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        <title>Frontiers in Genetics | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/genetics</link>
        <description>RSS Feed for Frontiers in Genetics | New and Recent Articles</description>
        <language>en-us</language>
        <generator>Frontiers Feed Generator,version:1</generator>
        <pubDate>2026-09-06T11:58:38.906+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1827187</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1827187</link>
        <title><![CDATA[Mechanisms of acquired resistance to osimertinib in EGFR T790M-Positive lung adenocarcinoma]]></title>
        <pubdate>2026-09-04T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Kefan Cui</author><author>Renjie Zhu</author><author>Jingmeng Li</author>
        <description><![CDATA[BackgroundThird-generation epidermal growth factor receptor tyrosine kinase inhibitor osimertinib serves as the gold standard therapy for treating NSCLC patients harboring EGFR T790M mutations. The clinical utility of this agent, however, faces considerable constraints due to the unavoidable emergence of acquired resistance mechanisms. Understanding the molecular basis of osimertinib resistance holds paramount importance for determining optimal follow-up treatment approaches.MethodsClinical information from 86 lung adenocarcinoma patients carrying EGFR T790M mutations who showed disease advancement following osimertinib therapy was examined retrospectively, spanning the period from January 2018 through December 2023. Genomic characterization was conducted via next-generation sequencing on tissue or liquid biopsy specimens collected after resistance developed. Protein expression alterations were assessed through immunohistochemical staining, while critical resistance pathways underwent validation using cell line models.ResultsAmong the 86-patient cohort, the median duration before disease progression reached 14.2 months. Genomic characterization identified these predominant resistance pathways: C797S mutations in EGFR (23.3%), amplification of MET (15.1%), amplification of HER2 (8.1%), mutations in PIK3CA (7.0%), transformation to small cell lung cancer (9.3%), and epithelial-mesenchymal transition (12.8%). Concurrent presence of multiple resistance mechanisms was detected in 24.4% of the patient population. Within the C797S mutation subset, 65.0% exhibited C797S/T790M in cis arrangement, 30.0% demonstrated trans arrangement, and 5.0% showed mixed configurations. Laboratory validation established that MET amplification confers resistance via bypass activation of both ERK and AKT signaling cascades. The poorest clinical outcomes were observed among patients undergoing histological transformation (median overall survival from confirmed progression: 8.3 months).ConclusionRemarkable heterogeneity characterizes the resistance mechanisms emerging against osimertinib in EGFR T790M-positive lung adenocarcinoma, with EGFR secondary mutations, bypass signaling pathway activation, and histological transformation representing the primary categories. Detection of specific resistance mechanisms enables tailored subsequent therapeutic approaches, with potential outcome improvements achievable through combination strategies incorporating targeted agents or immunotherapy.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1895515</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1895515</link>
        <title><![CDATA[HSTXGB: a hyperparameter self-tuning XGBoost method integrating pre- and post-processing for gene regulatory network inference]]></title>
        <pubdate>2026-09-04T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mingqing Huang</author><author>Shun Guo</author><author>Fengze Jiang</author><author>Yingnan Xiong</author><author>Xu Chen</author>
        <description><![CDATA[Clarifying gene regulatory networks (GRNs) remains one of the central challenges of systems biology and is crucial for elucidating pathogenesis and curing diseases. Various machine learning techniques have been developed for gene regulatory network inference, but identifying intricate interactions is still a fundamental problem. Here, we propose a network structure refinement scheme, termed HSTXGB (a hyperparameter self-tuning XGBoost method integrating pre- and post-processing), to infer GRNs from time-course expression data by leveraging the nonlinear modeling capability of XGBoost while integrating prior knowledge (e.g., knockout data) and posterior statistics (e.g., regulation probabilities). Specifically, HSTXGB first calculates regulation relationship confidences using a self-tuning XGBoost model, which accounts for temporal dependencies in gene expression. Then, two novel strategies are designed to integrate information from prior data and to incorporate statistical information, which correspond to fluctuations in knockout experiments and to regulatory frequency and intensity, respectively. The confirmatory experiments on the benchmark datasets from the DREAM challenge as well as the E. coli datasets (8 networks in total) demonstrated that our HSTXGB scheme achieves significantly better performance compared with eight other state-of-the-art methods.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1875383</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1875383</link>
        <title><![CDATA[Influence of homozygosity on genomic structural variation analyses for predicting ACL rupture risk in the Labrador Retriever and Rottweiler]]></title>
        <pubdate>2026-09-03T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mehdi Momen</author><author>Faris Hazim Mohamed Zaimir</author><author>Brian W. Davis</author><author>Susannah J. Sample</author><author>Peter Muir</author>
        <description><![CDATA[IntroductionAnterior cruciate ligament (ACL) rupture is a common orthopaedic disease in dogs, with varying prevalence and genetic susceptibility across different breeds. Here we investigate the association between genomic structural variation (SV) and ACL rupture risk in the Labrador Retriever and Rottweiler breeds.MethodsWe used 1,058 Labrador Retrievers (464 cases, 594 controls) and 108 Rottweilers (83 cases, 25 controls). Using breed‐specific de novo genome assemblies, we first characterized SV between Labrador Retriever and Rottweiler genomes to provide genomic context for breed-level differences. We then quantified runs of homozygosity (ROH) and evaluated the association between homozygosity measures (nROH, AVGROH, and FROH) and ACL rupture risk using breed‐specific and combined‐breed logistic regression models.ResultsThe association between homozygosity parameters and ACL rupture in the Labrador Retriever was not significant (P > 0.05 for all models). In contrast, inbreeding coefficient (FROH) was significantly associated with increased ACL rupture risk (OR = 2.011, 95% CI:1.120‐3.98, P‐value = 0.026) in the Rottweiler when sex and interaction effects were included in the model.ConclusionThese findings suggest a potential association between inbreeding and ACL rupture risk in Rottweilers. In addition, joint analysis of Labrador Retriever and Rottweiler data revealed multicollinearity between breed and homozygosity content, which highlights the heterogeneity of genetic risk factors across breeds. Our findings suggest that breed‐specific genetic models are crucial for understanding the genetic contribution to ACL rupture and for developing accurate genetic risk prediction tools. Given the relatively small and imbalanced Rottweiler dataset, independent validation in larger populations is warranted to further explore the potential breed‐specific genetic loci contributing to ACL rupture in the Rottweiler.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1889156</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1889156</link>
        <title><![CDATA[Spectrum and carrier frequency of DMD in Yueyang, China: a population-based analysis using NGS and MLPA]]></title>
        <pubdate>2026-09-03T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Qun Zhu</author><author>Ang Sun</author><author>Yuyao Zu</author><author>Yan Zeng</author><author>Liya Chen</author><author>Yuan Yang</author><author>Zhen Liu</author><author>Yuting Sun</author><author>Xuzhen Huang</author><author>Xiaobu Shen</author>
        <description><![CDATA[BackgroundDuchenne muscular dystrophy (DMD) is an X-linked recessive disorder caused by mutations in the DMD gene. Understanding the carrier frequency and mutation spectrum in specific populations is critical for genetic counseling and early intervention. However, data on DMD carrier frequency among women of childbearing age and early pregnancy in Yueyang City, China, remain limited. This study aimed to characterize the carrier rate and mutation profile to support preventive strategies and reduce disease incidence.MethodsA total of 25,611 women of childbearing age or early pregnancy from Yueyang City were enrolled. Combined next-generation sequencing and multiplex ligation-dependent probe amplification were used to detect pathogenic/likely pathogenic (P/LP) variants, copy number variants (CNVs), and small indels. Variants were classified per established guidelines. Carrier rates and geographical distribution were analyzed. Prenatal diagnosis was offered to identified carriers with follow-up to assess outcomes.ResultsTwenty-eight women were identified as P/LP carriers (0.11%), representing 25 distinct variants. CNVs constituted the majority (71.43%), with exon 45–55 deletions (64.29%) predominating over duplications (7.14%); notably, 13/18 CNVs clustered in this hotspot. SNVs and small indels accounted for the remaining 28.57%. Intra-regional variation was marked, with the highest rate in Yunxi District (0.74%). Additionally, 81 VUSs (51 distinct types) were detected, 66.67% being missense. One male fetus inheriting a maternal VUS developed DMD-like features postpartum. Overall, 12 variants (1 LP, 11 VUSs) were previously unreported, including a nonsense variant c.3502G>T (p.E1168*) classified as LP.ConclusionThis first population-based study in Yueyang City, China, characterized the DMD carrier frequency (0.11%) and mutation spectrum among women of childbearing age or in early pregnancy. It revealed geographical heterogeneity and a high prevalence of CNVs, especially exon 45–55 deletions. Crucially, it highlights the underappreciated screening value of VUS. We recommend focused attention on VUS, particularly those with Bayesian scores ≥3, in genetic counseling and prenatal diagnosis to improve preventive strategies and reduce DMD incidence.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1890433</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1890433</link>
        <title><![CDATA[Integrated transcriptomics approach identifies the upregulated SLC7A5, and associated pathways across different thyroid cancer cell types]]></title>
        <pubdate>2026-09-03T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Muhammad Naeem</author><author>Nan Wu</author><author>Yang Wu</author><author>Shahid Nawaz</author><author>Ren Jing</author><author>Yuanbin Luo</author><author>Shijian Yi</author>
        <description><![CDATA[Thyroid cancer is the most common type of endocrine malignancy, and its aggressive types are diagnosed at advanced stage due to limited treatment options. This study aimed to identify upregulated SLC7A5 across thyroid cancer cell types using an integrated transcriptomics approach. Total RNA was extracted from different samples. Differential expression analysis was performed through DESeq2. Functional enrichment analyses were performed to explore key pathways. The PPI network was built using the STRING database to investigate the functional relationships among significantly differentially expressed genes. Differential expression analysis revealed that SLC7A5 was significantly upregulated in KTC-1. GO and KEGG analyses were enriched with cell adhesion, protein binding, extracellular exosome, RNA processing, ECM-receptor interactions, and focal adhesion. The PPI network analysis showed the interaction of SLC7A5 with TERF1, CARD10, PSAT1, SIRPA, and MYC. Western blot analysis revealed that expression of mTOR was not elevated in KTC-1. Overall, these results could provide valuable insights for further validation in thyroid cancer therapy.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1847245</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1847245</link>
        <title><![CDATA[Opportunities to cultivate trust through communication behaviors]]></title>
        <pubdate>2026-09-03T00:00:00Z</pubdate>
        <category>Brief Research Report</category>
        <author>Mary Carol Barks</author><author>Claire Yballa</author><author>Alexandra Linker</author><author>Chau Amoeni</author><author>Gabrielle Cua</author><author>Malley Craig</author><author>Bridget Hein</author><author>Thomas May</author>
        <description><![CDATA[Sound scientific sample diversity will require attention to cultivating trust among populations underrepresented as biobank participants. While no particular group is the focus of this report, the observations presented may be particularly helpful for cultivating trust necessary for enrollment of underrepresented populations. Community engagement strategies indicate that such trust is built through relationships extending across the spectrum of biomedicine rather than focused exclusively on a particular research project. Central to these relationships are communication behaviors reflected in both research and clinical encounters. This ‘brief research report’ presents preliminary clinical research findings from a pilot analysis of return of genetic results conversations relevant to the cultivation of trust.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1836684</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1836684</link>
        <title><![CDATA[Preclinical evaluation of AL-001, a gene therapy for wet age-related macular degeneration]]></title>
        <pubdate>2026-09-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xuan Liu</author><author>Haiyan Liu</author><author>Lei Wang</author><author>Julia Zhao</author><author>Xingwang Xie</author><author>Long Jiang</author><author>Chunlin Adam Zhao</author>
        <description><![CDATA[BackgroundFrequent intravitreal administration of antivascular endothelial growth factor Vascular endothelial growth factor agents remains a major limitation in the management of wet age-related macular degeneration (wAMD). This study evaluated whether suprachoroidal delivery of an engineered recombinant adeno-associated viral (rAAV)-aflibercept vector could achieve sustained, targeted expression with improved efficacy and safety compared with intravitreal administration.MethodsAL-001, an engineered rAAV vector expressing aflibercept, was developed and characterized. Its expression profile was first assessed in New Zealand white rabbits following suprachoroidal space (SCS) injection. Efficacy, pharmacokinetics, and safety were then evaluated in a nonhuman primate model of laser-induced choroidal neovascularization (CNV), comparing SCS and intravitreal (IVT) administration routes.ResultsAL-001 efficiently expressed aflibercept in relevant ocular cells in vitro. In rabbits, SCS administration produced sustained aflibercept levels in ocular tissues. In the nonhuman primate CNV model, a single SCS injection of AL-001 showed favorable efficacy to IVT injection and a notable mild inflammatory response. At week 4, grade IV lesion incidence was 0% (0/48) after SCS administration versus 14.3% (6/42) after IVT administration (absolute difference, −14.3 percentage points; 95% CI, 3.7%–27.8%; P = 0.0258). Throughout follow-up, mean leakage area and grade IV lesion incidence remained 0 with SCS, versus IVT peaks of approximately 0.3 mm2 and 33.0%, respectively, declining to 0.03 mm2 and 2.0% by day 100. Both the medium and high doses decreased pathological vascular leakage and subretinal hyperreflective material. Vector administration preceded laser-induced CNV modeling, demonstrating that sustained intraocular aflibercept expression in the retina and choroid provided durable antiangiogenic protection. Pharmacokinetic analysis confirmed distinct ocular exposure profiles between routes, with viral genomes confined predominantly to the injected eye and no significant systemic accumulation. AL-001 was well tolerated, without sustained intraocular pressure elevation or severe ocular inflammation, and only mild-to-moderate treatment-emergent adverse events. Low pre-existing anti-AAV2 immunity and time-dependent neutralizing antibody responses postdosing, informing a translational model for patient stratification and redosing feasibility.ConclusionSuprachoroidal administration of AL-001 is well tolerated and provides durable, targeted aflibercept expression with pronounced antiangiogenic efficacy. These results support AL-001 as a promising, long-acting therapeutic candidate for wAMD.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1933643</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1933643</link>
        <title><![CDATA[DNA damage repair gene defects combined predict the efficacy of immune checkpoint inhibitors in metastatic castration-resistant prostate cancer: a retrospective cohort study]]></title>
        <pubdate>2026-09-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Kesong Qin</author><author>Gangqiang Hu</author><author>Erli Song</author>
        <description><![CDATA[BackgroundImmune checkpoint inhibitors (ICIs) yield heterogeneous benefit in metastatic castration-resistant prostate cancer (mCRPC), underscoring the unmet need for robust predictive biomarkers. DNA damage repair (DDR) gene defects encompass mechanistically distinct subtypes—homologous recombination repair (HRR) deficiency, mismatch repair deficiency/microsatellite instability-high (MMRd/MSI-H), and CDK12 inactivation—that may differentially modulate anti-tumor immunity. This study evaluated the combined predictive value of DDR mutation profiles, tumor mutational burden (TMB), and PD-L1 expression for ICI efficacy in mCRPC.MethodsIn this single-center retrospective cohort study conducted at PKUCare CNOOC Hospital (Tianjin, China), 152 patients with mCRPC who received ICI-containing therapy following ≥2 prior lines of systemic treatment were enrolled (January 2018–December 2023). Of these, 127 (83.6%) underwent tissue-based profiling with a validated 520-gene targeted NGS panel, and 25 (16.4%) were profiled by a validated 168-gene liquid biopsy panel. Patients were classified into four DDR subgroups: HRR-deficient, MMRd/MSI-H, CDK12-mutant, and DDR wild-type. Primary endpoints were objective response rate (ORR) and progression-free survival (PFS). Secondary endpoints included overall survival (OS), disease control rate (DCR), and prostate-specific antigen (PSA) response. Kaplan-Meier analysis, multivariate Cox regression, and ROC analysis were performed.ResultsAmong 152 patients, 101 (66.4%) harbored DDR alterations: 58 HRR-deficient (38.2%), 24 MMRd/MSI-H (15.8%), and 19 CDK12-mutant (12.5%). ORR was highest in MMRd/MSI-H (50.0%), followed by CDK12-mutant (26.3%), HRR-deficient (22.4%), and DDR wild-type (9.8%; p < 0.001). Median PFS was significantly longer across all DDR-mutant groups versus DDR wild-type (MMRd/MSI-H: 8.1 months; HR 0.31, 95% CI 0.18–0.53; p < 0.001). On multivariate analysis, DDR mutation subtype, TMB ≥10 mut/Mb, and liver metastasis were independent predictors of PFS. A composite biomarker integrating DDR status, TMB, and PD-L1 achieved the highest predictive accuracy (AUC 0.83, 95% CI 0.75–0.91). irAE rates did not differ significantly across subgroups (p = 0.614).ConclusionDDR gene mutation profiling, integrated with TMB and PD-L1 expression, provides clinically actionable stratification of mCRPC patients for ICI therapy. A composite DDR/TMB/PD-L1 biomarker panel warrants prospective validation in dedicated clinical trials.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1970828</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1970828</link>
        <title><![CDATA[Correction: Editorial: Hepatocellular carcinoma: from bench to bedside]]></title>
        <pubdate>2026-09-01T00:00:00Z</pubdate>
        <category>Correction</category>
        <author>Evin İşcan</author><author>Aaron B. Koenig</author><author>Xiaogang Wu</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1812702</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1812702</link>
        <title><![CDATA[Clinical implementation of next-generation sequencing in tertiary health system: the Rijeka retrospective study]]></title>
        <pubdate>2026-09-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Nina Pereza</author><author>Sanja Dević Pavlić</author><author>Tea Mladenić</author><author>Željka Hrupački</author><author>Dorotea Vukelić Drašković</author><author>Luca Lovrečić</author><author>Aleš Maver</author><author>Jadranka Vraneković</author><author>Iva Bilić Čače</author><author>Igor Prpić</author><author>Ivona Butorac Ahel</author><author>Vladimira Vuletić</author><author>Koraljka Benko</author><author>Tea Čaljkušić Mance</author><author>Marko Klarić</author><author>Nada Starčević Čizmarević</author><author>Ivana Babić Božović</author><author>Goran Hauser</author><author>Alen Ružić</author><author>Saša Ostojić</author><author>Borut Peterlin</author>
        <description><![CDATA[ObjectiveThis study aimed to assess the diagnostic yield, clinical indications, and utility of next-generation sequencing (NGS) testing since its implementation through collaboration between the University of Rijeka Faculty of Medicine and the Clinical Hospital Centre Rijeka.Materials and MethodsThis retrospective study included patients referred between 2018 and 2023 from the Clinical Hospital Centre Rijeka to the University of Rijeka Faculty of Medicine for genetic testing, primarily using exome sequencing.ResultsBetween April 2018 and December 2023, 412 patients were referred for exome sequencing, of whom 353 (85.7%) underwent diagnostic genetic testing. A notable increase in tests ordered was observed over time. Patients were most frequently referred from Pediatrics (55.0%), Neurology (29.5%), Cardiology (7.4%), Ophthalmology (3.4%), and others (4.7%). A diagnosis was confirmed in 103/353 patients, corresponding to an overall diagnostic yield of 29.2%, and an adjusted diagnostic yield of 27.2% after collapsing related individuals into single family units. In these confirmed cases, 83 distinct disorders involving 71 unique genes were identified, with most patients showing heterozygous variants and several recurrent disorders and genes. Variants of uncertain significance were reported in 35/353 (9.9%) patients.ConclusionThe 27.2% diagnostic yield demonstrates effective integration of NGS into tertiary clinical practice. The recent introduction of medical genetics specialization is expected to further improve referral quality, variant interpretation, and overall diagnostic outcomes.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1865110</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1865110</link>
        <title><![CDATA[Integrated proteomic and metabolomic analyses define the molecular architecture of acute mountain sickness]]></title>
        <pubdate>2026-09-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Wenjing Ding</author><author>Yifan Yang</author><author>Huaying Wei</author><author>Xinyu Hu</author><author>Haopeng Zhang</author><author>Ailifeila Aili</author><author>Xiaolan Chen</author><author>Qiqi Wang</author><author>Xinying Xue</author><author>Lei Pan</author>
        <description><![CDATA[BackgroundHypoxia-driven vascular, immune, and metabolic remodeling is a key biological process involved in cardiovascular diseases, cancer, and other complex systemic disorders. Acute mountain sickness (AMS) is an acute manifestation of hypobaric hypoxia, but its systemic molecular features remain incompletely defined.MethodsWe performed integrated plasma proteomic and metabolomic profiling in 81 healthy Han Chinese male participants after rapid high-altitude exposure. Differential analysis, weighted gene co-expression network analysis (WGCNA), tissue-specific protein mapping, regulatory network reconstruction, machine learning, and druggability assessment were applied to characterize AMS-associated molecular alterations and identify candidate biomarkers and targets.ResultsMulti-omics profiling identified 3,137 proteins and 4,104 metabolites and showed clear separation between AMS and non-AMS participants. AMS was characterized by coordinated thrombo-inflammatory activation, coagulation-related disturbance, and metabolic reprogramming, including suppression of oxidative phosphorylation-related signatures. WGCNA identified symptom associated proteomic and metabolomic modules linked to headache severity, oxygen saturation, and hemodynamic traits. Tissue-specific protein mapping revealed a liver-centered but multi-organ circulating proteomic architecture, suggesting hepatic secretory remodeling with additional neural and immune-system contributions. Regulatory network analysis highlighted NOTCH1 as a candidate upstream regulatory hub, whereas druggability analysis prioritized NOTCH1 and the antioxidant-related protein GSTA1 as translational candidates. An mRMR plus logistic regression classifier integrating 15 proteomic features and SpO2 achieved good discriminatory performance, with an AUC of 0.968 in the training cohort and 0.913 in the test cohort.ConclusionThis study defines a multi-layer molecular framework of human acute hypoxic stress, linking vascular regulation, inflammation, coagulation, metabolic remodeling, tissue origin, and biomarker prioritization. These findings provide mechanistic insight into AMS and support multi-omics-based biomarker discovery and target prioritization in hypoxia-associated systemic diseases.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1925751</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1925751</link>
        <title><![CDATA[Glycogen storage disease type VII (Tarui disease): a case report presenting a PFKM variant previously described only in canine models]]></title>
        <pubdate>2026-09-01T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Mariapia Griffo</author><author>Nicola Molitierno</author><author>Laura Napoli</author><author>Michela Ripolone</author><author>Simona Zanotti</author><author>Francesco Fortunato</author><author>Gabriele Tumminello</author><author>Maurizio Moggio</author><author>Marco Locatelli</author><author>Stefania Paola Corti</author><author>Giacomo Pietro  Comi</author><author>Dario Ronchi</author>
        <description><![CDATA[Glycogen storage disease type VII (GSD-VII), or Tarui disease, is a rare autosomal recessive disorder caused by biallelic loss-of-function variants in the PFKM gene encoding the muscle isoform of phosphofructokinase (PFK), a key enzyme of the glycolytic pathway. PFK deficiency impairs glycogen and glucose metabolism in skeletal muscle and erythrocytes, causing exercise intolerance, exertional myalgia, and myoglobinuria, and, in some cases, fixed proximal muscle weakness, as well as haemolytic anaemia. We report the case of an Italian woman with genetically confirmed GSD-VII harbouring a homozygous missense variant in PFKM (NM_000289.6:c.550C>T, p.Arg184Trp). This variant was previously identified in Wachtelhund dogs, a spontaneous animal model of PFK deficiency, but never reported in patients so far. PFK activity in skeletal muscle (PFKM) was found severely decreased and ultrastructural analysis revealed glycogen accumulation and mitochondrial alteration, supporting the pathogenetic role of the identified variant.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1802493</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1802493</link>
        <title><![CDATA[A workshop considering genetic research and data collection with American Indian and Alaska Native people outside of Tribal jurisdiction]]></title>
        <pubdate>2026-08-31T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Julie A. Beans</author><author>Jessica W. Blanchard</author><author>Vanessa Y. Hiratsuka</author><author>Taiawagi Helton</author><author>Stephanie Russo Carroll</author><author>Denise A. Dillard</author><author>Raymond Orr</author><author>Francine C. Gachupin</author><author>Sara C. Hull</author><author>Rodney C. Haring</author><author>Nanibaa’ A. Garrison</author><author>Bobby Saunkeah</author><author>Krystal S. Tsosie</author><author>Aaron J. Goldenberg</author><author>David Wilson</author><author>Richard R. Sharp</author><author>Joseph Yracheta</author><author>Erika Blacksher</author><author>R. Brian Woodbury</author><author>Dalaki Livingston</author><author>Paul Spicer</author>
        <description><![CDATA[IntroductionIn the United States (US), Tribes are sovereign nations and have the right to oversee research conducted with Tribal citizens. However, it is unclear who should approve research protocols when data from American Indian and Alaska Native (AIAN) people are collected off Tribal lands. As genetic research continues to advance and transform the delivery of healthcare, equitable inclusion of AIAN people is necessary, but oversight of research needs clarity.MethodsWe held a 3-day workshop with US thought leaders on genetic and other health research with AIAN people in urban areas to explore views and values on this issue and to discuss potential policy and practice solutions.ResultsThirty-six individuals attended. Solidarity surfaced as a foundational motivation for Tribal Nations to review research conducted with AIAN people, whether on Tribal lands or not. Understanding data from Indigenous perspectives was identified as a way to ensure appropriate AIAN community protections are in place. Three discrete areas to improve policy were suggested–Tribal, Academic Institution, and National–to protect AIAN people participating in research both on and off Tribal lands.DiscussionResearchers, whether Indigenous or not, must recognize Tribal sovereignty and operate in solidarity with the applicable and most appropriate ethical principles and regulations.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1932117</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1932117</link>
        <title><![CDATA[Case Report: Differential outcomes associated with the same pathogenic variant: long-term follow-up of a CHARGE syndrome case with a nonsense mutation c.6292C>T in the CHD gene]]></title>
        <pubdate>2026-08-31T00:00:00Z</pubdate>
        <category>Case Report</category>
        <author>Qiong-yu Wang</author><author>Jing-jing Huang</author><author>Fu-chun Wang</author><author>Jing-wei He</author>
        <description><![CDATA[BackgroundCHARGE syndrome (OMIM #214800) is a rare autosomal dominant multisystem disorder, most commonly attributable to de novo heterozygous loss-of-function pathogenic variants in the CHD7 gene. Pathogenic Pathogenic variants of CHD7 are distributed throughout the entire coding region, with nonsense and frameshift pathogenic variants predominating, and the vast majority constitute private mutations. Owing to its broad phenotypic spectrum and marked variability in expressivity, early diagnosis remains challenging. This article presents the long-term follow-up data of a female patient with genetically confirmed CHARGE syndrome, with particular emphasis on her clinical trajectory and outcomes achieved through multidisciplinary management.Case presentationThe patient was a full-term female born via spontaneous vaginal delivery in 2017, presenting with respiratory distress and feeding difficulties immediately after birth. Comprehensive evaluation revealed multisystem abnormalities involving the respiratory, cardiovascular, neurological, and sensory systems. Trio-based whole-exome sequencing identified a de novo heterozygous nonsense pathogenic variant, c.6292(EXON31)C>T (p.Arg2098*), in the CHD7 gene. Literature review indicated that this pathogenic variant had been previously reported in cases that all resulted in infantile death. In contrast, our patient, following active multidisciplinary management, achieved significant improvement in multiple organ functions and survived to school age, where she now adapts well to a special education school environment. This case provides the first evidence that this pathogenic variant is compatible with a favorable long-term outcome, highlighting substantial phenotypic heterogeneity and prognostic diversity even among individuals carrying an identical genetic alteration.ConclusionThis case highlights the critical importance of early genetic diagnosis and coordinated multidisciplinary management in CHARGE syndrome. By presenting divergent outcomes associated with the same pathogenic variant, our findings enrich the clinical evidence on CHD7 genotype–phenotype correlations. Even with severe neonatal multisystem involvement, proactive and individualized management can achieve favorable long-term outcomes.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1902866</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1902866</link>
        <title><![CDATA[Integrating machine learning and GWAS for variant prioritization in the INCIPE cohort highlights ABC transporter genes in chronic kidney disease]]></title>
        <pubdate>2026-08-31T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Dagnogo Dramane</author><author>Mirko Treccani</author><author>Laura Veschetti</author><author>N’Guessan Benedicte Sonia Koffi</author><author>Cristina Patuzzo</author><author>Pietro Manuel Ferraro</author><author>Giovanni Gambaro</author><author>Dago Dougba Noel</author><author>Giovanni Malerba</author>
        <description><![CDATA[IntroductionChronic kidney disease (CKD) is a major public health challenge, affecting approximately 674 million people worldwide and representing one of the fastest-growing causes of mortality. Since CKD is frequently asymptomatic in its early stages, the identification of novel genetic biomarkers may improve early detection and risk stratification. Genome-Wide Association Studies (GWAS) have identified numerous genetic loci associated with CKD and related traits; however, their performance is often limited in small and imbalanced cohorts, where reduced statistical power increases both false-positive and false-negative findings. Machine learning (ML) approaches can complement conventional GWAS by prioritizing biologically relevant genetic signals from high-dimensional genomic data.MethodsIn this study, we implemented a nested ensemble (NCBC) model composed of an undersampler and a CatBoostClassifier (CBC) to prioritize candidate genetic variants associated with CKD in the INCIPE cohort. Prioritized variants were functionally annotated and evaluated through enrichment analyses, GTEx gene expression profiling, and protein-protein interaction network analyses. Genes identified by the CKDGen Consortium were analysed as an external reference set and used to validate the biological relevance of the prioritized results.ResultsThe NCBC model outperformed conventional ML classifiers, achieving a ROC AUC score of 87.77%, compared to 50%–53% for the other evaluated models. Among the prioritized genes, 56.25% showed protein-protein interactions with genes previously reported by the CKDGen Consortium, whereas only 1.9% of randomly generated gene sets showed interactions.DiscussionOur study demonstrates that the NCBC model improves the prioritization of biologically plausible candidate variants in a small and imbalanced CKD cohort. Functional analyses suggested ABC transporter-related genes, including ABCA13, ABCA4, and ABCC4 genes, as promising candidate for future validation, with ABCA4 showing substantial expression in kidney tissues. Overall, these findings support the integration of ML with GWAS to prioritize candidate genes and investigate the genetic architecture of complex diseases.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1835653</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1835653</link>
        <title><![CDATA[Lymphangiogenesis-related gene signature–based risk model for prognostic assessment of cervical cancer: immune–metabolic characterization and molecular subtype analysis]]></title>
        <pubdate>2026-08-31T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xijing Fan</author><author>Lu Chen</author><author>Jing Xu</author><author>Shunjie Zheng</author><author>Qi Pan</author><author>Yifei Hu</author>
        <description><![CDATA[Background Lymphangiogenesis promotes tumor dissemination and may shape the immune contexture of cervical cancer, yet lymphangiogenesis-related prognostic stratification and its immunometabolic implications remain insufficiently defined in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC).MethodsTCGA-CESC transcriptomes and clinical data were obtained from UCSC Xena and integrated with normal cervix tissues from the Genotype-Tissue Expression Project after batch correction. Prognostic LYMRGs were first identified from the differentially expressed set using univariable Cox proportional hazards analysis. Candidate genes were then reduced using an L1-regularized Cox model (Least Absolute Shrinkage and Selection Operator), and the remaining markers were entered into a multivariable Cox regression to obtain the final coefficients and compute an individualized risk score. The model’s prognostic value was further assessed in an independent Gene Expression Omnibus dataset. In addition, expression patterns of the signature genes were leveraged for molecular subtyping of TCGA samples via non-negative matrix factorization (NMF). Immune infiltration and immunotherapy-associated characteristics were interrogated through a multi-algorithm strategy (single-sample gene set enrichment analysis, CIBERSORT, ESTIMATE, Tumor Immune Dysfunction and Exclusion (TIDE), and Immunophenoscore . Additional analyses included pathway enrichment (GSEA/GO/KEGG), drug sensitivity prediction (pRRophetic/CellMiner), and ceRNA network analysis.ResultsA six-gene LYMRG signature robustly stratified survival. High-risk patients had significantly worse overall survival in The Cancer Genome Atlas with AUCs of 0.819/0.801/0.801 at 1/3/5 years, and in GSE52903 (P = 0.001) with AUCs of 0.733/0.719/0.725. NMF identified two subtypes with distinct prognosis (P = 0.01) and divergent immune landscapes. Risk groups and subtypes exhibited consistent differences in immune infiltration, checkpoint expression, TIDE/IPS patterns, and pathway enrichment. Predicted chemosensitivity differed by risk group, and the ceRNA network suggested candidate upstream lncRNA regulators of the signature.ConclusionA lymphangiogenesis-related six-gene model enables clinically meaningful prognostic stratification of CESC and links lymphangiogenesis programs to distinct tumor immune phenotypes and therapeutic vulnerabilities.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1795147</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1795147</link>
        <title><![CDATA[Novel compound heterozygous SIL1 variants associated with Marinesco-Sjögren syndrome in a Chinese family]]></title>
        <pubdate>2026-08-28T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yizheng Jiang</author><author>Aojie Lian</author><author>Jialing Guo</author>
        <description><![CDATA[BackgroundMarinesco-Sjögren syndrome (MSS) is a rare and disabling genetic disorder caused primarily by pathogenic variants in the SIL1 gene. SIL1 functions as a nucleotide exchange factor for the molecular chaperone BiP within the endoplasmic reticulum (ER), which is essential for protein folding. This study aims to characterize a novel SIL1 compound heterozygous pathogenic mutation and investigate its disease-causing mechanism.MethodsWe determined a novel SIL1 compound heterozygous mutation information using whole exome sequencing and Sanger sequencing. RNA-seq, RT-qPCR and Western blot were employed to assess the impact of mutations on SIL1 RNA and protein levels. Immunofluorescence was used to monitor localization changes at the cellular level. Structural prediction and coimmunoprecipitation were utilized to investigate the effects of mutations on protein interactions.ResultsWe identified a 6-year-old girl with MSS carrying novel compound heterozygous variants in the SIL1 gene (c.570_572delCAA (p. Asn190del) and c.740C>T (p. Ala247Val)). Subsequent functional experiments revealed that the mutations show a reduction in SIL1 mRNA and protein levels. Structural prediction and coimmunoprecipitation indicate that the compound variants may be associated with the development of MSS by weakening SIL1-BiP binding.ConclusionsThese findings expand the SIL1 variant spectrum and provide preliminary functional evidence that the identified variants may affect SIL1 abundance and SIL1-BiP interaction, supporting their relevance to the MSS phenotype in this family.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1885466</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1885466</link>
        <title><![CDATA[Metabolomic analysis of children with congenital heart disease complicated by neurological developmental abnormalities and CHD7 mutations]]></title>
        <pubdate>2026-08-28T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xianghui Huang</author><author>Wanting Li</author><author>Ying Lin</author><author>Dan Li</author><author>Huiyue Zhang</author><author>Yuandan Chen</author><author>Wei Sheng</author><author>Deyi Zhuang</author>
        <description><![CDATA[ObjectiveThis study aimed to characterize the clinical features and identify serum differential metabolites in children with left-to-right shunt congenital heart disease (CHD) complicated by neurodevelopmental abnormalities (NDA) and harboring CHD7 mutations, to elucidate potential pathogenic mechanisms.MethodsA case-control study was conducted with three groups: seven children with CHD7-mutant CHD-NDA, 24 children with isolated CHD, and nine healthy controls. Serum metabolomic profiling was performed using untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) in both positive and negative ion modes.ResultsThe metabolomic profiles showed a tendency toward separation among the CHD7-mutant CHD-NDA, isolated CHD, and healthy control groups. Candidate differential metabolites were mainly enriched in steroid hormone biosynthesis, glyoxylate and dicarboxylate metabolism, ascorbate and aldarate metabolism, and glutathione metabolism in the CHD7-mutant group compared with the isolated CHD group. Compared with healthy controls, the CHD7-mutant group also showed candidate alterations related to steroid hormone biosynthesis, riboflavin metabolism, and folate biosynthesis. Two overlapping candidate metabolites, 11-deoxycortisol and 2-hydroxyestrone, were identified across pairwise comparisons and may represent potential metabolic markers related to steroid metabolism.ConclusionThe metabolic disturbances observed in children with CHD7-associated CHD-NDA may be related to steroid metabolism and hypothalamic-pituitary axis regulation. These preliminary findings suggest a potential metabolic link between CHD7 mutations, cardiac phenotypes, and neurodevelopmental abnormalities, warranting further validation in larger, sex-matched cohorts.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1881856</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1881856</link>
        <title><![CDATA[Homeostatic conflict as a driver for brain aging]]></title>
        <pubdate>2026-08-28T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Cristian A. Wulkop-Gil</author><author>Michael Petrascheck</author>
        <description><![CDATA[Mammalian tissue function depends on the balance between proliferative, mitotic cell populations and irreplaceable post-mitotic cells. Throughout life, aging progressively disrupts cell type balance and thus tissue function through opposing forces on different cell types. Aging promotes the aberrant proliferation or entry into pro-inflammatory senescent states of mitotic cells, while contributing to the functional erosion and, in vulnerable populations, loss of post-mitotic irreplaceable cells. The divergent age-associated vulnerabilities of mitotic and post-mitotic cells caused by aging generate a case of homeostatic conflict, in which tissue maintenance simultaneously demands the elimination of damaged mitotic cells and the preservation of irreplaceable ones. We examine the concept of homeostatic conflict using the aging brain as an example, and illustrate how the senescence-prone glia expand and acquire SASP-rich transcriptional states, while post-mitotic neurons undergo widespread loss of molecular identity and cell death, resulting in cell type imbalance and consequently tissue dysfunction. Based on the observed homeostatic conflict, we then devise potential context-sensitive therapeutic strategies by combining interventions that protect from ferroptosis to selectively protect irreplaceable cells with interventions that eliminate maladaptive ones to resolve the age-associated cell type imbalance and thus the underlying homeostatic conflict. We present homeostatic conflict as a concept that goes beyond the reductionist view in which numerous isolated processes promote aging in isolation, and provides a logical framework that integrates multiple processes and explains how their interaction drives age-associated dysfunction in a manner instructive to the development of pharmacological combination strategies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/fgene.2026.1900277</guid>
        <link>https://www.frontiersin.org/articles/10.3389/fgene.2026.1900277</link>
        <title><![CDATA[Machine learning-integrated multi-omics risk prediction for pulmonary fungal infection in COPD and lung cancer: a transcriptomic and immune profiling study]]></title>
        <pubdate>2026-08-28T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yibin Zhang</author><author>Lujun Dai</author>
        <description><![CDATA[BackgroundChronic obstructive pulmonary disease (COPD) and lung cancer are major risk factors for invasive pulmonary fungal infection (IPFI), carrying an attributable mortality of 30%–80%. Their coexistence further amplifies immunosuppression, while current diagnostic criteria remain inadequate for early risk identification.MethodsTranscriptomic data from the GEO dataset GSE296912 (scRNA-seq; 12,078 cells from normal and COPD lung tissue) and The Cancer Genome Atlas (TCGA)-lung adenocarcinoma (LUAD) bulk RNA-seq cohort (539 tumor and 59 normal samples) underwent differential expression and cross-omics integration analysis. Five machine learning models were constructed: logistic regression, SVM, random forest, XGBoost, and LASSO. Candidate genes were validated by qRT-PCR in A549 cells and THP-1-derived macrophages stimulated with heat-inactivated Aspergillus fumigatus conidia, a protocol selected to ensure BSL-2 biosafety compliance and isolate PAMP-mediated innate immune signaling. Model performance was evaluated using 5-fold stratified cross-validation with AUC, calibration curves, and decision curve analysis.ResultsSingle-cell transcriptomic analysis of 12,078 cells identified 14 distinct cell populations, with marked myeloid expansion and immune dysregulation in COPD lung tissue. Cross-omics integration with TCGA-LUAD data identified 1,145 shared genes (79 immune-related), converging on NF-κB, TLR4, and cytokine receptor signaling. The random forest model achieved excellent discriminative performance (5-fold CV AUC = 0.988), with Treg infiltration, TLR4, and MMP9 as the top predictors. qRT-PCR confirmed significant upregulation of all five candidate genes (DEFB4A, S100A8, IL-8, MMP9, and TLR4) in both A549 and THP-1 cells following fungal stimulation.ConclusionThis multi-omics machine learning model integrating scRNA-seq and TCGA transcriptomic data demonstrates excellent discriminative performance (AUC = 0.988), with mechanistic convergence of NF-κB, TLR4, and oncogenic signaling pathways identified across shared immune gene signatures. In vitro qRT-PCR validation confirms the biological relevance of five key antifungal immune genes, providing a transcriptomic foundation for future prospective IPFI risk stratification in patients with COPD and lung cancer.]]></description>
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