Functional & Integrative Genomics最新文献

{"title":"Comparative pan-genome analysis of Huperzia and Phlegmariurus and transcriptomics reveals thermal adaptation in Huperzia","authors":"Muzi Li,&nbsp;Yazhu Wu,&nbsp;Haibo Li,&nbsp;Zhongnian Zhang,&nbsp;Rui Qin,&nbsp;Jiahao Wen,&nbsp;Yeqin Xu,&nbsp;Chengcheng Bao,&nbsp;Dekai Wang","doi":"10.1007/s10142-025-01680-4","DOIUrl":"10.1007/s10142-025-01680-4","url":null,"abstract":"<div><p><i>Huperzia</i> and <i>Phlegmariurus</i> are ancient genera within the Lycopodiaceae family with significant medicinal value and ecological adaptability, yet the evolutionary dynamics and genetic diversity of their chloroplast genomes remain poorly characterized. Specifically, critical aspects such as intergeneric differences, phylogenetic relationships, and adaptive evolution within their chloroplast genomes remain insufficiently explored. This study analyzed the chloroplast genomes of 66 species from these two genera through comparative genomics to elucidate their structural dynamics and adaptive mechanisms. Results revealed that <i>Huperzia</i> chloroplast genomes (153–155 kb, GC content 36.25–36.39%) are significantly larger than those of <i>Phlegmariurus</i> (148–151 kb, GC content 33.78–34.26%), with pronounced differences in IR boundary dynamics, repetitive sequence distribution, nucleotide diversity, and codon usage bias. Phylogenetic and population structure analyses confirmed the monophyly of both genera and demonstrated significantly higher genetic diversity in <i>Phlegmariurus</i>, likely linked to adaptive radiation driven by humid tropical environments. Transcriptomic data revealed a temporally coordinated chloroplast response to heat stress in <i>Huperzia serrata</i>. Photosynthetic core genes (such as <i>psaB</i> and <i>rrna16</i>) were downregulated, leading to sustained functional impairment. In contrast, early stress-response genes (such as <i>rbcL</i> and <i>trnI-GAU</i>) peaked at 4 h to enhance carbon fixation and transport. Mid-phase repair genes (such as <i>ndhG</i> and <i>rps8</i>) exhibited inverted U-shaped expression patterns to activate electron transport and protein synthesis, whereas late-stage overexpression of <i>atpI</i> restored energy homeostasis. This coordinated regulatory mechanism illustrates a survival strategy of \"photosynthetic inhibition–stress compensation–energy reorganization\" for thermal adaptation. Future studies should integrate nuclear genome and epigenetic modification data to further unravel the synergistic nucleo-cytoplasmic interactions underlying environmental adaptation.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832303","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 analysis of Bacillus subtilis MBBL2 genomic characterization and comparative genomics","authors":"Hajra Sohail,&nbsp;Muhammad Naveed,&nbsp;Tariq Aziz,&nbsp;Rania Ali El Hadi Mohamed,&nbsp;Fakhria A. Al-Joufi","doi":"10.1007/s10142-025-01684-0","DOIUrl":"10.1007/s10142-025-01684-0","url":null,"abstract":"<div><p>This study presents the whole-genome sequencing and comprehensive analysis of <i>Bacillus subtilis MBBL2</i>, a strain isolated from soil samples in Lahore, Pakistan. The genome consists of 4,574,405 base pairs, with a GC content of 42.99%, and is assembled into 908 contigs. Using a range of bioinformatics tools, we performed genome assembly, functional annotation, secondary metabolite biosynthesis prediction, antimicrobial resistance (AMR) gene identification, and CRISPR array detection. The genome was initially assembled, achieving an average coverage of 126.534x, and its quality was also assessed to ensure completeness. Prokka was used to annotate 5,392 genes, including 5,033 protein-coding sequences, tRNAs, and rRNAs. Secondary metabolite biosynthesis clusters were identified revealing several important clusters involved in riboflavin, vitamin B6 biosynthesis, and antimicrobial peptide production via non-ribosomal peptide synthetase (NRPS). Notably, a novel bacteriocin gene cluster was detected, suggesting the strain’s potential as a source of antimicrobial peptides. AMR genes were identified highlighting resistance to various antibiotics. CRISPR arrays were also analyzed indicating the strain’s adaptive immune system. Genomic comparisons provided insights into the genetic diversity and evolutionary relationships of <i>Bacillus subtilis</i> strains. This study reveals the potential of <i>B. subtilis MBBL2</i> as a probiotic in aquaculture, with applications in sustainable practices such as biocontrol. The findings contribute valuable genomic resources to the <i>B. subtilis</i> research community and open avenues for future biotechnological applications.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832138","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: Integration of scRNA-seq and bulk tissue RNA-seq data to identify cancer-associated fibroblast-related gene RGMA as a potential treatment target for esophageal cancer","authors":"Yanqing Gao,&nbsp;Shuguang Bao,&nbsp;Bao Wen,&nbsp;Haoyuan Li,&nbsp;Qiang Guo,&nbsp;Ao Li,&nbsp;Luri Bao,&nbsp;Meitao Li,&nbsp;Bateer Han","doi":"10.1007/s10142-025-01681-3","DOIUrl":"10.1007/s10142-025-01681-3","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144814476","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 transcriptome analysis reveals the function of SoCER4 in alkanol synthesis in sugarcane","authors":"Yuting Zhou,&nbsp;Sangui Yi,&nbsp;Shuangcai Li,&nbsp;Zongling Liu","doi":"10.1007/s10142-025-01672-4","DOIUrl":"10.1007/s10142-025-01672-4","url":null,"abstract":"<div><p>The wax of sugarcane buds, especially alkanol, was correlated to sugarcane smut resistance in previous studies. Moreover, alkanol could induce smut teliospore germination. This study aimed to analyze wax-related genes in sugarcane buds. In this study, the wax contents in germinated sugarcane buds from smut-resistant Zhongzhe 9 (ZZ9) and smut-susceptible Guitang 42 (GT42) were measured, showing that total wax content and alkanol content of GT42 were significantly higher than that of ZZ9 after bud germination. The gene expression profiles of germinated buds from ZZ9 and GT42 were analyzed using transcriptome analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) terms for cutin, suberine, and wax biosynthesis were enriched between ZZ9 and GT42. In addition, a lipid transfer protein (<i>LTP)</i> gene (c97015.graph_c0) may be involved in wax transportation that caused higher wax content in GT42 buds, and a <i>SoCER4</i> gene (c120140.graph_c0) may play a key role in alkanol synthesis that caused higher alkanol content in GT42 buds. Here, the <i>SoCER4</i> gene was functionally characterized via overexpression in <i>Nicotiana benthamiana</i>. The alkanol contents of <i>SoCER4</i> transgenic <i>N. benthamiana</i> leaves were significantly higher than that of wild type, indicating <i>SoCER4</i> was responsible for alkanol synthesis. These results would be helpful in understanding alkanol synthesis in sugarcane buds.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768250","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":"CircNOX4 promotes proliferation and resistance by regulating the hsa-miR-6884-5p/YWHAG Axis and ERK signaling pathway in cholangiocarcinoma","authors":"Zhangdi Yan,&nbsp;Lixin Du,&nbsp;Yingdi Han,&nbsp;Kangshuai Li,&nbsp;Guoli Sheng,&nbsp;Xudong Wang,&nbsp;Yunjia Liu,&nbsp;Yuankun Zhang,&nbsp;Jian Deng,&nbsp;Zengli Liu,&nbsp;Yunfei Xu,&nbsp;Zongli Zhang,&nbsp;Yongchang Tang","doi":"10.1007/s10142-025-01668-0","DOIUrl":"10.1007/s10142-025-01668-0","url":null,"abstract":"<div><p>The biological function of circular RNAs (circRNAs) has been increasingly implicated in tumor drug resistance. However, their role in intrahepatic cholangiocarcinoma (ICC) remains poorly understood, and the underlying mechanisms are largely unexplored. In this study, we identified a key circRNA, circNOX4, through data mining and experimental validation in ICC. We found that circNOX4 was significantly upregulated in ICC tissues and its expression correlated with advanced clinicopathological features. Functional assays demonstrated that circNOX4 promoted ICC cell proliferation and tumor growth both in vitro and in vivo. Mechanistically, circNOX4 acted as a molecular sponge for hsa-miR-6884-5p, thereby upregulating YWHAG expression. YWHAG, in turn, interacted with RAF1, enhancing its phosphorylation and activating the ERK signaling pathway. This led to the nuclear translocation of phosphorylated ERK and subsequent promotion of ICC progression. Furthermore, we found that circNOX4 attenuated the anti-tumor efficacy of Trametinib. In summary, circNOX4 contributes to ICC progression and drug resistance through the hsa-miR-6884-5p/YWHAG/ERK axis, and may serve as a potential diagnostic marker, prognostic indicator, and therapeutic target in ICC.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740797","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":"Multiplex CRISPR-Cas9 editing of chlorophyll biosynthesis genes in chickpea via protoplast and Agrobacterium-mediated transformation","authors":"Samra Irum,&nbsp;Sudip Biswas,&nbsp;Mustafa Cilkiz,&nbsp;Nikolaos Tsakirpaloglou,&nbsp;Michael J. Thomson,&nbsp;Endang M. Septiningsih","doi":"10.1007/s10142-025-01665-3","DOIUrl":"10.1007/s10142-025-01665-3","url":null,"abstract":"<div><p>Chickpea is an important legume consumed worldwide and a rich source of protein. Chickpea is less amenable to recent gene editing techniques despite its economic significance. Accelerating the improvement process and enabling novel trait development in chickpea will require new approaches for genetic intervention. The CRISPR system has been used in different plant species to generate genetic variation and manipulate gene functions, facilitating studies on gene function and crop improvement. To implement genome editing in chickpea, genes involved in the chlorophyll biosynthesis pathway were selected as targets for gene editing. A construct (pTrans_100-Chbio) carrying gRNAs for chlorophyllide a oxygenase (<i>CAO</i>) and chlorophyll synthase (<i>CHLG</i>), along with the Cas9 protein, was introduced into chickpea protoplasts via PEG-mediated transformation. Multiple edits containing deletions and base insertions were identified after protoplast transformation, as confirmed by Sanger sequencing. Afterward, <i>Agrobacterium</i> transformation of explants was performed, resulting in the successful regeneration of pale and chimeric yellow tissues, subsequently confirmed as containing largely substitutions, as detected through deep amplicon sequencing. Edited plants showed yellowish leaves and lower chlorophyll content. Our results indicated that chlorophyll biosynthesis pathway genes played an essential role in chlorophyll degradation and ROS scavenging to regulate both natural and induced chickpea senescence. We established an efficient and feasible CRISPR/Cas9-based editing system in chickpea that successfully generates allelic mutations and phenotypic variation. The established platform can be a foundation for future functional studies and precise genome editing of additional agronomic traits, ultimately contributing to chickpea crop improvement and sustainable agriculture.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726376","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":"Integrated multi-omics analysis and machine learning refine molecular subtypes and prognosis in hepatocellular carcinoma through O-linked glycosylation genes","authors":"Minghao Li,&nbsp;Hongxu Li,&nbsp;Lei Liu,&nbsp;Qianyi Wei,&nbsp;Jie Gao,&nbsp;Bowen Hu,&nbsp;Zhihui Wang,&nbsp;Wenzhi Guo,&nbsp;Yi Zhang,&nbsp;Shuijun Zhang","doi":"10.1007/s10142-025-01669-z","DOIUrl":"10.1007/s10142-025-01669-z","url":null,"abstract":"<div><p>O-glycosylation significantly influences cellular physiological processes and disease regulation by modulating the structure, function, and stability of proteins. However, there is a notable gap in research focusing on O-glycosylation in relation to the prognosis of HCC patients. The study aimed to explore the expression and function of O-glycosylation genes in HCC from both bulk- and single-cell perspectives. Multi-omics data related to O-glycosylation identified by weighted gene co-expression network analysis (WGCNA). This was then combined with ten different clustering algorithms to construct molecular subtypes of high-resolution HCC. Cancer subtype 1 (CS1) is characterized by significant genomic variation, moderate immune cell infiltration, and immune function enrichment. Patients with CS2 have a better prognosis and are characterized by a stable genomic structure, an immune-hot phenotype with rich immune cell infiltration, and sensitivity to immunotherapy. CS3 is characterized by poor prognosis, outstanding genomic instability, and an immune-cold phenotype, but can benefit more from treatment with drugs such as sorafenib, cisplatin, paclitaxel, and gemcitabine. To further emphasize the role of O-glycosylation genes in individual HCC patients, we employed 59 machine-learning methods to construct and assess prognostic traits with improved generalizability. Microarray results indicated a pronounced upregulation of glycosylation hub genes involved in HCC stratification and modeling within HCC tumorous tissues. Altogether, our study highlights the importance of O-glycosylation for the assessment of HCC prognosis and treatment options by redefining HCC subtypes and constructing a consensus machine learning-driven prognostic signature (CMLS). This research establishes an optimized decision-making platform that enables the precise stratification of HCC patients, refines tumor treatment plans, and predicts patient survivability, with broad clinical implications.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726375","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":"Analysis of the AP2/ERF transcription factor family in Eriobotrya japonica and its role in exogenous melatonin-mediated regulation of salt stress","authors":"Ling Zhu,&nbsp;Fuhua Liu,&nbsp;Xin Lin,&nbsp;Tianyu Fu,&nbsp;Lin Zou,&nbsp;Yuanhai Pan,&nbsp;Rong Zou,&nbsp;Yang Zhao,&nbsp;Hanyao Zhang","doi":"10.1007/s10142-025-01667-1","DOIUrl":"10.1007/s10142-025-01667-1","url":null,"abstract":"<div><p>AP2/ERF transcription factors (TFs) are involved in various regulatory pathways related to plant growth, development, and stress responses. The growth of <i>Eriobotrya japonica</i>, a popular fruit and medicinal plant, is affected by salt stress. Currently, the functions of <i>E. japonica</i> AP2/ERF in response to salt stress and its role in alleviating salt stress caused by exogenous melatonin (MT) remain unclear. Therefore, in this study, a bioinformatics approach was used to analyze the AP2/ERF TF family of <i>E. japonica</i> and its expression patterns under exogenous MT-regulated salt stress. A total of 187 AP2/ERF TFs on 18 chromosomes were identified in <i>E. japonica</i>, and phylogenetic analyses classified them into four subfamilies: AP2, ERF, DREB, and RAV. Each subfamily contains a relatively large number of biotic or abiotic stresses and hormone related cis-acting elements. There are 61 DEGs of EjAP2/ERF involved in the regulation of NaCl stress by exogenous melatonin. Among these genes,, seven DEGs were involved in the response to ethylene and defense signals under salt stress. These genes are involved in the regulation of NaCl-stressed <i>E. japonica</i> by exogenous MT by activating or repressing the transcription of downstream target genes. Notably, <i>EjERF11</i>, <i>EjERF73</i>, and <i>EjERF86</i> may have functions similar to those of their homologous genes and may serve as vital genes for salt tolerance. This study is the first to investigate the functions of <i>EjAP2/ERF</i> genes in exogenous MT-regulated salt stress, and provides a theoretical foundation for exploring more features of <i>AP2/ERF</i> genes and a basis for breeding <i>E. japonica</i> with salt stress resistance.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717232","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":"UBE2C: a potential therapeutic target and prognostic biomarker for prostate cancer patients","authors":"Shan Li,&nbsp;Yang Liu,&nbsp;Xun Wu,&nbsp;Qiuning Zhang,&nbsp;Wenzhen Yuan","doi":"10.1007/s10142-025-01671-5","DOIUrl":"10.1007/s10142-025-01671-5","url":null,"abstract":"<div><p>UBE2C (Ubiquitin-conjugating enzyme E2C) has been confirmed to be closely associated with the progression of various cancers, but its specific role and clinical diagnostic and prognostic value in prostate cancer (PRAD) remain unclear. This study systematically assessed the expression characteristics, prognostic significance, and genetic mutations of UBE2C in cancer patients by integrating data from databases such as TCGA, GEO, cBioPortal, and COSMIC. Experimentally, we explored the biological functions of UBE2C in the occurrence and development of PRAD using various methods, including functional enrichment analysis, CCK8 cell proliferation assay, colony formation assay, Transwell migration and invasion assay, Edu staining, 3D tumor spheroid culture, cell cycle analysis, apoptosis detection, and xenograft tumor models. After knocking down UBE2C expression, the proliferation ability, migration and invasion ability of PRAD cells, as well as the growth of xenograft tumors, were all inhibited, and the cell cycle process and apoptosis were changed accordingly. These findings provide favorable experimental evidence and theoretical support for UBE2C as a novel molecular marker for prognosis assessment in solid tumors.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706015","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":"CRP and HNF1A collaborate to regulate the progression of laryngeal cancer through the Wnt signaling pathway","authors":"Zhigang Zhao,&nbsp;Xiaojing Zhu,&nbsp;Jinyuan Xu,&nbsp;Penglong Song,&nbsp;Yanan Sun,&nbsp;Zhenming Yang,&nbsp;Li Wang,&nbsp;Jiarui Zhang,&nbsp;Rui Zhao,&nbsp;Xiaoxue Chen,&nbsp;Wenjing Li,&nbsp;Linli Tian,&nbsp;Ming Liu","doi":"10.1007/s10142-025-01670-6","DOIUrl":"10.1007/s10142-025-01670-6","url":null,"abstract":"<div><p>We aim to investigate the regulatory mechanisms of CRP and HNF1A in laryngeal cancer (LC). Bioinformatics identified core genes and associated transcription factors. QRT-PCR evaluated mRNA expressions, while siRNA-transfection induced gene knockdown. Cell proliferation, apoptosis, migration, and invasion were evaluated via CCK-8, flow cytometry, wound-healing, and Transwell. The association between CRP and HNF1A was confirmed through dual luciferase assays, chromatin immunoprecipitation and electrophoretic mobility shift assay. Western blot investigated protein expressions, the association between CRP and the Wnt pathway was evaluated by β-catenin nuclear localization. Nude mouse tumorigenesis experiments validated tumor regulatory effects in vivo. Immunohistochemistry evaluated the in situ expression of proteins within the tumors. FMO2, PTCHD2, AKR1C4, PRSS27, CRP, and ANKRD37 were LC core genes, with HNF1A correlated with CRP. CRP and HNF1A were upregulated in human LC tissues (<i>p</i> &lt; 0.05). CRP/HNF1A knockdown induced decreased proliferation, migration, invasion, and enhanced apoptosis in TU686 cells (<i>p</i> &lt; 0.05), with the correlation between CRP and HNF1A confirmed experimentally. Upon HNF1A-knockdown, CRP, β-catenin, Wnt3a, and Vimentin were downregulated, while E-cadherin was upregulated (<i>p</i> &lt; 0.05). CRP-knockdown inhibited tumor growth and induced altered CRP, Ki67, and HNF1A expression, and consistent expressions for β-catenin, Wnt3a, E-Cadherin, and Vimentin (<i>p</i> &lt; 0.05). CRP and HNF1A promote LC progression through the Wnt signalling pathway and epithelial-mesenchymal transition.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12296761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717233","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}