Genes & genomics最新文献

{"title":"Prognostic and immunological role of LASP2 in clear cell renal cell carcinoma.","authors":"Libo Chen, Nanhui Chen, Zhouzhou Xie, Yuchen Xiao, Huiming Jiang","doi":"10.1007/s13258-024-01612-9","DOIUrl":"10.1007/s13258-024-01612-9","url":null,"abstract":"<p><strong>Background: </strong>Clear cell renal cell carcinoma (ccRCC) represents a common renal carcinoma subtype influenced by the immune microenvironment. LIM and SH3 Protein 2 (LASP2), an actin-binding protein within the nebulin family, contributes to cellular immunity and adhesion mechanisms.</p><p><strong>Objective: </strong>This study aimed to clarify the immunological and prognostic relevance of LASP2 in ccRCC.</p><p><strong>Methods: </strong>Using clinical and expression data from TCGA, LASP2 expression levels were analyzed alongside clinicopathological features in ccRCC patients. Validation was conducted through real-world samples and tissue microarrays. Comprehensive analysis using online databases examined genetic mutations, DNA methylation patterns, and immune microenvironment characteristics. Gene set enrichment analysis (GSEA) provided insights into LASP2's potential mechanisms in ccRCC.</p><p><strong>Results: </strong>LASP2 expression was notably reduced and correlated with adverse clinicopathological features and prognosis in ccRCC patients. Prognostic associations were identified across multiple CpG DNA methylation sites. LASP2 levels showed significant correlations with immune cell infiltration and checkpoint genes, including PDCD1 and CTLA4. GSEA findings highlighted LASP2's enrichment within metabolic pathways and signaling networks, such as fatty acid metabolism, TGF-β signaling, and epithelial-mesenchymal transition.</p><p><strong>Conclusion: </strong>LASP2 emerged as an immune-associated biomarker linked to poorer survival outcomes in ccRCC, suggesting its potential as a novel anti-cancer target and prognostic indicator in ccRCC.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"625-636"},"PeriodicalIF":1.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876918","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":"Alternative splicing of CHI3L1 regulates protein secretion through conformational changes.","authors":"Haesoo Jung, Yong-Eun Kim, Eun-Mi Kim, Kee K Kim","doi":"10.1007/s13258-025-01635-w","DOIUrl":"10.1007/s13258-025-01635-w","url":null,"abstract":"<p><strong>Background: </strong>Alternative splicing (AS) plays a crucial role in regulating protein function through the generation of structurally distinct isoforms.</p><p><strong>Objective: </strong>We identify a novel splicing event in Chitinase 3-like 1 (CHI3L1) that modulates its secretion through conformational changes.</p><p><strong>Methods: </strong>CHI3L1 alternative splicing was analyzed using the GTEx dataset. The regulation of CHI3L1 splicing was examined in response to THP-1 and BEAS-2B cells using RT-PCR. Structural modeling of CHI3L1 isoforms was conducted with AlphaFold to predict conformational changes caused by exon 8 exclusion. Protein expression and secretion levels of CHI3L1 isoforms were analyzed by Western blotting.</p><p><strong>Results: </strong>Analysis of the GTEx dataset revealed tissue-specific regulation of CHI3L1 exon 8, with pronounced exclusion in lung tissue. The splicing pattern of CHI3L1 was dynamically regulated during THP-1 macrophage differentiation and by cell density in lung-derived epithelial BEAS-2B cells, suggesting its responsiveness to cellular context. While both full-length and exon 8-excluded CHI3L1 proteins showed cytoplasmic localization, structural analysis using AlphaFold revealed that exon 8 exclusion significantly altered the orientation of the signal peptide. Consequently, exon 8-excluded CHI3L1 exhibited minimal secretion into the culture medium compared to the full-length protein.</p><p><strong>Conclusion: </strong>These findings demonstrate that alternative splicing-mediated exclusion of exon 8 serves as a novel regulatory mechanism controlling CHI3L1 secretion through conformational changes, providing new insights into the post-transcriptional regulation of secreted proteins.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"571-579"},"PeriodicalIF":1.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700370","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 transcriptome profiling of cardiac injury: insights from a neonatal mouse sepsis model.","authors":"Wenjin Feng, Huanqi Tang, Chengshuai Li, Xiaohui Kong, Xueyun Ren, Huabin Wang","doi":"10.1007/s13258-025-01632-z","DOIUrl":"10.1007/s13258-025-01632-z","url":null,"abstract":"<p><strong>Background: </strong>Neonatal sepsis is characterized by an excessive immune response, often leading to multiple organ failure, including cardiac injury, and is a major cause of morbidity and mortality in newborns. Understanding the molecular mechanisms of sepsis-induced cardiac injury is crucial for developing therapeutic strategies.</p><p><strong>Objective: </strong>To investigate transcriptomic changes and identify potential altered genes associated with cardiac injury in a neonatal sepsis model.</p><p><strong>Methods: </strong>A neonatal sepsis model was established by cecal slurry injection. RNA sequencing analysis was performed on cardiac tissues from sepsis and control groups, followed by functional enrichment analysis, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Interaction networks among mRNA, lncRNA, circRNA, and miRNA were constructed, and key regulatory genes were identified through protein-protein interaction (PPI) analysis.</p><p><strong>Results: </strong>A total of 1537 differentially expressed mRNAs, 287 lncRNAs, and 730 circRNAs were identified. Functional analysis revealed significant involvement in immune response and inflammatory regulation. PPI network analysis identified six key genes-Ccl5, Il-6, Pole, Mcm2, Mcm5, Mcm10-that were significantly expressed in sepsis-induced cardiac tissue. Additionally, lncRNAs and circRNAs were found to participate in myocardial injury by regulating immune and inflammatory pathways.</p><p><strong>Conclusions: </strong>This study identified six key genes involved in immune and inflammatory responses, playing critical roles in sepsis-induced cardiac injury in neonates. These findings provide new insights into the pathogenesis of sepsis-induced cardiac injury and offer potential therapeutic targets.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"599-613"},"PeriodicalIF":1.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669634","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":"Backtracking identification techniques for predicting unclear bacterial taxonomy at species level: molecular diagnosis-based bacterial classification.","authors":"Yeseul Choi, Jinuk Jeong, Minseo Kim, Seunghee Cha, Kyudong Han","doi":"10.1007/s13258-025-01634-x","DOIUrl":"10.1007/s13258-025-01634-x","url":null,"abstract":"<p><p>Bacterial 16S rRNA genes are widely used to classify bacterial communities within interesting environments (e.g., plants, water, human body) because they contain nine hyper-variable regions (V1-V9) reflecting a large number of sequence variation sites between species. Short-read sequencing platform (targeting partial region of 16S rRNA gene; approximately 150-500 bp) commonly used in the 16S-based microbiome study is favored by many researchers because it is economical and can generate highthroughput sequencing data faster than long-read sequencing platforms. However, this sequencing platform has technical limitations in that it cannot clarify bacterial classification at the species level compared to long-read sequencing technology, which can cover the unclassification issue due to sequence similarity between species by targeting the 16S full-length region. In recent microbiome research-related industries, species-level high-resolution microbial classification is considered a key challenge to secure microbial resources among institutions in the field. However, the long-read sequencing platforms currently offered are still under price adjustment (demanding higher cost than short-read sequencing platforms) and have the disadvantage of low base-calling accuracy compared to short-read sequencing platforms. Therefore, this brief communication introduces the'Molecular diagnosis-based bacterial classification' technology to predict candidate species by backtracking for unclassified bacterial taxonomy at the species level in the NGS-based 16S microbiome study.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"503-508"},"PeriodicalIF":1.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669545","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":"Report of two coinfections of human adenovirus and sapovirus in patients with acute gastroenteritis from China.","authors":"Xin Wang, Yaqing He, Mingda Hu, Wanqiu Liu, Kexin Li, Qiao Li, Shaofu Qiu, Lianqun Jin, Hailong Zhang, Boqian Wang, Chuanfu Zhang, Zhixi Peng, Long Chen, Xiaofeng Hu, Hongguang Ren, Hongbin Song","doi":"10.1007/s13258-025-01637-8","DOIUrl":"10.1007/s13258-025-01637-8","url":null,"abstract":"<p><strong>Background: </strong>Coinfections involving multiple diarrheal viruses have gained increasing recognition as a significant cause of acute gastroenteritis in recent years. Understanding the genetic diversity and evolutionary relationships of these viruses is crucial for effective outbreak identification and tracking.</p><p><strong>Objective: </strong>To report two cases of HAdV and SaV coinfections and elucidate the genetic diversity and evolutionary patterns of these viruses through whole-genome sequencing (WGS) and phylogenetic analysis.</p><p><strong>Methods: </strong>A total of 873 diarrheal stool samples were collected from sentinel hospitals in Shenzhen, China, in 2021. The collected stool samples were identified using RT-PCR and positive samples were subjected to WGS on the NovaSeq platform. phylogenetic trees were constructed using MEGA to analyze genetic relationships.</p><p><strong>Results: </strong>The sequencing results showed that both samples were human adenovirus type 41, which clustered in two distinct evolutionary clades. Additionally, we also retrieved the complete genome of sapovirus (GI.1 genotype) from the same sample. Phylogenetic analysis revealed that they were similar to previously reported strains, belonging to the clade predominating in China.</p><p><strong>Conclusions: </strong>This study reveals the genetic diversity of epidemic strains involved in coinfections of human adenovirus and sapovirus. The findings establish a groundwork for the identification and traces of acute gastroenteritis outbreaks.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"581-586"},"PeriodicalIF":1.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735758","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":"Extracellular nicotinamide phosphoribosyltransferase visfatin activates JAK2-STAT3 pathway in cancer-associated fibroblasts to promote colorectal cancer metastasis.","authors":"Yun Lei, Dan Shu, Jianyu Xia, Tao Zhang, He Wei","doi":"10.1007/s13258-024-01596-6","DOIUrl":"10.1007/s13258-024-01596-6","url":null,"abstract":"<p><strong>Background: </strong>Metastasis is one of the major challenges in the treatment of colorectal cancer (CRC), during which cancer-associated fibroblasts (CAFs) in the tumor microenvironment are critically involved.</p><p><strong>Objective: </strong>In this study, we aim to explore the regulatory role of extracellular nicotinamide phosphoribosyltransferase Visfatin and its impact on CRC metastasis.</p><p><strong>Methods: </strong>To examine the effect of visfatin on CAFs, human CRC tissue-derived CAFs were exposed to visfatin, and the expression of inflammatory factors, activation of JAK-STAT pathway and production of ROS in CAFs were assessed. To examine the effect of visfatin-treated CAFs on CRC metastasis, human CRC cell line SW480 or SW620 were cultured with the conditioned medium derived from visfatin-treated CAFs, and the invasion and migration ability of SW480 or SW620 cells were evaluated by transwell migration and matrigel invasion assays.</p><p><strong>Results: </strong>Our previous study found that visfatin, a secreted form of nicotinamide phosphoribosyltransferase that governs the rate-limiting step of NAD synthesis, promoted CRC metastasis. However, little is known about the effect of visfatin on CAFs. The conditioned medium derived from visfatin- treated CAFs promotes the migratory and invasive capability of CRC cells, and enhance lung metastasis in mouse model. Visfatin treatment stimulated the expression of a couple of inflammatory factors in CAFs, which was mediated by visfatin-induced activation of JAK- STAT pathway and accumulation of ROS. Inhibition of JAK-STAT pathway or neutralization of cellular ROS attenuated visfatin-mediated migration and invasion of CRC cells.</p><p><strong>Conclusions: </strong>The present work highlights a critical role of visfatin in the crosstalk between CRC cells and CAFs, which moonlight as a non-metabolic extracellular signal molecule to hijacks JAK-STAT pathway in CAFs to promote CRC metastasis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"615-624"},"PeriodicalIF":1.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12081565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791665","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":"A novel CLRN2 variant: expanding the mutation spectrum and its critical role in isolated hearing impairment.","authors":"Farooq Ahmad, Arif Mahmood, Ibrahim Abdullah Almazni, Afnan Mohammed Shakoori, Fatemah Alhakami, Qamre Alam, Muhammad Ismail, Muhammad Umair","doi":"10.1007/s13258-024-01590-y","DOIUrl":"10.1007/s13258-024-01590-y","url":null,"abstract":"<p><strong>Background: </strong>Biallelic variants in the CLRN2 gene have been reported to cause autosomal recessive profound hearing impairment in humans. CLRN2 belongs to the clarin gene family that encodes a tetraspan protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina.</p><p><strong>Methods: </strong>Here, we present a consanguineous family suffering from autosomal recessive non-syndromic profound hearing impairment (HI). We employed state of the art Whole exome sequencing (WES), Sanger sequencing followed by routine bioinformatics filtration steps and homology modeling to elucidate the effect of mutation at the protein level.</p><p><strong>Results: </strong>ES followed by Sanger sequencing revealed a novel homozygous nonsense variant in the CLRN2 gene [c.414 C > A; p.Cys138*]. Furthermore, insilico protein modeling of the wildtype and mutated version of the CLRN2 protein revealed large-scale changes that predict to compromise the routine normal function of the protein.</p><p><strong>Conclusion: </strong>Our finding further extends the mutations spectrum of CLRN2 gene and confirms its important role in hearing homeostasis and with developmental disorder in humans.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"417-423"},"PeriodicalIF":1.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498909","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":"BRN3A, a transcription factor, regulates the expression of genes involved in biological processes shaping the HPV induced cervical cancer.","authors":"Anand Prakash, Yashvant Patel, Jagat Kumar Roy","doi":"10.1007/s13258-025-01620-3","DOIUrl":"10.1007/s13258-025-01620-3","url":null,"abstract":"<p><strong>Background: </strong>Cervical cancer is the fourth most common cancer worldwide in females. This occurs primarily due to the infection of high-risk Human Papilloma Virus (HPV), although in advanced stages it requires support from host cellular factors. BRN3A is one such host cellular factors, whose expression remains high in cervical cancers and upregulates tumorigenic HPV gene expression. The effect of BRN3A on HPV-mediated cervical cancer and the underlying mechanism remains obscure.</p><p><strong>Objective: </strong>To investigates the effect of BRN3A on cancer-promoting biological processes in HPV-positive uterine cervix cancer cells.</p><p><strong>Methods: </strong>We have altered the expression of BRN3A through over-expression (OE) and knock-down (KD) constructs in cervical cancer cell line, SiHa, and did transcriptome profiling through next-generation RNA-sequencing, validation through RT-PCR and BRN3A binding study with in silico promoter study and ChIP PCR methods.</p><p><strong>Results: </strong>This study revealed a substantial change in the expression of several genes associated with cancer-promoting biological processes including viral processes, immune response, cell-death, cell-proliferation, different signaling pathways, etc. Additionally, promoter analysis through in silico mode revealed that a total of 32.7% of genes possess BRN3A binding sites at their promoters. Physical interaction of BRN3A with IFITM1, OAS3, ISG15, BCL2L1 and HSP90AB1 genes was also confirmed.</p><p><strong>Conclusions: </strong>The present study identified molecular targets of BRN3A and provided new insight into the pathogenesis of cervical cancer. According to our knowledge, this is the first report on the effect on eukaryotic transcriptomes after over-expression and knocking down BRN3A.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"487-501"},"PeriodicalIF":1.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052225","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":"Advances in cancer genomics and precision oncology.","authors":"Yonjong Heo, Woo-Jin Kim, Yong-Joon Cho, Jae-Won Jung, Nam-Soo Kim, Ik-Young Choi","doi":"10.1007/s13258-024-01614-7","DOIUrl":"10.1007/s13258-024-01614-7","url":null,"abstract":"<p><strong>Background: </strong>Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division. Utilization of next-generation sequencing in cancer gene panels has enabled the identification of actionable gene alterations in cancer patients to guide personalized precision medicine.</p><p><strong>Objective: </strong>The aim is to provide information that can identify actionable gene alterations, enabling personalized precision medicine for cancer patients.</p><p><strong>Results & discussion: </strong>Equipped with next-generation sequencing techniques, international collaboration programs on cancer genomics have identified numerous mutations, gene fusions, microsatellite variations, copy number variations, and epigenetics changes that promote the transformation of normal cells into tumors. Cancer classification has traditionally been based on cell type or tissue-of-origin and the morphological characteristics of the cancer. However, interactive genomic analyses have currently reclassified cancers based on systemic molecular-based taxonomy. Although all cancer-causing genes and mechanisms have yet to be completely understood or identified, personalized or precision medicine is now currently possible for some forms of cancer. Unlike the \"one-size-fits-all\" approach of traditional medicine, precision medicine allows for customized or personalized treatment based on genomic information.</p><p><strong>Conclusion: </strong>Despite the availability of numerous cancer gene panels, technological innovation in genomics and expansion of knowledge on the cancer genome will allow precision oncology to manage even more types of cancers.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"399-416"},"PeriodicalIF":1.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028557","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":"Integrative analysis of genetic variability and functional traits in lung adenocarcinoma epithelial cells via single-cell RNA sequencing, GWAS, bayesian deconvolution, and machine learning.","authors":"Chenggen Gao, Jintao Wu, Fangyan Zhong, Xianxin Yang, Hanwen Liu, Junming Lai, Jing Cai, Weimin Mao, Huijuan Xu","doi":"10.1007/s13258-025-01621-2","DOIUrl":"10.1007/s13258-025-01621-2","url":null,"abstract":"<p><strong>Background: </strong>Lung adenocarcinoma remains a leading cause of cancer-related mortality worldwide, characterized by high genetic and cellular heterogeneity, especially within the tumor microenvironment.</p><p><strong>Objective: </strong>This study integrates single-cell RNA sequencing (scRNA-seq) with genome-wide association studies (GWAS) using Bayesian deconvolution and machine learning techniques to unravel the genetic and functional complexity of lung adenocarcinoma epithelial cells.</p><p><strong>Methods: </strong>We performed scRNA-seq and GWAS analysis to identify critical cell populations affected by genetic variations. Bayesian deconvolution and machine learning techniques were applied to investigate tumor progression, prognosis, and immune-epithelial cell interactions, particularly focusing on immune checkpoint markers such as PD-L1 and CTLA-4.</p><p><strong>Results: </strong>Our analysis highlights the importance of genes like SLC2A1, which regulates glucose metabolism and correlates with tumor invasiveness and poor prognosis. Immune-epithelial interactions suggest a suppressive tumor microenvironment, potentially hindering immune responses. Additionally, machine learning models identify core prognostic genes such as F12, GOLM1, and S100P, which are significantly associated with patient survival.</p><p><strong>Conclusions: </strong>This comprehensive approach provides novel insights into lung adenocarcinoma biology, emphasizing the role of genetic and immune factors in tumor progression. The findings support the development of personalized therapeutic strategies targeting both tumor cells and the immune microenvironment.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"435-468"},"PeriodicalIF":1.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12000210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482886","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}