Omics A Journal of Integrative Biology最新文献

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Systems Biology of Mesial Temporal Lobe Epilepsy and Role of Iron-Related Gene Expression in Its Pathophysiology. 内侧颞叶癫痫的系统生物学及铁相关基因表达在其病理生理中的作用。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-03-01 Epub Date: 2026-02-04 DOI: 10.1177/15578100261419485
Divya Mundackal Sivaraman, Aisha Shaju, Geethu S Nair, Shabeesh Balan
{"title":"Systems Biology of Mesial Temporal Lobe Epilepsy and Role of Iron-Related Gene Expression in Its Pathophysiology.","authors":"Divya Mundackal Sivaraman, Aisha Shaju, Geethu S Nair, Shabeesh Balan","doi":"10.1177/15578100261419485","DOIUrl":"10.1177/15578100261419485","url":null,"abstract":"<p><p>Mesial temporal lobe epilepsy (MTLE) is the most common form of drug-resistant epilepsy in adults, yet its molecular pathogenesis remains elusive. While iron dysregulation has been implicated in MTLE, transcriptome-level regulation of iron-related genes in MTLE brain, including regional, subcellular, and pathology-specific patterns, remains largely unexplored. We analyzed publicly available nuclear and cytoplasmic RNA-sequencing data from hippocampal and cortical tissues of patients with MTLE with and without hippocampal sclerosis and controls. We identified differential expression among 562 curated iron-related genes, which constituted 1.46-2.95% of all differentially expressed genes across regions and compartments. These genes showed region- and compartment-specific expression profiles, with recurrent upregulation of <i>CH25H</i>, <i>TAL1</i>, <i>BTG2</i>, <i>TNF</i>, and <i>PTGIS</i> and consistent downregulation of <i>OGFOD3</i>. Protein-protein interaction and hub gene network analysis identified SLC40A1, CH25H, HBB, PTGIS, and CYP2C19 as central hubs linking iron transport, lipid metabolism, oxidative stress, and neuroprotection. Upstream regulatory analysis revealed enrichment of seizure-responsive immediate early genes (<i>EGR2</i>, <i>ATF3</i>, <i>JUN</i>) and neurogenic transcription factors (<i>NEUROD1</i>, <i>ASCL1</i>), with the former upregulated and the latter downregulated, indicating seizure-driven transcriptional reprogramming. Our analyses suggest potential regulatory links connecting iron homeostasis with apoptosis, osmotic balance, cholesterol metabolism, and pH/CO<sub>2</sub> buffering. Exploratory analysis showed a negative association between several iron-related genes, including <i>CYP26B1</i>, and seizure frequency in MTLE. Collectively, these findings reveal complex transcriptional programs governing iron dysregulation in MTLE. The results underscored coordinated regulation of inflammatory and metabolic pathways converging on iron homeostasis and neuronal stress responses in MTLE pathophysiology, providing a systems-level framework for potential prognosis and therapeutic targeting.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"177-190"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Systems Biology of Metabolic Dysregulation in Ankylosing Spondylitis Using scRNA-Seq Data. 使用scRNA-Seq数据研究强直性脊柱炎代谢失调的系统生物学。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-03-01 Epub Date: 2026-03-17 DOI: 10.1177/15578100261424002
Merve Yarıcı, Muhammed Erkan Karabekmez
{"title":"Systems Biology of Metabolic Dysregulation in Ankylosing Spondylitis Using scRNA-Seq Data.","authors":"Merve Yarıcı, Muhammed Erkan Karabekmez","doi":"10.1177/15578100261424002","DOIUrl":"10.1177/15578100261424002","url":null,"abstract":"<p><p>Ankylosing spondylitis (AS) is a prevalent autoimmune disorder that primarily affects the spinal joints, leading to chronic pain. Defining immune cell programs that contribute to AS is essential for the discovery of translational targets. Because immune function depends on metabolic state, we analyzed single-cell RNA sequencing data from peripheral blood mononuclear cells (PBMCs) of patients with AS and healthy controls (HCs), and constructed genome-scale metabolic models for each immune cell type to quantify differences in pathway activity and reaction fluxes between diseased and healthy conditions. Across datasets, AS showed consistent metabolic reprogramming, with increased flux through purine metabolism, fatty acid degradation, and glycolysis in CD14 monocytes and T cell subsets, including CD4 memory, CD4 naive, and CD8 T cells, indicating coordinated shifts in energy production and biosynthetic demand. To extend these findings, we constructed cell-type-specific protein-protein interaction networks and evaluated differential connectivity. We identified 63 rewired protein hubs across nine immune cell types. RPS11 emerged as a central hub linked to translation and prior evidence of AS pathogenesis. This integrative systems biology approach connects cell-type-specific metabolic alterations with rewired interaction hubs in an accessible clinical compartment, suggesting that PBMC-based multiomics signatures may support future biomarker development and therapeutic prioritization in autoimmune diseases.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":"30 3","pages":"146-157"},"PeriodicalIF":1.6,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147468935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Transcriptome-Based Machine Learning Models to Predict Antimicrobial Resistance in Pseudomonas aeruginosa. 基于转录组的机器学习模型预测铜绿假单胞菌抗菌素耐药性。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-02-01 Epub Date: 2025-12-30 DOI: 10.1177/15578100251408284
Ceyda Kula, Irem Erguven, Berkay Ozcelik, Gizem Gulfidan, Kazim Yalcin Arga
{"title":"Transcriptome-Based Machine Learning Models to Predict Antimicrobial Resistance in <i>Pseudomonas aeruginosa</i>.","authors":"Ceyda Kula, Irem Erguven, Berkay Ozcelik, Gizem Gulfidan, Kazim Yalcin Arga","doi":"10.1177/15578100251408284","DOIUrl":"10.1177/15578100251408284","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) is a growing threat in planetary health and demands innovative systems biology strategies for rapid and accurate detection of AMR and attendant resistance phenotypes. Chief among the AMR cases is <i>Pseudomonas aeruginosa</i> that exhibits remarkable genomic adaptability and contributes to multidrug resistance. This study aimed to evaluate the potential of transcriptome-based machine learning (ML) models to predict AMR in <i>P. aeruginosa</i> and attendant gene expression signatures. We integrated transcriptomic profiles of clinical isolates (<i>n</i> = 414) with ML algorithms to predict resistance to four antibiotics: ceftazidime, ciprofloxacin, meropenem, and tobramycin. ML models achieved high predictive accuracy, with the tobramycin model attaining 98.8% accuracy and 100% sensitivity. Each of the four antibiotics yielded distinct transcriptomic signatures enriched in pathways such as biofilm formation, membrane transport, virulence, and amino acid metabolism. Importantly, 10 gene signatures were identified across all four antibiotics, implicating them in core resistance mechanisms including oxidative stress response and iron acquisition. We further identified a core set of 10 mRNAs that are consistently deregulated in resistant isolates across all four drugs, pointing to a shared transcriptional program underpinning multidrug resistance. In conclusion, the transcriptome-based signatures reported herein (1) provide promising candidates for translational research toward development of mechanism-guided diagnostic assays for AMR in <i>P. aeruginosa</i>, and (2) attest to the potential of transcriptome-based ML models to predict AMR. Further studies and validation in independent cohorts are called for.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"94-104"},"PeriodicalIF":1.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145857105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Reproducible and Multi-Study Transcriptomic Integration with disint, Disease Integration and Clustering Toolkit, and Application to Drug Repositioning. 可重复和多研究转录组整合与分离,疾病整合和聚类工具包,并应用于药物重新定位。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-02-01 Epub Date: 2026-01-13 DOI: 10.1177/15578100251413812
Yi Cong, Naoki Osada, Toshinori Endo
{"title":"Reproducible and Multi-Study Transcriptomic Integration with <i>disint</i>, Disease Integration and Clustering Toolkit, and Application to Drug Repositioning.","authors":"Yi Cong, Naoki Osada, Toshinori Endo","doi":"10.1177/15578100251413812","DOIUrl":"https://doi.org/10.1177/15578100251413812","url":null,"abstract":"<p><p>Integrating Big Data, such as large-scale transcriptomic datasets across diseases, continues to be a major challenge. This is in part due to inconsistent preprocessing and the lack of a standardized, reproducible analytical framework. Existing pipelines often rely on manual parameter tuning and fragmented scripts, which limits cross-dataset comparability and downstream interpretability. We developed <i>disint</i> (disease integration and clustering toolkit), an open-source Python framework for standardized cross-dataset expression integration, embedding, and clustering. The pipeline implements housekeeping gene-based normalization, disease-specific log<sub>2</sub> fold-change computation, automated Uniform Manifold Approximation and Projection hyperparameter optimization, and adaptive K-means clustering. Building on its outputs, we further implemented a prototype downstream module, <i>disease reposition</i>, which extracts disease-specific gene signatures, evaluates their shared components, and explores potential drug repositioning candidates. The framework was validated on 28 transcriptomic datasets encompassing 34 disease categories and 386 samples, including 255 patient and 131 healthy control samples, covering 194,182 genes in total. These results highlight the reproducibility, scalability, and translational versatility of our proposed framework.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":"30 2","pages":"71-81"},"PeriodicalIF":1.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
A Comprehensive Analysis of Transcription Factor-microRNA Network in Six Different Major Cancers: Uncovering the Regulatory Backstages of Cancer. 六种主要癌症中转录因子- microrna网络的综合分析:揭示癌症的调控后台。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-02-01 Epub Date: 2026-01-07 DOI: 10.1177/15578100251408262
Krishnapriya Ramakrishnan, Vishal Ravi, Rajesh Raju, Debodipta Das, Niyas Rehman
{"title":"A Comprehensive Analysis of Transcription Factor-microRNA Network in Six Different Major Cancers: Uncovering the Regulatory Backstages of Cancer.","authors":"Krishnapriya Ramakrishnan, Vishal Ravi, Rajesh Raju, Debodipta Das, Niyas Rehman","doi":"10.1177/15578100251408262","DOIUrl":"https://doi.org/10.1177/15578100251408262","url":null,"abstract":"<p><p>Regulatory backstage of cancer involves complex multifactorial mechanisms. Among these, the posttranscriptional modulation between microRNA (miRNAs) and mRNAs is implicated as major regulatory mechanisms in different cancers. The tissue- and disease-specific regulation of miRNAs by transcription factors (TFs) further adds to the complexity of this system potentially impacting cancer pathogenesis. To uncover the major TFs impacting miRNA transcription in cancer, the differentially expressed miRNAs and mRNAs in six different cancer types, namely, liver hepatocellular carcinoma, lung adenocarcinoma, prostate adenocarcinoma, stomach adenocarcinoma, breast invasive carcinoma, and colon adenocarcinoma, were compiled from The Cancer Genome Atlas. Using bioinformatics approaches and the TransmiR database, we assembled the 374 TFs that transcriptionally regulate miRNAs through repression mechanisms, and the negatively correlating TF-miR pairs in each cancer type. Importantly, we found that <i>E2F1</i> and <i>EZH2</i>, primarily linked with cell proliferation and cell cycle regulation, are potential regulators of miRNA transcription in cancers. The comprehensive TF-miR pairs in each cancer type uncovered in this study represent the unique and shared constituents that could functionally affect the cancer pathology. Understanding the mechanisms that regulate miRNA transcription in different cancers could help understand the pathology of cancer from a novel perspective with shared TFs constitutive to multiple cancers. This may also open up new avenues for cancer therapeutic innovation, in which miRNA-based interventions might be able to target and be relevant to multiple cancers at once in the future.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":"30 2","pages":"120-130"},"PeriodicalIF":1.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Phosphorylation-Dependent Regulation and Interactions of the Neutral Amino Acid Transporter SLC6A15: Implications for Major Depression and Neuropsychiatric Disorders. 中性氨基酸转运体SLC6A15的磷酸化依赖性调控和相互作用:对重度抑郁症和神经精神疾病的影响。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-02-01 Epub Date: 2026-01-19 DOI: 10.1177/15578100251414655
Jaytha Thomas, Fathimathul Lubaba, Suhail Subair, Althaf Mahin, Athira Perunelly Gopalakrishnan, Prathik Basthikoppa Shivamurthy, Athira C Rajeev, Rajesh Raju
{"title":"Phosphorylation-Dependent Regulation and Interactions of the Neutral Amino Acid Transporter SLC6A15: Implications for Major Depression and Neuropsychiatric Disorders.","authors":"Jaytha Thomas, Fathimathul Lubaba, Suhail Subair, Althaf Mahin, Athira Perunelly Gopalakrishnan, Prathik Basthikoppa Shivamurthy, Athira C Rajeev, Rajesh Raju","doi":"10.1177/15578100251414655","DOIUrl":"https://doi.org/10.1177/15578100251414655","url":null,"abstract":"<p><p>SLC6A15, (sodium-dependent neutral amino acid transporter B(0)AT2), plays a crucial role in amino acid homeostasis and neuronal signaling, and it has been genetically and transcriptionally associated with major depressive disorder (MDD). However, the post-translational regulation of SLC6A15, particularly through phosphorylation, remains poorly understood. To address this knowledge gap, we report here curation of 3825 global phosphoproteomic datasets and layered statistical and bioinformatic analyses to uncover predominant phosphosites, co-phospho-regulated proteins, upstream kinases, and binary interactors of SLC6A15. Importantly, after stringent filtration, three sites, pS701, pS699, and pS687, were identified as the predominant sites of phosphorylation. Predicted upstream kinases included mitogen-activated protein kinase 3 (MAPK3) and cyclin-dependent kinase 12 (CDK12), suggesting regulatory control at these phosphorylation sites. Binary interactors such as tyrosine-protein kinase Lyn, epidermal growth factor receptor, and calnexin were found to have direct associations with stress-related pathways, indicating potential roles in stress-responsive signaling mechanisms. Pathway enrichment analysis of the high-confidence phosphosites in other proteins revealed significant enrichment of the ErbB signaling pathway, which is frequently dysregulated in MDD. Collectively, this study presents a comprehensive co-phospho-regulation-based catalog of SLC6A15, systematically mapping its key phosphorylation sites, regulatory kinases, and interaction partners. Identification of upstream kinases such as MAPK3 and CDK12 and enrichment of the ErbB signaling axis indicate a potential role of SLC6A15 in synaptic plasticity, neuronal signaling, and stress response mechanisms associated with depression. These findings uncover novel protein-protein relationships and phosphorylation-driven interactions, offering new insights into transporter regulation in neuropsychiatric disorders and potential therapeutic targets for MDD.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":"30 2","pages":"82-93"},"PeriodicalIF":1.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Phosphoregulation for Therapeutic Interventions in Cancer? Phosphoregulatory Map of Checkpoint Kinase 1 (CHK1) Uncovers Unexplored Regulatory Layers. 磷调控在癌症治疗干预中的作用?检查点激酶1 (CHK1)的磷酸化调控图谱揭示了未被探索的调控层。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-02-01 Epub Date: 2026-01-13 DOI: 10.1177/15578100251408291
Mejo George, Leona Dcunha, Levin John, Althaf Mahin, Diya Sanjeev, Athira Perunelly Gopalakrishnan, Mahammad Nisar, Prathik Basthikoppa Shivamurthy, Thottethodi Subrahmanya Keshava Prasad, Saptami Kanekar, Anoop Kumar G Velikkakath, Rajesh Raju
{"title":"Phosphoregulation for Therapeutic Interventions in Cancer? Phosphoregulatory Map of Checkpoint Kinase 1 (CHK1) Uncovers Unexplored Regulatory Layers.","authors":"Mejo George, Leona Dcunha, Levin John, Althaf Mahin, Diya Sanjeev, Athira Perunelly Gopalakrishnan, Mahammad Nisar, Prathik Basthikoppa Shivamurthy, Thottethodi Subrahmanya Keshava Prasad, Saptami Kanekar, Anoop Kumar G Velikkakath, Rajesh Raju","doi":"10.1177/15578100251408291","DOIUrl":"10.1177/15578100251408291","url":null,"abstract":"<p><p>Checkpoint kinase 1 (CHEK1/CHK1) is a serine/threonine kinase that is pivotal in maintaining genomic stability by regulating DNA replication, mitotic progression, and DNA damage response (DDR). Phosphorylation at distinct regulatory sites of CHK1 serves as a central signaling switch that tightly coordinates checkpoint control and DNA repair pathways. However, the broad phosphorylation network associated with the DNA repair pathway and CHK1 phosphorylation remains relatively underexplored, representing an untapped avenue with profound therapeutic potential. To bridge this discovery gap, we systematically analyzed global phosphoproteome datasets to visualize CHK1 phosphosites and their coregulated protein phosphosites, providing new insights into the functional networks governed by DDR signaling. The integrative analysis of 577 qualitative and 120 quantitative cellular phosphoproteomic datasets identified signatures of the CHK1 phosphorylation landscape. Our study visualized a strong co-occurrence of DDR-associated phosphosites in proteins, particularly with S280, and the Ataxia telangiectasia and Rad3-related protein-dependent S317 phosphosites in CHK1 located outside its kinase domain. Their coregulation analysis across CHK1 substrates, kinase regulators, and protein interactions uncovered connectivity between CHK1 phosphosites and DDR regulators. Collectively, our phosphosite-concordance approach reported here provides a regulatory map of CHK1 phosphorylation patterns, uncovering unexplored regulatory layers, and highlights new opportunities to explore mechanistic insights into CHK1 phosphoregulation as a target for therapeutic interventions in cancer.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"105-119"},"PeriodicalIF":1.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145857145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Immune-Suppressed, Not Immune-Cold: HMOX1-CD14-Immunoproteasome Axis and Structure-Guided Combination Pharmacotherapies in Isocitrate Dehydrogenase-Mutant Glioblastoma. 免疫抑制,非免疫冷:hmox1 - cd14 -免疫蛋白酶体轴和结构引导联合药物治疗异柠檬酸脱氢酶突变胶质母细胞瘤。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-01-01 Epub Date: 2025-12-24 DOI: 10.1177/15578100251408286
Sezin Gürkan Şali, Şeyma Çolakoğlu Özkaya, Betül Budak, Şükrü Güllüoğlu, Cevdet Nacar, Ömer Faruk Bayrak, Kazım Yalçın Arga, Ahmet İlter Güney
{"title":"Immune-Suppressed, Not Immune-Cold: HMOX1-CD14-Immunoproteasome Axis and Structure-Guided Combination Pharmacotherapies in Isocitrate Dehydrogenase-Mutant Glioblastoma.","authors":"Sezin Gürkan Şali, Şeyma Çolakoğlu Özkaya, Betül Budak, Şükrü Güllüoğlu, Cevdet Nacar, Ömer Faruk Bayrak, Kazım Yalçın Arga, Ahmet İlter Güney","doi":"10.1177/15578100251408286","DOIUrl":"10.1177/15578100251408286","url":null,"abstract":"<p><p>Glioblastoma (GBM) remains one of the most aggressive human malignancies, and its biological diversity is largely shaped by the isocitrate dehydrogenase (IDH) mutation status. Although apoptosis, autophagy, and ferroptosis have each been implicated in GBM pathophysiology, their coordinated regulation through the immunoproteasome (i-PSM) axis has not been systematically explored. Here, we integrated transcriptomic datasets from The Cancer Genome Atlas and The Chinese Glioma Genome Atlas with immune deconvolution and network analyses to map the IDH-specific crosstalk between i-PSM components and cell death programs. We identified a nine-gene signature (i.e., <i>CD14, HMOX1, CTSB, CTSS, RRAS, BAK1, FTH1, PRKCD,</i> and <i>CYBB</i>) that captures IDH-dependent immune and metabolic divergence. IDH-mutant (IDHmt) astrocytomas exhibited coordinated upregulation of <i>HMOX1</i> and <i>CD14</i>, suggesting an actively maintained, immunosuppressive niche rather than a merely \"immune-cold\" state. Receiver operating characteristic analyses demonstrated strong discrimination of IDH status (area under the curve ≥ 0.92 for key genes), whereas structure-guided docking nominated rational, multipathway combinations such as temozolomide + bortezomib, luteolin, or lovastatin. Collectively, this integrative omics approach reframes IDHmt GBM as a redox- and myeloid-driven suppressive ecosystem and provides a systems-level rationale for personalized, IDH-informed therapeutic strategies.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"19-34"},"PeriodicalIF":1.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145863278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Can We Develop Glioma Subtype-Specific Precision Medicines? An Integrative Machine Learning Pipeline for Biomarker Discovery and Drug Repurposing for Glioblastoma and Low-Grade Glioma. 我们能开发针对胶质瘤亚型的精准药物吗?用于胶质母细胞瘤和低级别胶质瘤生物标志物发现和药物再利用的综合机器学习管道。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-01-01 Epub Date: 2025-12-24 DOI: 10.1177/15578100251408278
Semra Melis Soyer, Elif Bengu Kizilay, Pemra Ozbek, Ceyda Kasavi
{"title":"Can We Develop Glioma Subtype-Specific Precision Medicines? An Integrative Machine Learning Pipeline for Biomarker Discovery and Drug Repurposing for Glioblastoma and Low-Grade Glioma.","authors":"Semra Melis Soyer, Elif Bengu Kizilay, Pemra Ozbek, Ceyda Kasavi","doi":"10.1177/15578100251408278","DOIUrl":"10.1177/15578100251408278","url":null,"abstract":"<p><p>Glioma remains a major clinical challenge due to its molecular heterogeneity and limited therapeutic options. While numerous biomarker and drug discovery efforts exist, most are restricted by small sample sizes, subtype-agnostic analyses, or limited integration of computational strategies. Here, we present an integrative machine learning-based systems pipeline for the identification of subtype-specific biomarkers and repurposed therapeutics for glioblastoma (GBM) and low-grade glioma (LGG). We report high-confidence, subtype-specific biomarker candidates by harnessing publicly available gene expression datasets and systematic analyses with oversampling strategies to balance class distributions, followed by feature selection algorithms. Specifically, 10 candidate genes with strong diagnostic potential were identified, including <i>RAB11FIP4</i>, <i>TYRO3</i>, <i>THEM5</i>, <i>SST</i>, <i>SMIM32</i>, <i>MIGA1</i>, <i>ARFGEF3</i>, and <i>ANK3</i> for GBM and <i>GUCA1A</i> and <i>CES4A</i> for LGG. Repurposed drug candidates were then predicted via signature-based prioritization and evaluated using molecular docking simulations, revealing six promising compounds for GBM (vandetanib, capecitabine, melatonin, agomelatine, ramelteon, and tasimelteon) and one for LGG (ambroxol). This study demonstrates the utility of combining class-balancing, feature selection, and drug repurposing pipelines to uncover clinically relevant glioma biomarkers and therapeutic candidates, thus providing a computational foundation for future experimental and translational validation in these brain cancers and neuro-oncology.</p>","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"43-55"},"PeriodicalIF":1.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145864511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Together, Shaping the Future: Our Collective Journey in Omics, Integrative Biology, AI, and the Future of Medicine. 共同塑造未来:我们在组学、综合生物学、人工智能和医学未来方面的集体旅程。
IF 1.6 3区 生物学
Omics A Journal of Integrative Biology Pub Date : 2026-01-01 Epub Date: 2025-12-16 DOI: 10.1177/15578100251408246
Biaoyang Lin
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