Functional & Integrative Genomics最新文献

Unveiling the role of adipokine-related genes in biliary atresia through transcriptomic analysis and machine learning 通过转录组学分析和机器学习揭示脂肪因子相关基因在胆道闭锁中的作用

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-07 DOI: 10.1007/s10142-026-02093-7

Yixuan Wang, Xiaoyang Liu, Dongming Wang, Peimin Hou, Weijing Mu, Yujie Zhang, Xingjian Liu, Yuqiang Sun, Qiangye Zhang, Aiwu Li

{"title":"Unveiling the role of adipokine-related genes in biliary atresia through transcriptomic analysis and machine learning","authors":"Yixuan Wang, Xiaoyang Liu, Dongming Wang, Peimin Hou, Weijing Mu, Yujie Zhang, Xingjian Liu, Yuqiang Sun, Qiangye Zhang, Aiwu Li","doi":"10.1007/s10142-026-02093-7","DOIUrl":"10.1007/s10142-026-02093-7","url":null,"abstract":"<div><h3>Background</h3><p>Biliary atresia (BA) is a devastating neonatal cholestatic disease characterized by progressive fibro-obliteration of the extrahepatic bile ducts. Although adipokine signaling is implicated in liver pathology, its key mediators in BA remain unclear.</p><h3>Methods</h3><p>We analyzed BA transcriptomic data (GSE46960) to identify differentially expressed genes (DEGs) and derived an adipokine-associated gene set (AdipoBA-GeneSet). An ensemble of 101 machine learning algorithms was employed to prioritize key genes. The diagnostic value, associated biological pathways, and immune infiltration patterns of key genes were investigated. The role of Leucine-Rich Alpha-2-Glycoprotein 1 (LRG1) was validated in a biliatresone-induced BA mouse model by upregulating its expression.</p><h3>Results</h3><p>We identified 522 DEGs in BA livers, refined to a 30-gene AdipoBA-GeneSet. Machine learning prioritized seven key genes from this adipokine-related gene set (LEPR, SPP1, LRG1, IL32, FBN1, IGF1, and SAA1). These genes showed excellent performance in distinguishing BA patients from normal controls and were linked to extracellular matrix organization and immune pathways. Immune infiltration analysis revealed that key gene expression correlated with specific immune cell subsets. Notably, the adipokine LRG1 was downregulated in BA, and its overexpression alleviated the disease phenotype, as evidenced by improved body weight, decreased bile duct wall-to-lumen ratio, attenuated hepatic fibrosis, and ameliorated hepatic steatosis.</p><h3>Conclusion</h3><p>This study identifies a novel adipokine-related gene signature in BA and highlights LRG1 as a key protector. LRG1 overexpression mitigates cholestatic injury and fibrotic progression in vivo, positioning it as a promising therapeutic target.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338699","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}

引用次数: 0

Transcriptomic insights into skin pigmentation differences between black and white skinned chickens 黑皮肤和白皮肤鸡皮肤色素沉着差异的转录组学研究

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-07 DOI: 10.1007/s10142-026-02105-6

Arti Jangra, Reena Arora, Ritika Gera, Rajesh Kumar, Meena Bagiyal, Pooja Chhabra, Upasna Sharma, Sonika Ahlawat, Rekha Sharma, N. H. Mohan

{"title":"Transcriptomic insights into skin pigmentation differences between black and white skinned chickens","authors":"Arti Jangra, Reena Arora, Ritika Gera, Rajesh Kumar, Meena Bagiyal, Pooja Chhabra, Upasna Sharma, Sonika Ahlawat, Rekha Sharma, N. H. Mohan","doi":"10.1007/s10142-026-02105-6","DOIUrl":"10.1007/s10142-026-02105-6","url":null,"abstract":"<div><p>The present study investigated the transcriptional differences between black skinned Kadaknath and white skinned Broiler chickens using RNA sequencing analysis of skin tissue. A total of 339 high confidence, differentially expressed genes with a log₂ fold change ≥ 4 were identified, of which 294 were upregulated in Kadaknath while 45 were upregulated in Broiler skin samples. Comparative gene expression analysis revealed strong activation of melanogenesis related pathways in black skin, indicating enhanced pigment synthesis and melanocyte activity. Pathway enrichment also underscored the role of biological processes related to melanin biosynthesis, ion homeostasis and mitochondrial regulation in Kadaknath. In contrast, Broiler skin showed enrichment of pathways associated with developmental regulation and tissue patterning, suggesting a greater role of transcriptional programs involved in skin development and structural organization. Gene co-expression network analysis also revealed distinct regulatory architectures between the two groups. Key genes identified in black skin were associated with structural and cytoskeletal functions, while developmental transcription factors and regulatory genes were enriched in white skin. These findings suggest that transcriptomic differences between the two chicken types are regulated by pigment synthesis pathways and developmental regulatory networks in in black and white skin, respectively. This study provides valuable insights into the transcriptional profiles associated with diverse skin types in chicken.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338700","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}

引用次数: 0

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-07 DOI: 10.1007/s10142-026-02108-3

Jingyi Qiu, Xiaoping Zhang, Xiao-Dan Hao

{"title":"Anoikis-related gene signatures and the tumor immune microenvironment: associations, mechanistic insights, and potential therapeutic implications","authors":"Jingyi Qiu, Xiaoping Zhang, Xiao-Dan Hao","doi":"10.1007/s10142-026-02108-3","DOIUrl":"10.1007/s10142-026-02108-3","url":null,"abstract":"<div><p>Anoikis resistance is a hallmark of malignant tumor cells, particularly those with high metastatic potential, and it has recently been closely linked to tumor immune evasion. Accumulating evidence links anoikis resistance to the immunosuppressive tumor microenvironment in which an anoikis-related index derived from a prognostic anoikis-related gene (ARG) signature stratifies patients into distinct immune landscapes and immune phenotypes. This review systematically summarizes the multiple roles of genes comprising this prognostic ARG signature in tumor immune regulation, including their association with immune cell recruitment and function, their utility as predictive biomarkers for prognosis and immunotherapy response, and therapeutic strategies targeting anoikis-related pathways to overcome resistance and reverse immune suppression. Moreover, the associations between the ARG signature characteristics, immunophenotype, and treatment response are not entirely consistent, varying not only across cancer types but also within the same cancer type when different gene signatures are used. Notably, while numerous transcriptomic studies have correlated ARG signatures with immune features across cancers, functional validation remains limited. Although the tumor cell-autonomous functions of some ARG signatures have been supported experimentally, systematic evidence directly demonstrating a causal relationship between specific ARG signatures and immune cell function remains scarce. By highlighting current progress and mechanistic gaps, this review aims to provide a theoretical foundation and potential targets for developing next-generation combination immunotherapies. Clinical trial number: Not applicable.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338782","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}

引用次数: 0

From LOX to JOX: Functional roles of jasmonate biosynthetic and catabolic genes in plant growth and stress responses 从LOX到JOX：茉莉酸生物合成和分解代谢基因在植物生长和胁迫反应中的功能作用

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-07 DOI: 10.1007/s10142-026-02110-9

Rui Wang, Teja Manda, Yao Zhang, Ali Movahedi, Liming Yang

{"title":"From LOX to JOX: Functional roles of jasmonate biosynthetic and catabolic genes in plant growth and stress responses","authors":"Rui Wang, Teja Manda, Yao Zhang, Ali Movahedi, Liming Yang","doi":"10.1007/s10142-026-02110-9","DOIUrl":"10.1007/s10142-026-02110-9","url":null,"abstract":"<div><p>Jasmonic acid (JA) is a central precursor in jasmonate metabolism, and its conjugate jasmonoyl-isoleucine (JA-Ile) serves as the major bioactive jasmonate that regulates plant growth, development, and responses to biotic and abiotic stresses. While extensive research has focused on JA-Ile-mediated signal transduction, particularly the COI1-JAZ-MYC module, less attention has been paid to the regulatory and broader systemic roles of genes involved in jasmonate biosynthesis and catabolism. This review systematically summarizes the multifaceted roles of key genes in the jasmonate biosynthesis and degradation pathway, such as <i>LOXs, AOSs, AOCs, OPRs, ACXs, MFPs, KATs</i>, <i>JAR1, CYP94s</i> and <i>JOXs/JAOs</i>, in plant growth and development, as well as in responses to biotic and abiotic stresses. We highlight that current evidence suggests that jasmonate biosynthesis and degradation are regulated through a complex network involving multiple gene families operating across different subcellular compartments. These genes are also reported to be associated with interactions between jasmonate metabolism and other signaling pathways, including light and hormones such as auxin, cytokinin, and ethylene. Finally, we identify current research gaps and propose future directions, including tissue-specific mechanisms, multi-signal integration, and applications in non-model plants.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338711","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}

引用次数: 0

Multi-omics data integration in bioinformatics: methods, applications, and the path toward biological reasoning 生物信息学中的多组学数据集成：方法、应用和生物推理的路径

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-07 DOI: 10.1007/s10142-026-02107-4

Emel Kabartan Çökeli, Furkan Cerrahoğlu

{"title":"Multi-omics data integration in bioinformatics: methods, applications, and the path toward biological reasoning","authors":"Emel Kabartan Çökeli, Furkan Cerrahoğlu","doi":"10.1007/s10142-026-02107-4","DOIUrl":"10.1007/s10142-026-02107-4","url":null,"abstract":"<div><p>High-throughput technologies now make it possible to simultaneously generate genomic, transcriptomic, epigenomic, proteomic, and metabolomic data. Spatial and single-cell platforms, in turn, provide cellular and spatial information in greater detail. Relying on a single omics method captures only a fraction of this complexity and often overlooks interactions across different layers. Despite these advances, clinical applications remain limited. This review examines integration strategies, along with their applications in various diseases, and the machine learning methods used to implement them. Rather than focusing solely on predictive performance, the aim is to support biological reasoning by formulating testable hypotheses, drawing causal inferences, and gaining insights that can guide clinical decisions. A reanalysis of a publicly available chronic lymphocytic leukemia dataset revealed that one data type was missing in approximately one-third of patients. When early and intermediate integration were combined with simple zero imputation, agreement dropped to chance and near-chance levels. In contrast, late integration, which does not require data imputation, was largely unaffected by this issue. This demonstrates that findings regarding integration strategies cannot be considered in isolation from how missing data are handled. The review also covers approaches that directly address missing data. Major barriers to clinical application include confounding batch effects, unreliable feature attribution when features are correlated, and deficiencies in clinical quality assurance. This review proposes four criteria to help identify models that not only ensure statistical validity but also genuinely support biological reasoning: mechanistic specificity, causal grounding, failure transparency, and decision relevance.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338783","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}

引用次数: 0

CircIKBKB promotes hepatocellular carcinoma stemness and EMT via TAF15-PTCH1-mediated Hedgehog activation CircIKBKB通过taf15 - ptch1介导的Hedgehog激活促进肝细胞癌的干细胞性和EMT

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-06 DOI: 10.1007/s10142-026-02062-0

Tingzhuang Yi, Kai Hu, Meini Pan, Xike Xie, Dengchong Ning, Jinyan Lan, Yibin Liang, Yongyu He, Gang Huang, Hong Huang, Yiheng Zhao, Peng Lei, Shengkui Tan, Rensheng Wang

{"title":"CircIKBKB promotes hepatocellular carcinoma stemness and EMT via TAF15-PTCH1-mediated Hedgehog activation","authors":"Tingzhuang Yi, Kai Hu, Meini Pan, Xike Xie, Dengchong Ning, Jinyan Lan, Yibin Liang, Yongyu He, Gang Huang, Hong Huang, Yiheng Zhao, Peng Lei, Shengkui Tan, Rensheng Wang","doi":"10.1007/s10142-026-02062-0","DOIUrl":"10.1007/s10142-026-02062-0","url":null,"abstract":"<div><p>Hepatocellular carcinoma (HCC) represents one of the leading causes of cancer-related mortality worldwide. Accumulating studies in recent years have confirmed that circular RNAs (circRNAs) are involved in the regulation of tumor initiation and progression. Nevertheless, the precise functions and underlying molecular mechanisms of circRNAs in HCC remain to be thoroughly investigated. In this study, we identified a circular RNA derived from the <i>IKBKB</i> gene, designated circIKBKB (database accession number: hsa_circ_0084102), which exhibits significantly elevated expression in HCC cell lines. Functional experiments demonstrated that circIKBKB promotes HCC cell proliferation, sustains cancer stemness properties, and induces epithelial-mesenchymal transition (EMT). Mechanistically, circIKBKB directly interacts with the RNA-binding protein TATA-box binding protein associated factor 15 (TAF15) and suppresses its polyubiquitination-mediated proteasomal degradation, thereby maintaining intracellular TAF15 protein stability. The upregulated TAF15 further binds to Patched 1 (<i>PTCH1</i>) mRNA and enhances its transcript stability, which consequently drives aberrant activation of the Hedgehog signaling pathway. Both in vitro and in vivo validation assays confirmed that overexpression of PTCH1 partially reversed the phenotypic effects induced by circIKBKB knockdown. Collectively, our findings uncover the regulatory mechanism of circIKBKB in mediating aberrant activation of the Hedgehog pathway in HCC, and this work may provide a potential interventional strategy for HCC treatment.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338503","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}

引用次数: 0

In silico prioritization with preliminary in vitro assessment of UV-328-associated molecular responses in colorectal cancer cells 大肠直肠癌细胞中uv -328相关分子反应的初步体外评估

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-05 DOI: 10.1007/s10142-026-02104-7

Shuangyi Sun, Zixia Xu, Jiaxiao Zheng, Lingli Hu

{"title":"In silico prioritization with preliminary in vitro assessment of UV-328-associated molecular responses in colorectal cancer cells","authors":"Shuangyi Sun, Zixia Xu, Jiaxiao Zheng, Lingli Hu","doi":"10.1007/s10142-026-02104-7","DOIUrl":"10.1007/s10142-026-02104-7","url":null,"abstract":"<div><p>2-(benzotriazole-2-yl)-4,6-bis(2-methylbutan-2-yl) phenol (UV-328) is a persistent benzotriazole ultraviolet stabilizer, but its potential relationship with colorectal cancer (CRC)-related molecular features and malignant cell phenotypes remains unclear. This study integrated public transcriptomic datasets, UV-328 target prediction, weighted gene co-expression network analysis (WGCNA), machine-learning, single-cell transcriptomic analysis, molecular docking, molecular dynamics (MD) simulation, and in vitro assays. Candidate targets were screened by intersecting CRC-associated genes with predicted UV-328 targets, followed by machine-learning-based feature prioritization, survival analysis, single-cell localization, structural modeling, and functional validation in CRC cells. The integrated workflow prioritized BRAF, DYRK1A, RXRB, RPS24, and TP53 as candidate predicted UV-328 targets. Single-cell analysis localized these genes mainly to epithelial compartments, providing a cell-type context for their interpretation. Docking, 100 ns MD simulations, and MM/PBSA analyses provided complementary structural and energetic support for the selected BRAF-, DYRK1A-, and RXRB–UV-328 candidate interactions. Short-term treatment with 10 µM UV-328 increased CCK-8 signals in SW480 and HCT116 cells and enhanced SW480 cell migration and invasion. Seven-day exposure to a nominal concentration of 10 nM UV-328 also increased CCK-8 signals in SW480, HCT116, and RKO cells. UV-328 treatment modestly increased DYRK1A protein abundance, whereas DYRK1A knockdown partially attenuated the associated CCK-8 response in SW480 cells. Together, these findings outline an integrated, hypothesis-generating framework connecting UV-328-associated molecular features with CRC-related cellular responses and prioritizing candidate targets for further mechanistic validation.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338119","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}

引用次数: 0

Discovery-locked cross-platform evaluation of a cervical epithelial transcriptional state 发现锁定的跨平台评估宫颈上皮转录状态

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-05 DOI: 10.1007/s10142-026-02088-4

Yihan Zheng, Huan Yi, Leilei Zhu, Jimiao Huang, Shihuang Liu, Xiangqin Zheng

{"title":"Discovery-locked cross-platform evaluation of a cervical epithelial transcriptional state","authors":"Yihan Zheng, Huan Yi, Leilei Zhu, Jimiao Huang, Shihuang Liu, Xiangqin Zheng","doi":"10.1007/s10142-026-02088-4","DOIUrl":"10.1007/s10142-026-02088-4","url":null,"abstract":"<div><p>Cross-platform claims about tumour-cell states can be inflated when each cohort is reanalysed to favour a new definition. We evaluated whether a cervical epithelial transcriptional state selected in one discovery cohort remained recoverable without changing its frozen genes or thresholds. E-MTAB-12,305 was the sole discovery cohort and contained 100,453 cells from ten samples; 11,224 cells were assigned to the discovery-defined epithelial state. We froze 123 sample-aware pseudobulk signatures and evaluated them in an external single-cell cohort, four Visium samples, a 22-sample Xenium cohort using an 11-gene proxy, and a local dataset containing 30,280 manually selected epithelial cells from 14 specimens representing 11 participants. Leave-one-sample-out analyses preserved gene-level direction in evaluable folds but showed sample-sensitive significance. Xenium scores exhibited within-score spatial clustering after joint-label coordinate permutations (median odds ratio 1.97; 19 of 22 odds ratios > 1). In the local cohort, patient-level associations with CytoTRACE2 were not significant, although within-participant cell-level correlations were consistently negative. Recomputed TCGA-CESC analyses did not support a stable prognostic association after accounting for score definition and time dependence. The results support a discovery-locked, cross-platform recovery framework and a context-dependent epithelial-state hypothesis, but not malignant identity, metastatic lineage, clinical prognosis, or causal communication.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149338271","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}

引用次数: 0

CLEC1B and RAC1 in peripheral immune remodeling associated with sleep disturbance: an exploratory integrative study cle1b和RAC1与睡眠障碍相关的外周免疫重塑：一项探索性综合研究

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-05 DOI: 10.1007/s10142-026-02102-9

Yangxiao Li, Changyuan Liu, Hong Zheng, Junhan Lin

{"title":"CLEC1B and RAC1 in peripheral immune remodeling associated with sleep disturbance: an exploratory integrative study","authors":"Yangxiao Li, Changyuan Liu, Hong Zheng, Junhan Lin","doi":"10.1007/s10142-026-02102-9","DOIUrl":"10.1007/s10142-026-02102-9","url":null,"abstract":"<div><p>Background: Sleep disturbance is closely linked to immune dysfunction, but the molecular features of associated peripheral immune remodeling remain incompletely defined. Results: In this exploratory study, we integrated blood eQTL data and GWAS summary statistics with mouse PBMC single-cell data, a human PBMC transcriptome cohort, and mouse PBMC measurements. The single-cell dataset comprised one control, one 24-hour sleep-deprivation, and one 48-hour sleep-deprivation library. Descriptive single-cell patterns showed contraction of the B-cell compartment and expansion of granulocytes. Mendelian randomization nominally prioritized <i>RAC1</i> and <i>CLEC1B</i>, with limited co-localization support. Both genes showed lower expression in the human cohort and were associated with altered B-cell communication and metabolic states. In mouse PBMCs (<i>n</i> = 3 per group), <i>Clec1b</i> qPCR showed a downward trend (<i>P</i> = 0.072), whereas <i>Rac1</i> qPCR expression was lower after sleep deprivation (<i>P</i> = 0.017). Lane-level western blot analysis also showed lower CLEC1B (<i>P</i> = 0.0056) and RAC1 (<i>P</i> = 0.0016) protein abundance. Conclusions: These exploratory integrative analyses nominate <i>CLEC1B</i> and <i>RAC1</i> as candidate genes associated with peripheral B-cell remodeling in a sleep-disturbance context. These hypothesis-generating findings warrant targeted functional studies of their roles in sleep-related immune remodeling.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149332045","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}

引用次数: 0

Genome-wide identification and integrative analysis of the cytochrome P450 superfamily in pea (Pisum sativum L.) reveals candidate genes associated with Aphanomyces root rot response 豌豆（Pisum sativum L.）细胞色素P450超家族的全基因组鉴定和综合分析揭示了与隐霉根腐病反应相关的候选基因。

IF 4 4区生物学

Functional & Integrative Genomics Pub Date : 2026-11-05 DOI: 10.1007/s10142-026-02095-5

Muhammad Sufyan Tahir, Sangeeta Dhaubhadel

{"title":"Genome-wide identification and integrative analysis of the cytochrome P450 superfamily in pea (Pisum sativum L.) reveals candidate genes associated with Aphanomyces root rot response","authors":"Muhammad Sufyan Tahir, Sangeeta Dhaubhadel","doi":"10.1007/s10142-026-02095-5","DOIUrl":"10.1007/s10142-026-02095-5","url":null,"abstract":"<div><p>Cytochrome P450 monooxygenases (P450) constitute one of the largest and most functionally diverse enzyme superfamilies in plants, underpinning the biosynthesis of a plethora of primary and specialized metabolites involved in growth and development as well as stress response. Here, we present the first integrated genome-wide analysis of the pea P450 superfamily (CYPome), combining phylogenetic, structural, evolutionary, transcriptional, and genetic approaches to identify defense-associated candidates. We identified 210 <i>P450</i> genes encoding 241 proteins in pea genome, classified into 45 CYP families across 10 clans. Comparative analyses revealed both highly conserved legume P450 lineages and a substantial fraction of pea-specific expansions, reflecting dynamic CYPome evolution. Gene structure and motif analyses confirmed conservation of core catalytic features, alongside family-specific variation consistent with functional diversification. A conserved core of many <i>PsP450</i> genes induced across multiple pea cultivars at a wide range of time points post <i>Aphanomyces euteiches</i> infection together with their expression in root tissue was discovered. Integration of aphanomyces root rot resistance-associated quantitative trait loci further refined candidate prioritization, identifying <i>PsP450s</i> that co-localized with resistance loci, exhibited strong co-expression with <i>PsIFS</i> genes, and were rapidly induced upon infection. Collectively, this integrative analysis defines the pea CYPome and identifies a focused set of high-confidence P450 candidates likely involved in defense-associated metabolic reprogramming during <i>A. euteiches</i> infection. These findings provide a foundational resource for functional genomics and offer promising targets for improving disease resistance in pea and related legume crops.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149332046","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}

引用次数: 0