Functional & Integrative Genomics最新文献

{"title":"MZB1-Driven Endoplasmic reticulum stress model as a predictor of breast cancer progression and survival","authors":"Purong Zhang,&nbsp;Rui Wang,&nbsp;Yuying Wang,&nbsp;Ning Zhang,&nbsp;Ke Luo","doi":"10.1007/s10142-025-01676-0","DOIUrl":"10.1007/s10142-025-01676-0","url":null,"abstract":"<div><p>Endoplasmic reticulum (ER) stress and its associated unfolded protein response (UPR) have been demonstrated to play a crucial role in cancer’s progression, but their prognostic significance in breast cancer (BC) remains unclear. In this study, a reliable ER-related gene signature was developed for the purpose of predicting BC prognosis and investigating the associated immune landscape. By utilizing public datasets and analytical methods, we developed a 16 ER-related gene risk signature and verified its efficacy in predicting prognosis in independent patient groups. Patients in the high-risk group exhibited significantly poorer survival rates. Single-cell analysis revealed that the low-risk group exhibited stronger immune interactions. Conversely, the high-risk group exhibiting elevated immune checkpoints may signify an immunosuppressive microenvironment or heightened sensitivity to immune checkpoint inhibitor therapy. In vitro and <i>vivo</i> experiments confirmed that knocking down the expression of Marginal Zone B And B1 Cell Specific Protein (MZB1) significantly inhibited the proliferation, invasion, and tumorigenesis of breast cancer. The 16 ER-related gene signature is capable of effectively categorizing breast cancer patients into different risk levels, thereby providing a basis for personalized therapy. MZB1 has been identified as a significant regulatory factor, suggesting its potential as a target for the treatment of breast cancer.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01676-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144914731","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":"Genomic insights into the antagonistic activity of Paenibacillus brasilensis PB24 against Fusarium oxysporum: implications for biocontrol and plant growth promotion strategies","authors":"Jackeline Rossetti Mateus,&nbsp;Isabella Dal’Rio,&nbsp;Antonio Pereira Ferreira,&nbsp;Jefferson Bomfim Silva Cypriano,&nbsp;Fernanda Abreu,&nbsp;Lucy Seldin","doi":"10.1007/s10142-025-01688-w","DOIUrl":"10.1007/s10142-025-01688-w","url":null,"abstract":"<div><p>Biotechnology and sustainable strategies are the way forward for increasing global food production. The use of plant growth-promoting bacteria to increase the productivity of important food crops helps reduce the need for land expansion, improves soil fertility and plant tolerance to adverse abiotic conditions, and increases the ability to combat phytopathogens. <i>Paenibacillus brasilensis</i> strain PB24 is an endospore-forming bacterium that promotes plant growth through various direct and indirect mechanisms. To improve the understanding of its ability to inhibit the fungus <i>Fusarium oxysporum</i>, which causes numerous agricultural pathologies, the potential of <i>P. brasilensis</i> PB24 as a producer of antifungal compounds was investigated. In vitro assays demonstrated fungicidal activity against <i>F. oxysporum</i> hyphae. Additionally, genome mining of <i>P. brasilensis</i> PB24 was conducted to identify biocontrol and plant growth-promoting traits. For the first time, these traits were compared with those of other <i>Paenibacillus</i> species, and several genetic similarities were identified. Genome mining revealed that strain PB24 produces several antimicrobial compounds, similar to fusaricidin and sevadicin, but retains substantial differences in their monomers, suggesting that they may be novel lipopeptides. A unique genetic cluster was characterized in the PB24 genome as a potential resource for the discovery of new compounds. The results demonstrate the biotechnological potential of <i>P. brasilensis</i> PB24 for plant growth and biocontrol of phytopathogens and provide a basis for the future development of sustainable biocontrol strategies and commercial bacterial formulations.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144909757","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 plastome analysis reveals evolutionary dynamics and codon usage patterns in Bidens (Asteraceae)","authors":"Ying Xue,&nbsp;Shaowei Qin,&nbsp;Zhangchen Xianyu,&nbsp;Haodi Wang,&nbsp;Jialei Yu,&nbsp;Xiaoyan Zhao,&nbsp;Xingxing Liang,&nbsp;Dong Li,&nbsp;Yunpeng Gai","doi":"10.1007/s10142-025-01699-7","DOIUrl":"10.1007/s10142-025-01699-7","url":null,"abstract":"<div><p>Plastome evolution in species-rich angiosperm lineages remains poorly understood despite recent advances in phylogenomics, particularly regarding the mechanistic drivers of codon usage bias (CUB) and their relationship to adaptive evolution. The genus <i>Bidens</i> (Asteraceae), comprising approximately 280 species, represents a morphologically diverse lineage with significant medicinal and economic value. Here, we assembled the complete plastid genome (plastome) of <i>Bidens alba</i> and conducted comprehensive comparative analyses across 31 <i>Bidens</i> species, integrating structural characterization, simple sequence repeat (SSR) distribution, codon usage bias assessment, and selection pressure analysis through Ka/Ks ratios and phylogenomic reconstruction. All plastomes exhibited the canonical angiosperm quadripartite structure (150,490 − 151,856 bp) with consistent AT bias (average GC content: 37.48%) and mononucleotide SSR predominance (37.43%). Twenty-nine high-frequency codons displayed strong AT preference, with multiple analytical approaches confirming natural selection as the primary driver of codon usage bias. The non-synonymous (Ka) /synonymous (Ks) substitution ratios revealed that most protein-coding genes showed evidence of purifying selection (Ka/Ks &lt; 0.5), though the <i>ycf2</i> and <i>accD</i> genes displayed elevated ratios suggesting adaptive evolution. Phylogenomic reconstruction supported <i>Bidens</i> monophyly with high bootstrap values and resolved species relationships with high confidence. Comparative structural analysis revealed exceptional genomic conservation across the genus, suggesting that while sequence evolution has occurred, the fundamental genomic architecture remains stable. These findings provide crucial insights into significant structural conservation across <i>Bidens</i> plastomes while demonstrating active sequence-level evolution, providing crucial insights into plastome evolutionary mechanisms within rapidly diversifying lineages and establish a robust genomic framework for understanding ecological adaptation and phylogenetic relationships in this ecologically important lineage.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144905135","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":"Cytosine base editor-mediated high-efficiency myostatin editing in Hu sheep","authors":"Y. Wang,&nbsp;W. J. Liu,&nbsp;C. H. Meng,&nbsp;H. L. Wang,&nbsp;Z. K. Cui,&nbsp;J. Zhang,&nbsp;J. L. Zhang,&nbsp;Y. Qian,&nbsp;Y. X. Li,&nbsp;S. X. Cao","doi":"10.1007/s10142-025-01698-8","DOIUrl":"10.1007/s10142-025-01698-8","url":null,"abstract":"<div><p>The cytosine base editor (CBE) enables precise C-to-T substitution without inducing DNA double-strand breaks, which offering a promising tool for editing livestock genomes to enhance economically valuable traits. In this study, using Hu sheep, characterized by high reproductive performance but suboptimal meat production as the research subject, two CBE-editing sgRNAs (sgM1 and sgM2) targeting the negative regulator Myostatin (<i>MSTN</i>) gene were designed. The results revealed a 75% editing efficiency of sgM2 at the parthenogenetically activated embryonic level with no detectable off-target effects. Thirty-four zygotes from five Hu sheep microinjected with sgM2 and CBE mRNA mixtures were transferred into four Hu sheep recipient ewes, yielding four lambs with confirmed <i>MSTN</i> editing and no off-target activity. Statistical analysis of growth performance data revealed that <i>MSTN</i>-edited Hu sheep exhibited significantly (<i>P</i> &lt; 0.05) higher body weights at 120–180 days, and significantly (<i>P</i> &lt; 0.05) enlarged muscle fiber cross-sectional areas compared to wild-type controls. Edited Hu sheep displayed reduced MSTN protein expression, elevated p-AKT levels, and diminished p-ERK and p-p38 signaling. In conclusion, <i>MSTN</i>-edited Hu sheep were highly efficient generated using CBE, and further analysis demonstrate that <i>MSTN</i> editing activates the <i>AKT</i> pathway while suppressing <i>MAPK</i> signaling, leading to muscle fiber hypertrophy and accelerated growth, which provides technical methodologies and breeding materials for developing fast-growing, meat-type Hu sheep-germplasm.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144905136","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: Decoding fungal communication networks: molecular signaling, genetic regulation, and ecological implications","authors":"Shumila Ishfaq,&nbsp;Hadiqa Anum,&nbsp;Tayyaba Shaheen,&nbsp;Sana Zulfiqar,&nbsp;Anila Ishfaq,&nbsp;Arslan Anjum,&nbsp;Umera Ramzan,&nbsp;Amna Rafiq,&nbsp; Mehboob-ur-Rahman,&nbsp;Wei Guo","doi":"10.1007/s10142-025-01652-8","DOIUrl":"10.1007/s10142-025-01652-8","url":null,"abstract":"","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896945","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 analysis of key flavonoid synthesis genes in the transcriptome of Cayratia Japonica and therapeutic target prediction for ulcerative colitis","authors":"Mengge Sun,&nbsp;Wanying Xie,&nbsp;Leiming Xu,&nbsp;Zhiwei Wang,&nbsp;Jinshibo Fan,&nbsp;Ziyang Xie,&nbsp;Jiawen Wu,&nbsp;Yijia Tao","doi":"10.1007/s10142-025-01695-x","DOIUrl":"10.1007/s10142-025-01695-x","url":null,"abstract":"<div><p><i>Cayratia japonica</i> is a traditional Chinese herbal plant rich in flavonoid compounds, with anti-inflammatory and anti-cancer properties. Although <i>Cayratia japonica</i> has been used for medicinal purposes for centuries, the mechanisms underlying flavonoid biosynthesis in this plant remain largely unexplored. In this study, combining transcriptomics and bioinformatics, we constructed a transcriptome database for three tissues of <i>Cayratia japonica</i>. We identified 38 unigenes related to the flavonoid biosynthetic pathway. Pearson’s correlation analysis indicated that the expression levels of three key enzyme-encoding genes in the flavonoid biosynthetic pathway (a 4-coumarate-CoA ligase gene (DN990) and two chalcone isomerase genes (DN1381, DN2421)) were significantly and positively correlated with the total flavonoid content. Subsequently, the tertiary structures of 4-coumarate-CoA ligase and chalcone isomerases were constructed, and structure-based docking analysis was carried o ut. The expression levels of 16 key enzyme genes in the flavonoid biosynthetic pathway were verified using quantitative reverse transcription-PCR. Four MYB transcription factors involved in flavonoid biosynthesis were also identified. In addition, five potentially important therapeutic targets for Ulcerative colitis were predicted through network pharmacological analysis. This study provides references for understanding the mechanisms involved in the regulation of key enzyme-encoding genes in the flavonoid biosynthetic pathway, as well as a scientific basis for the further development of the medicinal potential of <i>Cayratia japonica</i>.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896944","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":"Plastome structure, evolution and diversity of Frankincense-producing Boswellia genus","authors":"Sajjad Asaf,&nbsp;Yetunde A. Williams,&nbsp; Lubna,&nbsp;Jean-Jack M. Riethoven,&nbsp;Jason Eslamieh,&nbsp;Ahmed Al-Rawahi,&nbsp;Ahmed Al-Harrasi,&nbsp;Abdul Latif Khan","doi":"10.1007/s10142-025-01682-2","DOIUrl":"10.1007/s10142-025-01682-2","url":null,"abstract":"<div><p>The genus <i>Boswellia</i> is famous for its commercially important frankincense production. Additionally, it has unique ecological and taxonomic importance. However, the <i>Boswellia</i> species often face natural hybridization, and the lack of genomic datasets frequently contributes to taxonomic uncertainties. Here, we sequenced and analyzed the complete plastid genomes (plastomes) of six <i>Boswellia</i> species (<i>B. carteri</i>, <i>B. bullata</i>, <i>B. dioscoridis</i>, <i>B. elongata</i>, <i>B. serrata</i>, <i>B. frereana</i>, and a hybrid variant of <i>B. sacra</i> (<i>B. sacra</i> var. supersacra). The genome size of <i>Boswellia</i> plastomes is between 159,189 bp and 160,743 bp, displaying a typical structure with large single-copy (LSC; 86,811–88,054), small single-copy (SSC; 26,666–26,763), and inverted repeat (IR; 26,544–26,763) regions. The IR regions (~ 25,000 bp) are highly conserved across species, contributing to the stability of the plastome structure. Our study identified consistent gene content, typical of angiosperms, and showed that the IR boundaries remained unchanged across species. The simple sequence repeats revealed a range between 43 and 52 across the plastomes, with <i>B. sacra</i> exhibiting the highest count. We detected long, repetitive sequences that could serve as useful genetic markers for species differentiation. Nucleotide diversity analysis highlighted significant gene variations (<i>mat</i>K, <i>rbc</i>L, <i>rpl</i>14, and <i>rpo</i>C2). The results showed substantial genetic divergence in regions (<i>rpl</i>14, <i>mat</i>K, and <i>rpo</i>C2), demonstrating distinct variations among species. In evolutionary history, the <i>B. carteri</i> diverged around 4.2 million years ago (mya), while <i>B. sacra</i> and <i>B. serrata</i> separated by approximately 7.0 mya. The phylogenomic analysis supported the distinction between <i>B. carteri</i> and <i>B. sacra</i>, challenging prior claims that these are synonymous. These findings contribute to a deeper understanding of species boundaries within <i>Boswellia</i> and offer valuable resources for future DNA barcoding efforts.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893947","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":"A novel PADI6 splice-site variant induces non-canonical GC-AG splicing and embryonic arrest in humans","authors":"Huiling Hu,&nbsp;Jiaqi Sun,&nbsp;Fei Meng,&nbsp;Fei Gong,&nbsp;Ge Lin,&nbsp;Lizhi Leng,&nbsp;Wei Zheng","doi":"10.1007/s10142-025-01689-9","DOIUrl":"10.1007/s10142-025-01689-9","url":null,"abstract":"<div><p>Early embryonic arrest (EEA) represents the predominant cause of assisted reproductive technology (ART) failure. <i>PADI6</i> was a disease-associated gene identified for EEA. To date, 42 likely causal <i>PADI6</i> variants have been documented, predominantly located in exonic regions with clustering outside the N-terminal domain. Whole-exome sequencing identified candidate variants, with pedigree validation via Sanger sequencing. PCR amplification and sequencing of <i>PADI6</i> transcripts from arrested embryos characterized splicing alterations. Single-embryo RNA sequencing assessed transcriptomic perturbations in <i>PADI6</i>-variant carrier. We report a homozygous <i>PADI6</i> splicing variant (c.104_116 + 10del, p.Leu35_Gly39delinsTrpGluLeuCysGlnArgTrpGlnAlaAspArg) inducing non-canonical “GC-AG” splicing, causing a 13-bp exon 1 deletion and 31-bp intron 1 retention. This aberrant splicing altered the N-terminal domain, replacing five wild-type residues with eleven novel amino acids. Transcriptome analysis revealed dysregulation enriched in RNA metabolism pathways (down-regulated genes) and Rho GTPase signaling (up-regulated genes), with ribosomal dysfunction implicated as a potential pathogenic mechanism. This study expands the <i>PADI6</i> mutational landscape and provides the first transcriptome profiling of human embryos harboring <i>PADI6</i> variant. Our findings establish a framework for genetic counseling in female infertility characterized by embryonic arrest.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144869047","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":"Transcription factor BrEFM negatively regulates flowering time in Chinese cabbage","authors":"Xinlei Guo,&nbsp;Yuanyuan Zhang,&nbsp;Chunyang Feng,&nbsp;Yunduan Qin,&nbsp;Shuai Li,&nbsp;Yu Xu,&nbsp;Changwei Shen,&nbsp;Jingping Yuan","doi":"10.1007/s10142-025-01673-3","DOIUrl":"10.1007/s10142-025-01673-3","url":null,"abstract":"<div><p>Flowering represents a critical developmental transition in plants. In Chinese cabbage, precise regulation of flowering time is especially vital for optimizing yield and quality. In Chinese cabbage, <i>BrEFM</i> and many genes annotated as flowering-related are specifically expressed in leaf veins. However, whether it regulates flowering in Chinese cabbage remains unclear. Here, we cloned <i>BrEFM</i> and found that it encodes a 422-residue polypeptide with a conserved Myb-DNA-binding domain in its protein sequence. Expression pattern analysis showed that <i>BrEFM</i> exhibits the highest expression levels in leaf veins during the rosette and heading stages, while its expression peaks in buds during early pod-setting stage. Further analysis indicated <i>BrEFM</i> is primarily expressed in phloem cells of leaf veins. Subcellular localization analysis demonstrated that BrEFM localizes to the nucleus. Functional analysis revealed that heterologous overexpression of <i>BrEFM</i> resulted in delayed bolting and flowering in transgenic <i>Arabidopsis</i> plants. Conversely, <i>BrEFM</i>-silenced Chinese cabbage plants bolted and flowered earlier than control plants. This indicates that BrEFM negatively regulates flowering in Chinese cabbage. Quantitative real-time PCR analysis suggested that <i>BrEFM</i> likely regulates flowering by modulating the expression of <i>BrFT.1</i>, <i>BrFT.2</i>, <i>BrBFT</i>, <i>BrLFY</i>, <i>BrPI</i>, and <i>BrTSF</i> genes. Overall, this study provides insights into elucidating the molecular mechanisms of bolting in Chinese cabbage and offers valuable gene resources for breeding bolt-resistant varieties.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843182","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":"Prognostic and therapeutic implications related to glycosylation profiles of cancer-associated fibroblasts in colorectal cancer: insights from single-cell and bulk transcriptomics","authors":"Keji Chen,&nbsp;Huixia Huang,&nbsp;Zijuan Hu,&nbsp;Yifei Zhu,&nbsp;Yanxi Yao,&nbsp;Yaxian Wang,&nbsp;Jiayu Chen,&nbsp;Yuxue Li,&nbsp;Dawei Li,&nbsp;Ping Wei","doi":"10.1007/s10142-025-01675-1","DOIUrl":"10.1007/s10142-025-01675-1","url":null,"abstract":"<div><p>Glycosylation, a common post-translational modification of proteins, plays a role in numerous biological processes. However, the role of glycosylation in colorectal cancer (CRC) remains incompletely understood. In this study, we identified that CAFs exhibited the highest glycosylation levels in CRC. We classified 6 CAFs subgroups with distinct glycosylation profiles, revealing notable heterogeneity in functional activities, communication pathways, developmental trajectories, and metabolic states. Furthermore, we developed and validated a robust prognostic model capable of predicting CRC patient survival outcomes using 101 machine learning algorithms. The model stratified patients into high-risk and low-risk groups, where genetic and epigenetic alterations, immune infiltration patterns and responses to various therapeutic drugs varied significantly between the groups. In vitro experiments demonstrated that the key gene <i>CCDC85B</i> in the model influences the glycosylation levels of CRC and CD8 + T cell infiltration, underscoring its potential as an essential therapeutic target. These findings underscore the functional complexity within CAFs subgroups and highlight potential therapeutic targets for CRC treatment. These findings deepen our understanding of glycosylation and offer tools for prognosis, drug selection, and targeted therapy in CRC patients.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01675-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843180","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}