Biochemical Genetics最新文献

{"title":"Identification of Key Genes Related to SUMOylation and Potassium Channels and Their Mechanism of Influence on Pulmonary Arterial Hypertension.","authors":"Lingyun Gao, Wei Huang, Qianqian Wang, Sen Lei","doi":"10.1007/s10528-026-11388-0","DOIUrl":"10.1007/s10528-026-11388-0","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"7787-7807"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-Genome Deep Learning Predicts Chemotherapy Response in Colorectal Cancer.","authors":"Hossein Sadeghi, Fatemeh Seif","doi":"10.1007/s10528-026-11368-4","DOIUrl":"10.1007/s10528-026-11368-4","url":null,"abstract":"<p><p>Chemotherapy response in colorectal cancer (CRC) exhibits significant heterogeneity, with current clinical predictors failing to capture complex genomic determinants of resistance. We developed a hybrid deep learning framework integrating convolutional neural networks (CNNs) and bidirectional long short-term memory (BiLSTM) networks to analyze whole-genome somatic mutations, evolutionary conservation, chromatin accessibility, and 3D genome architecture in 2,546 TCGA patients. An attention mechanism identified predictive genomic regions. The model achieved an AUC of 0.92 (95% CI: 0.89-0.94) in cross-validation and 0.88 (95% CI: 0.85-0.91) in independent validation, outperforming clinical models (ΔAUC = +0.18, p < 0.001). Key predictors included non-coding variants in TP53, KRAS, and PIK3CA regulatory regions. Triple-positive patients (mutations in all 3 regions) had significantly worse progression-free survival (HR = 4.7, p < 0.001). Our framework enables accurate chemotherapy response prediction and reveals novel non-coding resistance mechanisms, advancing precision oncology in CRC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"7032-7051"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147661993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MiR-342-3p Attenuates Inflammation and Pyroptosis in Severe Community-Acquired Pneumonia by Targeting EP300.","authors":"Bo Song, Ruijuan Xu, Chenxi Cui, ShuMei Rao, Yingying Liu, Yilei Yang","doi":"10.1007/s10528-026-11344-y","DOIUrl":"10.1007/s10528-026-11344-y","url":null,"abstract":"<p><p>Community-acquired pneumonia (CAP), particularly severe CAP (SCAP), poses a significant clinical challenge with high mortality. MicroRNAs, including miR-342-3p, have been implicated in various pulmonary diseases, suggesting a potential role in SCAP. To examine the expression, functional mechanisms, and clinical relevance of miR-342-3p in SCAP. Bioinformatic analysis was performed on two independent GEO datasets (GSE196399 and GSE136390). Serum miR-342-3p levels were measured in a clinical cohort of 109 SCAP patients and 109 healthy controls by RT-qPCR, and its correlation with clinical prognosis was analyzed. An in vitro pneumonia model was established using LPS-stimulated MRC-5 cells. Gain-of-function experiments of miR-342-3p were achieved through mimic transfection. MiR-342-3p's involvement in inflammation, cytotoxicity, and pyroptosis was assessed via ELISA, western blot, CCK-8, and LDH assays. The interaction between miR-342-3p and EP300 was confirmed by dual-luciferase reporter and RNA pull-down assays, and its functional role was confirmed through rescue experiments. The downregulation of miR-342-3p in SCAP patient serum correlated with increased mortality. In vitro, miR-342-3p overexpression reduced LPS-induced inflammation and pyroptosis. Bioinformatics analysis confirmed that histone acetyltransferase EP300 is a candidate target gene for miR-342-3p. Mechanistically, miR-342-3p directly targeted and negatively regulated EP300. Overexpression of EP300 abolished the anti-inflammatory and anti-pyroptotic effects of miR-342-3p through the activation of NF-κB p65. MiR-342-3p acts as a protective factor in SCAP by targeting EP300 to inhibit inflammation and pyroptosis. These results indicate the potential of miR-342-3p as a biomarker and therapeutic target in SCAP.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6529-6545"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147455254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hedyotis diffusa Willd-Scutellaria barbata D.Don Suppresses Colorectal Cancer Liver Metastasis by Targeting hsa_circ_0039933-Mediated Epithelial-Mesenchymal Transition.","authors":"Shanmin Yuan, Sha Li, Cong Chen","doi":"10.1007/s10528-026-11392-4","DOIUrl":"10.1007/s10528-026-11392-4","url":null,"abstract":"<p><p>Colorectal cancer (CRC) liver metastasis remains a major cause of mortality, necessitating novel therapeutic strategies. Hedyotis diffusa Willd -Scutellaria barbata D.Don (HD-SB), a traditional Chinese herbal formulation, has demonstrated anti-tumor potential. However, its mechanism in CRC metastasis, particularly through the regulation of circular RNAs, remains unexplored. A CRC liver metastasis model was established in Balb/c nude mice via intrasplenic injection of HCT-15 cells. Mice received HD-SB treatment. Hematoxylin-eosin staining, Masson staining, and immunohistochemistry (Ki67 and Cytokeratin 19 [CK19]) were carried out to observe pathologic changes in CRC liver metastases. In vitro, HCT-15 cells were treated with tumor necrosis factor-α (TNF-α) to induce metastasis. hsa_circ_0039933 was knocked down and overexpressed in vitro. Transwell, wound healing, EdU, and cell counting kit-8 assays were employed to assess cell invasion, migration and proliferation, respectively. The levels of epithelial-mesenchymal transition (EMT) markers were evaluated by quantitative real-time polymerase chain reaction and western blot. HD-SB treatment dose-dependently reduced hepatic tumor nodules, fibrosis, Ki67 and CK19 expression in vivo, with high-dose HD-SB showing superior efficacy. EMT reverse (upregulated E-cadherin, downregulated N-cadherin/Vimentin) and hsa_circ_0039933 suppression were observed in HD-SB treated CRC mouse. In vitro, HD-SB attenuated TNF-α-induced proliferation, migration, and invasion, synergizing with hsa_circ_0039933 knockdown to suppress EMT and metastatic phenotypes. Conversely, hsa_circ_0039933 overexpression exacerbated TNF-α-driven aggressiveness, which was effectively counteracted by HD-SB. Collectively, HD-SB inhibits CRC liver metastasis by targeting hsa_circ_0039933 and modulating EMT. These findings highlight HD-SB as a promising circRNA-directed therapeutic agent for metastatic CRC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"7608-7627"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148196790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ANGPTL1 Inhibits the Growth, Migration, and Angiogenesis of Gastric Cancer Cells by Downregulating VEGFA Expression.","authors":"Lingli Jin, Guangxin Lu, Rui Shang, Junhua Hu, Chaobei Zhu, Tingting Yan","doi":"10.1007/s10528-026-11406-1","DOIUrl":"10.1007/s10528-026-11406-1","url":null,"abstract":"<p><p>Gastric cancer (GC) remains one of the most common malignant tumors worldwide, with high incidence and mortality rates. Angiopoietin-like protein 1 (ANGPTL1), a member of the ANGPTL family, is known to function as an anti-angiogenic factor and tumor suppressor. However, its role and underlying mechanisms in GC development have not been investigated and require further investigation. Protein expression levels were analyzed using western blotting and immunofluorescence (IF) assays. Cell viability was assessed using the CCK-8 assay, and cell proliferation was evaluated through colony formation assays. Cell migration and invasion were examined using Transwell assays. Angiogenic capacity was determined through tube formation assays. The VEGFA mRNA expression was detected through RT-qPCR. The level of VEGFA was confirmed through ELISA. The tumor size, volume and weight were confirmed through the in vivo assay. The CD31 protein expression was verified though IHC assay. ANGPTL1 was found to be expressed at lower levels in GC cells, and negatively correlated with VEGFA. ANGPTL1 significantly inhibited GC cell proliferation, migration, and invasion. Furthermore, ANGPTL1 suppressed angiogenesis in vitro. Mechanistically, it was observed that ANGPTL1 overexpression reduced VEGFA expression, and ANGPTL1 can interact with VEGFA. Importantly, reintroduction of VEGFA reversed the inhibitory effects of ANGPTL1 on GC progression. Lastly, VEGFA overexpression retarded the tumor growth in vivo. This study demonstrates that ANGPTL1 inhibits the growth, migration, and angiogenesis of GC cells by downregulating VEGFA expression. These findings suggest that ANGPTL1 may serve as a promising therapeutic target for gastric cancer treatment.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"7465-7481"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148142253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Klotho Attenuates Glucocorticoid-Induced Osteoblast Cytotoxicity Via Wnt Signaling Pathway Modulation.","authors":"Sen Wang, Miao He, Xiao Liang, Baoshan Li","doi":"10.1007/s10528-026-11390-6","DOIUrl":"10.1007/s10528-026-11390-6","url":null,"abstract":"<p><p>Glucocorticoids are commonly prescribed in clinical settings; however, their prolonged use at high doses can adversely affect human health. One significant complication following glucocorticoid therapy is glucocorticoid-induced osteoporosis (GIO), which is second in incidence only to senile osteoporosis. Based on previous research indicating that Klotho alleviates dexamethasone-induced osteoblast cytotoxicity through the NF-kB pathway, we aimed to explore the underlying mechanisms in greater depth. We assessed the impact of Lithium chloride (LiCl), a Wnt pathway activator, on glucocorticoid-induced cell cytotoxicity and viability. Cytotoxicity was specifically quantified by Annexin V/PI flow cytometry. We performed qRT-PCR and Western blotting analyzes to scrutinize the expressions of genes and proteins associated with both canonical and non-canonical Wnt signaling pathways. Dexamethasone treatment induced an upregulation of the non-canonical Wnt ligand, Wnt5a, and a downregulation of the canonical ligand, Wnt3a, along with its downstream marker, β-catenin. Transfection with Klotho counteracted these effects. Klotho has the potential to modulate both canonical and non-canonical Wnt signaling pathways, thereby counteracting osteoblast cytotoxicity induced by glucocorticoids.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"7340-7355"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147969451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FTO Deficiency Inhibits Vascular Endothelial Cell Apoptosis and Improved Mitophagy in Obesity-Related Hypertension by Enhancing NDRG1 m6A Methylation.","authors":"Qinglei Gan, Na Yang","doi":"10.1007/s10528-026-11410-5","DOIUrl":"10.1007/s10528-026-11410-5","url":null,"abstract":"<p><p>Vascular endothelial dysfunction contributes to obesity-related hypertension, yet its mechanisms remain unclear. This study examined the role of N6-methyladenosine (m6A) in this process using in vivo and in vitro models. C57BL/6J mice fed a high-fat diet (HFD) developed obesity-related hypertension, while oxidized low-density lipoprotein (ox-LDL)-treated human aortic endothelial cells (HAECs) simulated endothelial injury. Global m6A levels were assessed via dot blot, and m6A regulators were quantified by qPCR. Endothelial function was evaluated through viability (CCK-8), apoptosis (flow cytometry), and mitophagy (Western blot and immunofluorescence staining). Mechanistic studies included methylated RNA immunoprecipitation (MeRIP) and dual-luciferase assays. Results showed HFD reduced m6A levels but elevated Fto expression in mice, while ox-LDL decreased m6A levels and upregulated FTO in HAECs. FTO knockdown in HAECs enhanced viability and mitophagy while suppressing apoptosis under ox-LDL stress. Mechanistically, FTO silencing increased m6A methylation on NDRG1 mRNA, leading to its degradation via YTHDF2 recognition. NDRG1 overexpression reversed these effects, restoring apoptosis while reducing mitophagy and viability. These findings reveal that FTO depletion attenuates endothelial dysfunction in obesity-related hypertension by enhancing m6A-mediated suppression of NDRG1, highlighting the FTO/m6A/NDRG1/YTHDF2 axis as a therapeutic target for vascular protection.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"7523-7541"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148154866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitogenome of Rhabdophis swinhonis (Squamata: Colubridae): Its Comparative Description and Phylogenetic Position Within Colubridae.","authors":"Ya Su, Jingxue Luo, Fei Wu, Huina Song, Ji Wang, Guangxiang Zhu","doi":"10.1007/s10528-026-11359-5","DOIUrl":"10.1007/s10528-026-11359-5","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6794-6806"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Characterization of β-Glucosidase (TaBGLU) Genes in Bread Wheat and Their Expression Under Drought, Cold, and Combined Stress.","authors":"Khairiah Mubarak Alwutayd, Ashwag Shami, Ahmad M Alqudah, Samar G Thabet","doi":"10.1007/s10528-026-11342-0","DOIUrl":"10.1007/s10528-026-11342-0","url":null,"abstract":"<p><p>Glycoside hydrolase 1 (GH1) β-glucosidases were known to activate hormone conjugates and defense metabolites, yet their genomic organization and stress-response dynamics in wheat remained incompletely defined. We therefore performed an integrated characterization of TaBGLUs spanning phylogeny, gene structure and conserved motifs, subcellular localization, promoter cis-elements, Gene Ontology enrichment, protein-protein interaction networks, and targeted expression profiling. Wheat TaBGLUs partitioned into well-supported clades that shared canonical GH1 catalytic residues and a largely conserved motif scaffold. Subcellular localization predictions indicated predominant nuclear and chloroplast targeting, with a smaller cohort directed to secretory or endomembrane compartments. Promoters were enriched for light-responsive, hormone-related (ABA, JA/SA, auxin, GA) and stress-associated (MYB/WRKY, heat, low temperature) cis-elements, and functional annotations were consistent with roles in carbohydrate and cell-wall metabolism, hormone homeostasis, and defense. Network analysis revealed a densely connected TaBGLU submodule embedded within broader carbohydrate and defense interaction networks, suggesting coordinated or cooperative functions. Expression profiling under cold, drought, and combined drought and cold demonstrated broad stress inducibility, with early activation detected by 6 h, cold-responsive maxima typically at 12 h, drought-responsive peaks predominating at 24 h, and combined stress eliciting both earlier and more sustained expression maxima between 12-24 h. Representative strongly responsive genes included TaBGLU20, TaBGLU44, TaBGLU6, and TaBGLU23, which showed pronounced late induction under combined stress, TaBGLU30, which exhibited an earlier combined-stress peak, and TaBGLU12, which displayed a marked late drought-specific response. Taken together, this integrated genomic, regulatory, and expression atlas refined the wheat BGLU repertoire relative to previous gene model inventories, highlighted candidate TaBGLUs with central network positions and strong stress inducibility, and provided concrete entry points for functional validation and breeding for improved stress resilience.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6607-6631"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemical Complementarities of Neuroblastoma Tumor-Resident TCR CDR3s and CMV Antigens are Associated with a Better Outcome.","authors":"Kasey L Rigby, Rahul Jain, Etienne C Gozlan, Dorottya B Kacsoh, Tushar Singh, Andrea Chobrutskiy, Boris I Chobrutskiy, George Blanck","doi":"10.1007/s10528-026-11355-9","DOIUrl":"10.1007/s10528-026-11355-9","url":null,"abstract":"<p><p>A likely immune response to a virus can be detected via the presence of TCR CDR3s that (a) exactly match CDR3s known to bind viral antigens or (b) represent chemical complementarity to viral antigens. Previous studies, based on genomics approaches to characterizing anti-CMV TCR CDR3s in patient blood samples, have indicated the possibility that a systemic CMV infection is associated with worse outcomes for NBL, as well as for breast cancer. Thus, the association of NBL tumor-resident anti-CMV TCR CDR3s and patient outcomes was evaluated here, with results indicating that high levels of chemical complementarity between tumor-resident TCR CDR3s and CMV antigens represented a better outcome. This is in apparent contrast to results obtained via the previous study of blood sourced, anti-CMV TCR CDR3s representing a worse outcome. This study identified gene expression values associated with the tumor-specific anti-CMV TCR CDR3s, representing exact matches to known anti-CMV TCR CDR3s, which may assist in identifying a potential underlying mechanism effecting the better outcomes associated with the tumor-resident, anti-CMV TCR CDR3s. Overall, results here raise the question of whether an anti-CMV response directly against the tumor, or within the tumor microenvironment, is involved in reductions in tumor progression or responsiveness to treatment?</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6652-6671"},"PeriodicalIF":1.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147508548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}