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        <title>Frontiers in Genetics | Immunogenetics section | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/genetics/sections/immunogenetics</link>
        <description>RSS Feed for Immunogenetics section in the Frontiers in Genetics journal | New and Recent Articles</description>
        <language>en-us</language>
        <generator>Frontiers Feed Generator,version:1</generator>
        <pubDate>2026-05-02T04:34:11.316+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1771872</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1771872</link>
        <title><![CDATA[The role of pluripotency regulators in triple-negative breast cancer immune response]]></title>
        <pubdate>2026-04-23T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Carolina López-Santana</author><author>Fabio Mendez-Rivera</author><author>David A. Bernal-Estévez</author>
        <description><![CDATA[Triple-negative breast cancer (TNBC) is defined by the absence of estrogen, progesterone, and HER2 receptor expression. A critical challenge in managing TNBC is its high concentration of cancer stem cells (CSCs), which drives chemotherapy resistance and correlates with poor patient survival. In normal physiology, stem cell pluripotency and differentiation are governed by core transcription factors (such as Oct4, Sox2, Nanog, Klf4, and c-Myc) alongside key signaling networks, including the Notch, Wnt/β-catenin, and Sonic Hedgehog (Shh) pathways. During carcinogenesis, aberrant activation of these regulators in TNBC not only promotes the self-renewal of tumor cells but also actively facilitates immune evasion. Specifically, overexpressed pluripotency transcription factors enable cancer cells to downregulate antigen presentation molecules (e.g., MHC class I) and secrete immunomodulatory cytokines. Concurrently, dysregulated signaling, such as the Wnt/β-catenin pathway, inhibits dendritic cell maturation and recruits Myeloid-Derived Suppressor Cells (MDSCs) and regulatory T cells (Tregs) into the tumor microenvironment, thereby blunting the anti-tumor T cell response. This review examines the role of key pluripotency regulators in TNBC-mediated immune evasion, highlighting emerging immunotherapeutic strategies targeting these networks and summarizing current clinical research.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1786514</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1786514</link>
        <title><![CDATA[Identification of a novel HLA-G allele, HLA-G*01:66, using PolyseqOne and oxford nanopore sequencing]]></title>
        <pubdate>2026-03-04T00:00:00Z</pubdate>
        <category>Brief Research Report</category>
        <author>Ran Li</author><author>Liyan Sun</author><author>Siqi Cai</author>
        <description><![CDATA[HLA-G*01:66 differs from HLA-G*01:01:22:01 by one missense nucleotide substitution at position 508 in exon 3.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1775026</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1775026</link>
        <title><![CDATA[Integrative biology shows DPP4 affects inflammatory response to eclampsia and cell model growth via p65/NLRP3/ASC/Caspase-1 pathway]]></title>
        <pubdate>2026-03-04T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Zhimin Bian</author><author>Li Hao</author><author>Rongjuan Yang</author><author>Jianghui Sun</author>
        <description><![CDATA[Objective: Eclampsia severely endangers maternal and neonatal health, being a major contributor to emergency admissions, maternal mortality, and long-term complications. This study aimed to identify reliable biomarkers and explore potential therapeutic targets for improving the diagnosis, prevention, and management of eclampsia.Methods: Differential gene expression analysis was performed on the GSE60438 dataset. Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct gene modules and screen modules associated with pre-eclampsia. Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) were employed to annotate the biological functions and pathways of candidate genes. Immune cell infiltration was evaluated via the xCell algorithm. LASSO regression was utilized to identify hub genes, which was validated by RT-qPCR and Western blot in clinical samples (placental tissues and serum from pre-eclampsia patients). DPP4 knockdown experiments were conducted in HTR-8 cells to assess its effects on pro-inflammatory cytokines (IL-6, TNF-α) and trophoblast cell functions (migration, invasion, lumen formation). Additionally, the p65/NLRP3/ASC/Caspase-1 signaling pathway was examined to clarify the underlying molecular mechanism.Results: A total of 4,642 upregulated and 2,193 downregulated genes were identified in pre-eclampsia samples. WGCNA revealed nine gene modules, with the red module showing the strongest positive correlation and the magenta module exhibiting a negative correlation with pre-eclampsia. GO analysis indicated enrichment of candidate genes in chromosome organization, mitochondrial function, and DNA repair. GSEA identified key immune-related pathways, including cytokine production and chemokine signaling. LASSO regression pinpointed DPP4 as a hub gene, which was significantly upregulated in pre-eclampsia clinical samples. DPP4 knockdown in HTR-8 cells reduced IL-6 and TNF-α levels, impaired trophoblast migration, invasion, and lumen formation, and inhibited the phosphorylation of p65, NLRP3, ASC, and Caspase-1 in the p65/NLRP3/ASC/Caspase-1 signaling pathway.Conclusion: Targeting DPP4 may serve as an innovative strategy for regulating inflammatory signaling in eclampsia, with potential to alleviate maternal symptoms and improve pregnancy outcomes.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1745482</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1745482</link>
        <title><![CDATA[KIR AA individuals possess strong inhibitory KIR alleles alongside HLA ligands that are protective against leukemia in the Chinese population]]></title>
        <pubdate>2026-02-05T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Zhihui Deng</author><author>Jianxin Zhen</author><author>Yunan Li</author><author>Shuang Liang</author><author>Manru Zhang</author><author>Siqi Cai</author><author>Renhui Jiang</author><author>Zhichao Yang</author><author>Qiong Yu</author><author>Jinyong Wang</author><author>Jie Liu</author>
        <description><![CDATA[IntroductionThe killer-cell immunoglobulin-like receptor (KIR) gene cluster exhibits complicated diversity in haplotype content, copy-number variation (CNV), and allelic polymorphism. To date, 2,286 distinct KIR alleles have been released in the IPD-KIR Database. However, little is known about the impact of high-resolution-level KIR allelic polymorphisms on leukemia. Our previous study showed that the KIR AA genotype carrying more inhibitory genes conferred differential protection against leukemia in the Chinese Southern Han population. Herein, we hypothesized the impact of KIR alleles in the KIR A haplotype and cognate human leukocyte antigen (HLA) ligand on leukemia.MethodsThe study cohort included 318 ALL patients, 336 AML patients, and 306 unrelated healthy controls. All the study samples were subject to HLA-A, -B, and -C sequencing-based genotyping (PCR-SBT) and high-resolution KIR genotyping for all the seven functional KIR genes (KIR2DL1, KIR2DL3, KIR2DL4, KIR3DL1, KIR3DL2, KIR3DL3, and KIR2DS4) on the KIR A haplotype. HLA and KIR genotypes were assigned using Assign 4.7.1 software.ResultsIn the present study, our high-resolution genetic analysis revealed protective KIR–HLA interactions in individuals with the KIR AA genotype. The strong inhibitory KIR2DL1*00201+C2 interaction reduced ALL risk (p = 0.01), while KIR2DL1*00302 +C2 (p = 0.008), KIR2DL3*00201+C1 (p = 0.03), and KIR3DL1*00501+Bw4 80I (p = 0.008) interactions protected against AML (p < 0.05). However, the functionally weaker inhibitory KIR2DL1*004+C2 interaction conferred ALL risk (p = 0.01) in individuals with the KIR Bx genotype. Notably, we found that the allelic polymorphisms of the structure gene KIR3DL3 were associated with the occurrence of leukemia. KIR3DL3*001 tends to confer protection against AML (8.4% vs. 1.3%, p = 0.004, Pc = 0.06), whereas KIR3DL3*009 conferred susceptibility to AML (29.3% vs. 47.1%, p = 0.001, Pc = 0.016). KIR3DL3*001 differs from KIR3DL3*009 by an amino acid substitution of non-charged asparagine (N) to charged histidine (H) in its transmembrane domain, suggesting that this functional variant site KIR3DL3_N300H may play a critical role in the occurrence of leukemia in the Chinese population.ConclusionThese data suggest that KIR AA individuals possess strong inhibitory interactions of KIR alleles and HLA, arming KIR AA+ NK cells to meditate stronger alloreactivity and cytotoxicity against leukemia cells with lowered HLA expression. Our findings may provide valuable insights into leukemia pathogenesis and better understanding of the immune mechanisms.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1771063</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1771063</link>
        <title><![CDATA[Editorial: Genetics of pediatric immune-mediated diseases]]></title>
        <pubdate>2026-01-19T00:00:00Z</pubdate>
        <category>Editorial</category>
        <author>Sara Manti</author><author>Beatriz Elena Marciano</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1720056</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1720056</link>
        <title><![CDATA[Impacts of rs7528684 (−169T/C) on FCRL3, FOXP3, and IL-35 gene expressions and IgG-RF correlation: insights into the pathogenesis of rheumatoid arthritis]]></title>
        <pubdate>2026-01-02T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>S. Mohamed Muzammil</author><author>S. Asha Devi</author>
        <description><![CDATA[BackgroundThe Fc receptor-like protein 3 (FCRL3) gene encodes a transmembrane receptor that is predominantly expressed on the surfaces of regulatory T cells (Tregs). The single-nucleotide polymorphism (SNP) rs7528684 (−169T/C) in the FCRL3 gene has been hypothesised to enhance its expression, which in turn causes dysfunction of Tregs and results in loss of self-tolerance as well as diminished production of anti-inflammatory cytokines. This process triggers rapid proliferation of the autoreactive T cells and other immune cells, exacerbating the progression of rheumatoid arthritis (RA) and other autoimmune diseases.MethodsIn the current study, we screened the FCRL3 SNP rs7528684 to assess its association with the risk of RA in the Indian population. The screening was performed using high-resolution melting analysis, and the findings were confirmed via Sanger sequencing. We further analysed the impacts of rs7528684 on FCRL3, forkhead box protein 3 (FOXP3), and interleukin-35 (IL-35) gene expressions using quantitative real-time polymerase chain reaction. The gene expression correlation between FCRL3 and FOXP3 mRNA expression was analysed using Spearman’s rank correlation coefficient (ρ) analysis. Concurrently, the inflammatory serological biomarkers immunoglobulin G rheumatoid factor (IgG-RF) and C-reactive protein were evaluated in the RA patients.ResultsThe FCRL3 SNP rs7528684 C/C genotype was significantly associated with increased risk of RA in the Indian ethnicity (p = 0.0005). Furthermore, the C allele frequency was significantly elevated within the RA group (58.6%). Similarly, RA patients carrying the C/C genotype also exhibited higher FCRL3 mRNA expression levels than the controls (p = 0.0072). Additionally, FOXP3 and IL-35 mRNA expressions were downregulated in RA patients carrying the C/C genotype. The FCRL3 mRNA expression demonstrated a significant negative correlation with FOXP3 mRNA expression (ρ = - 0.5526, p = 0.0094, R2 = 0.3052) in RA patients. The results also showed positive correlations between the C/C genotype and IgG-RF-positive RA cases.ConclusionOur findings validate that the C/C genotype of the FCRL3 SNP rs7528684 is strongly associated with RA in the Indian ethnicity. This genotype is characterised by positive IgG-RF and upregulated FCRL3 and downregulated FOXP3 and IL-35 as key anti-inflammatory cytokines. Concurrently, FCRL3 and FOXP3 mRNA expression levels are inversely correlated.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1722527</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1722527</link>
        <title><![CDATA[Transcriptomic profiling of human endothelial cells infected with venezuelan equine encephalitis virus reveals NRF2 driven host reprogramming mediated by omaveloxolone treatment]]></title>
        <pubdate>2025-12-18T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mostafa Rezapour</author><author>Lorreta A. Opoku</author><author>Stephanie V. Trefry</author><author>Abbas Alili</author><author>Maame Konadu</author><author>Maria Galarza Dionisio</author><author>Metin Nafi Gurcan</author><author>Aarthi Narayanan</author>
        <description><![CDATA[IntroductionVenezuelan Equine Encephalitis virus (VEEV) is a mosquito-borne alphavirus that causes neurotropic disease with significant morbidity and mortality, especially in children. While interferon-stimulated genes (ISGs) are central to host defense, therapeutic modulation of host responses remains underexplored. Omaveloxolone (OMA), an FDA-approved NRF2 activator, has been proposed as a candidate for host-directed antiviral therapy.MethodsWe investigated transcriptomic responses of human umbilical vein endothelial cells (HUVECs) infected with VEEV TC-83 in the presence or absence of OMA at 24 hours post-infection using RNA-Seq. Differential expression analysis was performed with Generalized Linear Model with Quasi-Likelihood and Magnitude-Altitude Scoring (GLMQL-MAS), followed by Cross-MAS to distinguish shared and condition-specific programs.ResultsUntreated VEEV infection induced a canonical ISG signature including IFIT1-3, OASL, RSAD2, and MX1, together with cytokine and chemokine signaling (IL6, CXCL10, CXCL11), consistent with a strong proinflammatory and antiviral state. In contrast, OMA treatment elicited a broader shift, with 729 upregulated and 1,264 downregulated genes. Key OMA-induced genes (HMOX1, NQO1, GCLM, TXNRD1, SLC7A11) mapped to NRF2-dependent antioxidant, ferroptosis resistance, and detoxification pathways, accompanied by widespread repression of histone cluster genes. Cross-MAS revealed 695 OMA-unique upregulated genes, 86 untreated-unique genes, and 34 shared genes forming a compact interferon-centered antiviral backbone. Network analyses highlighted NRF2-driven antioxidant modules under OMA and cytokine-chemokine modules under untreated infection.DiscussionThese findings demonstrate that OMA redirects host transcription from an interferon-centric, inflammatory response toward an NRF2-driven cytoprotective program while preserving core antiviral mechanisms, which supports NRF2 activation as a therapeutic strategy against VEEV.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1661511</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1661511</link>
        <title><![CDATA[Emerging roles of natural killer cell ligands—HLA-E, HLA-F, HLA-G, MICA, and MICB—in in vitro fertilization outcomes]]></title>
        <pubdate>2025-11-13T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Itta Krishna Chaaithanya</author><author>Raja Rajalingam</author>
        <description><![CDATA[Infertility affects approximately one in six individuals globally and represents a complex public health concern influenced by a range of biological, environmental, and socioeconomic factors. In vitro fertilization (IVF) has emerged as a pivotal assisted reproductive technology (ART), yet its success is often hindered by recurrent implantation failure (RIF) and hypertensive complications such as preeclampsia (PE). Recent research highlights the critical role of the immune system particularly non-classical Human Leukocyte Antigen (HLA) class I molecules (HLA-G, HLA-E, HLA-F) and MHC class I chain-related proteins (MICA/B) in modulating maternal-fetal tolerance and determining IVF outcomes. This review synthesizes emerging evidence on the structure, expression, receptor interactions, and polymorphisms of these molecules, emphasizing their roles in embryo implantation, immune modulation, and pregnancy maintenance. Soluble HLA-G (sHLA-G) has shown promise as a biomarker for embryo viability, while variations in KIR–HLA interactions and polymorphisms in non-classical HLA genes have been linked to RIF and adverse reproductive outcomes. Despite promising findings, routine clinical testing of these markers remains limited due to methodological inconsistencies, lack of large-scale validation, and the multifactorial nature of implantation. Future research priorities include functional genomics, standardized diagnostic assays, AI-driven predictive tools, and translational trials of immunomodulatory therapies. Understanding the immunogenetic landscape offers new avenues for personalized reproductive care and improved IVF success rates.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1641956</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1641956</link>
        <title><![CDATA[A novel de novo IL2RG nonsense mutation in a pediatric patient with X-linked severe combined immunodeficiency]]></title>
        <pubdate>2025-10-07T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Lin Wang</author><author>Aiyan Ren</author><author>Yuanyuan He</author><author>Lu Wang</author><author>Sixi Wang</author><author>Xin Xie</author><author>Mei Tan</author><author>Yan Chen</author><author>Pei Huang</author><author>Zuochen Du</author>
        <description><![CDATA[ObjectiveThe study aims to describe the clinical manifestations, immunophenotype, and gene mutation characteristics of a child with X-linked severe combined immunodeficiency (X-SCID) caused by an IL2RG mutation (NM_000206.3; exon 2 c.216C > A, p.Cys72*), and to contextualize these findings through a review of reported cases of X-SCID associated with Talaromyces marneffei (T. marneffei) infection, highlighting the immunological and diagnostic relevance of the mutation.MethodsThe clinical data of a child with X-SCID caused by an IL2RG mutation were retrospectively analyzed. Whole-exome sequencing and Sanger sequencing were used to identify the mutation, and flow cytometry was employed for immunophenotypic analysis to assess the impact of the mutation on immune function. A literature review was performed on reported cases of X-SCID associated with T. marneffei infection identified in PubMed and Scopus.ResultsThe patient was a 4-month-old male infant presenting with chronic diarrhea, recurrent fever, and anemia, with poor response to antibiotic treatment. Laboratory tests indicated T. marneffei infection, significantly reduced T lymphocytes and NK cells, and decreased levels of immunoglobulins (IgG, IgA, IgE). Genetic testing revealed a de novo hemizygous mutation in the IL2RG gene (NM_000206.3; exon2 c.216C > A, p.Cys72*), which has not been previously reported. Flow cytometric analysis showed a severe reduction in T lymphocytes, absence of CD8 + T cells, reduced NK cells, and a normal number of B lymphocytes. Six cases of IL2RG gene mutation combined with T. marneffei infection were identified in the literature, most showing fever, hepatosplenomegaly and respiratory tract infection.ConclusionThis case of X-SCID caused by a novel de novo IL2RG mutation expands the known mutation spectrum and highlights its immunological and diagnostic relevance. The review of reported cases of X-SCID with T. marneffei infection further clarifies genotype–phenotype correlations and supports improved recognition of such rare presentations.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1686852</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1686852</link>
        <title><![CDATA[Editorial: Mitochondria in metabolic reprogramming and immune activation: the key gene and therapeutic target]]></title>
        <pubdate>2025-09-01T00:00:00Z</pubdate>
        <category>Editorial</category>
        <author>Yongzheng Guo</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1628428</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1628428</link>
        <title><![CDATA[Genetic association between STAT4 and primary Sjögren’s syndrome in Han Chinese women]]></title>
        <pubdate>2025-07-23T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Fangfang Li</author><author>Junhui Lu</author><author>Chao Cen</author><author>Wanqiu Zhen</author><author>Jiaojiao Zhang</author><author>Shengming Wang</author>
        <description><![CDATA[IntroductionSTAT4, a pivotal transcription factor governing immune and inflammatory responses, has been implicated in autoimmune pathogenesis. This case-control study aimed to examine the relationship between STAT4 single-nucleotide polymorphisms (SNPs) and primary Sjögren’s syndrome (pSS) in a female Chinese Han population, exploring potential genetic mechanisms underlying pSS susceptibility.MethodsSix STAT4 single-nucleotide polymorphisms (rs10931481, rs1400656, rs10168266, rs3821236, rs7601754, and rs10174238) were genotyped using MassARRAY, with STAT4 expression determined by quantitative real-time PCR and cytokine levels assessed via ELISA.ResultsThe rs10168266-C allele emerged as a significant risk factor for pSS, with CC homozygotes exhibiting elevated disease susceptibility compared to CT/TT carriers (Pc = 0.001, OR = 1.905). Conversely, the T allele conferred protection (Pc = 0.002, OR = 0.575), and CT genotypes were underrepresented in patients (Pc = 0.003, OR = 0.539). Notably, rs10168266-CC individuals displayed elevated STAT4 expression in peripheral blood mononuclear cells and elevated serum IL-6 levels compared to T allele carriers (both P < 0.05).DiscussionThis study represents the initial investigation to uncover the genetic association between the STAT4 gene and pSS in Han Chinese women. The rs10168266 polymorphism in the STAT4 gene is a novel genetic determinant of pSS susceptibility in female Chinese Han populations. The mechanism may involve dysregulation of IL-6 signaling driven by STAT4, offering a theoretical foundation for the advancement of gene therapy.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1619032</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1619032</link>
        <title><![CDATA[Editorial: Proficiency testing in histocompatibility and immunogenetics: current status and future perspectives]]></title>
        <pubdate>2025-06-05T00:00:00Z</pubdate>
        <category>Editorial</category>
        <author>Martin Petrek</author><author>Kelley M. K. Hitchman</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1506862</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1506862</link>
        <title><![CDATA[Disentangling effects of the DR and DQ isomers encoded by the HLA class II haplotype DRB1*15:01/DQB1*06:02 to help establish the true risk allele for FVIII inhibitor development in Hemophilia A]]></title>
        <pubdate>2025-04-09T00:00:00Z</pubdate>
        <category>Brief Research Report</category>
        <author>Vincent P. Diego</author><author>Bernadette W. Luu</author><author>Marcio A. Almeida</author><author>Raja Rajalingam</author><author>Marco Hofmann</author><author>Jacob A. Galan</author><author>Eron G. Manusov</author><author>Jerry S. Powell</author><author>Long V. Dinh</author><author>Henry Mead</author><author>Huy Huynh</author><author>Anne M. Verhagen</author><author>Juan M. Peralta</author><author>Paul V. Lehmann</author><author>Satish Kumar</author><author>Eli J. Fine</author><author>Joanne E. Curran</author><author>Harald H. Goring</author><author>Miguel A. Escobar</author><author>Sarah Williams-Blangero</author><author>Eugene Maraskovsky</author><author>John Blangero</author><author>Tom E. Howard</author>
        <description><![CDATA[IntroductionHemophilia A (HA) patients (HAPs) with the human leukocyte antigen (HLA)-class-II (HLAII) haplotype DRB1*15:01/DQB1*06:02, and thus antigen presenting cells which express HLAII β-polypeptide chains that form heterodimers of DR15- and DQ6-serotypes, respectively, have an increased risk of developing factor (F)VIII inhibitors (FEIs)—neutralizing antibodies against the therapeutic-FVIII-proteins (tFVIIIs) infused to prevent/arrest bleeding. As DRB1*15:01 and DQB1*06:02 exist in strong linkage disequilibrium, association analysis cannot determine which is the actual risk allele.MethodsTo establish the true risk allele of this haplotype, we analyzed the tFVIII-derived peptides (tFVIII-dPs) bound to either the DR or DQ molecules that comprise the individual HLAII repertoires expressed by monocyte-derived dendritic cells obtained from 25 normal blood donors and six HAPs, four without and two with FEIs. We performed log-linear mixed model analyses, where the dependent variable is the log of the measured peptide count. Under Model 1, we analyzed an HLAII allele predictor consisting of ten levels (four DRB1 and six DQB1 alleles) in the fixed effects and variables in the random effects to account for non-independence. Model 2—where the HLAII allele variable consisted of only DRB1*15:01 and DQB1*06:02—compares the HLAII alleles.ResultsRelative to the Model 1 reference, DRB1*15:01 and DQB1*06:02 significantly increased tFVIII-derived peptide counts, and DRB1*15:01 contributed significantly more than DQB1*06:02. Reported as risk ratios (RRs) and their 95% confidence interval (CI) lower- (LB) and upper-bound (UB), we found a RR (95% CI-LB, -UB) of 14.16 (10.38, 19.33) and 1.76 (1.24, 2.50) for DRB1*15:01 and DQB1*06:02, respectively. Under Model 2, we found an RR for DRB1*15:01 against DQB1*06:02 of 7.00 (5.80, 8.44).Discussion/conclusionOur results suggest that DRB1*15:01 is the offending HLAII allele and that DR15 allotypes underlie the increased FEI risk in HAPs.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1572987</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1572987</link>
        <title><![CDATA[Editorial: Novel applications of epitope biology to improve outcomes in transplantation]]></title>
        <pubdate>2025-02-26T00:00:00Z</pubdate>
        <category>Editorial</category>
        <author>James H. Lan</author><author>Robert Liwski</author><author>Alberto Cardoso Martins Lima</author><author>Sandra Tafulo</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2025.1505933</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2025.1505933</link>
        <title><![CDATA[Vitamin A family suppresses periodontitis by restoring mitochondrial metabolic reprogramming in macrophages through JAK-STAT pathway]]></title>
        <pubdate>2025-01-28T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Zishuo Cheng</author><author>Shun Huang</author><author>Qiya Tang</author><author>Danlan Zhang</author><author>Lan Huang</author>
        <description><![CDATA[ObjectiveMitochondrial metabolic reprogramming in macrophages is crucial in the development and progression of inflammation. Given vitamin A’s antioxidant properties and its therapeutic effects on inflammation, this study aims to elucidate how vitamin A influences mitochondrial metabolic reprogramming in inflammatory states, specifically in periodontitis, through genetic bioinformatics and experimental methods.MethodThe study utilized the GSE16134 dataset from the Gene Expression Omnibus (GEO) database, focusing on human periodontitis. Vitamin A-targeted genes (ATGs) were identified and analyzed using CIBERSORT to explore their role in inflammation. Cluster analysis revealed two phenotypes associated with ATGs, showing differential expression of genes like COX1, IL-1β, and STAT3, and immune activation patterns. Weighted Gene Co-expression Network Analysis (WGCNA) identified 145 markers correlated with ATG-guided phenotypes and inflammation. Machine learning models, combined with Gene Set Variation Analysis (GSVA), identified five key genes (RGS1, ACAT2, KDR, TUBB2A, TDO2) linked to periodontitis. Cell Type-Specific Enrichment Analysis (CSEA) highlighted macrophages as critical in metabolic reprogramming, validated by external datasets with an AUC of 0.856 in GSE10334 and 0.750 in GSE1730678. Experimental validation showed vitamin A’s role in suppressing endoplasmic reticulum stress and altering mitochondrial dynamics, as well as metabolic reprogramming influencing inflammation via the STAT3 pathway in RAW 264.7 cells.ResultsThe study identified 13 differentially expressed ATGs in periodontitis, showing strong correlations with inflammation, particularly in plasma cells, macrophages, dendritic cells, neutrophils, and mast cells. Two ATG-guided phenotypes were identified, differing in gene expression and immune activation. WGCNA and machine learning models identified 145 markers and five key genes associated with periodontitis. GSVA and CSEA analyses highlighted the JAK-STAT pathway and macrophage involvement in metabolic reprogramming. Experimental data confirmed vitamin A’s effects on mitochondrial dynamics and metabolic reprogramming through the STAT3 pathway.ConclusionThe study demonstrates that vitamin A’s therapeutic effect on periodontitis is mediated through JAK-STAT pathway-guided mitochondrial metabolic reprogramming in macrophages. It identifies two genetic and immune-related phenotypes and five genetic identifiers associated with periodontitis risk.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1502832</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1502832</link>
        <title><![CDATA[Global deletion of the immune cell transcription factor, T-bet, alters gut microbiota and insulin sensitivity in mice]]></title>
        <pubdate>2024-11-27T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>E. Stolarczyk</author><author>C. T. Vong</author><author>N. Garrido-Mesa</author><author>E. Marks</author><author>D. Abdel-Aziz</author><author>Q. Ju</author><author>I. Jackson</author><author>N. Powell</author><author>G. M. Lord</author><author>J. K. Howard</author>
        <description><![CDATA[The gut microbiota plays a role in energy homeostasis: its composition differs in lean and obese mice and may impact insulin sensitivity. The immune system has co-evolved with the gut microbiota, but direct regulation of microbial communities by the immune system and its metabolic impact is unclear. Mice lacking the immune cell specific transcription factor T-bet (Tbx21) are insulin sensitive. Compared with wild-type mice, T-bet deficient mice were found to have a higher proportion of colonic regulatory T cells despite significantly fewer colonic T cells, B cells and NK cells. Microbiota deletion by administration of antibiotics, increased colonic immune cell numbers. Furthermore, we report that T-bet−/− mice have an altered gut microbial composition and fecal short-chain fatty acid content, with an increase in butyrate production, compared with wild-type mice. Finally, in a proof-of concept study, we show that the enhanced insulin sensitivity observed in T-bet−/− mice is temporarily transmissible to antibiotic-treated wild-type mice through fecal transfer. Immune regulation of the gut microbiota by T-bet may be a novel pathway modulating insulin sensitivity.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1449301</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1449301</link>
        <title><![CDATA[epiArt: a graphical HLA eplet amino acid repertoire translation reveals the need for an epitope driven revision of allele group nomenclature]]></title>
        <pubdate>2024-10-16T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Ilias Doxiadis</author><author>Claudia Lehmann</author><author>Nils Lachmann</author><author>Henry Loeffler-Wirth</author>
        <description><![CDATA[IntroductionThe immune response after transplantation depends on recipient/donor HLA allele mismatches. To enhance our understanding of the relations of HLA alleles in terms of amino-acid polymorphisms and shared epitopes, we assessed pairwise sequence difference between HLA-alleles.MethodsWe translated amino-acid sequences of confirmed eplets into an atlas of HLA class I and II antigens, followed by visualization of the pairwise allele distances by means of antigen-specific disparity graphs in differential amino-acid space. We obtained an overview of relationships of all alleles of an antigen, corresponding similarity/dissimilarity structures, outliers, alleles with similarity to different antigen groups. Additionally, we calculated prevalence of the amino-acids for each polymorphic sequence position and visualized them in amino-acid motif plots of all alleles belonging to an antigen.ResultsOur visualizations show strongly varying intra-group heterogeneity of HLA class I and II alleles, as well as shared inter-group and inter-locus eplets and epitopes, indicating a benefit of epitope-based transplant matching: Single allele recipient/donor mismatches potentially refer to identical eplets, or to a set of multiple mismatched eplets.DiscussionThis data reveals inconsistencies in the HLA group nomenclature and consequently adds a new level of quality to allocation, motivating the definition of tolerable or taboo mismatches.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1442018</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1442018</link>
        <title><![CDATA[Improving long-term kidney allograft survival by rethinking HLA compatibility: from molecular matching to non-HLA genes]]></title>
        <pubdate>2024-10-02T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Aprajita Mattoo</author><author>Ian S. Jaffe</author><author>Brendan Keating</author><author>Robert A. Montgomery</author><author>Massimo Mangiola</author>
        <description><![CDATA[Optimizing immunologic compatibility in organ transplantation extends beyond the conventional approach of Human Leukocyte Antigen (HLA) antigen matching, which exhibits significant limitations. A broader comprehension of the roles of classical and non-classical HLA genes in transplantation is imperative for enhancing long-term graft survival. High-resolution molecular HLA genotyping, despite its inherent challenges, has emerged as the cornerstone for precise patient-donor compatibility assessment. Leveraging understanding of eplet biology and indirect immune activation, eplet mismatch calculators and the PIRCHE-II algorithm surpass traditional methods in predicting allograft rejection. Understanding minor histocompatibility antigens may also present an opportunity to personalize the compatibility process. While the application of molecular matching in deceased donor organ allocation presents multiple technical, logistical, and conceptual barriers, rendering it premature for mainstream use, several other areas of donor-recipient matching and post-transplant management are ready to incorporate molecular matching. Provision of molecular mismatch scores to physicians during potential organ offer evaluations could potentially amplify long-term outcomes. The implementation of molecular matching in living organ donation and kidney paired exchange programs is similarly viable. This article will explore the current understanding of immunologic matching in transplantation and the potential applications of epitope and non-epitope molecular biology and genetics in clinical transplantation.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1436194</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1436194</link>
        <title><![CDATA[Allogeneic mesenchymal stromal cell therapy in kidney transplantation: should repeated human leukocyte antigen mismatches be avoided?]]></title>
        <pubdate>2024-09-27T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Suzanne Bezstarosti</author><author>Pauline Erpicum</author><author>Gianni Maggipinto</author><author>Geertje J. Dreyer</author><author>Marlies E. J. Reinders</author><author>Soufian Meziyerh</author><author>Dave L. Roelen</author><author>Johan W. De Fijter</author><author>Jesper Kers</author><author>Laurent Weekers</author><author>Yves Beguin</author><author>François Jouret</author><author>Sebastiaan Heidt</author>
        <description><![CDATA[Mesenchymal stromal cells (MSCs) have immunomodulatory properties and are therefore considered promising tools in kidney transplantation. Although most studies have been conducted with autologous MSCs, using allogeneic MSCs as an off-the-shelf product is more feasible in clinical settings. However, allogeneic MSCs could potentially induce an immune response, which might eventually be directed towards the kidney allograft because of shared human leukocyte antigen (HLA) epitope mismatches between the kidney and MSC donor. In this study, we performed in-depth analyses of two cohorts (n = 20) that received third-party MSC therapy after kidney transplantation. While the Neptune Study from Leiden University Medical Center specifically selected MSC to avoid repeated HLA antigen mismatches between kidney and MSC donors, the study from the University of Liège did not perform specific MSC selection. The comparative analyses of amino acid mismatches between these cohorts showed that MSC selection to avoid repeated HLA mismatches at the split antigen level was not sufficient to prevent repeated mismatches at the amino acid level. However, repeated amino acid mismatches were not associated with the occurrence of donor-specific antibodies (DSAs). Thus, the clinical relevance of repeated amino acid mismatches seems to be limited with regard to the risk of DSA formation. Since DSA formation was limited (3 of 20 patients) in this study, larger studies are required to investigate the relevance of preventing repeated HLA mismatches in allogeneic MSC therapy in kidney transplantation.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2024.1444554</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2024.1444554</link>
        <title><![CDATA[Quantifying uncertainty of molecular mismatch introduced by mislabeled ancestry using haplotype-based HLA genotype imputation]]></title>
        <pubdate>2024-09-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Benedict M. Matern</author><author>Eric Spierings</author><author>Selle Bandstra</author><author>Abeer Madbouly</author><author>Stefan Schaub</author><author>Eric T. Weimer</author><author>Matthias Niemann</author>
        <description><![CDATA[IntroductionModern histocompatibility algorithms depend on the comparison and analysis of high-resolution HLA protein sequences and structures, especially when considering epitope-based algorithms, which aim to model the interactions involved in antibody or T cell binding. HLA genotype imputation can be performed in the cases where only low/intermediate-resolution HLA genotype is available or if specific loci are missing, and by providing an individuals’ race/ethnicity/ancestry information, imputation results can be more accurate. This study assesses the effect of imputing high-resolution genotypes on molecular mismatch scores under a variety of ancestry assumptions.MethodsWe compared molecular matching scores from “ground-truth” high-resolution genotypes against scores from genotypes which are imputed from low-resolution genotypes. Analysis was focused on a simulated patient-donor dataset and confirmed using two real-world datasets, and deviations were aggregated based on various ancestry assumptions.ResultsWe observed that using multiple imputation generally results in lower error in molecular matching scores compared to single imputation, and that using the correct ancestry assumptions can reduce error introduced during imputation.DiscussionWe conclude that for epitope analysis, imputation is a valuable and low-risk strategy, as long as care is taken regarding epitope analysis context, ancestry assumptions, and (multiple) imputation strategy.]]></description>
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