Functional & Integrative Genomics最新文献

{"title":"Integrative pooled transcriptomic analysis reveals shared and distinct molecular signatures in adult T-cell leukemia/lymphoma and peripheral T-cell lymphoma","authors":"Mohammad Mehdi Akbarin,&nbsp;Zahra Farjami,&nbsp;Hugo Ramírez Álvarez","doi":"10.1007/s10142-026-02041-5","DOIUrl":"10.1007/s10142-026-02041-5","url":null,"abstract":"<div><p>Adult T-cell leukemia/lymphoma (ATLL) and peripheral T-cell lymphomas (PTCLs) are aggressive neoplasms of mature T cells with poor prognosis and limited therapies. ATLL originates from HTLV-1 infection, while PTCL comprises heterogeneous subtypes without a defined etiologic factor. Comparative molecular profiling of these malignancies remains limited. We conducted an integrative pooled transcriptomic analysis of publicly available Gene Expression Omnibus (GEO) microarray datasets to compare ATLL, PTCL, and normal T-cell samples. Differential expression, functional enrichment, and protein–protein interaction (PPI) network analyses were performed using STRING, Cytoscape, and Gephi. Key hub genes and functional modules were further analyzed through KEGG and Enrichr databases. Comparative analyses revealed upregulation of extracellular matrix (ECM) components (<i>COL1A1</i>,<i> COL3A1</i>,<i> FN1</i>,<i> SPARC</i>,<i> THBS1</i>) and immune-regulatory molecules (<i>CD163</i>,<i> CXCL12–CXCR4</i>, complement subunits). Shared pathways included ECM–receptor interaction, focal adhesion, and PI3K–Akt signaling. PTCL showed enrichment in coagulation and angiogenesis, while ATLL displayed distinct enrichment of cytoskeletal, chemokine, immune-regulatory, and signaling-associated pathways. PPI networks identified ECM and chemokine signaling as key hubs, with subtype-specific modules related to immune regulation, proliferation, and metabolism. This integrative approach uncovers common and distinct oncogenic programs in ATLL and PTCL, emphasizing ECM remodeling and immune modulation as shared hallmarks. Hub genes such as <i>COL1A1</i>,<i> FN1</i>, and <i>CXCL12–CXCR4</i> may represent candidate molecular signatures that warrant validation in independent patient cohorts and functional studies before their clinical utility can be established.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-026-02041-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148917930","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":"Exploring the transcriptional crosstalk between adipose tissue and locoregional recurrence in breast cancer using independent component analysis","authors":"Marlous Arjaans,&nbsp;Bert van der Vegt,&nbsp;Renske Linstra,&nbsp;Rudolf S. N. Fehrmann,&nbsp;Arkajyoti Bhattacharya","doi":"10.1007/s10142-026-02012-w","DOIUrl":"10.1007/s10142-026-02012-w","url":null,"abstract":"<div><p>Locoregional recurrence (LRR) poses a persistent clinical challenge in breast cancer, with emerging evidence implicating the tumor-associated adipose tissue in modulating recurrence risk. This study investigates shared transcriptional programs between adipose tissue and breast tumors and examines their association with disease-free survival (DFS), particularly in the context of reconstructive surgery where adipose tissue from different body compartments are commonly used. We analyzed bulk gene expression data from 5,691 breast tumors and 978 human adipose tissue samples from different body compartments using consensus-independent component analysis (c-ICA) to identify transcriptional components (TCs). Gene set enrichment analysis (GSEA) and copy number alteration profiling were used for biological annotation. Associations between TCs and DFS were evaluated through univariate Cox regression. Key findings were validated using spatial transcriptomic and single-cell RNA sequencing datasets. Among the 411 TCs identified, 332 showed biological enrichment, and 35 were significantly associated with DFS. Four DFS-associated TCs (TC257, TC350, TC371, TC400) were enriched for adipogenesis-related genes and exhibited heightened activity in high-grade, triple-negative tumors and in patients with elevated BMI. Notably, TC350 was highly active in adipose tissue from common reconstructive donor sites (abdomen, omentum, subcutis) but not in native breast adipose tissue. Spatial transcriptomic and single-cell analyses confirmed the increased activity of these adipogenesis-related TCs in tumor regions and adipose cells. TC350 included <i>FABP4</i>, a gene previously linked to poor prognosis in breast cancer and considered as a potential new therapeutic target. Adipose tissue-derived transcriptional programs influence breast cancer prognosis and this seems to differ by tissue origin. These findings generate a hypothesis that donor site selection for adipose tissue in reconstructive surgery may impact LRR risk through adipogenesis-associated mechanisms. Further research is warranted to elucidate the biological and clinical implications of adipose–tumor transcriptional interactions.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-026-02012-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910498","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 truncated COL10A1 protein causes Schmid metaphyseal chondrodysplasia via protein downregulation and impairing α1 trimer formation and secretion","authors":"Zhe Sun,&nbsp;Yaqiong He,&nbsp;Ting Zhang,&nbsp;Yun Sun,&nbsp;Xiaobin Li,&nbsp;Guohua Yang,&nbsp;Shuo Zhang","doi":"10.1007/s10142-026-02044-2","DOIUrl":"10.1007/s10142-026-02044-2","url":null,"abstract":"<div><p>Schmid-type metaphyseal chondrodysplasia (SMCD) is primarily caused by mutations in the <i>COL10A1</i> gene. This study reports a novel frameshift mutation, c.1940dup (p.Asn647Lysfs*2), identified in a Chinese SMCD pedigree. The mutation did not alter messenger RNA levels but significantly reduced <i>COL10A1</i> protein expression. The mutant protein lacks the C-terminal 33 amino acids, resulting in a truncated polypeptide of 648 residues with a lower molecular weight than the wild-type protein. Degradation kinetics analysis showed no evidence of accelerated turnover. Notably, even under complete inhibition of degradation pathways, mutant protein expression remained substantially lower than that of wild-type, suggesting a potential defect in translational efficiency. Furthermore, the mutation severely disrupted the assembly of the characteristic collagen X trimer and led to markedly reduced extracellular secretion, as measured by accumulated protein levels in conditioned medium. These findings demonstrate that the c.1940dup mutation contributes to SMCD pathogenesis through coordinated mechanisms involving protein truncation, reduced expression, probable translational deficiency, and defective trimer formation and secretion, thereby revealing new potential therapeutic targets.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904822","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":"Age-associated chromatin repression of Hippo-Yap signaling drives oogonial stem cell decline in chicken","authors":"Jiahui Wei,&nbsp;Jin Wang,&nbsp;Hongcai Sun,&nbsp;Wenhui Wu,&nbsp;Qing Sun,&nbsp;Yuxiao Ma,&nbsp;Guiyu Zhu","doi":"10.1007/s10142-026-02038-0","DOIUrl":"10.1007/s10142-026-02038-0","url":null,"abstract":"<div><p>Oogonial stem cells (OSCs) are a type of reproductive germline stem cell present in the ovaries of adult animals after birth. They have been proposed to contribute to follicle renewal and could be associated with reproductive longevity, yet the molecular mechanism contribute to OSC malfunction during aging in chicken remain unclear. Here, we show that OSC number and proliferative capacity decline significantly from pre-laying to late-laying stages, accompanied by increased follicular atresia. RNA-seq analysis revealed a global reduction in transcriptional activity in aged OSCs. ChIP-seq demonstrated elevated H3K27me3 deposition, particularly at promoter regions, which correlated with repression of proliferation-related genes in the Hippo pathway including YAP1 and TEAD1. Pharmacological inhibition of H3K27me3 reduced repressive chromatin marks, restored Hippo pathway gene expression, and significantly enhanced OSC proliferation. Conversely, YAP1 knockdown attenuated proliferation-associated gene expression. These findings indicate that age-dependent H3K27me3 accumulation suppresses OSC proliferation through epigenetic repression of the Hippo–YAP axis, providing mechanistic insight into ovarian aging and a potential strategy to extend the laying cycle in poultry.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904835","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":"NFS1 activates PI3K/AKT/mTOR signaling to upregulate GPX4 expression and enhance ferroptosis resistance in osteosarcoma","authors":"Yu-Nan Man,&nbsp;Jing-Tang Li,&nbsp;Tao Zhang,&nbsp;Ying-peng Xu,&nbsp;Ya-yun Liu","doi":"10.1007/s10142-026-02040-6","DOIUrl":"10.1007/s10142-026-02040-6","url":null,"abstract":"<div><p>Osteosarcoma continues to exhibit poor survival outcomes due to chemoresistance and metastasis, with metabolic reprogramming and ferroptosis resistance being key features of tumor heterogeneity, yet their upstream regulators remain poorly defined. NFS1, a cysteine desulfurase essential for iron–sulfur cluster biogenesis, protects multiple cancers from ferroptosis, but its role in osteosarcoma is unknown. In this study, we performed a transcriptomic meta-analysis and found that NFS1 expression was significantly upregulated in osteosarcoma tissues, with further elevation in metastatic lesions, and high NFS1 expression correlated with poor overall survival. Genome‑wide CRISPR screening data revealed a marked NFS1 dependency in osteosarcoma cell lines. Functionally, NFS1 promoted cell proliferation, migration, and invasion, whereas its knockdown suppressed these phenotypes. Using single‑cell RNA sequencing data from 27 osteosarcoma specimens, we applied a multi‑algorithm glycolytic scoring framework and observed NFS1 enrichment in highly glycolytic malignant cells, along with an association with PI3K/AKT/mTOR pathway activation. Mechanistically, NFS1 selectively enhanced PI3K, AKT, and mTOR phosphorylation without altering total protein levels, and upregulated GPX4, a central ferroptosis suppressor, leading to elevated ferroptosis resistance scores in NFS1‑high malignant cells. Collectively, these findings identify a previously unrecognized NFS1–PI3K/AKT/mTOR–GPX4 regulatory axis in osteosarcoma, linking metabolic reprogramming to ferroptosis resistance, and suggest that NFS1 functions as an oncogenic driver, as well as a promising prognostic biomarker and therapeutic target in osteosarcoma.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13550047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904830","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":"Dynamic and non-additive gene regulation shapes maize responses to simultaneous salt and cold stress","authors":"Jinlei Han,&nbsp;Yan Dai,&nbsp;Chen Xu,&nbsp;Jialiang Zhou,&nbsp;Chenjia Xu,&nbsp;Kai Wang,&nbsp;Qi Chen","doi":"10.1007/s10142-026-02034-4","DOIUrl":"10.1007/s10142-026-02034-4","url":null,"abstract":"<div><p>Salt and cold stresses often occur together in nature and severely impact crop productivity, yet their transcriptional regulation remains poorly understood. Here, we conducted a time-series transcriptomic analysis of maize under salt, cold, and their combination at 0, 6, 12, and 24 h. Differential expression analysis revealed dynamic, condition-specific gene responses grouped into eight distinct temporal patterns. Promoter motif analysis of genes within each pattern identified 5–39 significantly enriched motifs, with over 40% lacking known counterparts, suggesting the involvement of previously uncharacterized cis-regulatory elements in stress-responsive transcriptional regulation. By comparing combined stress responses to the sum of single-stress effects, we found that about 74% of DEGs showed non-additive patterns, suggesting that combined stress triggers a distinct transcriptional program. Evolutionary analysis showed that additive DEGs tend to be more recently evolved, subject to weaker purifying selection, and enriched in transposed duplications, contrasting with the stronger constraint observed in non-additive DEGs. WGCNA identified 24 co-expression modules, among which 65 hub DEGs were detected in modules significantly correlated with specific stress conditions. Furthermore, we reconstructed 228, 20, and 200 sequential transcription factor cascades spanning 6 h, 12 h, and 24 h under cold, salt, and combined stress, respectively, with no cascade shared across all three conditions. Together, these results reveal that maize responses to combined salt and cold stress are largely non-additive and temporally dynamic, with distinct evolutionary patterns underlying different response types, offering insights and candidate regulators for enhancing crop stress resilience.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148896277","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":"Context-dependent effects of MIR100HG on tumorigenic phenotypes and p38/MAPK–AKT signaling in hepatocellular carcinoma","authors":"Esra Tokay,&nbsp;Sevin Avsar Koc,&nbsp;Aylin Turkoglu Dulger,&nbsp;Rümeysa Alacam,&nbsp;Nelin Hacioglu,&nbsp;Meltem Alper,&nbsp;Feray Kockar","doi":"10.1007/s10142-026-02033-5","DOIUrl":"10.1007/s10142-026-02033-5","url":null,"abstract":"<div><p>Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide and is characterized by a hypoxic tumor microenvironment that promotes tumor progression, cellular adaptation, and therapeutic resistance. Increasing evidence indicates that long non-coding RNAs (lncRNAs) play critical roles in regulating tumor-associated signaling networks; however, the contribution of MIR100HG to hepatocellular carcinoma progression, particularly under hypoxic conditions, remains insufficiently understood. In this study, we investigated the expression pattern and functional significance of MIR100HG in hepatocellular carcinoma using epithelial-like Hep3B and mesenchymal-like SNU-398 cells, together with non-tumor hepatocytes (Clone-9). Gain- and loss-of-function approaches were employed to evaluate the impact of MIR100HG on tumor-associated cellular phenotypes under both normoxic and hypoxic conditions. Functional assays demonstrated that MIR100HG overexpression significantly enhanced cell proliferation, clonogenic potential, migration, and invasion, whereas MIR100HG silencing markedly suppressed these tumorigenic properties and increased apoptotic cell death. Mechanistic analyses revealed that MIR100HG promotes oncogenic signaling through the p38/MAPK and AKT pathways under normoxic conditions, whereas MIR100HG depletion reduced the phosphorylation of these key signaling proteins. Notably, additional pathway analyses under hypoxia-mimicking conditions revealed a distinct signaling response, in which the MIR100HG-associated activation of p38/MAPK and AKT observed under normoxia was not maintained. Moreover, the expression patterns of AKT-associated regulatory genes, including GAS6 and PTEN, were reversed under hypoxia-mimicking conditions. These findings suggest that the effects of MIR100HG on oncogenic signaling are highly dependent on the cellular oxygenation context and that hypoxia reshapes the downstream signaling consequences of MIR100HG expression in HCC cells. Collectively, our findings identify MIR100HG as a hypoxia-associated oncogenic regulator that enhances tumorigenic phenotypes and promotes survival signaling in hepatocellular carcinoma. These results highlight MIR100HG as a potential biomarker and therapeutic target in liver cancer and provide new insights into the molecular mechanisms underlying hypoxia-driven tumor progression.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890582","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":"Comprehensive analysis of synonymous codon usage bias and evolutionary dynamics in the chloroplast genomes of eight Coptis species","authors":"Shuang Yang,&nbsp;Xiaolei Yu,&nbsp;Yu Chen","doi":"10.1007/s10142-026-02035-3","DOIUrl":"10.1007/s10142-026-02035-3","url":null,"abstract":"<div><p><i>Coptis</i> is a medically important genus renowned for producing valuable isoquinoline alkaloids. Although its chloroplast genomes encode key components for photosynthesis and plastid gene expression, the evolutionary constraints acting on their coding sequences and synonymous codon usage remain poorly resolved. Here, we combined a transparent taxon-level sampling strategy with comparative analyses of chloroplast CDSs from eight <i>Coptis</i> taxa. We quantified nucleotide composition, relative synonymous codon usage, effective number of codons, neutrality and PR2 patterns, and correspondence analysis, and then integrated these results with a core-CDS distance analysis and gene-wise pairwise dN/dS estimates. The chloroplast genomes showed a conserved AT-rich composition, especially at the third codon position (GC3 approximately 30.3–30.8%), with a consistent GC1 &gt; GC2 &gt; GC3 trend. Thirty preferred codons were detected, 28 ending in A/T, and eleven optimal codons were shared across the genus. The core-CDS distance analysis recovered a close relationship between <i>C. chinensis</i> and <i>C. chinensis var. brevisepala</i>, whereas most coding genes showed dN/dS values below one, consistent with pervasive purifying constraint. Across 48 consistently filtered CDSs, GC3s was negatively associated with mean dN (Spearman rho = -0.404, <i>P</i> = 0.00439) and CAI was positively associated with mean dN (rho = 0.303, <i>P</i> = 0.0361), whereas the remaining associations were not significant (all P &gt; = 0.0972). These results extend codon-usage analysis by linking synonymous-site composition to coding-sequence evolution within <i>Coptis</i>, while providing a hypothesis-generating resource for future plastid engineering studies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148896243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of STK35L1 as a potential prognostic biomarker in breast carcinoma, and its expression exhibits high correlation with EGFR activity","authors":"Saloni Bage,&nbsp;Arpana Yadav,&nbsp;Kritika Gaur,&nbsp;Kritika Gahlot,&nbsp;Mukul Purva,&nbsp;Mahesh Saini,&nbsp;Sunita Dadarwal,&nbsp;Pragya Gehlot,&nbsp;Sudhanshu Kumari,&nbsp;Shyam Bhutra,&nbsp;Devesh Madhukar Sawant,&nbsp;Daniela Brünnert,&nbsp;Neena Kasliwal,&nbsp;Pankaj Goyal","doi":"10.1007/s10142-026-02021-9","DOIUrl":"10.1007/s10142-026-02021-9","url":null,"abstract":"<div><p>Breast cancer (BC) is the second most prevalent malignancy after lung cancer, and the life expectancy is still very low due to therapeutic resistance and tumor relapse. It is crucial to identify novel biomarkers that can serve as potential therapeutic targets. In TNBC, aberrant activation of EGFR has also been implicated in the development of drug resistance. STK35L1 is a critical regulator of diverse cellular processes, including apoptosis and DNA damage. Notably, STK35L1 promotes drug resistance and regulates glycolysis and apoptosis through AKT signaling. The oncogenic role of STK35L1 is established in various cancers, including osteosarcoma, colorectal cancer, and acute myeloid leukemia. However, its association in BC has not yet been explored. In this study, we found that <i>STK35L1</i> was significantly upregulated in multiple cancers, and its higher expression was associated with poor survival outcomes in BC patients. <i>STK35L1</i> was differentially upregulated across all BC subtypes. An association between <i>EGFR</i> and <i>STK35L1</i> expression was observed in normal breast tissues but not in BC. Interestingly, compared with normal breast tissue, <i>EGFR</i> mRNA expression is downregulated in BC tissues, with the greatest downregulation in the luminal B subtype and the least in TNBC. Furthermore, EGFR inhibition with gefitinib increased STAT3 phosphorylation at Tyr-705, and <i>STK35L1</i> and <i>EGFR</i> gene expression were significantly upregulated. These data suggest that EGFR-STAT3 signaling may regulate <i>STK35L1</i> and <i>EGFR</i> expression. In conclusion, we report an association of STK35L1 and EGFR in BC, highlighting STK35L1 as a potential prognostic biomarker and therapeutic target.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890621","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":"Heterologous expression of DobHLH25 from Dendrobium officinale enhances drought tolerance in Arabidopsis","authors":"Qingxia Liu,&nbsp;Jian Wang,&nbsp;Yan Zhang,&nbsp;Rong Wang,&nbsp;Youya Liu,&nbsp;Jingzhong Chen,&nbsp;Bo Wang,&nbsp;Ningmei Chen,&nbsp;Qingwen Sun,&nbsp;Ronghui Gu,&nbsp;Yuan Huang","doi":"10.1007/s10142-026-02032-6","DOIUrl":"10.1007/s10142-026-02032-6","url":null,"abstract":"<div><p>Drought stress severely constrains the growth, yield, and accumulation of bioactive compounds in <i>Dendrobium officinale</i> (<i>D. officinale</i>), a valuable medicinal orchid, and this challenge is exacerbated under simulated wild cultivation where plants are inevitably exposed to recurring water deficits. Basic helix-loop-helix (bHLH) transcription factors are well-established regulators of plant abiotic stress responses. However, the molecular mechanisms by which bHLH transcription factors respond to drought stress in this species remain largely unknown. In this study, a bHLH transcription factor gene, <i>DobHLH25</i>, was cloned from <i>D. officinale</i>. Phylogenetic analysis revealed that <i>DobHLH25</i> shares the highest sequence identity with its ortholog in <i>Dendrobium nobile</i>. Additionally, subcellular localization analysis indicated that DobHLH25 is targeted to the nucleus and possesses a functional transcriptional activation domain. Expression pattern analysis showed that <i>DobHLH25</i> is most abundantly expressed in old leaves, and its expression in roots, stems, and leaves is induced by polyethylene glycol treatments. Heterologous expression of <i>DobHLH25</i> in <i>Arabidopsis thaliana</i> resulted in higher seed germination rates and longer root lengths under mannitol-induced osmotic stress compared to wild-type plants. Under drought stress, <i>DobHLH25</i> heterologous expression lines exhibited higher survival rates, reduced leaf water loss, lower malondialdehyde accumulation, and increased proline content. Moreover, the activities of antioxidant enzymes such as superoxide dismutase and peroxidase were significantly enhanced, and the expression levels of multiple drought-responsive genes were markedly upregulated. Collectively, these findings suggest a correlation between <i>DobHLH25</i> expression and plant drought tolerance, as evidenced by reduced oxidative damage, increased osmolyte accumulation, enhanced antioxidant enzyme activities, and upregulation of drought-responsive genes. Together, these results suggest that <i>DobHLH25</i> plays a positive role in drought tolerance, and provides a basis for future dissection of its regulatory network in <i>D. officinale</i>.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"26 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890614","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}