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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Mol. Neurosci.</journal-id>
<journal-title>Frontiers in Molecular Neuroscience</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Mol. Neurosci.</abbrev-journal-title>
<issn pub-type="epub">1662-5099</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fnmol.2023.1186279</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Molecular Neuroscience</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Hemokinin-1 induces transcriptomic alterations in pain-related signaling processes in rat primary sensory neurons independent of NK1 tachykinin receptor activation</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Tak&#x000E1;cs-Lov&#x000E1;sz</surname> <given-names>Krisztina</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/2190223/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Acz&#x000E9;l</surname> <given-names>Timea</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/2527757/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Borb&#x000E9;ly</surname> <given-names>&#x000C9;va</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="corresp" rid="c001"><sup>&#x0002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/30951/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Sz&#x00151;ke</surname> <given-names>&#x000C9;va</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/846198/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Czuni</surname> <given-names>Lilla</given-names></name>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/2528321/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Urb&#x000E1;n</surname> <given-names>P&#x000E9;ter</given-names></name>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Gyenesei</surname> <given-names>Attila</given-names></name>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Helyes</surname> <given-names>Zsuzsanna</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<xref ref-type="aff" rid="aff5"><sup>5</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/488917/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Kun</surname> <given-names>J&#x000F3;zsef</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/2291668/overview"/>
</contrib>
<contrib contrib-type="author">
<name><surname>B&#x000F6;lcskei</surname> <given-names>Kata</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Department of Pharmacology and Pharmacotherapy, Medical School and Centre for Neuroscience, University of P&#x000E9;cs</institution>, <addr-line>P&#x000E9;cs</addr-line>, <country>Hungary</country></aff>
<aff id="aff2"><sup>2</sup><institution>National Laboratory for Drug Research and Development</institution>, <addr-line>Budapest</addr-line>, <country>Hungary</country></aff>
<aff id="aff3"><sup>3</sup><institution>Hungarian Research Network, PTE HUN-REN Chronic Research Group</institution>, <addr-line>Budapest</addr-line>, <country>Hungary</country></aff>
<aff id="aff4"><sup>4</sup><institution>Szent&#x000E1;gothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of P&#x000E9;cs</institution>, <addr-line>P&#x000E9;cs</addr-line>, <country>Hungary</country></aff>
<aff id="aff5"><sup>5</sup><institution>PharmInVivo Ltd.</institution>, <addr-line>P&#x000E9;cs</addr-line>, <country>Hungary</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Manuela Simonetti, Heidelberg University, Germany</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Temugin Berta, University of Cincinnati, United States; Bang Sangsu, Duke University, United States</p></fn>
<corresp id="c001">&#x0002A;Correspondence: &#x000C9;va Borb&#x000E9;ly <email>eva.borbely&#x00040;aok.pte.hu</email></corresp>
</author-notes>
<pub-date pub-type="epub">
<day>27</day>
<month>10</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2023</year>
</pub-date>
<volume>16</volume>
<elocation-id>1186279</elocation-id>
<history>
<date date-type="received">
<day>14</day>
<month>03</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>18</day>
<month>09</month>
<year>2023</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x000A9; 2023 Tak&#x000E1;cs-Lov&#x000E1;sz, Acz&#x000E9;l, Borb&#x000E9;ly, Sz&#x00151;ke, Czuni, Urb&#x000E1;n, Gyenesei, Helyes, Kun and B&#x000F6;lcskei.</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Tak&#x000E1;cs-Lov&#x000E1;sz, Acz&#x000E9;l, Borb&#x000E9;ly, Sz&#x00151;ke, Czuni, Urb&#x000E1;n, Gyenesei, Helyes, Kun and B&#x000F6;lcskei</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<abstract>
<p>The tachykinin hemokinin-1 (HK-1) is involved in immunological processes, inflammation, and pain. Although the neurokinin 1 receptor (NK1R) is described as its main target, several effects are mediated by currently unidentified receptor(s). The role of HK-1 in pain is controversial, depending on the involvement of peripheral and central sensitization mechanisms in different models. We earlier showed the ability of HK-1 to activate the trigeminovascular system, but the mechanisms need to be clarified. Therefore, in this study, we investigated HK-1-induced transcriptomic alterations in cultured rat trigeminal ganglion (TRG) primary sensory neurons. HK-1 was applied for 6 or 24 h in 1 &#x003BC;M causing calcium-influx in these neurons, 500 nM not inducing calcium-entry was used for comparison. Next-generation sequencing was performed on the isolated RNA, and transcriptomic changes were analyzed to identify differentially expressed (DE) genes. Functional analysis was performed for gene annotation using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome databases. NK1R and Neurokinin receptor 2 (NK2R) were not detected. Neurokinin receptor 3 (NK3R) was around the detection limit, which suggests the involvement of other NKR isoforms or other receptors in HK-1-induced sensory neuronal activation. We found protease-activated receptor 1 (PAR1) and epidermal growth factor receptor (EGFR) as DE genes in calcium signaling. The transmembrane protein anthrax toxin receptor 2 (ANTXR2), a potential novel pain-related target, was upregulated. Acid-sensing ion channel 1; 3 (Asic1,3), N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptors decreased, myelin production and maintenance related genes (Mbp, Pmp2, Myef2, Mpz) and GNDF changed by HK-1 treatment. Our data showed time and dose-dependent effects of HK-1 in TRG cell culture. Result showed calcium signaling as altered event, however, we did not detect any of NK receptors. Presumably, the activation of TRG neurons is independent of NK receptors. ANTXR2 is a potential new target, PAR-1 has also important role in pain, however their connection to HK-1 is unknown. These findings might highlight new targets or key mediators to solve how HK-1 acts on TRG.</p></abstract>
<kwd-group>
<kwd>trigeminal ganglion</kwd>
<kwd>cell culture</kwd>
<kwd>transcriptomics</kwd>
<kwd>pain</kwd>
<kwd>migraine</kwd>
<kwd>Mrgpr-ANTXR2</kwd>
<kwd>tac4</kwd>
</kwd-group>
<counts>
<fig-count count="7"/>
<table-count count="7"/>
<equation-count count="0"/>
<ref-count count="87"/>
<page-count count="23"/>
<word-count count="12236"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-at-acceptance</meta-name>
<meta-value>Molecular Signalling and Pathways</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="s1">
<title>1. Introduction</title>
<p>Tachykinins represent a neuropeptide family widely distributed in the body. The first members of this family were substance P (SP), neurokinin A (NKA), derived from the preprotachykinin A/Tac1 gene, and neurokinin B (NKB), encoded by the preprotachykinin B/Tac3 gene (Borb&#x000E9;ly and Helyes, <xref ref-type="bibr" rid="B11">2017</xref>). Other members of this family have also been identified: neuropeptide K (NPK) (Roth et al., <xref ref-type="bibr" rid="B57">1985</xref>), neuropeptide &#x003B3; (NP&#x003B3;) (Kage et al., <xref ref-type="bibr" rid="B30">1988</xref>), hemokinin-1 (HK-1), and endokinins (EKs) (Kurtz et al., <xref ref-type="bibr" rid="B31">2002</xref>). HK-1 encoded by the preprotachykinin C/Tac4 gene was discovered 20 years ago in B lymphocytes (Zhang et al., <xref ref-type="bibr" rid="B85">2000</xref>), and similar to SP, it was shown in several immune cell types, including myeloid (polymorphonuclear granulocytes and eosinophils), lymphoid, dendritic cells, neurons, and microglia (Borb&#x000E9;ly and Helyes, <xref ref-type="bibr" rid="B11">2017</xref>). This widespread expression of HK-1 in diverse cell types might be related to a broad range of physiological and pathophysiological functions by activating a multitude of signaling pathways, which are currently not understood. HK-1 induces a variety of physiological and pathophysiological functions in the immune and hematopoietic systems, gastrointestinal tract, airways, cardiovascular, endocrine, and neural systems, bone, joints, and cancer. The role of HK-1 in pain is contradictory and likely to be concentration/dose dependent (Borb&#x000E9;ly and Helyes, <xref ref-type="bibr" rid="B11">2017</xref>). In mice, centrally administered HK-1 caused scratching (Borb&#x000E9;ly and Helyes, <xref ref-type="bibr" rid="B11">2017</xref>), licking, and biting at low doses (Watanabe et al., <xref ref-type="bibr" rid="B79">2010</xref>). Intrathecally injected HK-1 was analgesic in nanomolar concentrations in an NK1- or opioid receptor-dependent manner, but hyperalgesic in picomolar concentrations (Fu et al., <xref ref-type="bibr" rid="B24">2005</xref>).</p>
<p>Tachykinins possess a differential affinity for the three tachykinin receptors. HK and EKs have the highest affinity for NK1R, similar to SP (Satake et al., <xref ref-type="bibr" rid="B64">2013</xref>; Steinhoff et al., <xref ref-type="bibr" rid="B68">2014</xref>). They are all G protein-coupled receptors of the rhodopsin family. Signaling through the NK receptors is complex with multiple directions: (1) G<sub>q</sub>-related: activation of phospholipase C, resulting in inositol trisphosphate and diacylglycerol formation, mobilization of Ca<sup>2&#x0002B;</sup> from intracellular stores, and activation of protein kinase C; (2) G<sub>s</sub>-related activation of adenylyl cyclase, resulting in the cAMP formation and protein kinase A (PKA) activation; or (3) activation of phospholipase A2 and arachidonic acid production (Steinhoff et al., <xref ref-type="bibr" rid="B68">2014</xref>; Garcia-Recio and Gasc&#x000F3;n, <xref ref-type="bibr" rid="B25">2015</xref>). The existence of a specific receptor for HK-1 is currently intensively investigated (Duffy et al., <xref ref-type="bibr" rid="B19">2003</xref>). It was shown that an NK1R antagonist did not inhibit pain caused by HK-1 in different concentrations, suggesting a specific HK-1 target/receptor (Watanabe et al., <xref ref-type="bibr" rid="B79">2010</xref>). NK1R antagonists were developed as analgesic drug candidates, but they failed in human pain conditions. This might be due to different NK1R splice variants linked to distinct binding and activation mechanisms and/or a currently unidentified receptor (Zhang et al., <xref ref-type="bibr" rid="B85">2000</xref>; Borb&#x000E9;ly and Helyes, <xref ref-type="bibr" rid="B11">2017</xref>; Hunyady et al., <xref ref-type="bibr" rid="B28">2019</xref>; Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>). Our research group earlier showed that HK-1 mediated chronic adjuvant-induced inflammation and related pain (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B10">2013</xref>) and neuropathic and neurogenic inflammatory hyperalgesia via NK1 receptor activation (Hunyady et al., <xref ref-type="bibr" rid="B28">2019</xref>). Interestingly, we recently demonstrated that unlike SP, HK-1 activates primary sensory neurons by inducing calcium influx via an NK1R-independent mechanism (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>). NK1R was shown to interact with the Mas-related G protein receptors (Mrgr) in certain pain-related mechanisms (Zhou et al., <xref ref-type="bibr" rid="B87">2015</xref>). The human Mrgprx2, which is an ortholog of the rat Mrgprb5, was described as a potential target for HK-1 in mast cells to cause degranulation (Manorak et al., <xref ref-type="bibr" rid="B41">2018</xref>). However, naturally occurring variants of Mrgprx2 lose HK-1 binding ability, showing the high importance of receptor variants (Alkanfari et al., <xref ref-type="bibr" rid="B3">2018</xref>).</p>
<p>Based on a broad range of data demonstrating proinflammatory and pronociceptive functions of HK-1 in different organs partially independently of NK1 receptor activation (Hunyady et al., <xref ref-type="bibr" rid="B28">2019</xref>; Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>), our main aim was to identify the molecular mechanisms responsible for these actions. Our recent results demonstrated NK1R-independent calcium influx in cultured trigeminal ganglion cells induced by 1 &#x003BC;M, but not 500 nM HK-1 (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>). In the present study, we investigated the concentration- and treatment duration-dependent intracellular signaling mechanisms and pathways in these primary sensory neurons using an unbiased transcriptomic approach.</p>
</sec>
<sec sec-type="materials and methods" id="s2">
<title>2. Materials and methods</title>
<sec>
<title>2.1. Primary cultures of TG neurons and treatment protocols</title>
<p>Primary cell cultures of TG neuron cells were extracted from 1&#x02013;4-day-old Wistar rat pups as described earlier (Szoke et al., <xref ref-type="bibr" rid="B71">2000</xref>). TG cells were dissected and washed in several steps. Afterward, TG cells were plated on poly-D-lysin-coated glass coverslips and grown in a nutrient-supplemented medium for the experiment. The earlier washing steps and the cell culture medium recipe are detailed elsewhere (Tak&#x000E1;cs-Lov&#x000E1;sz et al., <xref ref-type="bibr" rid="B72">2022</xref>). According to an earlier calcium influx, cell cultures were treated with HK-1 (Sigma Aldrich, solved in culture media) in two concentrations: 500 nM (no evoked calcium influx) and 1 &#x003BC;M [evoked calcium influx in an earlier study (Tak&#x000E1;cs-Lov&#x000E1;sz et al., <xref ref-type="bibr" rid="B72">2022</xref>)]. Untreated cultures were used as controls. After 6 h and 24 h of HK-1 administration, samples were collected for RNA isolation. Except for the HK-1 500 nM 24 h condition, which was repeated in duplicates, other conditions were repeated in triplicate.</p>
</sec>
<sec>
<title>2.2. Illumina library preparation and sequencing</title>
<p>In order to provide a complete gene expression profile, RNA sequencing was performed (Fang and Cui, <xref ref-type="bibr" rid="B21">2011</xref>). The library for Illumina sequencing was made using the QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). A total of 400 ng of total RNA was used for first-strand cDNA generation using an oligodT primer followed by RNA removal. The second strand synthesis was followed by random priming, and the products were purified with magnetic beads. Finally, the libraries were amplified and barcoded using PCR. All libraries were quality-checked on the TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) to examine if adapter dimers formed during PCR. The QuantSeq libraries were sequenced using the Illumina NextSeq550 platform to produce 75 bp single-end reads.</p>
</sec>
<sec>
<title>2.3. Bioinformatics</title>
<p>The sequencing reads were aligned against the <italic>Rattus norvegicus</italic> reference genome (Rnor 6.0 Ensembl release) with STAR v2.5.3a (Dobin et al., <xref ref-type="bibr" rid="B17">2013</xref>). Following alignment, reads were associated with known protein-coding genes, and the number of reads aligned within each gene was counted using HTSeq library v0.11.1 (Anders et al., <xref ref-type="bibr" rid="B4">2015</xref>). Gene count data were normalized using the trimmed mean of M values (TMM) normalization method of the edgeR R/Bioconductor package (v3.28, R v3.6.0, Bioconductor v3.9) (Robinson et al., <xref ref-type="bibr" rid="B56">2010</xref>). Data were further log-transformed using the voom approach for statistical evaluation (Law et al., <xref ref-type="bibr" rid="B33">2014</xref>) in the limma package (Ritchie et al., <xref ref-type="bibr" rid="B55">2015</xref>). Fold change (FC) values between the compared groups resulting from the linear modeling process and moderated <italic>t</italic>-test <italic>p-</italic>values relative to a minimum required fold change threshold were calculated by the limma package. When determining differentially expressed (DE) genes, filtering thresholds were set to at least FC 1,2 and <italic>p</italic>-value 0.05 when the HK-1 1 &#x003BC;M 24 h and HK-1 500 nM 6 h treatments were compared to the untreated control group, and to FC 1.3 and <italic>p</italic>-value 0.05 for the HK-1 1 &#x003BC;M 6 h vs. untreated control, and to FC 2 and <italic>p</italic>-value 0.05 for HK-1 500 nM 24 h vs. untreated control group comparison. Normalized counts were represented as transcripts per million (TPM) values. Functional analysis (annotations of genes) was prepared using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome databases. Detection of functional enrichment was performed in the differentially expressed gene list (DE list enrichment: Fisher&#x00027;s exact test for GO, hypergeometric test for KEGG and Reactome) and toward the top of the list when all genes have been ranked according to the evidence for being differentially expressed (ranked list enrichment: non-parametric Kolmogorov&#x02013;Smirnov test for GO and KEGG, hypergeometric test for Reactome) applying the topGO v2.37.0, ReactomePA v1.30.0, and gage v2.36.0 packages. The pathview package v1.26.0 (Luo and Brouwer, <xref ref-type="bibr" rid="B40">2013</xref>) was used to visualize mapping data to KEGG pathways. GO terms were merged using the Revigo tool (tiny resulting list set up) for extracting the most relevant terms.</p>
</sec>
<sec>
<title>2.4. Validation of gene expression fold changes by RT-qPCR</title>
<p>To validate certain up and downregulated genes together with unaltered ones determined by RNA sequencing, 200 ng RNA per sample was used for reverse transcription with the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Primers were designed with Primer-BLAST (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/tools/primer-blast/">https://www.ncbi.nlm.nih.gov/tools/primer-blast/</ext-link>) for the genes selected on the basis of the transcriptomics results [nuclear receptor subfamily 4 group A member 1 (Nr4a1), solute carrier family 25 member 5 (Slc25a5), fibroblast growth factor receptor 1 (Fgfr1), heat shock protein HSP 90-alpha (Hsp90aa1), integrin subunit alpha 4 (Itga4), NADH: ubiquinone oxidoreductase subunit B6 (Ndufb6), F2r/PAR1, G protein subunit beta 2 (Gnb2), G protein subunit alpha I1 (Gnai1), fibroblast growth factor 5 (Fgf5)], and they are demonstrated in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S1</xref>. The reactions were carried out with SensiFAST SYBR<sup>&#x000AE;</sup> Lo-ROX mix (Meridian BioScience) reagents in triplicate using 1 &#x003BC;l of cDNA per well in a Bio-Rad CFX96 real-time cycler. The amplification program was as follows: 95 &#x000B0;C for 120 s, 40 cycles at 95 &#x000B0;C for 5 s, 58 &#x000B0;C for 10s, and 60 &#x000B0;C for 30 s. The geometric mean of the CT values for the two housekeeping genes was determined to obtain the &#x00394;CT for each gene of interest. The &#x00394;&#x00394;CT values were calculated by subtracting the &#x00394;CT value of the control sample from the &#x00394;CT of the treated sample. Relative fold changes in gene expression were calculated using the comparative 2&#x02013;&#x00394;&#x00394;Ct method (Livak and Schmittgen, <xref ref-type="bibr" rid="B39">2001</xref>).</p>
</sec>
</sec>
<sec sec-type="results" id="s3">
<title>3. Results</title>
<sec>
<title>3.1. DE genes</title>
<p>Extracting the most important and relevant DE genes helps to understand the effects and intracellular signaling mechanisms of HK-1. In average rank, the p and FC values were taken into account shows the most relevant ranked gene list for all groups (<xref ref-type="table" rid="T1">Table 1</xref>). After 24 h of response to 1 &#x003BC;M HK-1, which we previously showed induces calcium influx in trigeminal primary sensory neurons, acid-sensing ion channel subunit 3 (Asic3), Glutamate ionotropic receptor NMDA type subunit 1 (Grin1), and C-C motif chemokine ligand 7 (Ccl7) were downregulated. At the earlier, 6 h timepoint, 1 &#x003BC;M HK-1 downregulated Slc25a5, while upregulating myelin-associated glycoprotein (Mag). For 6 h results, Mag, Itga4, and the LBH regulator of the Wnt signaling pathway (Lbb) were at the top of the list and upregulated independently of concentration.</p>
<table-wrap position="float" id="T1">
<label>Table 1</label>
<caption><p>Collection of the first 30 average ranked genes with FC value for all cases.</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th valign="top" align="left"><bold>avgRank</bold></th>
<th valign="top" align="center" colspan="3"><bold>HK-1 1</bold>&#x003BC;<bold>M_24h</bold></th>
<th valign="top" align="center" colspan="3"><bold>HK-1 1</bold>&#x003BC;<bold>M_6h</bold></th>
<th valign="top" align="center" colspan="3"><bold>HK-1 500 nM 24h</bold></th>
<th valign="top" align="center" colspan="3"><bold>HK-1 500 nM 6h</bold></th>
</tr>
</thead>
<tbody>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<td/>
<td valign="top" align="left"><bold>Description</bold></td>
<td valign="top" align="left"><bold>Gene</bold></td>
<td valign="top" align="left"><bold>FC</bold></td>
<td valign="top" align="left"><bold>Description</bold></td>
<td valign="top" align="left"><bold>Gene</bold></td>
<td valign="top" align="left"><bold>FC</bold></td>
<td valign="top" align="left"><bold>Description</bold></td>
<td valign="top" align="left"><bold>Gene</bold></td>
<td valign="top" align="left"><bold>FC</bold></td>
<td valign="top" align="left"><bold>Description</bold></td>
<td valign="top" align="left"><bold>Gene</bold></td>
<td valign="top" align="left"><bold>FC</bold></td>
</tr>
<tr>
<td valign="top" align="left">1</td>
<td valign="top" align="left">Receptor (chemosensory) transporter protein 4</td>
<td valign="top" align="left">Rtp4</td>
<td valign="top" align="left">&#x02212;5.0</td>
<td valign="top" align="left">Integrin subunit alpha 4</td>
<td valign="top" align="left">Itga4</td>
<td valign="top" align="left">7.5</td>
<td valign="top" align="left">Nuclear receptor subfamily 4, group A, member 1</td>
<td valign="top" align="left">Nr4a1</td>
<td valign="top" align="left">30.2</td>
<td valign="top" align="left">H1.1 linker histone, cluster member</td>
<td valign="top" align="left">H1f1</td>
<td valign="top" align="left">11.9</td>
</tr>
<tr>
<td valign="top" align="left">2</td>
<td valign="top" align="left">Limb and CNS expressed 1</td>
<td valign="top" align="left">Lix1</td>
<td valign="top" align="left">&#x02212;4.1</td>
<td valign="top" align="left">Mitogen-activated protein kinase kinase kinase 20</td>
<td valign="top" align="left">Map3k20</td>
<td valign="top" align="left">4.4</td>
<td valign="top" align="left">Solute carrier family 25 member 5</td>
<td valign="top" align="left">Slc25a5</td>
<td valign="top" align="left">15.3</td>
<td valign="top" align="left">Integrin subunit alpha 4</td>
<td valign="top" align="left">Itga4</td>
<td valign="top" align="left">4.4</td>
</tr>
<tr>
<td valign="top" align="left">3</td>
<td valign="top" align="left">Potassium voltage-gated channel-interacting protein 1</td>
<td valign="top" align="left">Kcnip1</td>
<td valign="top" align="left">&#x02212;3.9</td>
<td valign="top" align="left">LBH regulator of WNT signaling pathway</td>
<td valign="top" align="left">Lbh</td>
<td valign="top" align="left">4.1</td>
<td valign="top" align="left">Cellular communication network factor 1</td>
<td valign="top" align="left">Ccn1</td>
<td valign="top" align="left">19.5</td>
<td valign="top" align="left">Betacellulin</td>
<td valign="top" align="left">Btc</td>
<td valign="top" align="left">3.6</td>
</tr>
<tr>
<td valign="top" align="left">4</td>
<td valign="top" align="left">Glycine receptor, beta</td>
<td valign="top" align="left">Glrb</td>
<td valign="top" align="left">&#x02212;3.2</td>
<td valign="top" align="left">H1.1 linker histone, cluster member</td>
<td valign="top" align="left">H1f1</td>
<td valign="top" align="left">15.1</td>
<td valign="top" align="left">Ring finger protein 5</td>
<td valign="top" align="left">Rnf5</td>
<td valign="top" align="left">28.8</td>
<td valign="top" align="left">Insulin-like growth factor 2 mRNA binding protein 3</td>
<td valign="top" align="left">Igf2bp3</td>
<td valign="top" align="left">3.9</td>
</tr>
<tr>
<td valign="top" align="left">5</td>
<td valign="top" align="left">Transmembrane protein 45b</td>
<td valign="top" align="left">Tmem45b</td>
<td valign="top" align="left">&#x02212;3.3</td>
<td valign="top" align="left">Solute carrier family 25 member 5</td>
<td valign="top" align="left">Slc25a5</td>
<td valign="top" align="left">&#x02212;4.5</td>
<td valign="top" align="left">U2 small nuclear RNA auxiliary factor 2</td>
<td valign="top" align="left">U2af2</td>
<td valign="top" align="left">&#x02212;9.3</td>
<td valign="top" align="left">LBH regulator of WNT signaling pathway</td>
<td valign="top" align="left">Lbh</td>
<td valign="top" align="left">2.7</td>
</tr>
<tr>
<td valign="top" align="left">6</td>
<td valign="top" align="left">Ras-like without CAAX 2</td>
<td valign="top" align="left">Rit2</td>
<td valign="top" align="left">&#x02212;2.8</td>
<td valign="top" align="left">H1.4 linker histone, cluster member</td>
<td valign="top" align="left">H1f4</td>
<td valign="top" align="left">3.8</td>
<td valign="top" align="left">Basic transcription factor 3</td>
<td valign="top" align="left">Btf3</td>
<td valign="top" align="left">10.1</td>
<td valign="top" align="left">Cysteine and glycine-rich protein 2</td>
<td valign="top" align="left">Csrp2</td>
<td valign="top" align="left">3.3</td>
</tr>
<tr>
<td valign="top" align="left">7</td>
<td valign="top" align="left">Chondromodulin</td>
<td valign="top" align="left">Cnmd</td>
<td valign="top" align="left">&#x02212;5.1</td>
<td valign="top" align="left">tropomyosin 4</td>
<td valign="top" align="left">Tpm4</td>
<td valign="top" align="left">3.7</td>
<td valign="top" align="left">Ribosomal protein S13</td>
<td valign="top" align="left">Rps13</td>
<td valign="top" align="left">11.6</td>
<td valign="top" align="left">Exocyst complex component 1 like</td>
<td valign="top" align="left">Exoc1l</td>
<td valign="top" align="left">&#x02212;3.2</td>
</tr>
<tr>
<td valign="top" align="left">8</td>
<td valign="top" align="left">Radical S-adenosyl methionine domain containing 2</td>
<td valign="top" align="left">Rsad2</td>
<td valign="top" align="left">&#x02212;4.6</td>
<td valign="top" align="left">shootin 1</td>
<td valign="top" align="left">Shtn1</td>
<td valign="top" align="left">3.9</td>
<td valign="top" align="left">Dihydropyrimidinase-like 3</td>
<td valign="top" align="left">Dpysl3</td>
<td valign="top" align="left">&#x02212;6.6</td>
<td valign="top" align="left">H1.4 linker histone, cluster member</td>
<td valign="top" align="left">H1f4</td>
<td valign="top" align="left">2.6</td>
</tr>
<tr>
<td valign="top" align="left">9</td>
<td valign="top" align="left">Diacylglycerol kinase, gamma</td>
<td valign="top" align="left">Dgkg</td>
<td valign="top" align="left">&#x02212;2.9</td>
<td valign="top" align="left">La ribonucleoprotein 4B</td>
<td valign="top" align="left">Larp4b</td>
<td valign="top" align="left">4.0</td>
<td/>
<td valign="top" align="left">AC141489.1</td>
<td valign="top" align="left">6.9</td>
<td valign="top" align="left">H1.5 linker histone, cluster member</td>
<td valign="top" align="left">H1f5</td>
<td valign="top" align="left">6.5</td>
</tr>
<tr>
<td valign="top" align="left">10</td>
<td valign="top" align="left">RT1 class II, locus Db1</td>
<td valign="top" align="left">RT1-Db1</td>
<td valign="top" align="left">&#x02212;2.4</td>
<td valign="top" align="left">High mobility group AT-hook 1</td>
<td valign="top" align="left">Hmga1</td>
<td valign="top" align="left">4.2</td>
<td valign="top" align="left">La ribonucleoprotein 4B</td>
<td valign="top" align="left">Larp4b</td>
<td valign="top" align="left">&#x02212;6.0</td>
<td valign="top" align="left">Serine protease 12</td>
<td valign="top" align="left">Prss12</td>
<td valign="top" align="left">2.6</td>
</tr>
<tr>
<td valign="top" align="left">11</td>
<td valign="top" align="left">Expressed sequence AI593442</td>
<td valign="top" align="left">LOC100125362</td>
<td valign="top" align="left">&#x02212;2.7</td>
<td valign="top" align="left">Dihydropyrimidinase-like 3</td>
<td valign="top" align="left">Dpysl3</td>
<td valign="top" align="left">3.6</td>
<td valign="top" align="left">Cilia and flagella associated protein 20</td>
<td valign="top" align="left">Cfap20</td>
<td valign="top" align="left">7.2</td>
<td valign="top" align="left">Mitochondrially encoded NADH dehydrogenase 6</td>
<td valign="top" align="left">Mt-nd6</td>
<td valign="top" align="left">&#x02212;2.4</td>
</tr>
<tr>
<td valign="top" align="left">12</td>
<td valign="top" align="left">Inhibin subunit beta B</td>
<td valign="top" align="left">Inhbb</td>
<td valign="top" align="left">&#x02212;2.7</td>
<td valign="top" align="left">BMP2 inducible kinase</td>
<td valign="top" align="left">Bmp2k</td>
<td valign="top" align="left">3.7</td>
<td valign="top" align="left">Hexokinase 1</td>
<td valign="top" align="left">Hk1</td>
<td valign="top" align="left">&#x02212;6.9</td>
<td valign="top" align="left">Catenin beta 1</td>
<td valign="top" align="left">Ctnnb1</td>
<td valign="top" align="left">5.6</td>
</tr>
<tr>
<td valign="top" align="left">13</td>
<td valign="top" align="left">Elastin</td>
<td valign="top" align="left">Eln</td>
<td valign="top" align="left">&#x02212;2.5</td>
<td valign="top" align="left">TIAM Rac1 associated GEF 1</td>
<td valign="top" align="left">Tiam1</td>
<td valign="top" align="left">3.9</td>
<td valign="top" align="left">Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-5</td>
<td valign="top" align="left">LOC108349548</td>
<td valign="top" align="left">5.4</td>
<td valign="top" align="left">Ly6/Plaur domain containing 1</td>
<td valign="top" align="left">Lypd1</td>
<td valign="top" align="left">3.0</td>
</tr>
<tr>
<td valign="top" align="left">14</td>
<td valign="top" align="left">Acid-sensing ion channel subunit 3</td>
<td valign="top" align="left">Asic3</td>
<td valign="top" align="left">&#x02212;2.9</td>
<td valign="top" align="left">U2 small nuclear RNA auxiliary factor 2</td>
<td valign="top" align="left">U2af2</td>
<td valign="top" align="left">5.0</td>
<td valign="top" align="left">Mesoderm specific transcript</td>
<td valign="top" align="left">Mest</td>
<td valign="top" align="left">&#x02212;5.8</td>
<td valign="top" align="left">Apolipoprotein E</td>
<td valign="top" align="left">Apoe</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td valign="top" align="left">15</td>
<td valign="top" align="left">Guanosine monophosphate reductase</td>
<td valign="top" align="left">Gmpr</td>
<td valign="top" align="left">&#x02212;2.3</td>
<td valign="top" align="left">Serine/threonine kinase 10</td>
<td valign="top" align="left">Stk10</td>
<td valign="top" align="left">3.6</td>
<td valign="top" align="left">Sorting nexin 7</td>
<td valign="top" align="left">Snx7</td>
<td valign="top" align="left">&#x02212;5.8</td>
<td valign="top" align="left">shootin 1</td>
<td valign="top" align="left">Shtn1</td>
<td valign="top" align="left">2.6</td>
</tr>
<tr>
<td valign="top" align="left">16</td>
<td valign="top" align="left">Dispatched RND transporter family member 2</td>
<td valign="top" align="left">Disp2</td>
<td valign="top" align="left">&#x02212;2.2</td>
<td valign="top" align="left">H1.2 linker histone, cluster member</td>
<td valign="top" align="left">H1f2</td>
<td valign="top" align="left">6.4</td>
<td valign="top" align="left">ANKH inorganic pyrophosphate transport regulator</td>
<td valign="top" align="left">Ankh</td>
<td valign="top" align="left">&#x02212;6.9</td>
<td/>
<td valign="top" align="left">AABR07035787.1</td>
<td valign="top" align="left">2.5</td>
</tr>
<tr>
<td valign="top" align="left">17</td>
<td valign="top" align="left">Glutamate ionotropic receptor NMDA type subunit 1</td>
<td valign="top" align="left">Grin1</td>
<td valign="top" align="left">&#x02212;2.3</td>
<td valign="top" align="left">Heat shock protein family A (Hsp70) member 9</td>
<td valign="top" align="left">Hspa9</td>
<td valign="top" align="left">3.3</td>
<td valign="top" align="left">Translin-associated factor X</td>
<td valign="top" align="left">Tsnax</td>
<td valign="top" align="left">7.9</td>
<td valign="top" align="left">Scm-like with four mbt domains 2</td>
<td valign="top" align="left">Sfmbt2</td>
<td valign="top" align="left">4.1</td>
</tr>
<tr>
<td valign="top" align="left">18</td>
<td valign="top" align="left">Homer scaffold protein 3</td>
<td valign="top" align="left">Homer3</td>
<td valign="top" align="left">&#x02212;2.2</td>
<td valign="top" align="left">Myotubularin-related protein 2</td>
<td valign="top" align="left">Mtmr2</td>
<td valign="top" align="left">4.1</td>
<td valign="top" align="left">Pyruvate kinase M1/2</td>
<td valign="top" align="left">Pkm</td>
<td valign="top" align="left">&#x02212;8.5</td>
<td valign="top" align="left">Cysteine and glycine-rich protein 1</td>
<td valign="top" align="left">Csrp1</td>
<td valign="top" align="left">2.4</td>
</tr>
<tr>
<td valign="top" align="left">19</td>
<td valign="top" align="left">Transmembrane protein 72</td>
<td valign="top" align="left">Tmem72</td>
<td valign="top" align="left">&#x02212;2.8</td>
<td valign="top" align="left">ANKH inorganic pyrophosphate transport regulator</td>
<td valign="top" align="left">Ankh</td>
<td valign="top" align="left">4.3</td>
<td valign="top" align="left">Signal recognition particle 9</td>
<td valign="top" align="left">Srp9</td>
<td valign="top" align="left">4.8</td>
<td valign="top" align="left">Lipoprotein lipase</td>
<td valign="top" align="left">Lpl</td>
<td valign="top" align="left">&#x02212;2.3</td>
</tr>
<tr>
<td valign="top" align="left">20</td>
<td valign="top" align="left">Microsomal glutathione S-transferase 3</td>
<td valign="top" align="left">Mgst3</td>
<td valign="top" align="left">&#x02212;4.1</td>
<td valign="top" align="left">RAP2A, member of the RAS oncogene family</td>
<td valign="top" align="left">Rap2a</td>
<td valign="top" align="left">3.2</td>
<td valign="top" align="left">Formin binding protein 1</td>
<td valign="top" align="left">Fnbp1</td>
<td valign="top" align="left">&#x02212;6.4</td>
<td valign="top" align="left">DEAD (Asp-Glu-Ala-Asp) box polypeptide 3</td>
<td valign="top" align="left">Ddx3</td>
<td valign="top" align="left">3.8</td>
</tr>
<tr>
<td valign="top" align="left">21</td>
<td valign="top" align="left">Protein phosphatase 2C-like domain containing 1</td>
<td valign="top" align="left">Pp2d1</td>
<td valign="top" align="left">&#x02212;2.2</td>
<td valign="top" align="left">Myb/SANT DNA binding domain containing 2</td>
<td valign="top" align="left">Msantd2</td>
<td valign="top" align="left">4.5</td>
<td valign="top" align="left">Discoidin, CUB, and LCCL domain containing 2</td>
<td valign="top" align="left">Dcbld2</td>
<td valign="top" align="left">&#x02212;4.8</td>
<td valign="top" align="left">Lysophosphatidic acid receptor 4</td>
<td valign="top" align="left">Lpar4</td>
<td valign="top" align="left">3.6</td>
</tr>
<tr>
<td valign="top" align="left">22</td>
<td valign="top" align="left">Gap junction protein, beta 1</td>
<td valign="top" align="left">Gjb1</td>
<td valign="top" align="left">&#x02212;2.2</td>
<td valign="top" align="left">Filamin A interacting protein 1-like</td>
<td valign="top" align="left">Filip1l</td>
<td valign="top" align="left">3.7</td>
<td/>
<td valign="top" align="left">AABR07028615.1</td>
<td valign="top" align="left">&#x02212;5.2</td>
<td valign="top" align="left">Insulin-like growth factor 2</td>
<td valign="top" align="left">Igf2</td>
<td valign="top" align="left">2.4</td>
</tr>
<tr>
<td valign="top" align="left">23</td>
<td valign="top" align="left">C-C motif chemokine ligand 7</td>
<td valign="top" align="left">Ccl7</td>
<td valign="top" align="left">&#x02212;2.4</td>
<td valign="top" align="left">G protein subunit beta 2</td>
<td valign="top" align="left">Gnb2</td>
<td valign="top" align="left">&#x02212;6.5</td>
<td valign="top" align="left">RNA polymerase II subunit D</td>
<td valign="top" align="left">Polr2d</td>
<td valign="top" align="left">10.5</td>
<td valign="top" align="left">CUE domain containing 2</td>
<td valign="top" align="left">Cuedc2</td>
<td valign="top" align="left">2.5</td>
</tr>
<tr>
<td valign="top" align="left">24</td>
<td valign="top" align="left">Pleckstrin homology and RhoGEF domain containing G6</td>
<td valign="top" align="left">Plekhg6</td>
<td valign="top" align="left">&#x02212;2.4</td>
<td valign="top" align="left">Nebulin</td>
<td valign="top" align="left">Neb</td>
<td valign="top" align="left">3.3</td>
<td/>
<td valign="top" align="left">AABR07057617.1</td>
<td valign="top" align="left">6.3</td>
<td valign="top" align="left">Adrenomedullin</td>
<td valign="top" align="left">Adm</td>
<td valign="top" align="left">&#x02212;2.4</td>
</tr>
<tr>
<td valign="top" align="left">25</td>
<td valign="top" align="left">Synaptotagmin 6</td>
<td valign="top" align="left">Syt6</td>
<td valign="top" align="left">&#x02212;2.6</td>
<td valign="top" align="left">Jumonji and AT-rich interaction domain containing 2</td>
<td valign="top" align="left">Jarid2</td>
<td valign="top" align="left">3.6</td>
<td valign="top" align="left">Golgin A7</td>
<td valign="top" align="left">Golga7</td>
<td valign="top" align="left">6.8</td>
<td valign="top" align="left">Myelin-associated glycoprotein</td>
<td valign="top" align="left">Mag</td>
<td valign="top" align="left">2.8</td>
</tr>
<tr>
<td valign="top" align="left">26</td>
<td valign="top" align="left">Frizzled class Receptor 1</td>
<td valign="top" align="left">Fzd1</td>
<td valign="top" align="left">2.0</td>
<td valign="top" align="left">Cellular communication network factor 1</td>
<td valign="top" align="left">Ccn1</td>
<td valign="top" align="left">&#x02212;3.6</td>
<td valign="top" align="left">Selenoprotein F</td>
<td valign="top" align="left">Selenof</td>
<td valign="top" align="left">5.1</td>
<td valign="top" align="left">Calponin 1</td>
<td valign="top" align="left">Cnn1</td>
<td valign="top" align="left">3.3</td>
</tr>
<tr>
<td valign="top" align="left">27</td>
<td valign="top" align="left">rabphilin 3A</td>
<td valign="top" align="left">Rph3a</td>
<td valign="top" align="left">&#x02212;2.4</td>
<td valign="top" align="left">Transcription activation suppressor family member 2</td>
<td valign="top" align="left">Tasor2</td>
<td valign="top" align="left">3.1</td>
<td valign="top" align="left">cystatin B</td>
<td valign="top" align="left">Cstb</td>
<td valign="top" align="left">5.4</td>
<td valign="top" align="left">Capping actin protein, gelsolin like</td>
<td valign="top" align="left">Capg</td>
<td valign="top" align="left">2.8</td>
</tr>
<tr>
<td valign="top" align="left">28</td>
<td valign="top" align="left">Methionine sulfoxide reductase B2</td>
<td valign="top" align="left">Msrb2</td>
<td valign="top" align="left">&#x02212;2.4</td>
<td valign="top" align="left">Sprouty-related, EVH1 domain containing 1</td>
<td valign="top" align="left">Spred1</td>
<td valign="top" align="left">3.7</td>
<td valign="top" align="left">host cell factor C1</td>
<td valign="top" align="left">Hcfc1</td>
<td valign="top" align="left">&#x02212;7.4</td>
<td valign="top" align="left">Oxysterol binding protein 2</td>
<td valign="top" align="left">Osbp2</td>
<td valign="top" align="left">2.3</td>
</tr>
<tr>
<td valign="top" align="left">29</td>
<td valign="top" align="left">Solute carrier family 16, member 13</td>
<td valign="top" align="left">Slc16a13</td>
<td valign="top" align="left">2.0</td>
<td valign="top" align="left">Myelin-associated glycoprotein</td>
<td valign="top" align="left">Mag</td>
<td valign="top" align="left">4.0</td>
<td valign="top" align="left">Protocadherin gamma subfamily C, 3</td>
<td valign="top" align="left">Pcdhgc3</td>
<td valign="top" align="left">&#x02212;5.4</td>
<td valign="top" align="left">Cyclin-dependent kinase inhibitor 1C</td>
<td valign="top" align="left">Cdkn1c</td>
<td valign="top" align="left">2.4</td>
</tr>
<tr>
<td valign="top" align="left">30</td>
<td valign="top" align="left">Reprimo, TP53 dependent G2 arrest mediator homolog</td>
<td valign="top" align="left">Rprm</td>
<td valign="top" align="left">&#x02212;2.0</td>
<td valign="top" align="left">Nuclear receptor subfamily 4, group A, member 1</td>
<td valign="top" align="left">Nr4a1</td>
<td valign="top" align="left">&#x02212;6.1</td>
<td valign="top" align="left">NADH:ubiquinone oxidoreductase subunit B6</td>
<td valign="top" align="left">Ndufb6</td>
<td valign="top" align="left">18.3</td>
<td valign="top" align="left">Ankyrin repeat domain 1</td>
<td valign="top" align="left">Ankrd1</td>
<td valign="top" align="left">&#x02212;5.1</td>
</tr></tbody>
</table>
</table-wrap>
<p>The 500 nM HK-1 concentration, which did not evoke calcium influx in our earlier studies, downregulated Slc25a5 at 24 h and upregulated Ndufb6. Additionally, mitochondrially encoded NADH dehydrogenase 6 (Mt-nd6) was downregulated in the HK-1 500 nM 6 h group. <xref ref-type="supplementary-material" rid="SM1">Supplementary Images I1</xref>&#x02013;<xref ref-type="supplementary-material" rid="SM1">I4</xref> show heatmaps of all DE genes for different concentrations at different sampling times.</p>
<p>Similarly, altered DE genes over time (both at the 6 h and 24 h timepoints) in response to the same HK-1 concentration may yield insight into the key mechanisms and effects. <xref ref-type="fig" rid="F1">Figure 1</xref> shows the numerical representation of DE genes across all groups and a summary of different group comparisons. Most DE genes were detected in response to 500 nM HK-1 treatment after 24h, where Nr4a1, Slc25a5, F2r, Ndufb6, and Gnb2 were upregulated, which were confirmed by qPCR (FC: 1.726-; 1.783; 2.205; 2.105; 1.445, respectively). Itga4, Fgf5, and Gnai1 were upregulated, and Ndufb6, Gnb2, and F2r were downregulated 6h after 1 &#x003BC;M HK-1 treatment, as determined both by sequencing and qPCR (FC: 2.942; 3.652; 1.14;&#x02212;1.15;&#x02212;1.01;&#x02212;1.08). Unaltered genes were Fgfr1 and Gnai1 according to RNA sequencing and qPCR (FC: 1.385; 1.365) 24h after 1 &#x003BC;M HK-1 treatment. Although qPCR confirmed all these alterations obtained with sequencing, 24 h after 500 nM HK-1 treatment, Fgfr1 changes were different with the two techniques: it was downregulated according to RNA sequencing but upregulated by PCR (FC: 1.18). The qPCR results are shown in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S2</xref>.</p>
<fig id="F1" position="float">
<label>Figure 1</label>
<caption><p>Number of DE genes for all groups. Insert tables show the FC values of the DE genes for the respective comparisons. <bold>(A)</bold> Panel demonstrates the upregulated genes and <bold>(B)</bold> shows the numbers of downregulated genes.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0001.tif"/>
</fig>
<p>In response to 1 &#x003BC;M HK-1, the expression of three genes, Itga4, ANTXR cell adhesion molecule 2 (Antxr2), and teneurin transmembrane protein 3 (Tenm3), changed similarly (<xref ref-type="fig" rid="F1">Figure 1</xref>). There was only one DE gene after 500 nM HK-1, Cxcl9 (C-X-C motif chemokine ligand 9), which was downregulated. Results for 24 h include less common DE genes, showing a greater concentration-dependent effect of HK-1. The common DE genes expressed in differently treated groups at the same timepoints showed 30 upregulated and 6 downregulated genes at 6 h and 3 upregulated and 5 downregulated genes at 24 h.</p>
<p>Common DE genes independent of the HK-1 concentration (and the calcium influx-inducing potential) at both timepoints are shown in <xref ref-type="table" rid="T2">Tables 2</xref>, <xref ref-type="table" rid="T3">3</xref>. Antxr2 and Itga4 at 6 h were concentration-independently upregulated. Serine protease 12 (Prss12), T cell differentiation protein (Mal), and Mag were also upregulated, but the expression level of voltage-gated sodium channel beta subunit 4 (Scn4b) was decreased at 6 h after both concentrations. Regarding concentration-independent results at 24 h, frizzled class receptor 1 (Fzd1) and 3-hydroxyacyl-CoA dehydratase 2 (Hacd2) were upregulated, and rabphilin 3A (Rph3a), gamma-aminobutyric acid type A receptor alpha2 subunit (Gabra2), ryanodine receptor 2 (Ryr2) Mag, and voltage-gated sodium channel alpha subunit 1 (Scn1a) were downregulated. There were significant DE genes with potential importance in neuronal and inflammatory functions, but they are not in the top 30 ranked gene lists (<xref ref-type="table" rid="T4">Table 4</xref>). In response to 1 &#x003BC;M HK-1 potassium voltage-gated channel-interacting protein 4 (Kcnip4), myelin basic protein (Mbp) was downregulated and Gpr108 was upregulated at 24 h, while fibroblast growth factor 9 (Fgf9), Ndufb6, Myelin expression factor 2 (Myef2), myelin protein zero (Mpzc), and GDNF were upregulated at 6 h. Interestingly, 500 nM HK-1 downregulated PACAP, while upregulating peripheral myelin protein 2 (Pmp2), glial cell-derived neurotrophic factor (GDNF) at 6 h, transmembrane protein 128 (Tmem128), and integrin subunit alpha V (Itgav) at 24 h.</p>
<table-wrap position="float" id="T2">
<label>Table 2</label>
<caption><p>Common DE genes for the 1&#x003BC;M and 500 nM HK-1 concentrations at 6 h. Red means upregulated, while green shows downregulated DE genes.</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th valign="top" align="left"><bold>geneSymbol</bold></th>
<th valign="top" align="center"><bold>Description</bold></th>
<th valign="top" align="center"><bold>EntrezIDs</bold></th>
<th valign="top" align="center"><bold>EntrezID</bold></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Antxr2</td>
<td valign="top" align="center">Anthrax toxin receptor 2</td>
<td valign="top" align="center">305633</td>
<td valign="top" align="center">305633</td>
</tr>
<tr>
<td valign="top" align="left">Bmp2k</td>
<td valign="top" align="center">BMP2 inducible kinase</td>
<td valign="top" align="center">NA</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left">Btc</td>
<td valign="top" align="center">Betacellulin</td>
<td valign="top" align="center">64022</td>
<td valign="top" align="center">64022</td>
</tr>
<tr>
<td valign="top" align="left">Lypd1</td>
<td valign="top" align="center">Ly6/Plaur domain containing 1</td>
<td valign="top" align="center">360838</td>
<td valign="top" align="center">360838</td>
</tr>
<tr>
<td valign="top" align="left">Csrp2</td>
<td valign="top" align="center">Cysteine and glycine-rich protein 2</td>
<td valign="top" align="center">29317</td>
<td valign="top" align="center">29317</td>
</tr>
<tr>
<td valign="top" align="left">Rnd3</td>
<td valign="top" align="center">Rho family GTPase 3</td>
<td valign="top" align="center">295588</td>
<td valign="top" align="center">295588</td>
</tr>
<tr>
<td valign="top" align="left">Itga4</td>
<td valign="top" align="center">Integrin subunit alpha 4</td>
<td valign="top" align="center">311144</td>
<td valign="top" align="center">311144</td>
</tr>
<tr>
<td valign="top" align="left">Zwilch</td>
<td valign="top" align="center">Zwilch kinetochore protein</td>
<td valign="top" align="center">691493</td>
<td valign="top" align="center">691493</td>
</tr>
<tr>
<td valign="top" align="left">Ankh</td>
<td valign="top" align="center">ANKH inorganic pyrophosphate transport regulator</td>
<td valign="top" align="center">114506</td>
<td valign="top" align="center">114506</td>
</tr>
<tr>
<td valign="top" align="left">Epb41l2</td>
<td valign="top" align="center">Erythrocyte membrane protein band 4.1-like 2</td>
<td valign="top" align="center">309557</td>
<td valign="top" align="center">309557</td>
</tr>
<tr>
<td valign="top" align="left">Capg</td>
<td valign="top" align="center">Capping actin protein, gelsolin like</td>
<td valign="top" align="center">297339</td>
<td valign="top" align="center">297339</td>
</tr>
<tr>
<td valign="top" align="left">Inhba</td>
<td valign="top" align="center">Inhibin beta A subunit</td>
<td valign="top" align="center">29200</td>
<td valign="top" align="center">29200</td>
</tr>
<tr>
<td valign="top" align="left">Prss12</td>
<td valign="top" align="center">Protease, serine 12</td>
<td valign="top" align="center">85266</td>
<td valign="top" align="center">85266</td>
</tr>
<tr>
<td valign="top" align="left">Mal</td>
<td valign="top" align="center">Mal, T-cell differentiation protein</td>
<td valign="top" align="center">25263</td>
<td valign="top" align="center">25263</td>
</tr>
<tr>
<td valign="top" align="left">Tpm4</td>
<td valign="top" align="center">Tropomyosin 4</td>
<td valign="top" align="center">24852</td>
<td valign="top" align="center">24852</td>
</tr>
<tr>
<td valign="top" align="left">Hist1h1a</td>
<td valign="top" align="center">Histone cluster 1 H1 family member a</td>
<td valign="top" align="center">291145</td>
<td valign="top" align="center">291145</td>
</tr>
<tr>
<td valign="top" align="left">Shtn1</td>
<td valign="top" align="center">Shootin 1</td>
<td valign="top" align="center">292139</td>
<td valign="top" align="center">292139</td>
</tr>
<tr>
<td valign="top" align="left">Rnf40</td>
<td valign="top" align="center">Ring finger protein 40</td>
<td valign="top" align="center">266712</td>
<td valign="top" align="center">266712</td>
</tr>
<tr>
<td valign="top" align="left">Cuedc2</td>
<td valign="top" align="center">CUE domain containing 2</td>
<td valign="top" align="center">294009</td>
<td valign="top" align="center">294009</td>
</tr>
<tr>
<td valign="top" align="left">Mag</td>
<td valign="top" align="center">Myelin-associated glycoprotein</td>
<td valign="top" align="center">29409</td>
<td valign="top" align="center">29409</td>
</tr>
<tr>
<td valign="top" align="left">Fgf5</td>
<td valign="top" align="center">Fibroblast growth factor 5</td>
<td valign="top" align="center">60662</td>
<td valign="top" align="center">60662</td>
</tr>
<tr>
<td valign="top" align="left">Ctnnd1</td>
<td valign="top" align="center">Catenin delta 1</td>
<td valign="top" align="center">311163</td>
<td valign="top" align="center">311163</td>
</tr>
<tr>
<td valign="top" align="left">Lbh</td>
<td valign="top" align="center">Limb bud and heart development</td>
<td valign="top" align="center">683626</td>
<td valign="top" align="center">683626</td>
</tr>
<tr>
<td valign="top" align="left">Otud7b</td>
<td valign="top" align="center">OTU deubiquitinase 7B</td>
<td valign="top" align="center">310677</td>
<td valign="top" align="center">310677</td>
</tr>
<tr>
<td valign="top" align="left">Hist1h1d</td>
<td valign="top" align="center">Histone cluster 1, H1d</td>
<td valign="top" align="center">201097</td>
<td valign="top" align="center">201097</td>
</tr>
<tr>
<td valign="top" align="left">Hist1h1c</td>
<td valign="top" align="center">Histone cluster 1 H1 family member c</td>
<td valign="top" align="center">684681</td>
<td valign="top" align="center">684681</td>
</tr>
<tr>
<td valign="top" align="left">NA</td>
<td valign="top" align="center">NA</td>
<td valign="top" align="center">NA</td>
<td valign="top" align="center">NA</td>
</tr>
<tr>
<td valign="top" align="left">Cdkn1c</td>
<td valign="top" align="center">Cyclin-dependent kinase inhibitor 1C</td>
<td valign="top" align="center">246060</td>
<td valign="top" align="center">246060</td>
</tr>
<tr>
<td valign="top" align="left">LOC103692716</td>
<td valign="top" align="center">Heat shock protein HSP 90-alpha</td>
<td valign="top" align="center">299331</td>
<td valign="top" align="center">299331</td>
</tr>
<tr>
<td valign="top" align="left">Hist1h1b</td>
<td valign="top" align="center">Histone cluster 1 H1 family member b</td>
<td valign="top" align="center">680522</td>
<td valign="top" align="center">680522</td>
</tr>
<tr>
<td valign="top" align="left">Tmem176b</td>
<td valign="top" align="center">Transmembrane protein 176B</td>
<td valign="top" align="center">171411</td>
<td valign="top" align="center">171411</td>
</tr>
<tr>
<td valign="top" align="left">Ankrd1</td>
<td valign="top" align="center">Ankyrin repeat domain 1</td>
<td valign="top" align="center">27064</td>
<td valign="top" align="center">27064</td>
</tr>
<tr>
<td valign="top" align="left">Scn4b</td>
<td valign="top" align="center">Sodium voltage-gated channel beta subunit 4</td>
<td valign="top" align="center">315611</td>
<td valign="top" align="center">315611</td>
</tr>
<tr>
<td valign="top" align="left">Susd2</td>
<td valign="top" align="center">Sushi domain containing 2</td>
<td valign="top" align="center">294335</td>
<td valign="top" align="center">294335</td>
</tr>
<tr>
<td valign="top" align="left">Cbx6</td>
<td valign="top" align="center">Chromobox 6</td>
<td valign="top" align="center">315136</td>
<td valign="top" align="center">315136</td>
</tr>
<tr>
<td valign="top" align="left">LOC686911</td>
<td valign="top" align="center">Similar to exocyst complex component 1 (exocyst complex component Sec3)</td>
<td valign="top" align="center">686911</td>
<td valign="top" align="center">686911</td>
</tr></tbody>
</table>
</table-wrap>
<table-wrap position="float" id="T3">
<label>Table 3</label>
<caption><p>Common DE genes for both doses at 24 h. Red means upregulated DEs, whereas green shows downregulated Des.</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th valign="top" align="left"><bold>geneSymbol</bold></th>
<th valign="top" align="left"><bold>Description</bold></th>
<th valign="top" align="center"><bold>EntrezIDs</bold></th>
<th valign="top" align="center"><bold>EntrezID</bold></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Fzd1</td>
<td valign="top" align="left">Frizzled class receptor 1</td>
<td valign="top" align="center">58868</td>
<td valign="top" align="center">58868</td>
</tr>
<tr>
<td valign="top" align="left">Hacd2</td>
<td valign="top" align="left">3-hydroxyacyl-CoA dehydratase 2</td>
<td/>
<td/>
</tr>
<tr>
<td valign="top" align="left">Cfap20</td>
<td valign="top" align="left">Cilia and flagella-associated protein 20</td>
<td valign="top" align="center">307642</td>
<td valign="top" align="center">307642</td>
</tr>
<tr>
<td valign="top" align="left">Rph3a</td>
<td valign="top" align="left">Rabphilin 3A</td>
<td valign="top" align="center">171039</td>
<td valign="top" align="center">171039</td>
</tr>
<tr>
<td valign="top" align="left">Gabra2</td>
<td valign="top" align="left">Gamma-aminobutyric acid type A receptor alpha2 subunit</td>
<td valign="top" align="center">289606</td>
<td valign="top" align="center">289606</td>
</tr>
<tr>
<td valign="top" align="left">Ryr2</td>
<td valign="top" align="left">Ryanodine receptor 2</td>
<td valign="top" align="center">689560</td>
<td valign="top" align="center">689560</td>
</tr>
<tr>
<td valign="top" align="left">Mag</td>
<td valign="top" align="left">Myelin-associated glycoprotein</td>
<td valign="top" align="center">29409</td>
<td valign="top" align="center">29409</td>
</tr>
<tr>
<td valign="top" align="left">Scn1a</td>
<td valign="top" align="left">Sodium voltage-gated channel alpha subunit 1</td>
<td valign="top" align="center">81574</td>
<td valign="top" align="center">81574</td>
</tr></tbody>
</table>
</table-wrap>
<table-wrap position="float" id="T4">
<label>Table 4</label>
<caption><p>FC, p, and avgRank values for other possible relevant and significant DE genes for all groups.</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th/>
<th valign="top" align="center"><bold>Description</bold></th>
<th valign="top" align="center"><bold>gene</bold></th>
<th valign="top" align="center"><bold>FC</bold></th>
<th valign="top" align="center"><bold><italic>P</italic>-value</bold></th>
<th valign="top" align="center"><bold>avgRank</bold></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">HK-1 1 &#x003BC;M 24 h</td>
<td valign="top" align="center">Myelin basic protein</td>
<td valign="top" align="center">Mbp</td>
<td valign="top" align="center">&#x02212;1.64</td>
<td valign="top" align="center">0.037</td>
<td valign="top" align="center">120</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">G protein-coupled receptor 108</td>
<td valign="top" align="center">Gpr108</td>
<td valign="top" align="center">1.52</td>
<td valign="top" align="center">2.30E&#x02212;02</td>
<td valign="top" align="center">190</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Potassium voltage-gated channel-interacting protein 4</td>
<td valign="top" align="center">Kcnip4</td>
<td valign="top" align="center">&#x02212;1.91</td>
<td valign="top" align="center">4.50E&#x02212;02</td>
<td valign="top" align="center">85</td>
</tr>
<tr>
<td valign="top" align="left">HK-1 500 nM 6 h</td>
<td valign="top" align="center">Peripheral myelin protein 2</td>
<td valign="top" align="center">Pmp2</td>
<td valign="top" align="center">1.69</td>
<td valign="top" align="center">4.79E&#x02212;02</td>
<td valign="top" align="center">318</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">PACAP (pituitary adenylate cyclase-activating polypeptide)</td>
<td valign="top" align="center">Adcyap1</td>
<td valign="top" align="center">&#x02212;1.74</td>
<td valign="top" align="center">4.5E&#x02212;02</td>
<td valign="top" align="center">280</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Glial cell-derived neurotrophic factor</td>
<td valign="top" align="center">GNDF</td>
<td valign="top" align="center">1.84</td>
<td valign="top" align="center">4.42E&#x02212;02</td>
<td valign="top" align="center">223</td>
</tr>
<tr>
<td valign="top" align="left">HK-1 500 nM 24 h</td>
<td valign="top" align="center">NADH:ubiquinone oxidoreductase subunit B6</td>
<td valign="top" align="center">Ndufb6</td>
<td valign="top" align="center">18.27</td>
<td valign="top" align="center">1.57E&#x02212;06</td>
<td valign="top" align="center">30</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Transmembrane protein 128</td>
<td valign="top" align="center">Tmem128</td>
<td valign="top" align="center">3.59</td>
<td valign="top" align="center">1.26E&#x02212;04</td>
<td valign="top" align="center">156</td>
</tr>
<tr>
<td valign="top" align="left">HK-1 1 &#x003BC;M 6 h</td>
<td valign="top" align="center">Myelin expression factor 2</td>
<td valign="top" align="center">Myef2</td>
<td valign="top" align="center">2.7</td>
<td valign="top" align="center">3.09E&#x02212;04</td>
<td valign="top" align="center">105</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Fibroblast growth factor 5</td>
<td valign="top" align="center">Fgf5</td>
<td valign="top" align="center">4.91</td>
<td valign="top" align="center">2.03E&#x02212;02</td>
<td valign="top" align="center">48</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Fibroblast growth factor 9</td>
<td valign="top" align="center">Fgf9</td>
<td valign="top" align="center">&#x02212;3.28</td>
<td valign="top" align="center">1.40E&#x02212;02</td>
<td valign="top" align="center">57</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Myelin protein zero</td>
<td valign="top" align="center">Mpz</td>
<td valign="top" align="center">2.0</td>
<td valign="top" align="center">3.63E&#x02212;02</td>
<td valign="top" align="center">548</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">NADH:ubiquinone oxidoreductase subunit B6</td>
<td valign="top" align="center">Ndufb6</td>
<td valign="top" align="center">&#x02212;2.7</td>
<td valign="top" align="center">2.87E&#x02212;02</td>
<td valign="top" align="center">304</td>
</tr>
 <tr>
<td/>
<td valign="top" align="center">Glial cell-derived neurotrophic factor</td>
<td valign="top" align="center">GNDF</td>
<td valign="top" align="center">2.8</td>
<td valign="top" align="center">5.63E&#x02212;04</td>
<td valign="top" align="center">101</td>
</tr></tbody>
</table>
</table-wrap>
</sec>
<sec>
<title>3.2. Potential targets for HK-1</title>
<p>The mRNA level of the Tacr3 receptor was detected around the detection limit, showing that low expression of Tacr1 and Tacr2 was not found in these primary cell cultures. This result was confirmed by earlier, unpublished findings with primary cell cultures from adult rat trigeminal ganglia showing similar expression patterns of these receptors. The TPM values of these receptors in different primary cultures are shown in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S3</xref>. No significant difference was detected between the HK-1-treated and control groups; the overlapping receptors are shown in <xref ref-type="fig" rid="F2">Figure 2</xref>. To identify potential target molecules, we collected relevant receptors related to neural and/or inflammatory mechanisms based on different gene databases. Notably, the MAS-related G protein-coupled receptor, member B5 (Mrgprb5), was detected in all groups, however, with transcripts per million (TPM) below 2. <xref ref-type="fig" rid="F3">Figure 3</xref> shows receptors present in control primary sensory neuronal cultures at 6 h and 24 h. Abbreviations for receptors can be found in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S4</xref>. The expressions of the receptors were similar at 6 h and 24 h. Rack1, Ngfr, and Ednrb were detected at very high TPM at both sampling timepoints. Tnfrsf12a, Adipor1, and Adipor2 were also present in both concentrations. Ntrk1, P2rx3, and F2r were also expressed in both cases, highlighting the possible impact on pain transmission and calcium ion flow. Cxcr4 was found at 6 h. <xref ref-type="fig" rid="F2">Figure 2</xref> shows the DE receptors. Adipor2 at 500 nM 24 h was downregulated; F2r at 1 &#x003BC;M 6 h was, however, upregulated at 500 nM 24 h. Not only F2r but also Egfr expression was upregulated at 1 &#x003BC;M 6 h. An interesting result was the expression change in transient receptor potential melastatin 3,7,8 (Trpm3,7,8) cation channels at 500 nM 24 h. <xref ref-type="supplementary-material" rid="SM1">Supplementary Image I5</xref> shows important receptors for all treatment conditions.</p>
<fig id="F2" position="float">
<label>Figure 2</label>
<caption><p>TPM values of receptors in control primary sensory neuronal cultures 6 h and 24 h. All data are shown in the <xref ref-type="supplementary-material" rid="SM1">Supplementary Image I1</xref>. Receptors having a TPM &#x0003E;10 with specific roles in neural mechanisms are demonstrated here. Functions of receptors were filtered based on public databases (<ext-link ext-link-type="uri" xlink:href="https://rgd.mcw.edu/">https://rgd.mcw.edu/</ext-link>, <ext-link ext-link-type="uri" xlink:href="https://www.genecards.org/">https://www.genecards.org/</ext-link>, and <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov">https://www.ncbi.nlm.nih.gov</ext-link>).</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0002.tif"/>
</fig>
<fig id="F3" position="float">
<label>Figure 3</label>
<caption><p>FC value of significant differentially expressed genes in primary sensory neuron cultures of the trigeminal ganglia in response to two HK-1 concentrations after 6 h and 24 h treatment durations. Abbreviations are shown in <xref ref-type="supplementary-material" rid="SM1">Supplementary Table S4</xref>. All DE genes can be found in <xref ref-type="supplementary-material" rid="SM1">Supplementary Images I2</xref>&#x02013;<xref ref-type="supplementary-material" rid="SM1">I5</xref>.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0003.tif"/>
</fig>
</sec>
<sec>
<title>3.3. Signaling pathways influenced by HK-1 treatments</title>
<p>Significantly altered pathways 6 h after 500 nM and 1 &#x003BC;M HK-1 treatment determined by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were predominantly related to calcium and Wnt signaling (<xref ref-type="table" rid="T5">Table 5</xref>). <xref ref-type="fig" rid="F4">Figure 4</xref> shows calcium signaling pathways with significant DE genes and represents the FC values of DE genes involved in this process. Among receptors, F2r had shown down-, Egfr upregulation. The transcriptomic level of Slc25a5 and Prkaca (protein kinase CAMP-activated catalytic subunit alpha) has changed negatively, and that of Gna11 (G protein subunit Alpha 11) and Prkacb (protein kinase cAMP-activated catalytic subunit beta) has changed positively.</p>
<table-wrap position="float" id="T5">
<label>Table 5</label>
<caption><p>Pathways from the KEGG database for HK-1 1 &#x003BC;M 6h group.</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th valign="top" align="left"><bold>KEGG.ID</bold></th>
<th valign="top" align="center"><bold>Term</bold></th>
<th valign="top" align="center"><bold>Annotated</bold></th>
<th valign="top" align="center"><bold>significant</bold></th>
<th valign="top" align="center"><bold>Expected</bold></th>
<th valign="top" align="center"><bold>P.Value</bold></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map04540">4540</ext-link></td>
<td valign="top" align="center">Gap junction</td>
<td valign="top" align="center">55</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">1.8588850</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map4530">4530</ext-link></td>
<td valign="top" align="center">Tight junction</td>
<td valign="top" align="center">70</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">2.3658537</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map04520">4520</ext-link></td>
<td valign="top" align="center">Adherens junction</td>
<td valign="top" align="center">52</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">1.7574913</td>
<td valign="top" align="center">0.007</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map4962">4962</ext-link></td>
<td valign="top" align="center">Vasopressin-regulated water reabsorption</td>
<td valign="top" align="center">33</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1.1153310</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map04916">4916</ext-link></td>
<td valign="top" align="center">Melanogenesis</td>
<td valign="top" align="center">51</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">1.7236934</td>
<td valign="top" align="center">0.007</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map5218">5218</ext-link></td>
<td valign="top" align="center">Melanoma</td>
<td valign="top" align="center">40</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1.3519164</td>
<td valign="top" align="center">0.010</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map04020">4020</ext-link></td>
<td valign="top" align="center">Calcium signaling pathway</td>
<td valign="top" align="center">67</td>
<td valign="top" align="center">6</td>
<td valign="top" align="center">2.2644599</td>
<td valign="top" align="center">0.024</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map4912">4912</ext-link></td>
<td valign="top" align="center">GnRH signaling pathway</td>
<td valign="top" align="center">57</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1.9264808</td>
<td valign="top" align="center">0.042</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map04310">4310</ext-link></td>
<td valign="top" align="center">Wnt signaling pathway</td>
<td valign="top" align="center">91</td>
<td valign="top" align="center">7</td>
<td valign="top" align="center">3.0756098</td>
<td valign="top" align="center">0.032</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map4730">4730</ext-link></td>
<td valign="top" align="center">Long-term depression</td>
<td valign="top" align="center">38</td>
<td valign="top" align="center">4</td>
<td valign="top" align="center">1.2843206</td>
<td valign="top" align="center">0.038</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map04914">4914</ext-link></td>
<td valign="top" align="center">Progesterone-mediated oocyte maturation</td>
<td valign="top" align="center">57</td>
<td valign="top" align="center">5</td>
<td valign="top" align="center">1.9264808</td>
<td valign="top" align="center">0.042</td>
</tr>
<tr>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.genome.jp/dbget-bin/www_bget?pathway:map5200">5200</ext-link></td>
<td valign="top" align="center">Pathways in cancer</td>
<td valign="top" align="center">188</td>
<td valign="top" align="center">11</td>
<td valign="top" align="center">6.3540070</td>
<td valign="top" align="center">0.049</td>
</tr></tbody>
</table>
<table-wrap-foot>
<p>Significant column shows the number of DE genes from annotated genes of a given pathway. Pathway was altered significantly if a p-value of &#x02264; 0.05. Pathways, having a Significant score &#x02265; 4 were thought of as interesting findings.</p>
</table-wrap-foot>
</table-wrap>
<fig id="F4" position="float">
<label>Figure 4</label>
<caption><p>Genes involved in the calcium signaling pathway from the KEGG database. Colored rectangle is for the altered expression of genes at 6 h of HK-1 1 &#x003BC;M. Color means Z-score calculated from fold change value; green means downregulated, and red means upregulated.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0004.tif"/>
</fig>
<p>The Gene Ontology (GO) database provides information on the functions of genes. <xref ref-type="table" rid="T6">Tables 6A&#x02013;D</xref> shows the collected GO terms for all treated groups, simplified with the Revigo tool. <xref ref-type="table" rid="T6">Table 6A</xref> shows GO results for the HK-1 1 &#x003BC;M 6 h group. Protein kinase inhibitor activity, protein kinase A regulatory subunit binding, and thyroid hormone receptor binding are present in this list. Synaptic cleft was found to be a significant GO term in the 6 h results independent of the HK-1 concentration. Interestingly, biological processes altered by 500 nM HK-1 at 6 h (<xref ref-type="table" rid="T6">Table 6B</xref>) included the adenylate cyclase-activating G protein-coupled receptor signaling pathway, positive regulation of T cell-mediated immunity, neutrophil chemotaxis, positive regulation of leukocyte adhesion to vascular endothelial cells, and highlighting possible immunological functions. Notable cellular components were the synaptic cleft, T-tubule, and myelin sheath, and remarkable molecular functions were adrenergic receptor binding, NADH dehydrogenase activity, and cAMP binding. GO results revealed that 1 &#x003BC;M HK-1 treatment significantly altered the glutamate and insulin receptor signaling pathways at the 24-h timepoint, which are intracellular responses to calcium ions, as shown in <xref ref-type="table" rid="T6">Table 6C</xref>. A notable affected cellular component was the synaptic vesicle. Among modified molecular functions, we found ligand-gated ion channel activity, postsynaptic neurotransmitter receptor activity, and sodium channel activity (<xref ref-type="table" rid="T6">Table 6C</xref>). Meanwhile, 500 nM HK-1 at the same timepoint regulated presynapse assembly, cGMP-mediated signaling, mitochondrial ATP synthesis-coupled electron transport, Schwann cell proliferation, cell fate specification, positive regulation of dendritic spine development, positive regulation of cold-induced thermogenesis, and ceramide biosynthetic processes. As significant molecular functions, palmitoyltransferase activity, fibroblast growth factor binding, oxidoreductase activity, and acting on peroxide as an acceptor were found (<xref ref-type="table" rid="T6">Table 6D</xref>).</p>
<table-wrap position="float" id="T6">
<label>Table 6</label>
<caption><p>A&#x02013;D. GO terms for each group merged with the Revigo tool.</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th valign="top" align="left"><bold>6h HK-1 1&#x003BC;M</bold></th>
<th valign="top" align="left"><bold>GO ID</bold></th>
<th valign="top" align="left"><bold>Name</bold></th>
<th valign="top" align="left"><bold>Value (logP)</bold></th>
</tr>
</thead>
<tbody>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(A)</bold></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Biological processes</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007062">GO:0007062</ext-link></td>
<td valign="top" align="left">Sister chromatid cohesion</td>
<td valign="top" align="left">&#x02212;4.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007063">GO:0007063</ext-link></td>
<td valign="top" align="left">Regulation of sister chromatid cohesion</td>
<td valign="top" align="left">&#x02212;3.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0048538">GO:0048538</ext-link></td>
<td valign="top" align="left">Thymus development</td>
<td valign="top" align="left">&#x02212;2.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0080182">GO:0080182</ext-link></td>
<td valign="top" align="left">Histone H3-K4 trimethylation</td>
<td valign="top" align="left">&#x02212;2.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1903429">GO:1903429</ext-link></td>
<td valign="top" align="left">Regulation of cell maturation</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051973">GO:0051973</ext-link></td>
<td valign="top" align="left">Positive regulation of telomerase activity</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008589">GO:0008589</ext-link></td>
<td valign="top" align="left">Regulation of smoothened signaling pathway</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0071108">GO:0071108</ext-link></td>
<td valign="top" align="left">Protein K48-linked deubiquitination</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0038083">GO:0038083</ext-link></td>
<td valign="top" align="left">Peptidyl-tyrosine autophosphorylation</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045992">GO:0045992</ext-link></td>
<td valign="top" align="left">Negative regulation of embryonic development</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0035019">GO:0035019</ext-link></td>
<td valign="top" align="left">Somatic stem cell population maintenance</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Cellular component</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000786">GO:0000786</ext-link></td>
<td valign="top" align="left">Nucleosome</td>
<td valign="top" align="left">&#x02212;2.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0043083">GO:0043083</ext-link></td>
<td valign="top" align="left">Synaptic cleft</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0014704">GO:0014704</ext-link></td>
<td valign="top" align="left">Intercalated disc</td>
<td valign="top" align="left">&#x02212;1.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0099738">GO:0099738</ext-link></td>
<td valign="top" align="left">Cell cortex region</td>
<td valign="top" align="left">&#x02212;2.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045120">GO:0045120</ext-link></td>
<td valign="top" align="left">Pronucleus</td>
<td valign="top" align="left">&#x02212;1.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031519">GO:0031519</ext-link></td>
<td valign="top" align="left">PcG protein complex</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000307">GO:0000307</ext-link></td>
<td valign="top" align="left">Cyclin-dependent protein kinase holoenzyme complex</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044815">GO:0044815</ext-link></td>
<td valign="top" align="left">DNA packaging complex</td>
<td valign="top" align="left">&#x02212;2.1</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005868">GO:0005868</ext-link></td>
<td valign="top" align="left">Cytoplasmic dynein Complex</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004860">GO:0004860</ext-link></td>
<td valign="top" align="left">Protein kinase inhibitor activity</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0018024">GO:0018024</ext-link></td>
<td valign="top" align="left">Histone-lysine N-methyltransferase activity</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Molecular function</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0034237">GO:0034237</ext-link></td>
<td valign="top" align="left">Protein kinase A regulatory subunit binding</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0048027">GO:0048027</ext-link></td>
<td valign="top" align="left">mRNA 5&#x00027;-UTR binding</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0042562">GO:0042562</ext-link></td>
<td valign="top" align="left">Hormone binding</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0090079">GO:0090079</ext-link></td>
<td valign="top" align="left">Translation regulator activity, nucleic acid binding</td>
<td valign="top" align="left">&#x02212;2.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031490">GO:0031490</ext-link></td>
<td valign="top" align="left">Chromatin DNA binding</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046966">GO:0046966</ext-link></td>
<td valign="top" align="left">Thyroid hormone receptor binding</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0070182">GO:0070182</ext-link></td>
<td valign="top" align="left">DNA polymerase binding</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051018">GO:0051018</ext-link></td>
<td valign="top" align="left">Protein kinase A binding</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<td valign="top" align="left"><bold>6h HK-1 500 nM</bold></td>
<td valign="top" align="left"><bold>GO ID</bold></td>
<td valign="top" align="left"><bold>Name</bold></td>
<td valign="top" align="left"><bold>Value (logP)</bold></td>
</tr>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(B)</bold></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Biological process</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016584">GO:0016584</ext-link></td>
<td valign="top" align="left">Nucleosome positioning</td>
<td valign="top" align="left">&#x02212;3.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0035627">GO:0035627</ext-link></td>
<td valign="top" align="left">Ceramide transport</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0060788">GO:0060788</ext-link></td>
<td valign="top" align="left">Ectodermal placode formation</td>
<td valign="top" align="left">&#x02212;3.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007189">GO:0007189</ext-link></td>
<td valign="top" align="left">Adenylate cyclase-activating G protein-coupled receptor signaling pathway</td>
<td valign="top" align="left">&#x02212;3.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046464">GO:0046464</ext-link></td>
<td valign="top" align="left">Acylglycerol catabolic process</td>
<td valign="top" align="left">&#x02212;3.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0002711">GO:0002711</ext-link></td>
<td valign="top" align="left">Positive regulation of T cell-mediated immunity</td>
<td valign="top" align="left">&#x02212;2.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010801">GO:0010801</ext-link></td>
<td valign="top" align="left">Negative regulation of peptidyl-threonine phosphorylation</td>
<td valign="top" align="left">&#x02212;3.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0055093">GO:0055093</ext-link></td>
<td valign="top" align="left">Response to hyperoxia</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030593">GO:0030593</ext-link></td>
<td valign="top" align="left">Neutrophil chemotaxis</td>
<td valign="top" align="left">&#x02212;3.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><bold><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0019226">GO:0019226</ext-link></bold></td>
<td valign="top" align="left"><bold>Transmission of nerve impulse</bold></td>
<td valign="top" align="left"><bold>&#x02212;2.5</bold></td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><bold><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0055094">GO:0055094</ext-link></bold></td>
<td valign="top" align="left"><bold>Response to lipoprotein particle</bold></td>
<td valign="top" align="left"><bold>&#x02212;2.4</bold></td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><bold><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0035094">GO:0035094</ext-link></bold></td>
<td valign="top" align="left"><bold>Response to nicotine</bold></td>
<td valign="top" align="left"><bold>&#x02212;2.4</bold></td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><bold><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0043537">GO:0043537</ext-link></bold></td>
<td valign="top" align="left"><bold>Negative regulation of blood vessel endothelial cell migration</bold></td>
<td valign="top" align="left"><bold>&#x02212;2.6</bold></td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><bold><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0071696">GO:0071696</ext-link></bold></td>
<td valign="top" align="left"><bold>Ectodermal placode development</bold></td>
<td valign="top" align="left"><bold>&#x02212;3.4</bold></td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><bold><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1904996">GO:1904996</ext-link></bold></td>
<td valign="top" align="left"><bold>Positive regulation of leukocyte adhesion to vascular endothelial cell</bold></td>
<td valign="top" align="left"><bold>&#x02212;2.3</bold></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Cellular component</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000786">GO:0000786</ext-link></td>
<td valign="top" align="left">Nucleosome</td>
<td valign="top" align="left">&#x02212;3.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0043083">GO:0043083</ext-link></td>
<td valign="top" align="left">Synaptic cleft</td>
<td valign="top" align="left">&#x02212;3.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030315">GO:0030315</ext-link></td>
<td valign="top" align="left">T-tubule</td>
<td valign="top" align="left">&#x02212;3.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0043209">GO:0043209</ext-link></td>
<td valign="top" align="left">Myelin sheath</td>
<td valign="top" align="left">&#x02212;3.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0099092">GO:0099092</ext-link></td>
<td valign="top" align="left">Postsynaptic density, intracellular component</td>
<td valign="top" align="left">&#x02212;3.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044815">GO:0044815</ext-link></td>
<td valign="top" align="left">DNA packaging complex</td>
<td valign="top" align="left">&#x02212;3.2</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Molecular function</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004112">GO:0004112</ext-link></td>
<td valign="top" align="left">Cyclic-nucleotide phosphodiesterase activity</td>
<td valign="top" align="left">&#x02212;2.1</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030296">GO:0030296</ext-link></td>
<td valign="top" align="left">Protein tyrosine kinase activator activity</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031690">GO:0031690</ext-link></td>
<td valign="top" align="left">Adrenergic receptor binding</td>
<td valign="top" align="left">&#x02212;4.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0120013">GO:0120013</ext-link></td>
<td valign="top" align="left">Lipid transfer activity</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0097001">GO:0097001</ext-link></td>
<td valign="top" align="left">Ceramide binding</td>
<td valign="top" align="left">&#x02212;3.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016835">GO:0016835</ext-link></td>
<td valign="top" align="left">Carbon&#x02013;oxygen lyase activity</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031490">GO:0031490</ext-link></td>
<td valign="top" align="left">Chromatin DNA binding</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003954">GO:0003954</ext-link></td>
<td valign="top" align="left">NADH dehydrogenase activity</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030552">GO:0030552</ext-link></td>
<td valign="top" align="left">cAMP binding</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030551">GO:0030551</ext-link></td>
<td valign="top" align="left">Cyclic nucleotide binding</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0043394">GO:0043394</ext-link></td>
<td valign="top" align="left">Proteoglycan binding</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<td valign="top" align="left"><bold>24h HK-1 1</bold> &#x003BC;<bold>M</bold></td>
<td valign="top" align="left"><bold>GO ID</bold></td>
<td valign="top" align="left"><bold>Name</bold></td>
<td valign="top" align="left"><bold>Value (logP)</bold></td>
</tr>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(C)</bold></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Biological process</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007215">GO:0007215</ext-link></td>
<td valign="top" align="left">Glutamate receptor signaling pathway</td>
<td valign="top" align="left">&#x02212;2.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007606">GO:0007606</ext-link></td>
<td valign="top" align="left">Sensory perception of chemical stimulus</td>
<td valign="top" align="left">&#x02212;2.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046834">GO:0046834</ext-link></td>
<td valign="top" align="left">Lipid phosphorylation</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046626">GO:0046626</ext-link></td>
<td valign="top" align="left">Regulation of insulin receptor signaling pathway</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045639">GO:0045639</ext-link></td>
<td valign="top" align="left">Positive regulation of myeloid cell differentiation</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0014075">GO:0014075</ext-link></td>
<td valign="top" align="left">Response to amine</td>
<td valign="top" align="left">&#x02212;2.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0097366">GO:0097366</ext-link></td>
<td valign="top" align="left">Response to bronchodilator</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0071277">GO:0071277</ext-link></td>
<td valign="top" align="left">Cellular response to calcium ion</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0050868">GO:0050868</ext-link></td>
<td valign="top" align="left">Negative regulation of T cell activation</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Cellular component</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0098797">GO:0098797</ext-link></td>
<td valign="top" align="left">Plasma membrane protein complex</td>
<td valign="top" align="left">&#x02212;2.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008021">GO:0008021</ext-link></td>
<td valign="top" align="left">Synaptic vesicle</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Molecular function</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005085">GO:0005085</ext-link></td>
<td valign="top" align="left">Guanyl-nucleotide exchange factor activity</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005544">GO:0005544</ext-link></td>
<td valign="top" align="left">Calcium-dependent phospholipid binding</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0015276">GO:0015276</ext-link></td>
<td valign="top" align="left">Ligand-gated ion channel activity</td>
<td valign="top" align="left">&#x02212;4.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030594">GO:0030594</ext-link></td>
<td valign="top" align="left">Neurotransmitter receptor activity</td>
<td valign="top" align="left">&#x02212;3.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0098960">GO:0098960</ext-link></td>
<td valign="top" align="left">Postsynaptic neurotransmitter receptor activity</td>
<td valign="top" align="left">&#x02212;3.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005125">GO:0005125</ext-link></td>
<td valign="top" align="left">Cytokine activity</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005272">GO:0005272</ext-link></td>
<td valign="top" align="left">Sodium channel activity</td>
<td valign="top" align="left">&#x02212;2.9</td>
</tr>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<td valign="top" align="left"><bold>HK-1 500 nM at 24 h</bold></td>
<td valign="top" align="left"><bold>GO ID</bold></td>
<td valign="top" align="left"><bold>Name</bold></td>
<td valign="top" align="left"><bold>Value (logP)</bold></td>
</tr>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(D)</bold></td>
</tr>
<tr>
<td valign="top" align="left"><bold>Biological process</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051973">GO:0051973</ext-link></td>
<td valign="top" align="left">Positive regulation of telomerase activity</td>
<td valign="top" align="left">&#x02212;3.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0097066">GO:0097066</ext-link></td>
<td valign="top" align="left">Response to thyroid hormone</td>
<td valign="top" align="left">&#x02212;2.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1903537">GO:1903537</ext-link></td>
<td valign="top" align="left">Meiotic cell cycle process involved in oocyte maturation</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0080182">GO:0080182</ext-link></td>
<td valign="top" align="left">Histone H3-K4 trimethylation</td>
<td valign="top" align="left">&#x02212;2.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0050432">GO:0050432</ext-link></td>
<td valign="top" align="left">Catecholamine secretion</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td/>
<td valign="top" align="left">chromosome condensation</td>
<td valign="top" align="left">&#x02212;2.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030261">GO:0030261</ext-link></td>
<td valign="top" align="left">Regulation of the meiotic cell cycle process involved in oocyte maturation</td>
<td valign="top" align="left">&#x02212;2.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1903538">GO:1903538</ext-link></td>
<td valign="top" align="left">Negative regulation of stem cell differentiation</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:2000737">GO:2000737</ext-link></td>
<td valign="top" align="left">Regulation of presynapse assembly</td>
<td valign="top" align="left">&#x02212;2.0</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1905606">GO:1905606</ext-link></td>
<td valign="top" align="left">Regulation of anion transmembrane transport</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1903959">GO:1903959</ext-link></td>
<td valign="top" align="left">cGMP-mediated signaling</td>
<td valign="top" align="left">&#x02212;2.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0019934">GO:0019934</ext-link></td>
<td valign="top" align="left">Mitochondrial ATP synthesis-coupled electron transport</td>
<td valign="top" align="left">&#x02212;2.1</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0042775">GO:0042775</ext-link></td>
<td valign="top" align="left">Somatic stem cell population maintenance</td>
<td valign="top" align="left">&#x02212;1.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0035019">GO:0035019</ext-link></td>
<td valign="top" align="left">Positive regulation of coagulation</td>
<td valign="top" align="left">&#x02212;2.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0050820">GO:0050820</ext-link></td>
<td valign="top" align="left">Protein homotrimerization</td>
<td valign="top" align="left">&#x02212;1.7</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0070207">GO:0070207</ext-link></td>
<td valign="top" align="left">Receptor recycling</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0001881">GO:0001881</ext-link></td>
<td valign="top" align="left">Schwann cell proliferation</td>
<td valign="top" align="left">&#x02212;2.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0014010">GO:0014010</ext-link></td>
<td valign="top" align="left">Negative regulation of the BMP signaling pathway</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0030514">GO:0030514</ext-link></td>
<td valign="top" align="left">Endodermal cell differentiation</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0035987">GO:0035987</ext-link></td>
<td valign="top" align="left">Regulation of translational initiation</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006446">GO:0006446</ext-link></td>
<td valign="top" align="left">Cell fate specification</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0001708">GO:0001708</ext-link></td>
<td valign="top" align="left">Negative regulation of chromatin organization</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1905268">GO:1905268</ext-link></td>
<td valign="top" align="left">Cerebral cortex cell migration</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0021795">GO:0021795</ext-link></td>
<td valign="top" align="left">DNA methylation or demethylation</td>
<td valign="top" align="left">&#x02212;2.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044728">GO:0044728</ext-link></td>
<td valign="top" align="left">Protein palmitoylation</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0018345">GO:0018345</ext-link></td>
<td valign="top" align="left">Positive regulation of dendritic spine development</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0060999">GO:0060999</ext-link></td>
<td valign="top" align="left">Presynapse assembly</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0099054">GO:0099054</ext-link></td>
<td valign="top" align="left">Regulation of phospholipase activity</td>
<td valign="top" align="left">&#x02212;2.3</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010517">GO:0010517</ext-link></td>
<td valign="top" align="left">Positive regulation of neurotransmitter transport</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051590">GO:0051590</ext-link></td>
<td valign="top" align="left">Regulation of stem cell differentiation</td>
<td valign="top" align="left">&#x02212;1.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:2000736">GO:2000736</ext-link></td>
<td valign="top" align="left">Regulation of cell maturation</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:1903429">GO:1903429</ext-link></td>
<td valign="top" align="left">Positive regulation of cold-induced thermogenesis</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0120162">GO:0120162</ext-link></td>
<td valign="top" align="left">Ceramide biosynthetic process</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Cellular component</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0046513">GO:0046513</ext-link></td>
<td valign="top" align="left">Nucleosome</td>
<td valign="top" align="left">&#x02212;4.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000786">GO:0000786</ext-link></td>
<td valign="top" align="left">DNA packaging complex</td>
<td valign="top" align="left">&#x02212;3.8</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0044815">GO:0044815</ext-link></td>
<td valign="top" align="left">Cytoplasmic dynein complex</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005868">GO:0005868</ext-link></td>
<td valign="top" align="left">Polysomal ribosome</td>
<td valign="top" align="left">&#x02212;1.5</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0042788">GO:0042788</ext-link></td>
<td valign="top" align="left">Cyclin-dependent protein kinase holoenzyme complex</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Molecular function</bold></td>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000307">GO:0000307</ext-link></td>
<td valign="top" align="left">Antioxidant activity</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016209">GO:0016209</ext-link></td>
<td valign="top" align="left">Palmitoyltransferase activity</td>
<td valign="top" align="left">&#x02212;2.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016409">GO:0016409</ext-link></td>
<td valign="top" align="left">Fibroblast growth factor binding</td>
<td valign="top" align="left">&#x02212;2.2</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0017134">GO:0017134</ext-link></td>
<td valign="top" align="left">Kinesin binding</td>
<td valign="top" align="left">&#x02212;1.9</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0019894">GO:0019894</ext-link></td>
<td valign="top" align="left">Translation initiation factor binding</td>
<td valign="top" align="left">&#x02212;1.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031369">GO:0031369</ext-link></td>
<td valign="top" align="left">Cadherin binding</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045296">GO:0045296</ext-link></td>
<td valign="top" align="left">3&#x00027;,5&#x00027;-cyclic-nucleotide phosphodiesterase activity</td>
<td valign="top" align="left">&#x02212;2.6</td>
</tr>
<tr>
<td/>
<td valign="top" align="left"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004114">GO:0004114</ext-link></td>
<td valign="top" align="left">Oxidoreductase activity, acting on peroxide as acceptor</td>
<td valign="top" align="left">&#x02212;1.4</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec>
<title>3.4. HK-1-induced signaling pathways</title>
<p><xref ref-type="table" rid="T7">Table 7</xref> shows results gained from the pathway database Reactome with DE genes for HK-1 1 &#x003BC;M 6 h, 500 nM 6 h, and 24 h groups. There was no significant finding for the HK-1 1 &#x003BC;M 24 h group. Noteworthy terms for HK-1 1 &#x003BC;M 6 h were apoptosis, signal amplification, programmed cell death, G alpha (s) signaling events, chaperone-mediated autophagy, and opioid signaling. ADP signaling through P2Y purinoreceptor 12 and opioid signaling were also important results for HK-1 500 nM 6 h group. Additional relevant terms for HK-1 500 nM 6 h treatment group were oxidative stress-induced senescence and GABA receptor activation. Common results for two concentrations at 6 h are the G alpha (s) signaling events, showing potential concentration- and calcium influx-independent effects of HK-1. Moreover, GPCR, GPCR ligand binding, and glycosphingolipid metabolism are important terms for HK-1 500 nM 6 h.</p>
<table-wrap position="float" id="T7">
<label>Table 7</label>
<caption><p>Reactome results for HK-1 1&#x003BC;M 6h (A), HK-1 500 nM 24h (B), and HK-1 500 nM 6h (C).</p></caption> 
<table frame="box" rules="all">
<thead>
<tr style="background-color:&#x00023;919498;color:&#x00023;ffffff">
<th valign="top" align="left"><bold>Reactome ID</bold></th>
<th valign="top" align="center"><bold>Term</bold></th>
<th valign="top" align="center"><bold>Gene ratio</bold></th>
<th valign="top" align="center"><bold><italic>P-</italic>value</bold></th>
</tr>
</thead>
<tbody>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(A)</bold></td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559584</td>
<td valign="top" align="center">Formation of senescence-associated heterochromatin Foci (SAHF)</td>
<td valign="top" align="center">6/12</td>
<td valign="top" align="center">1.1E-06</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559586</td>
<td valign="top" align="center">DNA damage/telomere stress-induced senescence</td>
<td valign="top" align="center">6/30</td>
<td valign="top" align="center">4.3E-04</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-9009391</td>
<td valign="top" align="center">Extra-nuclear estrogen signaling</td>
<td valign="top" align="center">6/40</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-109581</td>
<td valign="top" align="center">Apoptosis</td>
<td valign="top" align="center">7/54</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-392518</td>
<td valign="top" align="center">Signal amplification</td>
<td valign="top" align="center">4/17</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-69231</td>
<td valign="top" align="center">Cyclin D-associated events in G1</td>
<td valign="top" align="center">5/28</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-69236</td>
<td valign="top" align="center">G1 Phase</td>
<td valign="top" align="center">5/28</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-75153</td>
<td valign="top" align="center">Apoptotic execution phase</td>
<td valign="top" align="center">5/29</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-163685</td>
<td valign="top" align="center">Integration of energy metabolism</td>
<td valign="top" align="center">6/43</td>
<td valign="top" align="center">0.003</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-5357801</td>
<td valign="top" align="center">Programmed cell death</td>
<td valign="top" align="center">7/58</td>
<td valign="top" align="center">0.003</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2500257</td>
<td valign="top" align="center">Resolution of sister chromatid cohesion</td>
<td valign="top" align="center">8/75</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-418555</td>
<td valign="top" align="center">G alpha (s) signaling events</td>
<td valign="top" align="center">5/33</td>
<td valign="top" align="center">0.005</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-392170</td>
<td valign="top" align="center">ADP signaling through P2Y purinoceptor 12</td>
<td valign="top" align="center">3/12</td>
<td valign="top" align="center">0.007</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-5223345</td>
<td valign="top" align="center">Miscellaneous transport and binding events</td>
<td valign="top" align="center">3/12</td>
<td valign="top" align="center">0.007</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-202040</td>
<td valign="top" align="center">G protein activation</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-400042</td>
<td valign="top" align="center">Adrenaline and noradrenaline inhibit insulin secretion</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-418592</td>
<td valign="top" align="center">ADP signaling through P2Y purinoceptor 1</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-428930</td>
<td valign="top" align="center">Thromboxane signaling through TP receptor</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-9613829</td>
<td valign="top" align="center">Chaperone-mediated autophagy</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-111885</td>
<td valign="top" align="center">Opioid signaling</td>
<td valign="top" align="center">5/38</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(B)</bold></td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-432040</td>
<td valign="top" align="center">Vasopressin regulates renal water homeostasis via Aquaporins</td>
<td valign="top" align="center">4/15</td>
<td valign="top" align="center">6.00E-04</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-445717</td>
<td valign="top" align="center">Aquaporin-mediated transport</td>
<td valign="top" align="center">4/15</td>
<td valign="top" align="center">6.00E-04</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-163685</td>
<td valign="top" align="center">Integration of energy metabolism</td>
<td valign="top" align="center">6/43</td>
<td valign="top" align="center">0.001</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-8939211</td>
<td valign="top" align="center">ESR-mediated signaling</td>
<td valign="top" align="center">8/76</td>
<td valign="top" align="center">0.001</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-9018519</td>
<td valign="top" align="center">Estrogen-dependent gene expression</td>
<td valign="top" align="center">5/33</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-111885</td>
<td valign="top" align="center">Opioid signaling</td>
<td valign="top" align="center">5/38</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559584</td>
<td valign="top" align="center">Formation of senescence-associated heterochromatin foci (SAHF)</td>
<td valign="top" align="center">3/12</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-392170</td>
<td valign="top" align="center">ADP signaling through P2Y purinoceptor 12</td>
<td valign="top" align="center">3/12</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-202040</td>
<td valign="top" align="center">G protein activation</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.005</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-400042</td>
<td valign="top" align="center">Adrenaline and noradrenaline inhibit insulin secretion</td>
<td valign="top" align="center">3/13</td>
<td valign="top" align="center">0.005</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559583</td>
<td valign="top" align="center">Cellular senescence</td>
<td valign="top" align="center">7/77</td>
<td valign="top" align="center">0.005</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-199977</td>
<td valign="top" align="center">ER to Golgi anterograde transport</td>
<td valign="top" align="center">8/100</td>
<td valign="top" align="center">0.006</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-9006931</td>
<td valign="top" align="center">Signaling by nuclear receptors</td>
<td valign="top" align="center">8/100</td>
<td valign="top" align="center">0.006</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-211000</td>
<td valign="top" align="center">Gene silencing by RNA</td>
<td valign="top" align="center">5/43</td>
<td valign="top" align="center">0.006</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-112409</td>
<td valign="top" align="center">RAF-independent MAPK1/3 activation</td>
<td valign="top" align="center">3/15</td>
<td valign="top" align="center">0.007</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-8936459</td>
<td valign="top" align="center">RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function</td>
<td valign="top" align="center">3/15</td>
<td valign="top" align="center">0.007</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559580</td>
<td valign="top" align="center">Oxidative stress-induced senescence</td>
<td valign="top" align="center">4/29</td>
<td valign="top" align="center">0.008</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-75153</td>
<td valign="top" align="center">Apoptotic execution phase</td>
<td valign="top" align="center">4/29</td>
<td valign="top" align="center">0.008</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559586</td>
<td valign="top" align="center">DNA damage/telomere stress-induced senescence</td>
<td valign="top" align="center">4/30</td>
<td valign="top" align="center">0.009</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-6807878</td>
<td valign="top" align="center">COPI-mediated anterograde transport</td>
<td valign="top" align="center">6/67</td>
<td valign="top" align="center">0.010</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-392518</td>
<td valign="top" align="center">Signal amplification</td>
<td valign="top" align="center">3/17</td>
<td valign="top" align="center">0.011</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2299718</td>
<td valign="top" align="center">Condensation of prophase chromosomes</td>
<td valign="top" align="center">3/18</td>
<td valign="top" align="center">0.013</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-977443</td>
<td valign="top" align="center">GABA receptor activation</td>
<td valign="top" align="center">3/18</td>
<td valign="top" align="center">0.013</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-977444</td>
<td valign="top" align="center">GABA B receptor activation</td>
<td valign="top" align="center">3/18</td>
<td valign="top" align="center">0.013</td>
</tr>
<tr style="background-color:#dee1e1">
<td valign="top" align="left" colspan="4"><bold>(C)</bold></td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559584</td>
<td valign="top" align="center">Formation of senescence-associated heterochromatin Foci (SAHF)</td>
<td valign="top" align="center">5/12</td>
<td valign="top" align="center">2.35E-05</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-372790</td>
<td valign="top" align="center">Signaling by GPCR</td>
<td valign="top" align="center">16/185</td>
<td valign="top" align="center">3.04E-04</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559586</td>
<td valign="top" align="center">DNA damage/telomere stress-induced senescence</td>
<td valign="top" align="center">6/30</td>
<td valign="top" align="center">3.5E-04</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-388396</td>
<td valign="top" align="center">GPCR downstream signaling</td>
<td valign="top" align="center">15/181</td>
<td valign="top" align="center">7.48E-04</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-500792</td>
<td valign="top" align="center">GPCR ligand binding</td>
<td valign="top" align="center">7/54</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-75153</td>
<td valign="top" align="center">Apoptotic execution phase</td>
<td valign="top" align="center">5/29</td>
<td valign="top" align="center">0.002</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-1660662</td>
<td valign="top" align="center">Glycosphingolipid metabolism</td>
<td valign="top" align="center">4/19</td>
<td valign="top" align="center">0.003</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2559583</td>
<td valign="top" align="center">Cellular senescence</td>
<td valign="top" align="center">8/77</td>
<td valign="top" align="center">0.003</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-190828</td>
<td valign="top" align="center">Gap junction trafficking</td>
<td valign="top" align="center">4/20</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-157858</td>
<td valign="top" align="center">Gap junction trafficking and regulation</td>
<td valign="top" align="center">4/21</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-190861</td>
<td valign="top" align="center">Gap junction assembly</td>
<td valign="top" align="center">3/12</td>
<td valign="top" align="center">0.006</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-418555</td>
<td valign="top" align="center">G alpha (s) signaling events</td>
<td valign="top" align="center">5/33</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-2262752</td>
<td valign="top" align="center">Cellular responses to stress</td>
<td valign="top" align="center">17/258</td>
<td valign="top" align="center">0.004</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-8953897</td>
<td valign="top" align="center">Cellular responses to external stimuli</td>
<td valign="top" align="center">17/260</td>
<td valign="top" align="center">0.005</td>
</tr>
<tr>
<td valign="top" align="left">R-RNO-5218920</td>
<td valign="top" align="center">VEGFR2-mediated vascular permeability</td>
<td valign="top" align="center">4/23</td>
<td valign="top" align="center">0.006</td>
</tr></tbody>
</table>
<table-wrap-foot>
<p>Results were relevant and significant, if FDR &#x0003C; 0.25 and a p-value of &#x0003C; 0.05. The total number of background genes was 3890. Terms are in order according to p increasing value showing less statistical significance. Date ratio shows DE genes/genes involved in the Reactome pathway.</p>
</table-wrap-foot>
</table-wrap></sec>
</sec>
<sec sec-type="discussion" id="s4">
<title>4. Discussion</title>
<p>We demonstrate here the first transcriptomic data on the signaling pathways of HK-1 in rat primary sensory neurons, focusing on potential HK-1 targets, mechanisms of action, and DE genes involved in pain transmission and inflammation. The effect of HK-1 is complex, concentration dependent, and time dependent. Our findings support the well-described nociceptive actions of HK-1 and might explain the divergent neuronal activation processes. Since HK-1 is likely to act both on the primary sensory neurons and satellite glia cells, in this study we extract knowledge on these interactions to mimic <italic>in vivo</italic> conditions (Sakai et al., <xref ref-type="bibr" rid="B61">2012</xref>; Theoharides et al., <xref ref-type="bibr" rid="B75">2019</xref>).</p>
<p>Peripheral inflammatory and neuroinflammatory mechanisms resulting from complex interactions of immune cells, glial cells, and neurons play crucial roles in several diseases, including chronic pain (Siiskonen and Harvima, <xref ref-type="bibr" rid="B66">2019</xref>). Itga4 and Antxr2 were upregulated for both concentrations, Tenm3 for 1 &#x003BC;M and Cxcl9 was downregulated after 500 nM at both timepoints. Itga4 encodes CD49d (alpha 4), one chain of very late antigen 4 (VLA-4), which belongs to adhesive molecules that activate the inflammatory process by facilitating the migration of immune cells into the central nervous system. The role of VLA-4 in genetic predisposition to chronic neuroinflammatory diseases has been demonstrated by several studies (Andreoli et al., <xref ref-type="bibr" rid="B5">2007</xref>; Odoherty et al., <xref ref-type="bibr" rid="B49">2007</xref>; Correia et al., <xref ref-type="bibr" rid="B16">2009</xref>), supporting our findings in sensory neurons. Anthrax toxin components binding to ANTXR2, highly expressed on primary sensory neurons, were shown to inhibit inflammatory and neuropathic mechanical and thermal hyperalgesia (Yang et al., <xref ref-type="bibr" rid="B82">2022</xref>). Tenm3 encodes a transmembrane protein also related to pain (Rouillard et al., <xref ref-type="bibr" rid="B59">2016</xref>). Chemokines (CXCL4, CXCL9, CXCL10, and CXCL11) are important nociceptive mediators produced by neurons, microglia, and/or astroglia (Colvin et al., <xref ref-type="bibr" rid="B15">2004</xref>). The CXCR3 receptor is expressed predominantly on T cells activated by CXCL9, CXCL10, and CXCL11 (Ransohoff, <xref ref-type="bibr" rid="B54">2009</xref>). A CXCR3 receptor antagonist was recently shown to inhibit glia activation and neuropathic pain and enhance the effectiveness of morphine (Piotrowska et al., <xref ref-type="bibr" rid="B52">2018</xref>). We showed the upregulation of Prss12, Mal, and Mag, but the downregulation of the Na<sub>v</sub> beta subunit 4 (Scn4b) 6 h after both HK-1 concentrations. Motopsyn/Prss12 can activate the PAR receptor in astrocytes and trigger glutamate release to activate neuronal NMDA receptors (Lee et al., <xref ref-type="bibr" rid="B34">2007</xref>; W&#x000F3;jtowicz et al., <xref ref-type="bibr" rid="B80">2015</xref>). MAL is a protein predominantly expressed by oligodendrocytes and Schwann cells and inhibits peripheral nerve myelination (Buser et al., <xref ref-type="bibr" rid="B13">2009</xref>). Voltage-gated sodium channels (Na<sub>v</sub>) initiate the action potential in excitable cells, and their mutations are implicated in chronic pain (Namadurai et al., <xref ref-type="bibr" rid="B45">2015</xref>).</p>
<p><xref ref-type="fig" rid="F5">Figure 5</xref> represents a summary of DE genes in different conditions. Both HK-1 concentrations resulted in more downregulated than upregulated genes at 24 h. Rph3a, Gabra2, Ryr2, Mag, and Scn1a were downregulated, while Hacd2 was upregulated. Hacd2 plays an important role in long-chain fatty acid biogenesis involved in neuronal membrane functions. Tachykinin receptors interact with Ryr2 in the endoplasmic reticulum, releasing calcium (Lin et al., <xref ref-type="bibr" rid="B37">2005</xref>). The interaction of Rph3A with the NMDA receptor in hippocampal neurons plays a crucial role in synaptic retention and long-term potentiation. Moreover, Rph3A can also interact with AMPA receptors (Franchini et al., <xref ref-type="bibr" rid="B22">2022</xref>). Notably, we have found remarkable upregulation of Fzd1 expressed by astrocytes and involved in their cross-talks (L&#x00027;Episcopo et al., <xref ref-type="bibr" rid="B35">2011</xref>, <xref ref-type="bibr" rid="B36">2018</xref>). Increased levels of myelin-associated proteins, including Mag and Mbp proteins, were demonstrated through Activin A oligodendroglial ACVR1B-mediated white matter remyelination after ischemic stroke in mice (Zheng et al., <xref ref-type="bibr" rid="B86">2021</xref>).</p>
<fig id="F5" position="float">
<label>Figure 5</label>
<caption><p>Summary of DE genes found in different treatment conditions: red columns refer to the respective group comparisons and the black columns demonstrate the shared DE genes of two or more groups. H: HK-1.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0005.tif"/>
</fig>
<p>One of the most interesting issues is assigning potential targets for HK-1. Interestingly, the Tacr genes encoding tachykinin receptors were expressed around the detection limit in the primary sensory neuron cultures. These results are similar to the dorsal root ganglia data from Linnarson and co-workers (<ext-link ext-link-type="uri" xlink:href="http://linnarssonlab.org/drg/">http://linnarssonlab.org/drg/</ext-link>). In human primary sensory neurons, Tac receptors were also detected at a low level (LaPaglia et al., <xref ref-type="bibr" rid="B32">2018</xref>). Tachykinin receptors with three NK1R isoforms are expressed in primary sensory neurons of the rat trigeminal system (Beaujouan et al., <xref ref-type="bibr" rid="B9">1999</xref>, <xref ref-type="bibr" rid="B8">2002</xref>; Page, <xref ref-type="bibr" rid="B50">2005</xref>; Garcia-Recio and Gasc&#x000F3;n, <xref ref-type="bibr" rid="B25">2015</xref>; Edvinsson et al., <xref ref-type="bibr" rid="B20">2021</xref>), which we could not detect by our sequencing technique in the cultures derived from neonatal rats. The lack of a functionally active NK1 receptor in our system is supported by no calcium influx in response to SP treatment (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>).</p>
<p>HK-1 at 1 &#x003BC;M induced calcium signaling-related transcriptomic alterations 6 h later, which is supported by our earlier fluorescent calcium influx data, which was not inhibited either by the NK1 receptor antagonist CP99994 or NK1R deletion (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>). In calcium signaling processes, F2r and EGFR receptors were DEs (<xref ref-type="fig" rid="F6">Figures 6</xref>, <xref ref-type="fig" rid="F7">7</xref>). F2r/PAR1 was downregulated, while the EGFR was upregulated. NK1R signaling by SP can activate tyrosine kinase receptors such as EGFR, and PAR1 can activate EGFR (Castagliuolo et al., <xref ref-type="bibr" rid="B14">2000</xref>; Arora et al., <xref ref-type="bibr" rid="B6">2008</xref>). This is supported by our earlier <italic>in vivo</italic> findings that in HK-1-deficient mice, the PAR agonist mast cell tryptase-induced arthritic pain was decreased (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B12">2020</xref>). Mast cells were shown to be involved in fibromyalgia-related pain (Theoharides et al., <xref ref-type="bibr" rid="B75">2019</xref>). Interestingly, Nr4a1 was downregulated 6 h after 1 &#x003BC;M and upregulated 24 h after 500 nM HK-1. Nr4a1 is an orphan nuclear receptor (Safe et al., <xref ref-type="bibr" rid="B60">2016</xref>) involved in innate and adaptive immune responses in leukocytes (Shaked et al., <xref ref-type="bibr" rid="B65">2015</xref>), which is downregulated and inactivated during neuroinflammation (Palumbo-Zerr et al., <xref ref-type="bibr" rid="B51">2015</xref>; Shaked et al., <xref ref-type="bibr" rid="B65">2015</xref>; Xiong et al., <xref ref-type="bibr" rid="B81">2020</xref>). NR4a1 suppresses inflammatory responses driven by interferon (IFN) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-&#x003BA;B) signaling (Freire and Conneely, <xref ref-type="bibr" rid="B23">2018</xref>) and microglia polarization (Rothe et al., <xref ref-type="bibr" rid="B58">2017</xref>). Calcium influx might inhibit CXCL9 production and consequently decrease T cell activation (Mishra and Lal, <xref ref-type="bibr" rid="B44">2021</xref>). Downregulated Slc25a5 might lead to mitochondrial dysfunction (Babenko et al., <xref ref-type="bibr" rid="B7">2018</xref>), which is involved in several chronic pain conditions (Meeus et al., <xref ref-type="bibr" rid="B43">2013</xref>; van den Ameele et al., <xref ref-type="bibr" rid="B76">2020</xref>; Yousuf et al., <xref ref-type="bibr" rid="B83">2020</xref>) related to reactive oxygen species generation and nociceptor sensitization (Salvemini et al., <xref ref-type="bibr" rid="B63">2011</xref>). Intracellular calcium homeostasis, regulated mainly by the mitochondria, endoplasmic reticulum, and nucleus, determines neuronal excitability. Nuclear calcium sensor 1 (NCS-1) was suggested to modulate the expression of mitochondrial genes (Simons et al., <xref ref-type="bibr" rid="B67">2019</xref>) together with the ATP sensor transporter Slc25a5 (Zhang et al., <xref ref-type="bibr" rid="B84">2009</xref>). Dysfunction of Grin1, an NMDA receptor subunit, has been associated with several neurological disorders (Intson et al., <xref ref-type="bibr" rid="B29">2019</xref>). Gria 2 is an AMPA receptor subunit having a major role in calcium permeation and voltage rectification; its abnormal functions also play a role in neural pathophysiologies (Salpietro et al., <xref ref-type="bibr" rid="B62">2019</xref>). Downregulation of Grin1 and Gria 2 might decrease calcium concentration after a longer time, influencing neuronal survival (Guo and Ma, <xref ref-type="bibr" rid="B26">2021</xref>). Several TRP channels are involved in sensory functions (Nilius et al., <xref ref-type="bibr" rid="B47">2003</xref>; Voets et al., <xref ref-type="bibr" rid="B77">2004</xref>, <xref ref-type="bibr" rid="B78">2005</xref>; Nilius and Sage, <xref ref-type="bibr" rid="B48">2005</xref>), and their expression or functional changes alter neuronal responsiveness (Nilius and Owsianik, <xref ref-type="bibr" rid="B46">2011</xref>). TRPM 3,7,8 were downregulated 24 h after 500 nM HK-1, which is the opposite of what we earlier found in response to another sensory neuropeptide, PACAP (Tak&#x000E1;cs-Lov&#x000E1;sz et al., <xref ref-type="bibr" rid="B72">2022</xref>). Notably, PACAP was downregulated 6 h after 500 nM HK-1, suggesting a potential link between the effects of these two peptides on TRP channel expression. The mitochondrial complex I Ndufb6 subunit was significantly downregulated, similar to PACAP (Tak&#x000E1;cs-Lov&#x000E1;sz et al., <xref ref-type="bibr" rid="B72">2022</xref>). <xref ref-type="fig" rid="F6">Figure 6</xref> demonstrates these findings in network.</p>
<fig id="F6" position="float">
<label>Figure 6</label>
<caption><p>Summary of calcium influx-related gene expression changes after 1 &#x003BC;M HK-1 treatment. Red means upregulated, green means downregulated genes, and the gray arrow shows the 24-h effect. Protein kinase A (PKA) was up and downregulated in different concentrations. Yellow rectangular means G &#x003B1; s signaling, and blue means G &#x003B1; q/11 signaling. Gray rectangular demonstrates 24 h result. Abbreviations: G protein subunit alpha I1 (GnaI), G protein subunit beta 2 (GNB2), acid-sensing ion channel subunit 1,3 (Asic1; Asic3), potassium two pore domain channel subfamily K member 3 (Kcnk3), taste 1 receptor member (Tas1r2), adenylyl cyclase (AC), cyclic adenosine monophosphate (cAMP), G protein subunit gamma 3 (Gng3), and sodium voltage-gated channel beta subunit 4 (SCN4B) having a potential role in nociceptive sensation.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0006.tif"/>
</fig>
<fig id="F7" position="float">
<label>Figure 7</label>
<caption><p>FC value of significant DE genes at 6 h of HK-1 1 &#x003BC;M involved in calcium signaling pathways. Red means upregulated genes and green shows downregulated genes. Abbreviations can be found in the <xref ref-type="supplementary-material" rid="SM1">Supplementary material</xref>. Asterisks denote these genes were found significant DE genes (&#x0002A;<italic>p</italic> &#x0003C; 0,05; &#x0002A;&#x0002A;<italic>p</italic> &#x0003C; 0,01; &#x0002A;&#x0002A;&#x0002A;<italic>p</italic> &#x0003C; 0,001) as analyzed by moderated t-test.</p></caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fnmol-16-1186279-g0007.tif"/>
</fig>
<p>Our previous <italic>in vivo</italic> data demonstrated the pain-mediating role of HK-1 in several acute and chronic orofacial, neuropathic, and inflammatory pain models (partial sciatic nerve ligation, acute, and chronic CFA and mast cell tryptase-induced, as well as K/BxN serum-transfer arthritis models) (Borb&#x000E9;ly et al., <xref ref-type="bibr" rid="B10">2013</xref>, <xref ref-type="bibr" rid="B12">2020</xref>; Acz&#x000E9;l et al., <xref ref-type="bibr" rid="B2">2018</xref>; Hunyady et al., <xref ref-type="bibr" rid="B28">2019</xref>). Although it is difficult to directly compare the present results with <italic>in vivo</italic> conditions, several similarities can be determined between gene expressions in the mouse TRG after adjuvant-induced orofacial inflammation and the present TRG culture experiment following HK-1 treatment. We earlier showed that the HK-1 encoding <italic>Tac4</italic> gene was upregulated in the TRG in the adjuvant-induced model. Meanwhile, fibroblast growth factor 13 (Fgf13, also termed as glia activating factor) was downregulated in wild-type mice, but upregulated in HK-1-deficient ones (Acz&#x000E9;l et al., <xref ref-type="bibr" rid="B1">2020</xref>). This well correlates with the Fgf9 downregulation we observed in the present study in response to 1 &#x003BC;M 6 h later. Fgfs are involved in neuron&#x02013;glia interactions and glia proliferation, mediating neuroinflammatory mechanisms (Stork et al., <xref ref-type="bibr" rid="B70">2014</xref>). Furthermore, an orphan G protein-coupled receptor, Gpr62, playing a role in axo-myelinic signaling, was upregulated in the TRG of adjuvant-treated wild-type mice (Hay et al., <xref ref-type="bibr" rid="B27">2021</xref>) similar to Gpr108 upregulation after 1 &#x003BC;M HK-1 in the present experiment to inhibit Toll-like receptor-triggered inflammatory responses (Dong et al., <xref ref-type="bibr" rid="B18">2018</xref>). The voltage-gated K<sup>&#x0002B;</sup> channel-interacting protein 9 (Kcnj9) was also downregulated in the TRG after adjuvant injection (Acz&#x000E9;l et al., <xref ref-type="bibr" rid="B1">2020</xref>), which supports our findings on the Kcnip4 downregulations in the present model. Inward-rectifying K&#x0002B; currents have been shown to change in the trigeminal ganglia during peripheral inflammation (Takeda et al., <xref ref-type="bibr" rid="B73">2011</xref>). Transmembrane protein 100 (Tmem100) was upregulated in the TRG in the <italic>in vivo</italic> mouse model, while in our cell system the expressions of related members of this protein family, Tmem128, significantly increased. Integrin subunit alpha 7 (Itga7) involved in glia proliferation (Tan et al., <xref ref-type="bibr" rid="B74">2022</xref>), was also downregulated both in the mouse model (Acz&#x000E9;l et al., <xref ref-type="bibr" rid="B1">2020</xref>) and in the present cell culture study Itgav both are expressed on glial cells (Mapps et al., <xref ref-type="bibr" rid="B42">2022</xref>). RNA-Seq literature data demonstrated Kcnj9, F2rl2 (PAR3) upregulation in the DRG in a neuropathic pain model similar to what we found for F2r and PAR1 (Stevens et al., <xref ref-type="bibr" rid="B69">2020</xref>). Validation of the RNA sequencing data with qPCR showed a good correlation for all investigated genes except Fgfr1. However, such discrepancies are not unusual based on the literature data; others described that these two techniques provide similar results in 87.9% (Protasio et al., <xref ref-type="bibr" rid="B53">2013</xref>) and 95.2% of genes (Liu et al., <xref ref-type="bibr" rid="B38">2014</xref>), which is in agreement with the present findings.</p>
<p>In conclusion, this is the first approach to determining transcriptomic alterations induced by HK-1 in primary sensory neurons that might be related to their activation mechanisms and pain. We showed concentration- and time-dependent actions and identified potential pain-related processes such as microglial&#x02013;neuron or GPCR interactions, myelin-associated gene expression, and orphan GPCRs having roles in GABAergic pathways by modifying NMDA and AMPA receptor subunits, demonstrating that not just neurons, but mast cells and glia cells might be affected by HK-1. The effects specific to the 1 &#x003BC;M (sodium channel activity, neurotransmitter receptor activity, cytokine activity) were potentially calcium influx-dependent, as we earlier showed that the 1 &#x003BC;M, but not the 500 nM concentration, induced a calcium signal in this experimental paradigm. Although the target(s) of HK-1 cannot be determined on the basis of the present results, it is not likely to be the NK1 tachykinin receptor. Identifying the receptor might open novel perspectives in analgesic research.</p>
</sec>
<sec sec-type="data-availability" id="s5">
<title>Data availability statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be at: <ext-link ext-link-type="uri" xlink:href="https://www.ebi.ac.uk/ena">https://www.ebi.ac.uk/ena</ext-link>, PRJEB47291.</p>
</sec>
<sec sec-type="ethics-statement" id="s6">
<title>Ethics statement</title>
<p>The animal studies were approved by the Ethical Committee on Use of Laboratory Animals at the University of P&#x000E9;cs (permission no: BA02/2000-51/2017). The studies were conducted in accordance with the local legislation and institutional requirements. Written informed consent was obtained from the owners for the participation of their animals in this study.</p>
</sec>
<sec sec-type="author-contributions" id="s7">
<title>Author contributions</title>
<p>&#x000C9;B, &#x000C9;S, KB, and ZH: conceptualization. TA and KB: methodology. JK: software. JK, KT-L, LC, and PU: validation. KT-L and JK: formal analysis, data curation, and visualization. ZH: investigation and supervision. AG and ZH: resources and funding acquisition. KT-L: writing&#x02014;original draft preparation. KT-L, &#x000C9;B, &#x000C9;S, KB, and ZH: writing&#x02014;review and editing. All authors contributed to the article and approved the submitted version.</p>
</sec>
</body>
<back>
<sec sec-type="funding-information" id="s8">
<title>Funding</title>
<p>This research was supported by the National Brain Research Program 3.0 (NAP-3; Chronic Pain Research Group) and the National Research Development and Innovation Office grants OTKA FK132587 and FK137951. AG and JK were supported by the grants GINOP-2.3.4-15-2020-00010, GINOP-2.3.1-20-2020-00001, and Educating Experts of the Future: Developing Bioinformatics and Biostatistics Competencies of European Biomedical Students (BECOMING, 2019-1-HU01-KA203-061251). Bioinformatics infrastructure was supported by ELIXIR Hungary (<ext-link ext-link-type="uri" xlink:href="https://www.bioinformatics.hu/">https://www.bioinformatics.hu/</ext-link>). Project no. TKP 2021-EGA-16 has been implemented with the support provided by the National Research, Development, and Innovation Fund of Hungary, financed under the EGA 16 funding scheme. The research was performed in collaboration with the Genomics and Bioinformatics Core Facility at the Szent&#x000E1;gothai Research Centre of the University of P&#x000E9;cs. This project was supported by the National Research, Development, and Innovation Office (PharmaLab, RRF-2.3.1-21-2022-00015). RRF-2.3.1-21-2022-00015 has been implemented with the support of the European Union. &#x000C9;B was supported by the J&#x000E1;nos Bolyai Research Scholarship of the Hungarian Academy of Sciences (BO/00592/19/5).</p>
</sec>
<ack><p>The authors wish to thank Cec&#x000ED;lia Disztl for expert technical assistance and the Genomics and Bioinformatics Core Facility at the Szent&#x000E1;gothai Research Centre of the University of P&#x000E9;cs and the E&#x000F6;tv&#x000F6;s L&#x000F3;r&#x000E1;nd Research Network (ELKH-PTE changed to HUN-REN E&#x000F6;tv&#x000F6;s L&#x000F3;r&#x000E1;nd Research Network to Hungarian Research Network Chronic Pain Research Group). The authors wish to thank Prof. Dr. Bal&#x000E1;zs Gyorffy and his Oncological Biomarker Research Group, ELKH Research Centre for Natural Sciences, for their contribution to the development of the bioinformatics pipelines.</p>
</ack>
<sec sec-type="COI-statement" id="conf1">
<title>Conflict of interest</title>
<p>ZH was employed by the company PharmInVivo Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec sec-type="disclaimer" id="s9">
<title>Publisher&#x00027;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec sec-type="supplementary-material" id="s10">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fnmol.2023.1186279/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fnmol.2023.1186279/full#supplementary-material</ext-link></p>
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