Genes & genomics最新文献

{"title":"Association of MSH2, MSH6, and MLH1 polymorphisms with susceptibility and survival in lung cancer patients.","authors":"Jing Cheng, Chao Zuo, Dongli Yang, Yi Liu, Yu Wang, Yongchao Qiao","doi":"10.1007/s13258-025-01681-4","DOIUrl":"10.1007/s13258-025-01681-4","url":null,"abstract":"<p><strong>Background: </strong>Lung cancer (LC) is the leading cause of cancer-related deaths globally. Genetic variants in mismatch repair (MMR) genes, such as MutS homolog 2 (MSH2), MutS homolog 6 (MSH6) and MutL homolog 1 (MLH1), may influence individual susceptibility and clinical outcomes in LC.</p><p><strong>Objective: </strong>This study investigated the associations of genetic polymorphisms in MSH2, MSH6, and MLH1 with susceptibility and survival outcomes in lung cancer patients in the Guangxi Zhuang population.</p><p><strong>Methods: </strong>This study included a cohort of 192 LC patients and 262 healthy controls. The association of MSH2, MSH6, and MLH1 polymorphisms with susceptibility to small cell lung cancer (SCLC), lung adenocarcinoma (LUAD), and lung squamous carcinoma (LUSC) was evaluated using case-control methods, and protein expression differences were analysed by immunohistochemistry. The genotypes of genetic variations were detected using high-throughput SNP-scan technology. The Kaplan-Meier survival curve and log-rank test were used to assess the influence of individual genetic variants on prognostic outcomes in lung cancer patients.</p><p><strong>Results: </strong>Multivariate logistic regression identified significant associations of rs2303428 and rs1042821 with increased lung cancer risk, especially in SCLC and LUSC. The GA and GG genotypes of rs1042821 were linked to higher SCLC risk (OR = 4.415 and 2.685; P = 0.019), the TC genotype of rs2303428 was associated with elevated LUSC risk (OR = 3.993; P = 0.034). No associations were found for rs1800734 or in LUAD. Immunohistochemistry showed increased MSH2 and MSH6 expression in risk genotypes, with no genotype-related changes in MLH1. In LUAD, the CC genotype of rs2300789 was associated with poorer overall survival compared to TC (P = 0.047), with no significant differences in other comparisons.</p><p><strong>Conclusion: </strong>rs2303428 and rs1042821 polymorphisms were associated with increased lung cancer susceptibility and altered protein expression. Additionally, the CC genotype of rs2300789 was linked to poorer overall survival in LUAD.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1277-1291"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145029539","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":"L1CAM enhances autophagy via inhibition of p38 phosphorylation in colorectal cancer development and progression.","authors":"Xiaojin Hu, Ting Wu, Yan Xie, Jin Zhou, Cong Liu, Lei Shi, Liangxi Xie, Hongtai Shi","doi":"10.1007/s13258-025-01697-w","DOIUrl":"10.1007/s13258-025-01697-w","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer (CRC) is a common gastrointestinal tumor with a high incidence worldwide. L1 cell adhesion molecule (L1CAM) is highly expressed in CRC tissues and can promote tumor growth and metastasis. Autophagy regulates oncogenesis and tumor progression through context-dependent mechanisms and is regulated by multiple signaling pathways, including the p38 MAPK signaling pathway.</p><p><strong>Objective: </strong>However, the relationship between L1CAM and autophagy is not known yet. In this study, we are trying to dissect the role of L1CAM-autophagy interaction in the development and progression of CRC and its underlying mechanism.</p><p><strong>Methods: </strong>Stable L1CAM knockdown was achieved in SW480 and HT29 cells via lentiviral transduction of specific shRNAs. Autophagic flux was detected using western blotting and Tandem mRFP-GFP-LC3 assay. The protein levels were measured via western blotting. Cell proliferation was tested via CCK-8 proliferation assay and Edu staining. Apoptosis was evaluated using flow cytometry.</p><p><strong>Results: </strong>We found that upon L1CAM knockdown, the phosphorylation of p38 was enhanced, and autophagy was weakened. When p38 phosphorylation was inhibited, the inhibitory effect of L1CAM knockdown on autophagy was restored. And L1CAM can promote cell proliferation and inhibit cell apoptosis.</p><p><strong>Conclusions: </strong>Taken together, these findings indicate that L1CAM promotes autophagy by inhibiting the phosphorylation of p38, and that it also promotes cell proliferation and inhibits cell apoptosis in colon cancer cells. L1CAM might be as a new target in CRC therapy.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1333-1342"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145426690","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":"Correction to: Comprehensive analysis the diagnosis, malignant progression and immune infiltrate of ANXA6 in prostate cancer.","authors":"Banggao Huang, Kewei Yang","doi":"10.1007/s13258-023-01425-2","DOIUrl":"10.1007/s13258-023-01425-2","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1383"},"PeriodicalIF":1.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10001946","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":"Expression profiling of flowering time pathway in the L-ascorbate peroxidase 9 (APX9) near-isogenic line derived from an interspecific cross between Korean Japonica rice (Oryza sativa L.) and Oryza rufipogon.","authors":"Yun-A Jeon, Hyun-Sook Lee, Cheryl Adeva, Sang-Nag Ahn, Kyu-Chan Shim","doi":"10.1007/s13258-025-01683-2","DOIUrl":"10.1007/s13258-025-01683-2","url":null,"abstract":"<p><strong>Background: </strong>Flowering time (referred to as heading date in rice) is a characteristic controlled by quantitative trait loci (QTLs). Heading date is an important agronomic trait that determines yield in rice and is precisely regulated by various exogenous and endogenous factors.</p><p><strong>Objective: </strong>To investigate the role of the ascorbate peroxidase 9 (APX9) gene in the flowering mechanism, we examined the expression levels of flowering time regulators under long-day conditions (14 h light/10 hours dark) and natural long-day conditions.</p><p><strong>Methods: </strong>A BC₄F₇ near-isogenic line (NIL), derived from an interspecific cross between the Korean elite japonica cultivar (cv. Hwaseong, Oryza sativa L.) and Oryza rufipogon (IRGC 105491), was used in this study to identify and characterize candidate genes associated with heading traits. The NIL contains a small O. rufipogon chromosome segment harboring the APX9 gene. In addition, overexpression and T-DNA insertion knockout transgenic lines were used to examine the function of APX9 gene.</p><p><strong>Results: </strong>The NIL exhibited delayed flowering under both controlled and natural long-day conditions compared to Hwaseong. Real-time PCR analysis indicated that APX9 influences the upstream pathway of flowering time regulation. Over-expression lines showed delayed flowering relative to Hwaseong, whereas T-DNA mutants flowered earlier than the control cultivar, Dongjin. These findings support a role for APX9 in modulating flowering time in rice.</p><p><strong>Conclusion: </strong>The APX9 is known for its antioxidant activity and its response to various abiotic stresses. The APX9 may play a role in the upstream regulation of the flowering pathway. These findings will be valuable in understanding the effect of APX9 during flowering stages. It would also be interesting to explore the relationship between hydrogen peroxide (H₂O₂₎ levels and the APX9 gene in signaling events related to heading.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1163-1174"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145112901","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":"The influences of genetic polymorphisms in three candidate genes on the athletic performance of Korean athletes.","authors":"Jae Koo Lee, Byung Yong Kang","doi":"10.1007/s13258-025-01678-z","DOIUrl":"10.1007/s13258-025-01678-z","url":null,"abstract":"<p><strong>Backgound: </strong>It is known that in addition to environmental factors such as the athlete's own efforts or the qualities of the coach, genetic predisposition can also have a significant impact on achievements in the sports field.</p><p><strong>Objective: </strong>For this reason, this study tried to analyze whether single nucleotide polymorphisms (SNPs) in the myostatin, hemochromatosis(HFE) and estrogen receptor 1 (ESR1) genes, which are known to affect muscular strength, cardiorespiratory endurance and flexibility, respectively, could significantly affect the athletic performance of endurance or power/sprint events in Korean population.</p><p><strong>Methods: </strong>A total of 192 Korean unrelated participants were recruited in this study. They were divided into two groups: controls (n = 72) and track-field athletes (n = 120), which included throwing athletes (n = 39) and distance runners (n = 81). Also, the determination of the genotypes constituting the SNP markers in the three kinds of candidate genes mentioned above was performed using TaqMan method.</p><p><strong>Results: </strong>Among the three kinds of SNP markers studied, only the rs1799945 polymorphism in the HFE gene was observed to be significantly associated with endurance performance in Korean athletes (p < 0.05).</p><p><strong>Conclusion: </strong>Therefore, our results suggest that the rs1799945 polymorphism in the HFE gene may be one of useful genetic markers for endurance performance in Korean athletes. Further studies using larger sample sizes and various sports events are needed to replicate our results.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1229-1238"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145299793","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":"Identification of a hypoxia-related gene signature associated with childhood asthma.","authors":"Wenlie Chen, Yuanlu Huang, Li Lei, Rui Zhang, Li Fu, Jinwen Liao, Shaohua Wang, Zhenzhuang Zou","doi":"10.1007/s13258-025-01665-4","DOIUrl":"10.1007/s13258-025-01665-4","url":null,"abstract":"<p><strong>Background: </strong>Hypoxia is a significant manifestation of severe asthma in children. An early and accurate diagnosis is crucial for enhancing treatment outcomes and mitigating long-term complications. This study aims to utilize bioinformatics analysis to investigate hypoxia-related genes (HRGs) in childhood asthma.</p><p><strong>Objective: </strong>This study aims to develop a diagnostic model and identify key hypoxia-related biomarkers in childhood asthma based on transcriptomic data analysis.</p><p><strong>Methods: </strong>Hypoxia-related differentially expressed genes (HRDEGs) were identified from bronchial epithelial transcriptomes (GSE27011/GSE40732 datasets) using limma analysis. A diagnostic model was developed using LASSO regression, and hub genes were identified via protein-protein interaction (PPI) networks. Asthma subtyping and immune microenvironment characterization were conducted using ConsensusClusterPlus and CIBERSORTx, respectively. Experimental validation in house dust mite (HDM)-induced asthmatic mice confirmed transcriptional changes in candidate genes.</p><p><strong>Results: </strong>We obtained 19 HRDEGs and 11 model genes (AHR, AKR1C3, ELP3, GNAL, GZMB, LPP, MAFG, PDGFD, PPP1R12B, SYNE2, and TAF15). Regression analyses demonstrated the model's robust diagnostic performance. PPI analysis identified 10 hub genes associated with asthma, with AKR1C3 showing high diagnostic accuracy for different molecular subtypes. Immune infiltration analysis indicated significant correlations between hub genes and eight immune cell types, including B cells, effector T cells, cytotoxic T cells, regulatory T cells (Tregs), monocytes, mast cells, eosinophils, and neutrophils.</p><p><strong>Conclusions: </strong>In this study, a hypoxia-related gene signature associated with childhood asthma was identified. These findings not only highlight potential therapeutic targets for asthma but also offer new insights into its pathogenesis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1199-1215"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144872874","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":"NPR1 modulates DNA replication in vascular endothelial cells via the transcription factor E2F2.","authors":"Fengqing Zhang, Hong Tang, Xiaocheng Mao, Simin Xiong, Yiqi Wan, Wei Yuan, Hongfei Liu","doi":"10.1007/s13258-025-01682-3","DOIUrl":"10.1007/s13258-025-01682-3","url":null,"abstract":"<p><strong>Background: </strong>Natriuretic peptide receptor 1 (NPR1) plays a crucial role in maintaining the functionality of vascular endothelial cells. However, its role in regulating DNA replication and genome stability in endothelial cells remains unexplored.</p><p><strong>Objective: </strong>This study aimed to investigate whether NPR1 deficiency disrupts DNA replication and induces DNA damage in human umbilical vein endothelial cells (HUVECs), and to explore the mechanistic role of the E2F transcription factor 2 (E2F2) in this process.</p><p><strong>Methods: </strong>RNA-sequencing analysis was performed in NPR1-deficient HUVECs. EdU incorporation assay quantified DNA replication activity. qPCR or RNA-seq evaluated expression of DNA replication-related genes. DNA damage levels were assessed via phosphorylated histone H2AX (γH2AX). The proteins of NPR1, E2F2 and γH2AX were examined by Western blot. E2F2 was knocked down or overexpressed in NPR1-deficient HUVECs to validate its regulatory role.</p><p><strong>Results: </strong>DNA replication related genes were downregulated in NPR1-knockdown HUVECs. This result was supported by a decrease of EdU positive rate of HUVECs upon NPR1 deficiency. Downregulation of DNA replication genes (DSCC1, EXO1, MCM4, MCM6, TREX1 and CCNE2) was observed in NPR1-deficient cells. NPR1 knockdown increased γH2AX, particularly in EdU-positive cells. NPR1 silencing reduced the expression of E2F2. E2F2 knockdown mimicked NPR1 deficiency, suppressing DNA replication genes and increasing DNA damage. Additionally, overexpression of E2F2 recovered the DNA replication and mitigated DNA damage in NPR1-knockdown HUVECs.</p><p><strong>Conclusions: </strong>NPR1 deficiency declines DNA replication activity and induces DNA damage in vascular endothelial cell by inhibiting E2F2 expression. This provides further insights into the underlying mechanism on NPR1 in the regulation of the functionality of vascular endothelial cells.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1217-1228"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274342","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":"PSM-SMOTE: propensity score matching and synthetic minority oversampling for handling unbalanced microbiome data.","authors":"Jeongsup Moon, Zhe Liu, Taesung Park","doi":"10.1007/s13258-025-01688-x","DOIUrl":"10.1007/s13258-025-01688-x","url":null,"abstract":"<p><strong>Background: </strong>Predictive models using microbiome data often suffer from covariate imbalance and class imbalance, biasing results. Propensity Score Matching (PSM) balances covariates but reduces sample size, while borderline synthetic minority oversampling technique (borderline-SMOTE) oversamples minority classes but can generate uninformative examples.</p><p><strong>Objective: </strong>To develop and evaluate PSM-SMOTE, a novel hybrid sampling method that integrates PSM and borderline-SMOTE to handle both covariate and class imbalance in microbiome data.</p><p><strong>Methods: </strong>We developed PSM-SMOTE, a three-step hybrid sampling algorithm for microbiome data: (1) PSM at four caliper levels to balance covariates, (2) selection of at least ten robust differential markers via seven statistical tests with false discovery rate correction, and (3) application of borderline-SMOTE on the marker-based distance matrix to oversample minority classes. We evaluated PSM-SMOTE on three publicly available microbiome case-control datasets: pancreatic ductal adenocarcinoma (PDAC), colorectal cancer (CRC), and obesity, using logistic regression (LR), random forest (RF), and support vector machine (SVM) classifiers. Performance was assessed via area under the ROC curve (AUC).</p><p><strong>Results: </strong>PSM-SMOTE improved test AUCs in multiple model-dataset combinations compared with using PSM alone. Notably, for the RF model, PSM-SMOTE consistently enhanced AUC across nearly all oversampling settings in the PDAC and obesity cohorts. For the SVM model, PSM-SMOTE also achieved a significant AUC increase in the CRC cohort. For the LR model, PSM-SMOTE showed modest improvement under strict matching.</p><p><strong>Conclusion: </strong>PSM-SMOTE effectively addresses dual imbalance in microbiome data and consistently enhances performance, providing a practical solution for imbalanced data analyses.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1175-1185"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225195","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":"Identification of microbiome markers for ordered groups.","authors":"Jaehong Yu, Md Mozaffar Hosain, Taesung Park","doi":"10.1007/s13258-025-01673-4","DOIUrl":"10.1007/s13258-025-01673-4","url":null,"abstract":"<p><strong>Background: </strong>Identifying microbiome markers associated with ordered phenotypes, such as disease stages or severity levels, is crucial for understanding disease progression and advancing precision medicine. Despite this importance, most existing methods for differential abundance analysis are designed for binary group comparisons and do not incorporate ordinal information, limiting their ability to capture trends across ordered categories.</p><p><strong>Objective: </strong>To develop and evaluate statistical methods that explicitly account for ordinal phenotype structure in microbiome data, addressing challenges such as sparsity and zero inflation, and improving the detection of meaningful microbial associations.</p><p><strong>Methods: </strong>In this study, we propose and evaluate three novel approaches specifically tailored for microbiome association analysis with ordered groups: the binary optimal test, the linear trend test, and the proportional odds model-based permutation test (POMp). These methods explicitly account for the ordinal structure of phenotypes and address the sparsity and zero-inflation commonly observed in microbiome data through permutation-based inference. We applied the proposed methods to three publicly available gut microbiome datasets, including two related to obesity and one concerning colorectal cancer.</p><p><strong>Results: </strong>All three proposed methods successfully identified differentially abundant features (DAFs) that exhibited stronger ordinal associations compared to those identified by existing methods. In particular, POMp consistently outperformed other approaches in terms of correlation with phenotype order, demonstrating its potential to identify biologically relevant markers.</p><p><strong>Conclusion: </strong>The findings of this study highlight the importance of incorporating ordinal information in microbiome studies and provide robust statistical tools for advancing microbial biomarker discovery in complex disease contexts.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1133-1145"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069338","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":"Assembly of a high-quality Polypterus senegalus diploid genome.","authors":"Jeong Woen Shin, Bo-Mi Kim, Jun Kim, Jae-Sung Rhee","doi":"10.1007/s13258-025-01685-0","DOIUrl":"10.1007/s13258-025-01685-0","url":null,"abstract":"<p><strong>Background: </strong>Polypterus senegalus is a major actinopterygian fish that provides vital insights into vertebrate terrestrial adaptation. Advances in sequencing technologies have enabled improvements to the reference genome of P. senegalus, highlighting the need to expand research on this species.</p><p><strong>Objective: </strong>In this study, we sought to construct high-quality, partially-phased, assemblies of the P. senegalus genome using high-fidelity long-read sequencing data.</p><p><strong>Methods: </strong>First, partially-phased assemblies of P. senegalus genome using PacBio HiFi data. And then, our assemblies were compared with a previously published genome in terms of total length, contiguity, base-level accuracy, and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness, including resolution of repetitive regions and identification of telomere-telomere chromosomes.</p><p><strong>Results: </strong>Compared with a previously published genome, our assemblies exhibit improved quality in overall quality. A total of 20,940 genes were annotated employing integrated short-read and long-read RNA sequencing data. Transcriptomics revealed the gene-expression relationships between 12 tissue types and the distinct expression patterns of genes associated with key evolutionary traits, such as aerial respiration, angiogenesis, and limb flexibility. Notably, several genes including Tcf21, Foxf1, and Tbx3a were coordinately expressed in the lungs and swim bladder, supporting shared origins and developmental patterns. Analyses of the correlations among tissues revealed physiological similarities between the lungs, kidneys, and spleen.</p><p><strong>Conclusion: </strong>Our results provide a valuable genomic resource for P. senegalus and offer novel insights into the molecular basis of vertebrate organ evolution and adaptation.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"1187-1197"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206211","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}