Genes & genomics最新文献

{"title":"Comparative analysis of spatial expression patterns of ectopic olfactory receptors.","authors":"Elina Pokharel, Jae-Kwang Jung, Jae-Young Kim, Wern-Joo Sohn","doi":"10.1007/s13258-026-01747-x","DOIUrl":"10.1007/s13258-026-01747-x","url":null,"abstract":"<p><strong>Background: </strong>The oral mucosa comprises anatomically and functionally distinct regions that differ in their degree of keratinization and barrier properties. Ectopic olfactory receptors (OR) have been detected in the oral mucosa. However, their expression patterns and potential roles remain poorly understood.</p><p><strong>Objective: </strong>This study aimed to characterize the molecular features and regional differences of structurally and functionally distinct oral mucosal tissues through unbiased transcriptomic analysis, and to explore the potential involvement of ectopic ORs as chemosensory components within this context.</p><p><strong>Methods: </strong>Gingival, buccal, and palatal mucosal tissues were collected by full-thickness excision from 8-week-old adult mice. Total RNA was extracted and sequenced. Differentially expressed genes (DEGs) and expression patterns were analyzed via bioinformatic approaches, and selected genes were validated by RT-qPCR.</p><p><strong>Results: </strong>Buccal, gingival, and palatal epithelia exhibited distinct transcriptional profiles, with gingiva and palate showing higher mutual correlation compared with buccal mucosa. Buccal tissue was enriched for genes associated with muscle activity and cytoskeletal organization, whereas genes related to keratinization and epithelial differentiation related genes were relatively underrepresented. Pairwise differential expression analysis indicated greater molecular divergence between buccal and masticatory mucosa than between gingiva and palate. Pattern-based transcriptomic analysis defined a global expression topology across oral mucosal tissues, in which ectopic ORs and associated genes were nonrandomly distributed. Several ORs displayed tissue-biased expression patterns linked to keratinization, calcium signaling, and GPCR-related pathways.</p><p><strong>Conclusion: </strong>These findings demonstrate that buccal, gingival, and palatal epithelia constitute transcriptionally and functionally distinct compartments of the oral mucosa. The regional embedding of ectopic ORs within tissue-specific expression architecture suggests a potential role for chemosensory mechanisms in shaping site-specific physiological responses, providing a molecular framework for understanding chemical sensing in the oral mucosa.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"683-696"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147354896","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":"Cochlear synaptic vulnerability scales with pathological noise intensity in a noise-induced hearing loss model.","authors":"Byeonghyeon Lee, Tae-Jun Kwon, Hyun Tae Kim, Un-Kyung Kim","doi":"10.1007/s13258-026-01748-w","DOIUrl":"10.1007/s13258-026-01748-w","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"697-708"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147354900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Histone lactatation-related genes GPR19 and SLC22A16 are important diagnostic markers and drug treatment targets for prostate cancer.","authors":"Yunkun Yan, Zhuo Li, Mushi Ye, Jianchang Li","doi":"10.1007/s13258-026-01740-4","DOIUrl":"10.1007/s13258-026-01740-4","url":null,"abstract":"<p><strong>Background: </strong>Histone lactylation is an emerging epigenetic modification involved in tumor progression, but its transcriptional characteristics and clinical relevance in prostate cancer (PCa) remain poorly understood.</p><p><strong>Purpose: </strong>To preliminarily explore histone lactylation-related transcriptional features in prostate cancer and identify potential diagnostic biomarkers.</p><p><strong>Methods: </strong>The TCGA-PRAD dataset was used as the training cohort and the GSE46602 dataset as the validation cohort. Based on histone lactylation-related genes (HLRGs) reported in the literature, single-sample gene set enrichment analysis (ssGSEA) scores were calculated to characterize histone lactylation-related transcriptional states. Differentially expressed genes were identified between tumor and normal tissues, as well as between highand low-ssGSEA score groups, and overlapping genes were selected for further analysis. Mendelian randomization (MR) analysis was then applied to identify genes significantly associated with PCa, and receiver operating characteristic (ROC) curves were used to evaluate their discriminatory performance. Functional enrichment and regulatory network analyses were also performed. In addition, gene expression was examined in prostate-related cell lines, and gene knockdown experiments were conducted to preliminarily assess the effects on prostate cancer cell viability and proliferation.</p><p><strong>Results: </strong>GPR19 and SLC22A16 were ultimately identified as candidate biomarkers. Both genes were significantly upregulated in prostate cancer tissues and cell lines. Functional analyses indicated that GPR19 and SLC22A16 were associated with the \"cell cycle\" and \"aminoacyl-tRNA biosynthesis\" pathways, respectively. In vitro experiments showed that knockdown of SLC22A16 significantly suppressed the viability and proliferation of PC-3 cells.</p><p><strong>Conclusion: </strong>Based on histone lactylation-related transcriptional features, this study preliminarily identified GPR19 and SLC22A16 as genes associated with prostate cancer and provided supportive evidence for their potential biological relevance. Further studies are required to elucidate their regulatory mechanisms and clinical significance.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"659-671"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147283357","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":"Ferroptosis modulation by Toxoplasma gondii suppresses sodium iodate-driven age-related macular degeneration.","authors":"Xin-Cheng Wang, Guan-Hao Hong, Yu-Sun Yun, In-Wook Choi, Jaemin Yuk, Guang-Ho Cha","doi":"10.1007/s13258-026-01757-9","DOIUrl":"10.1007/s13258-026-01757-9","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"767-781"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147485341","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":"Ubiquilin 1 Inhibits intracellular proliferation of Salmonella enterica serovar Typhimurium through Xenophagy.","authors":"In Sook Jeon, Yong-Hee Lee, Jin Tae Hong, Won Seop Kim, Jae-Cheon Shin, Hak-Kyo Lee, Joong-Kook Choi","doi":"10.1007/s13258-026-01755-x","DOIUrl":"10.1007/s13258-026-01755-x","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"755-766"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147485353","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":"Comparative transcriptomic profiling reveals metabolic and regulatory features of Drosophila melanogaster S2 cells relative to newly hatched larval tissues.","authors":"Deng Chao, Yang Hui","doi":"10.1007/s13258-025-01725-9","DOIUrl":"10.1007/s13258-025-01725-9","url":null,"abstract":"<p><strong>Background: </strong>Drosophila melanogaster S2 cells are widely used as an in vitro model system and have undergone extensive adaptation during long-term culture. Understanding how their transcriptional programs differ from in vivo tissues is essential for interpreting their biological characteristics and experimental utility.</p><p><strong>Objective: </strong>This study aimed to characterize transcriptomic differences between Drosophila S2 cells and newly hatched larval tissues, with a focus on identifying metabolic, regulatory, and proliferative features associated with the long-term maintenance of S2 cells in vitro.</p><p><strong>Methods: </strong>RNA sequencing was performed on S2 cells and newly hatched larvae. Differentially expressed genes (DEGs) were identified using edgeR (FDR < 0.05, |log2FC| ≥ 1). Gene Ontology (GO) and KEGG enrichment analyses were used to investigate functional changes. Protein-protein interaction (PPI) networks were constructed based on STRING data to identify hub genes, and selected genes were validated using quantitative real-time PCR (qRT-PCR).</p><p><strong>Results: </strong>A total of 5,937 DEGs were detected between S2 cells and larval tissues. S2 cells displayed pronounced upregulation of genes linked to amino acid metabolism, lipid biosynthesis, cell cycle progression, protein turnover, and RNA interference pathways, whereas genes associated with development and differentiation were broadly downregulated. PPI analysis highlighted 10 hub genes-including P5CS, GluProRS, ND-ACP, Ubi-p63E, and Dcr-2-that represent central nodes in metabolic regulation, protein homeostasis, transcriptional control, and stress response. These features collectively reflect a transcriptional state shaped by long-term in vitro adaptation.</p><p><strong>Conclusions: </strong>This comparative analysis provides a comprehensive overview of transcriptomic and regulatory differences between S2 cells and in vivo larval tissues. The results clarify key molecular characteristics of S2 cells and offer a useful reference for their application in functional genomics, metabolism research, and cell-based assays.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"721-732"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147432358","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":"GWAS reveals common SLX4 variants associated with telomere length and hypertension in individuals of African ancestry.","authors":"Nicole Benfield, Prisca K Thami, James Ware, Laura Collopy","doi":"10.1007/s13258-026-01746-y","DOIUrl":"10.1007/s13258-026-01746-y","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"673-682"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13149702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146258009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selection of heat stress-tolerant cultivars from radish and analysis of gene expression under high-temperature.","authors":"Jae-Han Choi, Won Byoung Chae, Man-Ho Oh","doi":"10.1007/s13258-026-01766-8","DOIUrl":"10.1007/s13258-026-01766-8","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"783-796"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769561","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":"Resolving repetitive and telomeric regions through a high-contiguity genome assembly of the African Turquoise killifish.","authors":"Nagyeong Kim, Chang-Myung Oh, Yumi Kim, Jun Kim","doi":"10.1007/s13258-026-01738-y","DOIUrl":"10.1007/s13258-026-01738-y","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"747-754"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147480394","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":"c-Myc regulated long noncoding RNA TRD-AS1 to affect the progression of oral squamous cell carcinoma.","authors":"Ziyue Feng, Yuxuan Han, Xiaofeng Qin, Miaoting Fu, Xiangyang Li, Youming Zhu","doi":"10.1007/s13258-026-01745-z","DOIUrl":"10.1007/s13258-026-01745-z","url":null,"abstract":"<p><strong>Background: </strong>Oral squamous cell carcinoma (OSCC) progression is closely associated with dysregulated oncogenic transcription programs and noncoding RNA networks. c-Myc is a key transcription factor in tumor biology, but the role of c-Myc-regulated long noncoding RNAs such as TRD-AS1 (LNC TRD-AS1) in OSCC progression remains to be clarified.</p><p><strong>Objective: </strong>To investigate the effect of c-Myc-regulated LNC TRD-AS1 on the progression of OSCC.</p><p><strong>Methods: </strong>The effects of c-Myc on LNC TRD-AS1 were detected. Expression of c-Myc and LNC TRD-AS1 in OSCC and paracancerous tissues. Dual luciferase reporter assay verified the binding of c-Myc to the promoter region of LNC TRD-AS1. The localization of LNC TRD-AS1 in OSCC was determined by nucleocytoplasmic isolation assay and RNA FISH experiments. The effects of overexpression, knockdown of LNC TRD-AS1 and rescue experiments on migration, metabolism, and proliferation of OSCC cells were observed by quantitative real-time polymerase chain reaction (qRT-PCR), western blots, scratch tests, Transwell assays, medium color and pH changes, ATP measurement, CCK-8 assays, and colony formation assays.</p><p><strong>Results: </strong>It was found that c-Myc positively regulated the expression of LNC TRD-AS1 in OSCC cell lines and tissues. The binding of c-Myc to the LNC TRD-AS1 promoter region was verified by dual-luciferase reporter assays. Both nucleoplasmic separation assays and RNA FISH showed that LNC TRD-AS1 was localized to the nuclei in OSCC cells. Overexpression of LNC TRD-AS1 promoted migration, metabolism and proliferation in OSCC cell lines, while knockdown had the opposite effect.</p><p><strong>Conclusion: </strong>c-Myc positively regulated LNC TRD-AS1 in OSCC. LNC TRD-AS1 affected the migration, proliferation and metabolism of OSCC by affecting the tumor acid metabolism.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"709-720"},"PeriodicalIF":1.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147432417","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}