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        <title>Experimental Biology and Medicine | Genomics, Proteomics and Bioinformatics section | New and Recent Articles</title>
        <link>https://www.ebm-journal.org/journals/experimental-biology-and-medicine/sections/genomics-proteomics-and-bioinformatics</link>
        <description>RSS Feed for Genomics, Proteomics and Bioinformatics section in the Experimental Biology and Medicine journal | New and Recent Articles</description>
        <language>en-us</language>
        <generator>Frontiers Feed Generator,version:1</generator>
        <pubDate>2026-04-06T17:47:27.576+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2026.10929</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2026.10929</link>
        <title><![CDATA[Global MyoG research 2004–2024: a bibliometric analysis of trends and translational implications]]></title>
        <pubdate>2026-03-05T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Luoming Hu</author><author>Weizhong Zhuang</author><author>Weimin Chen</author><author>Song Yang</author><author>Shuo Chen</author><author>Xin Wang</author><author>Qiang Gao</author><author>Jimei Chen</author>
        <description><![CDATA[Myogenin (MyoG) is a core myogenic transcription factor that orchestrates myoblast differentiation and myofiber maturation and has been increasingly implicated in skeletal muscle degeneration and rhabdomyosarcoma, yet its global research landscape has not been systematically characterized. In this study, we performed a bibliometric analysis of MyoG-related publications from 2004 to 2024 retrieved from the Web of Science Core Collection. A total of 402 articles authored by 2,402 researchers from 1,148 institutions across 165 countries and regions were analyzed using VOSviewer, CiteSpace and R-based bibliometric tools. We quantified annual publication output, identified leading countries, institutions, authors and journals, and reconstructed collaboration, co-citation and keyword co-occurrence networks to delineate thematic evolution. The global pattern showed a multipolar structure dominated by the United States and China, with European institutions forming an additional hub and emerging countries contributing with growing but comparatively lower impact. Research hotspots exhibited a clear progression from early work on molecular mechanisms (DNA binding, MyoD family interactions, chromatin remodelling) toward regenerative biology (satellite cell regulation, muscle regeneration) and, more recently, disease-oriented studies focused on muscle atrophy, Duchenne muscular dystrophy and rhabdomyosarcoma. Landmark co-cited studies established MyoG as an indispensable regulator of skeletal muscle differentiation and highlighted its expanding relevance in pathological remodelling and therapeutic targeting. Future work is expected to concentrate on decoding MyoG-centred regulatory networks in degenerative muscle disease, integrating single-cell and spatial transcriptomics with functional genomics and multi-omics, and developing MyoG-based diagnostic and targeted therapeutic strategies. Despite the intrinsic limitations of single-database and citation-based approaches, this study provides a panoramic overview of two decades of MyoG research and offers a structured framework to guide future basic and translational investigations in muscle biology and oncology.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2026.10709</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2026.10709</link>
        <title><![CDATA[Identification of potential hub genes related to ferroptosis and hypoxia in dilated cardiomyopathy: a bioinformatic analysis with preliminary experimental validation]]></title>
        <pubdate>2026-03-02T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xiqin Wang</author><author>Chrismis Novalinda Ginting</author><author>William Leslie</author>
        <description><![CDATA[The study aims to explore the potential role of ferroptosis and hypoxia in dilated cardiomyopathy (DCM). GSE120895, GSE17800, GSE112556, ferroptosis-related genes (FRGs), and hypoxia-related genes (HRGs) were downloaded from the public dataset. Ferroptosis- and hypoxia-related differentially expressed genes (DEGs) and DCM-related genes were obtained. Subsequentially, hub genes were identified, and their diagnostic values were assessed. Next, immune cell infiltration analysis, drug prediction and molecular docking were carried out based on the hub genes. Finally, the hub gene TGM2 was preliminarily verified in vitro. A total of 18 ferroptosis- and hypoxia-related DEGs and 315 DCM-related genes were acquired. Subsequently, 6 hub genes (PPP1R15A, TGM2, MAP3K5, USP7, SESN2, and ADAM23) were obtained and have potential diagnostic value. Immune infiltration analysis showed that CD56dim natural killer (NK) cells, macrophages, monocytes, NK cells, and NK T cells were significantly infiltrated in DCM patients. Furthermore, the lncRNA-miRNA-mRNA network was constructed. Moreover, 16 drugs were predicted, and the binding energy between atorvastatin and TGM2 was −2.79 kcal/mol. In vitro verification showed that TGM2, PPP1R15A and SESN2 were up-regulated in DOX-induced AC16 cardiomyocyte injury. After knocking down TGM2, the expressions of α-actinin and cTnT were increased, and the expression level of HIF-1α was inhibited. Dual luciferase assay showed that hsa-miR-291-5p exerted its regulatory effect by directly binding to TGM2. Flow cytometry results showed that TGM2 had no significant effect on the apoptosis of AC16 cells. Our findings may provide new ideas for the diagnosis and treatment of DCM.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2026.10894</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2026.10894</link>
        <title><![CDATA[The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals]]></title>
        <pubdate>2026-02-23T00:00:00Z</pubdate>
        <category>Brief Communication</category>
        <author>Inna Burakova</author><author>Yuliya Smirnova</author><author>Polina Morozova</author><author>Svetlana Pogorelova</author><author>Olga Kryukova</author><author>Tatiana Kislova</author><author>Olga Korneeva</author><author>Mikhail Syromyatnikov</author>
        <description><![CDATA[It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2026.10745</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2026.10745</link>
        <title><![CDATA[Poliovirus receptor (PVR) expression as a predictor of relapse in colorectal cancer: bioinformatics and virtual screening]]></title>
        <pubdate>2026-02-13T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Sulaiman S. Alhudaithi</author><author>Muhamed Hamza R. Salih</author><author>Zaid H. AlHusseini</author><author>Sarah M. Almufadhili</author><author>Noura Alelayani</author><author>Ahmed H. Bakheit</author><author>Hamad M. Alkahtani</author><author>Hanadi H. Asiri</author><author>Ali A. Alshamrani</author><author>Ali R. Alhoshani</author><author>Moureq R. Alotaibi</author><author>Homood M. As Sobeai</author>
        <description><![CDATA[Colorectal cancer (CRC) is one of the most frequently diagnosed malignancies worldwide. Despite advancements in CRC treatment strategies in recent years, disease recurrence remains a major problem; relapsed patients have a poorer prognosis and higher mortality risk. Several factors have been associated with CRC relapse. However, the role of immune checkpoints in CRC recurrence remains elusive. In this work, we aimed to investigate immune checkpoint genes correlated with recurrence in CRC, evaluate their potential as prognostic biomarkers, and identify promising immune checkpoint inhibitors through molecular docking and molecular dynamics simulations. Clinical, genetic, and epigenetic data of relapsed and relapse-free CRC patients in the Cancer Genome Atlas were retrieved from the cBioportal database and evaluated. Subsequently, molecular docking and molecular dynamics simulations studies were conducted to identify suitable poliovirus receptor (PVR)/TIGIT binders. PVR is a ligand for TIGIT and competes with CD226. The crystal structure used for docking was obtained from the Protein Data Bank (PDB ID: 3UDW). Using this investigative approach, clinical parameters data revealed that among immune checkpoint genes, the PVR gene was significantly upregulated in relapsed patients. That upregulation was strongly correlated with diagnosis age, Aneuploidy, fraction genome alterations, and mutation count. Furthermore, free survival analysis showed that patients exhibiting elevated PVR levels were 2.16 times more likely to relapse than those with low PVR expression (p = 0.039). Virtual screening identified 106 natural compounds as potential binders at the PVR/TIGIT interface. Molecular docking and molecular dynamics simulations identified three binders that exhibit favorable interactions with PVR, with ZINC001848443492 emerging as the most promising. The results underscore the potential role of PVR as a prognostic biomarker for relapse in CRC. Future studies, including TIGIT-PVR blockade assays and assessments of the impact of predicted PVR/TIGIT interface binders on T cell function, are necessary to validate this study’s findings.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2026.10893</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2026.10893</link>
        <title><![CDATA[Expanding the clinical and genetic spectrum of RHO-associated retinitis pigmentosa]]></title>
        <pubdate>2026-02-04T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Rebeca A. S. Amaral</author><author>Olivia A. Zin</author><author>Rosane G. Resende</author><author>Debora N. Moraes</author><author>Mariana V. Salles</author><author>Gabriela D. Rodrigues</author><author>Fabiana L. Motta</author><author>Juliana M. F. Sallum</author>
        <description><![CDATA[The majority of cases of autosomal-dominant retinitis pigmentosa (adRP) are associated with rhodopsin (RHO) variants. More than 290 pathogenic variants responsible for 25%–30% of adRP cases have been identified to date. This retrospective report focuses on RHO and RP cases in the Brazilian population. Patients with molecular confirmation of pathogenic variants in the RHO gene were included. Their clinical and genetic data were analyzed. Segregation analyses were included where possible. Cases were classified as generalized RP or sector RP according to fundus examinations and imaging data. The medical records of 43 patients from 34 families with RHO-associated RP were reviewed. Twenty-two disease-causing variants of the RHO gene and four previously unreported variants (c.317G>T; c.937-2A>T, c.272_283del, and c.530+1G>C) were identified. The majority of cases involved missense variants. The most prevalent variant was c.551A>G, p.(Gln184Arg), which was identified in seven patients (21%) from four families. One patient presented with the splice donor variant c.530+1G>C in the homozygous state, which was classified as pathogenic. Thirty-two patients presented with a generalized RP phenotype, and six patients were diagnosed with sector RP. This study provides information on the clinical and genetic features of RHO-associated RP in the Brazilian population, expanding the spectrum of RHO gene disease-causing variant frequencies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10866</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10866</link>
        <title><![CDATA[Integrated tear proteomics define the molecular blueprint of corneal epithelial repair]]></title>
        <pubdate>2026-02-02T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Nadege Feret</author><author>Marilou Decoudu</author><author>Jerome Vialaret</author><author>Christophe Hirtz</author><author>Karine Loulier</author><author>Vincent Daien</author><author>Frederic Michon</author>
        <description><![CDATA[Tears are easy to collect, repeatable, and reflect the state of the corneal surface—attributes that make them attractive for bedside monitoring after surgery or injury. We performed a cross-species meta-analysis of tear proteomes from patients undergoing photorefractive keratectomy (PRK) and from mice after mechanical epithelial abrasion to define molecular programs that are both conserved and clinically actionable. Roughly one-third of the injury response was shared between species, centering on innate immune activation (complement/acute phase), epithelial migration and cytoskeletal remodeling, and a calibrated suppression of proteolysis. From this overlap we distilled a small, secreted tear panel that stages injury and early resolution in both species: transferrin and hemopexin (iron/heme scavenging), albumin (vascular leak), apolipoprotein A-I (barrier lipid transport), and the coagulation modulators kininogen-1 and α2-antiplasmin (protease/fibrinolysis control). This panel rises at the first post-injury sampling (D0 in humans; 6–12 h in mice) and trends toward baseline during recovery (D3 in humans; ∼24 h in mice), providing a practical kinetic signature for clinical decision-making. Standardized sampling at D0/D3 can therefore quantify acute damage and early healing, enable pharmacodynamic readouts for anti-inflammatory or barrier-stabilizing therapies, and support risk stratification after epithelial procedures. Species-specific differences (human: secretory/immune surveillance; mouse: mitochondrial/metabolic reboot) clarify which preclinical signals are most likely to translate. Together, these findings establish a conserved tear blueprint of corneal repair and nominate a minimal, deployable biomarker set to accelerate clinical monitoring and therapeutic development in ocular surface disease.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2026.10906</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2026.10906</link>
        <title><![CDATA[Causal effects of antibody-mediated immunity to pathogens on five ophthalmic diseases: a Mendelian randomization study]]></title>
        <pubdate>2026-01-30T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Liduo Pan</author><author>Jian Deng</author><author>Jianli Yang</author><author>Meng Wang</author><author>Zheng Chen</author><author>Tao Wang</author><author>Yonghao Li</author>
        <description><![CDATA[While immune responses related to infections have been linked to ocular diseases, their causal role remains to be established. This study aimed to assess the causal relationship between antibody-mediated immune responses to infectious agents and five ocular conditions: chronic iridocyclitis (CIR), scleritis, wet age-related macular degeneration (AMD), diabetic retinopathy (DR), and glaucoma. We performed a two-sample Mendelian randomization (MR) analysis using GWAS data to assess causality between antibody responses to 46 pathogens and five ophthalmic diseases. The instrumental variables were Single nucleotide polymorphisms (SNPs). Causal estimates were primarily generated via the inverse-variance weighted method, supplemented by MR-Egger and weighted median methods. A Bonferroni-corrected threshold of P < 2.17 × 10−4 was applied. Sensitivity analyses included Cochran’s Q, MR-Egger, and MR-PRESSO for heterogeneity and pleiotropy. Reverse MR was performed to assess bidirectionality. Forward MR identified causal effects of infection-induced immune responses on ocular diseases. Epstein-Barr virus (EBV) ZEBRA antibodies were positively correlated with CIR, whereas Varicella zoster virus glycoproteins E and I antibodies were associated with scleritis and DR as risk factors. Genetically predicted anti-polyomavirus 2 IgG seropositivity (JCV IgG+) was identified as a risk factor for DR, wet AMD and glaucoma. In contrast, The EBV EBNA-1 antibody is associated with DR, wet AMD, and glaucoma as a protective factor, whereas the EBV VCA18 antibody is negatively associated with wet AMD. Reverse MR analysis indicated that DR may elevate JCV VP1 antibody levels. This study provides the first genetic evidence of a causal link between pathogen-specific immune responses and ocular diseases, offering a foundation for targeted immunomodulatory and personalized therapies.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10771</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10771</link>
        <title><![CDATA[Altered MCF2L-AS1 expression and correlation with the prognosis of diabetic nephropathy]]></title>
        <pubdate>2026-01-22T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Nastaran Injinari</author><author>Morteza Hadizadeh</author><author>Nasim Namiranian</author><author>Seyed Mehdi Kalantar</author><author>Ali Dehghani Firoozabadi</author><author>Samira Asadollahi</author>
        <description><![CDATA[Although diabetic nephropathy (DN) stands as a prominent complication in individuals with diabetes, the specific molecular mechanisms remain unclear. In this study, we focused on one newly discovered lncRNA, MCF2L-AS1, and its target gene, BCOR, in individuals with various levels of DN. Twenty-eight participants with different stages of DN (14 early stage and 14 late stage), 12 non-diabetic individuals, and 12 with T2DM without microvascular complications were selected. The qPCR was done, and one-way ANOVA assessed gene expression. ROC curves analysis and Spearman correlations between levels of expression and clinicopathological parameters were explored. The expression of MCF2L-AS1 decreased in the early and late DN groups compared to the type 2 diabetes (T2DM) (P = 0.01 and P = 0.03, respectively) and non-diabetic groups (P = 0.01 and P = 0.03, respectively). However, BCOR gene expression analysis revealed that there was no significant difference between the groups (P = 0.27). MCF2L-AS1 levels negatively correlated with microalbuminuria (P = 0.003, r = −0.41), but not with creatinine (Cr) (P = 0.058, r = −0.29). Moreover, there was no correlation between BCOR and microalbumin (P = 0.85, r = 0.02) and Cr (P = 0.49, r = 0.10). ROC curves underscored significant diagnostic accuracy for MCF2L-AS1 in distinguishing DN from people without kidney diseases (P < 0.05). This study introduces MCF2L-AS1 as a potential key player in the molecular landscape of DN, shedding light on its multifaceted interactions. The results provide a basis for further exploration and therapeutic interventions in the management of DN.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10776</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10776</link>
        <title><![CDATA[Machine learning-based comprehensive analysis of m6A RNA methylation regulators in colorectal cancer: implications for prognosis, immune microenvironment, and immunotherapy response]]></title>
        <pubdate>2026-01-14T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Feifei Kong</author><author>Jiawei Feng</author><author>Haixia Shan</author><author>Youlong Zhu</author><author>Ling-Jun Zhu</author>
        <description><![CDATA[N6-methyladenosine (m6A) RNA methylation regulators have been implicated in colorectal cancer (CRC) progression. However, systematic evaluation using multiple machine learning approaches for prognostic prediction remains limited. This study aimed to develop and validate machine learning models for CRC prognosis based on m6A regulators and assess their potential for immunotherapy response prediction. We analyzed 1,047 CRC patients from TCGA and GEO databases (70% training, 30% validation). Twenty machine learning algorithms were systematically evaluated, with LASSO regression selecting optimal features from 27 m6A regulators. SHAP analysis provided model interpretability. Immune microenvironment characterization and immunotherapy response prediction were performed using established computational methods. LASSO regression selected eight m6A regulators (IGF2BP2, METTL3, HNRNPA2B1, METTL14, YTHDF2, VIRMA, FTO, ALKBH5) for model construction. Among 20 algorithms tested, Random Forest achieved optimal performance (training AUC = 0.895, validation AUC = 0.847). SHAP analysis identified IGF2BP2 (mean |SHAP| = 0.42) and METTL3 (mean |SHAP| = 0.36) as primary contributors to risk prediction. Risk stratification showed significant survival differences (HR = 2.41, 95% CI: 1.73–3.36, p < 0.001). Low-risk patients demonstrated enhanced immune infiltration with higher CD8+ T cells (17.8% vs. 10.2%, p < 0.001) and better predicted immunotherapy response rates (36.5% vs. 20.3%, p = 0.006). Our systematic machine learning analysis demonstrates that m6A regulators can effectively predict CRC prognosis and immunotherapy response. The eight-gene signature provides a practical tool for clinical risk assessment and treatment decision-making.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10864</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10864</link>
        <title><![CDATA[Tear proteomic analysis in keratoconus patients and potential biomarkers: a case-control study]]></title>
        <pubdate>2026-01-12T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Daniel de Almeida Borges</author><author>Marcos Rodrigo Alborghetti</author><author>Romenia Ramos Domingues</author><author>Adriana Franco Paes Leme</author><author>Mônica Alves</author>
        <description><![CDATA[Keratoconus is a corneal ectasia whose pathophysiological mechanisms, including biomolecular alterations and genetic influences, remain poorly understood. Recent studies have shown altered cytokine levels, increased proteinase activity, and other potential mediators in the tear film and corneal tissue, highlighting a possible involvement of inflammatory pathways in the pathophysiology of keratoconus. This observational study aims to characterize the tear proteome of keratoconus patients and compare it to a control group, reporting potential disease biomarkers in the tear film. 23 keratoconus patients were selected at the Cornea and External Diseases Outpatient Clinic of the Clinics Hospital of UNICAMP. The control group consisted of 17 age- and sex-matched participants. All study subjects underwent corneal tomography (Pentacam). Tear film samples were collected and sent for proteomic evaluation by mass spectrometry at the National Biosciences Laboratory (LNBio). After quantification, univariate and multivariate statistical analyses were performed. A total of 353 proteins were identified and quantified, of which 25 showed statistical differences in the univariate analysis (t-test), and 19 were selected in the multivariate analysis (PLS-DA). There was an overlap of 7 proteins identified in both uni- and multivariate analyses: chitinase-3-like protein 2, prosaposin, zymogen granule protein 16 homolog B, procollagen-lysine,2-oxoglutarate 5-dioxygenase 1, secretoglobin family 1D member 1, albumin, and Ig kappa chain V-I region. Thirty-seven proteins showed statistically significant variation between the keratoconus and control groups. Proteomic analysis revealed differentially expressed proteins in the tear film of keratoconus patients. We report the identified proteomic profile, which includes potential biomarkers that may help elucidate the disease’s pathophysiology.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10533</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10533</link>
        <title><![CDATA[TIMAP downregulation in Burkitt’s lymphoma reveals key molecules and signaling pathways in B-cell lymphomagenesis]]></title>
        <pubdate>2025-10-15T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Marya Obeidat</author><author>Saleh Tadros</author><author>Batool Ismail</author><author>Ayah Al-Khaldi</author>
        <description><![CDATA[Burkitt’s lymphoma (BL) is an aggressive subtype of B-cell non-Hodgkin’s lymphoma, known for its rapid tumor growth and poor prognosis. Transforming growth factor beta-inhibited membrane-associated protein (TIMAP) is a regulatory subunit of protein phosphatase 1 catalytic subunit, enriched in lymphoid tissues, and upregulated in various cancers. Despite suggestions that TIMAP promotes lymphomagenesis in a c-myc-driven model, its precise role remains unclear. This study aimed to investigate the contribution of TIMAP to B-cell lymphomagenesis by examining transcriptomic changes upon TIMAP downregulation in BL cells. Raji BL cells were transfected with 2′Fluoro Arabinonucleic acid (FANA)-antisense oligonucleotides (ASO) targeting TIMAP (FANA-ASO-TIMAP) or a scramble control (FANA-ASO-Scramble). TIMAP expression was significantly reduced at the mRNA (0.70 ± 0.04, p = 0.001) and protein levels (median = 0.73, IQR = 0.13, p = 0.002). RNA sequencing identified 2,368 differentially expressed genes (DEGs), of which 1,326 were upregulated, and 1,042 were downregulated. Gene Ontology analysis revealed that the DEGs were primarily involved in cellular processes, DNA replication, intracellular signal transduction, and apoptosis. Pathways related to lymphoma progression, such as B-cell receptor signaling, p53 signaling, and mTOR signaling, were notably affected. Key genes such as PAK3, LINC00487, AID, PURPL, and BCL2 were among the most dysregulated, highlighting TIMAP’s role in critical oncogenic pathways in B-cell Lymphoma. These findings suggest that TIMAP is a key regulator of gene expression and signaling pathways in B-cell lymphomagenesis and could serve as a potential therapeutic target for novel treatments.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10610</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10610</link>
        <title><![CDATA[Glaucoma and cardiovascular disease: a bidirectional two-sample Mendelian randomization analysis]]></title>
        <pubdate>2025-10-15T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Dongdong Jin</author><author>Jie Sun</author><author>Wei Zhang</author><author>Mingxuan Zhang</author><author>Chengfang Li</author>
        <description><![CDATA[Many studies reported that glaucoma is associated with cardiovascular disease (CVD). This study aims to investigate the potential causal relationship between glaucoma and CVD using a bidirectional two-sample Mendelian randomization (MR) analysis. The genome-wide association studies (GWAS) of glaucoma and CVD were downloaded from the IEU OpenGWAS project. The CVD included unstable angina pectoris (UAP), coronary artery disease (CAD), high blood pressure (HBP), myocardial infarct (MI), heart failure (HF), ischemic stroke (IS), atrial fibrillation (AF), and pulmonary embolism (PE). The inverse variance weighting (IVW) analysis was the primary method in MR analysis. Meanwhile, sensitivity analysis and statistical power tests were performed. The random effects IVW method showed a causal relationship between glaucoma and a decreased risk of MI (Odds ratio (OR): 0.94, 95% confidence interval (CI): 0.89–0.99; P = 0.012). In the reverse MR analysis, genetic susceptibility of UAP (OR: 1.12, 95% CI: 1.02–1.23; P = 0.022), CAD (OR: 1.1, 95% CI: 1–1.21; P = 0.041), and HBP (OR: 1.83, 95% CI: 1.25–2.67; P = 0.002) was significantly linked to an increased risk of glaucoma. MR-Egger (P = 0.005) and IVW (P = 0.005) methods found that HBP presented different degrees of heterogeneity. The random effects IVW method also demonstrated that HBP is the risk factor for glaucoma (P = 0.0017). Although reverse MR initially suggested a potential association between CAD and glaucoma, MVMR showed no causal relationship after adjusting for obesity and BMI. The MR analysis found that glaucoma serves as a protective factor for MI, while UAP and HBP were risk factors for glaucoma in the European population, which may contribute to preventing and managing glaucoma and CVD.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10599</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10599</link>
        <title><![CDATA[Unveiling the dual role of CD3G: a diagnostic biomarker for depression and its oncogenic implications]]></title>
        <pubdate>2025-10-01T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Hai Gao</author><author>Ting Wu</author><author>Jihui Xue</author><author>Jing Liu</author><author>Dongmei Wen</author><author>Guanwei Huang</author>
        <description><![CDATA[Depression has been increasingly associated with immune system dysregulation. This study investigates the potential of CD3 Gamma Subunit of T-Cell Receptor Complex (CD3G) as a diagnostic marker for depression, while also examining its role across various cancer types. Comparative analyses of immune cell infiltration and pathway activities were conducted using single-sample Gene Set Enrichment Analysis (ssGSEA) on datasets GSE98793. Depression patients were defined based on clinical diagnoses and compared to healthy controls (HC) without any psychiatric disorders. Differentially expressed genes (DEGs) were identified, followed by weighted gene co-expression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) and logistic regression to pinpoint independent diagnostic markers. Functional enrichment analyses were performed to explore the biological implications of CD3G expression in depression. Pan-cancer analyses were also conducted to investigate CD3G’s role in cancer. Depression patients exhibited significant decreases in CD8 T cells, cytotoxic cells, T cells, T helper cells, Tgd, and Th2 cells, with increased levels of dendritic cells and neutrophils compared to HC. Immune pathway activities showed increased antimicrobial, chemokine, cytokine, and TNF family member activities, with decreased TCR signaling activity in depression patients. CD3G was identified as a key immune-related gene and independent diagnostic marker for depression, validated by GSE76826 dataset. Low CD3G expression in depression was associated with enhanced immune response and inflammatory pathways. In pan-cancer analysis, CD3G was upregulated in numerous cancers and correlated with immune cell infiltration and oncogenic pathways. The study highlights significant dysregulation in immune cell infiltration and pathway activities in depression, with CD3G emerging as a critical immune-related gene and potential diagnostic marker. CD3G’s role in immune modulation and cancer underscores its relevance in both depression and oncology, suggesting potential therapeutic targets and prognostic indicators.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10632</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10632</link>
        <title><![CDATA[Multi-omics analysis identifies the unique high-FDCSP basal cells in triple-negative breast cancer]]></title>
        <pubdate>2025-09-25T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Xinya Lu</author><author>Zhen Chen</author><author>Ying Shao</author>
        <description><![CDATA[Follicular dendritic cell secreted protein (FDCSP) is highly expressed in various cancers and has been implicated in tumor migration and invasion, yet its role in triple-negative breast cancer (TNBC) remains poorly understood. Our findings revealed that FDCSP expression was significantly elevated in TNBC compared to normal breast tissue, whereas its expression was significantly reduced in non-TNBC. In TNBC, high FDCSP expression was associated with an increased mutation rate of TP53 and influenced the infiltration of B cells and macrophages. Single-cell transcriptome analysis demonstrated that FDCSP was predominantly highly expressed in basal cells but exhibited low expression in luminal epithelial cells. This observation was further corroborated by spatial transcriptome (ST) analysis. Immunohistochemistry (IHC) assay also confirmed the distinct expression patterns of FDCSP. Cell-cell interaction and receptor-ligand pair analyses indicated that macrophages could interact with the receptor epidermal growth factor receptor (EGFR) in FDCSP highly expressed basal cells by secreting transforming growth factor-β1 (TGF-β1). Then, the co-localization of FDCSP and EGFR in TNBC basal cells was verified by IHC and immunofluorescence (IF) assay. Additionally, we discovered that FDCSP possesses strong predictive capabilities for distinguishing between responders and non-responders to Immune checkpoint blockade (ICB) treatment. Finally, leveraging the CARE database, we identified 14 potential FDCSP-related target drugs. These findings highlight the unique expression pattern of FDCSP in breast cancer, revealing FDCSP as a promising target for therapeutic strategies in TNBC.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10623</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10623</link>
        <title><![CDATA[Prognostic significance and therapeutic implications of redox metabolism-related genes in head and neck squamous cell carcinoma]]></title>
        <pubdate>2025-09-19T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Lina Yang</author><author>Jingyu Hai</author><author>Jiayi Liu</author><author>Shaohua Shen</author><author>Lin Su</author><author>Juan Sun</author>
        <description><![CDATA[Head and neck squamous cell carcinomas (HNSC) are associated with alterations in redox metabolism. This study aims to identify differentially expressed genes (DEGs) related to redox metabolism in HNSC and assess their prognostic values. We utilized the limma package for identifying redox metabolism-related DEGs and performed univariate and multivariate Cox regression analyses to evaluate their prognostic significance. Gene set variation analysis (GSVA), immune cell infiltration analysis, and single-cell RNA sequencing were utilized to explore the relationships between gene expression and tumor processes. Chemotherapy sensitivity was assessed based on ERP44 expression levels. Additionally, pan-cancer analysis was conducted to evaluate ERP44 expression and its prognostic value across different cancer types. The analysis identified several DEGs with significant prognostic value, including ERP44, which was significantly associated with poor prognosis in HNSC patients. High ERP44 expression correlated with reduced overall survival, disease-specific survival, and progression-free interval. ERP44 was notably overexpressed in tumor tissues and associated with key oncogenic pathways and immune cell infiltration patterns. Chemotherapeutic drug sensitivity analysis revealed that high ERP44 expression increased sensitivity to Paclitaxel, Vinblastine, and Sorafenib but decreased sensitivity to Rapamycin. Pan-cancer analysis indicated that ERP44 is differentially expressed and prognostic across multiple cancer types. Our findings highlight the crucial role of redox metabolism-related DEGs, particularly ERP44, in HNSC progression and prognosis. ERP44 serves as a potential biomarker for prognosis and therapeutic response, warranting further research into its biological functions and potential as a therapeutic target.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10430</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10430</link>
        <title><![CDATA[RNA binding proteins potentially regulate alternative splicing of immune-related genes during the progression of coronary artery disease]]></title>
        <pubdate>2025-08-29T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yulin Miao</author><author>Lei Wang</author><author>Gang Zhao</author><author>Wei Gou</author><author>Shan Chen</author><author>Chao Ding</author><author>Zongxin Li</author><author>Fengli Gao</author>
        <description><![CDATA[RNA-binding proteins (RBPs) are crucial in disease as they regulate the biological functions of RNA. However, their role in coronary artery disease (CAD) progression remains unclear. RNA-seq from peripheral blood of CAD patients and no-CAD controls was analyzed to compare differentially expressed genes (DEGs) and explore their potential functions. The distribution of immune cells was assessed by CIBERSORT algorithm. Alternative splicing (AS) pattern was quantified by SUVA. Immune-related AS events (ASEs) were screened via ImmPort database. Co-expression network of ASEs, differentially expressed RBPs (DERBPs), mitochondrion and apoptosis genes, and immune cells was constructed to clarify their potential functions. A total of 1521 DEGs were detected, including 99 DERBPs, which were mainly downregulated and enriched in mRNA processing, RNA splicing, mRNA transport, and innate immune response pathways in CAD. Seven DERBPs (ANG, C4BPA, DDX60, IFIH1, IPO7, MATR3, OTUD4) were associated with immune function. Analysis of the immune cell fraction demonstrated significant increase in macrophage M0 and CD8 T cells and decrease in resting dendritic cells and activated memory CD4 T cells. Immune-related ASEs correlated with atherosclerotic stenosis were mainly the complex “alt3p/alt5p” splicing types. DERBP-AS’s co-expression identified a key A5′SS event of CTSB gene. Co-expression of this event with TST and SYNCRIP may lead to a change in the proportion of macrophage M0 and CD8 T cells, respectively. The mitochondrion and apoptosis genes were also dysregulated in CAD and correlated with four DERBPs. In conclusion, RBPs have potential regulatory role in the progression of CAD by regulating the ASEs of immune-related genes and mediating immune cells composition. These findings highlight RBPs as potential therapeutic targets for CAD.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10452</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10452</link>
        <title><![CDATA[Integrated analysis of metabolome and microbiome in a mouse model of sodium valproate-induced autism]]></title>
        <pubdate>2025-08-29T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Shuzhen Zhao</author><author>Xinyan Zhang</author><author>Yanqiu Miao</author><author>Xueya Gao</author><author>Qiuhua Wan</author><author>Wei Qiu</author><author>Haixia Si</author><author>Yingjie Han</author><author>Xiao Du</author><author>Yuanyuan Feng</author><author>Lianhua Liu</author><author>Yuqing Chen</author>
        <description><![CDATA[Sodium valproate (SV) has been shown to induce autism in animal models. In this study, the SV method was used to establish a mouse model of autism, and anxiety-like behaviours and learning memory performance were evaluated by behavioural tests. The effects of SV on metabolic profiles and gut microbiota were assessed by integrating gas chromatography-mass spectrometry and 16S ribosomal RNA gene sequencing. Correlations between metabolites and gut microbiota were determined using Spearman correlation coefficient. Behavioral tests, including the three-chambered social assay, repetitive behaviors, open field test, elevated plus-maze test, and novel object recognition test, demonstrated that SV treatment exacerbated anxiety-like behaviors and impeded spatial learning and memory in mice. SV disrupted metabolic pathways in hippocampus, cortex, intestine, and serum, affecting primarily valine, leucine and isoleucine biosynthesis, glycerophospholipid metabolism and glutathione metabolism and so on. SV also altered gut microbiota at the genus level, decreasing the abundances of Dubosiella, Faecalibaculum, Clostridia_UCG-014, Bifidobacterium, and Alloprevotella, while increase the abundances of Lactobacillus, Alistipes, and Lachnospiraceae in intestine. The results of correlation analysis showed that in hippocampus, Bifidobacterium was positively correlated with serine and glycine, while Alistipes was negatively correlated with them. These findings suggested that SV may contribute to the development of autism progression by altering the gut microbiota abundances and metabolite profiles. This may provide new direction for the management of autism.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10544</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10544</link>
        <title><![CDATA[Dietary-related characteristics and cataract risk: evidence from a mendelian randomization study]]></title>
        <pubdate>2025-08-04T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Chen Li</author><author>Yicheng Lu</author><author>Mingxuan Chen</author><author>Qing Zhang</author><author>Zhe Zhang</author><author>Wenqun Xi</author><author>Weihua Yang</author>
        <description><![CDATA[Cataract is the leading cause of blindness globally, imposing a significant socioeconomic burden. While diet is associated with various eye diseases, the causal relationship between dietary-related characteristics (DRCs) and cataract remains unclear. This study investigates the causal associations between DRCs and cataract using Mendelian randomization (MR) to provide insights into potential dietary interventions for cataract prevention. We conducted a two-sample MR analysis using data from the open GWAS database, focusing on individuals of European descent. Instrumental variables were selected based on stringent criteria, and multiple MR methods were applied to estimate causal effects. Sensitivity analyses assessed the robustness of the findings. Significant causal associations were found between oily fish intake (OR = 0.86) and variation in diet (OR = 1.26) with cataract. Sensitivity analyses supported the robustness of these findings. Mediation effect analysis suggested that the intake of oily fish might indirectly influence cataract risk through metabolites. This study provides evidence for causal relationships between specific DRCs and cataract, highlighting the potential role of dietary interventions in cataract prevention.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10593</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10593</link>
        <title><![CDATA[Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing]]></title>
        <pubdate>2025-07-17T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Eleonora Sabetta</author><author>Karin Rallmann</author><author>Jonas Bergquist</author><author>Pille Taba</author><author>Abigail L. Pfaff</author><author>Bal Hari Poudel</author><author>Davide Ferrari</author><author>Massimo Locatelli</author><author>Sulev Kõks</author>
        <description><![CDATA[Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder presenting progressive weakness of the bulbar and extremity muscles, leading to a wide-ranging clinical phenotype. More than 30 genes have been associated to genetically inherited ALS yet, approximately 85%–90% of ALS cases are sporadic. Short tandem repeats expansions, have recently been found in clinically diagnosed ALS patients and are currently investigated as potential genetic biomarkers. In this paper we compare the investigation of pathological tandem repeat expansions on a group of ALS patients by comparing the standard short-read sequencing (SRS) technique with a long-read-sequencing (LRS) method which has recently become more accessible. Blood samples from 47 sporadic ALS cases were subjected to SRS by Illumina Whole Genome Sequencing. The genome-wide tandem repeat expansions were genotyped using GangSTR, while wANNOVAR was used for variant annotation. Uncertain cases were further explored using LRS. SRS identified pathological expansions in HTT, ATXN2, and CACNA1A genes in one patient, which were not confirmed with LRS. The latter identified large tandem repeat expansions in the C9orf72 gene of one patient that were missed by SRS. Our findings suggest that LRS should be preferred to SRS for accurate identification of pathological tandem repeat expansions.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.ebm-journal.org/articles/10.3389/ebm.2025.10128</guid>
        <link>https://www.ebm-journal.org/articles/10.3389/ebm.2025.10128</link>
        <title><![CDATA[An innovative full-size pathogenic tandem duplication mutation precise detection system based on next-generation sequencing]]></title>
        <pubdate>2025-07-11T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Li-Li Zhang</author><author>Zhe Wang</author><author>Ying Zhou</author><author>Dai-Yang Li</author><author>Xiao-Nian Tu</author><author>Yu-Xia Li</author><author>Ke-Ming Du</author><author>Zhong-Zheng Zheng</author>
        <description><![CDATA[Accurate identifying internal tandem duplication (ITD) mutation is indispensable for diagnosis and prognosis of acute myeloid leukemia (AML) patients, but specialized full-size detection tools are lacking. Therefore, we aimed to develop a reliable system for accurate assessment of ITD mutations of various size ranges and improve prognosis for AML. Bone marrow samples from AML patients from December 2021 to March 2022 were collected for methodology establishment. After a large-scale sample testing by next-generation sequencing (NGS), a short-read tandem duplication recognition system based on soft-clip was established. During performance validation, the lower detection limit was set to a parameter close to capillary electrophoresis (“gold standard”) by adjusting reference values (sensitivity 3–5%). Data simulation was performed using the FLT3 gene CDS as wild-type data. Methodological concordance of this system with capillary electrophoresis was analyzed. The applicability to other pathogenic tandem duplication mutations was validated. We have developed an innovative NGS-based system named “ITDFinder” for accurate detection of ITD mutations, with the lower detection limit of 4%, corresponding to a sequencing depth of 1000X. Compared to capillary electrophoresis, ITDFinder exhibited good consistency (mean difference: −0.0085) in mutation detection and correlation across various length of ITD. Clinical case validation (n = 1,032) showed an overall agreement rate of 96.5% between the two approaches used for characterization. In addition, data simulation results suggested that the new system could observe BCOR-ITD and KMT2A-PTD mutations (depths, 500–1300X; mutation rates, 0.04–0.8). The innovative mutation detection system is appropriate to small-to large-sized ITDs and other pathogenic tandem duplication mutations, expected to save 96.3% of the workload. This offers significant potential for accurate clinical assessment of ITD mutations and subsequent prognosis in AML patients.]]></description>
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