Molecular omics最新文献_第3页

A practical guide to experimental design and power analysis for metaproteomics studies. b宏蛋白质组学研究的实验设计和功率分析实用指南。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-03-06 DOI: 10.1093/molecular-omics/aaiag014

Luman Wang, Qianyi Zhou, Yutong Li, Feng Sun, Xin Zhou, Leyuan Li

{"title":"A practical guide to experimental design and power analysis for metaproteomics studies.","authors":"Luman Wang, Qianyi Zhou, Yutong Li, Feng Sun, Xin Zhou, Leyuan Li","doi":"10.1093/molecular-omics/aaiag014","DOIUrl":"10.1093/molecular-omics/aaiag014","url":null,"abstract":"Metaproteomics is an effective tool for characterizing the functional profiles of microbial communities by directly identifying and quantifying abundances. However, prospective power analysis and sample-size estimation are often overlooked at the study design stage in metaproteomics, which can result in underpowered experiments and reduced ability to detect biologically meaningful effects. In this study, we present a practical, end-to-end workflow for conducting power analysis prior to data collection. We focus on three common experimental designs: between-group comparisons, parallelized perturbation experiments, and beta diversity analyses. To tailored these experimental designs, we consider three major statistical approaches for power estimation: parametric tests (e.g. t-test, ANOVA), non-parametric tests (e.g. Wilcoxon rank-sum test, Kruskal-Wallis test), and distance-based multivariate methods (e.g. PERMANOVA using Bray-Curtis). By presenting detailed case studies, we provide practical guidance on how to calculate effect sizes, generate simulated datasets, and estimate statistical power across varying sample sizes. We also supply corresponding visualizations for each scenario to support sample-size determination and power assessment. This framework is intended to help researchers optimize sample size, improve experimental efficiency, and reduce costs, thereby enabling more reliable and interpretable biological insights from metaproteomic studies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147504345","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

You are what you degrade: tracking the cellular fates of the proteasomal degradome. 你就是你所降解的：跟踪蛋白酶体降解的细胞命运。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/momics/aaiaf002

Duno S Dantis, Darci J Trader

{"title":"You are what you degrade: tracking the cellular fates of the proteasomal degradome.","authors":"Duno S Dantis, Darci J Trader","doi":"10.1093/momics/aaiaf002","DOIUrl":"10.1093/momics/aaiaf002","url":null,"abstract":"The ubiquitin-proteasome system (UPS) is the primary protein degradation machinery in eukaryotic cells, composed of multiple proteasome isoforms. It plays critical roles in cellular proliferation, metabolism, immune regulation, oxidative stress, and aging, making it a long-standing focus of biological and therapeutic research. Recently, the UPS has been harnessed for the targeted degradation of disease-relevant proteins using proximity-inducing agents such as proteolysis-targeting chimeras and molecular glue degraders, which have transformed our understanding of druggability. Despite these advances, major gaps remain, particularly in understanding the proteasome's functional heterogeneity across biological contexts. Traditional research emphasizes proteasome structure, subunit function, and substrate features to guide chemical tool and therapeutic development. However, an often-overlooked aspect is the proteasomal degradome, the repertoire of peptide fragments generated during protein degradation. These peptides can exhibit biological activities distinct from their parent proteins, and pathogens, including viruses, have evolved mechanisms to block their production to evade immune detection. Thus, degradome characterization is essential to fully appreciate the proteasome's role in shaping cellular phenotypes in both healthy and diseased states. This review highlights recent studies exploring the degradome, with particular attention to -omic technologies applied to profile and interrogate these peptide products. By focusing on degradation outcomes rather than only the machinery, we aim to underscore the importance of tracing proteasome-derived peptides and their biological consequences. Ultimately, this perspective will broaden our understanding of the UPS while suggesting new avenues for therapeutic exploitation beyond current strategies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201898","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

Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation. 放大到重排基因组：应用细胞学，基因组学和转录组学方法的管道结构变异解释。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/molecular-omics/aaiag006

Maria Gridina, Timofey Lagunov, Polina Belokopytova, Nikita Torgunakov, Artem Nurislamov, Darya A Yurchenko, Zhanna G Markova, Tatiana V Markova, Yana Stepanchuk, Galina Koksharova, Pavel Orlov, Anna Subbotovskaia, Oxana Ryzhkova, Nadezhda V Shilova, Veniamin Fishman

{"title":"Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation.","authors":"Maria Gridina, Timofey Lagunov, Polina Belokopytova, Nikita Torgunakov, Artem Nurislamov, Darya A Yurchenko, Zhanna G Markova, Tatiana V Markova, Yana Stepanchuk, Galina Koksharova, Pavel Orlov, Anna Subbotovskaia, Oxana Ryzhkova, Nadezhda V Shilova, Veniamin Fishman","doi":"10.1093/molecular-omics/aaiag006","DOIUrl":"10.1093/molecular-omics/aaiag006","url":null,"abstract":"Recent advances in genomic technologies have greatly enhanced our understanding of genotype-phenotype relationships and improved the diagnosis of genetic diseases. However, the dissection of complex structural variants (SVs) remains challenging due to the limitations of current methods in resolving their breakpoints and interpreting phenotypes involving multiple disrupted genes. In this study, we demonstrate how an integrative approach-combining molecular cytogenetic, genomic, and transcriptomic methods-enables the detection and structural and functional characterization of complex SVs affecting the MBD5, USP34, and XPO1 genes. Our findings underscore the utility of the Exo-C, a modified chromosome conformation capture technique in resolving complex rearrangements. We also report, for the first time, a composite neurodevelopmental phenotype resulting from the combined effects of MBD5-associated intellectual disability and 2p15p16.1 microdeletion syndromes.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142985","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

A mass spectrometry-based approach identifies a putative plasma protein biomarker signature for early diabetic kidney disease diagnosis. 一种基于质谱的方法确定了早期糖尿病肾病诊断的推定血浆蛋白生物标志物。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/molecular-omics/aaiag003

Sumaiya Nazli, Kip Zimmerman, Zeeshan Hamid, Arisbeth Camarillo Reyes, Katharyn Wallis, Avinash Jadhav, Abhijit Mallick, Tiffany Chambers, Heather A Newman, Lei Cao, Shaymaa M Abousaad, Christine Adhiambo, Elimelda M Ongeri, Robert H Newman, Michael Olivier

{"title":"A mass spectrometry-based approach identifies a putative plasma protein biomarker signature for early diabetic kidney disease diagnosis.","authors":"Sumaiya Nazli, Kip Zimmerman, Zeeshan Hamid, Arisbeth Camarillo Reyes, Katharyn Wallis, Avinash Jadhav, Abhijit Mallick, Tiffany Chambers, Heather A Newman, Lei Cao, Shaymaa M Abousaad, Christine Adhiambo, Elimelda M Ongeri, Robert H Newman, Michael Olivier","doi":"10.1093/molecular-omics/aaiag003","DOIUrl":"10.1093/molecular-omics/aaiag003","url":null,"abstract":"Diabetic kidney disease (DKD) is the leading cause of kidney failure among diabetic patients. At the time of clinical diagnosis, kidney function has already significantly deteriorated, limiting treatment options. We developed a novel approach using tandem mass tags (TMT) labelling to identify kidney proteins in plasma samples and putative protein biomarker signatures that distinguish patients with DKD or reduced kidney function from control individuals. Plasma samples from 28 patients from the NC A&T Men's Minority Health Initiative Cohort included 7 healthy controls, 7 patients with diabetes and microalbuminuria (DM), and 2 patients with DKD. In addition, our sample set included 12 individuals with DM but no detectable microalbuminuria. Plasma samples were depleted, and analysed using TMT labelling with kidney lysate as a reference sample to identify potentially kidney-derived proteins in plasma that could indicate early kidney cell damage and protein leakage. A total of 424 proteins were identified in the plasma samples. Of these, the Human Protein Atlas labels 375 as proteins expressed in the kidney and 4 proteins as kidney-enriched. We identified 13 proteins whose abundance levels were different between patients with kidney injury and controls (P < .05). Using sparse partial least squares discriminant analysis, we identified a biomarker signature of four plasma proteins that confidently distinguish samples from individuals with kidney injury and control individuals. Interestingly, samples from DM patients without any detectable kidney dysfunction align between the controls and individuals with kidney damage, suggesting that some of these individuals are more similar in their biomarker signature to DKD patients and may be progressing to microalbuminuria.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125921","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

Paxillin mediates endothelial cell migration and angiogenesis following spinal cord injury: a transcriptomic and functional analysis. 帕罗西林介导脊髓损伤后内皮细胞迁移和血管生成：转录组学和功能分析。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-22 DOI: 10.1093/momics/aaiaf001

Manjeet Chopra, Jaidev Sharma, Aditya A Singh, Zarna Pathak, Priyanka Patel Vats, Vibhor Kumar, Amit Mandoli, Hemant Kumar

{"title":"Paxillin mediates endothelial cell migration and angiogenesis following spinal cord injury: a transcriptomic and functional analysis.","authors":"Manjeet Chopra, Jaidev Sharma, Aditya A Singh, Zarna Pathak, Priyanka Patel Vats, Vibhor Kumar, Amit Mandoli, Hemant Kumar","doi":"10.1093/momics/aaiaf001","DOIUrl":"10.1093/momics/aaiaf001","url":null,"abstract":"Spinal cord injury (SCI) is a destructive neurological condition that leads to significant functional deficits in the affected individual. To map the altered pathways within the lesion epicentre and the surrounding rostrocaudal segments, we performed RNA-sequencing on injured spinal cord tissue. Samples were collected from three regions-rostral, epicentre, and caudal-at Days 1, 14, and 28 post-injury to systematically profile the transcriptomic changes and identify pathways associated with angiogenesis following SCI. Gene set enrichment analysis revealed enriched pathways, including hepatocyte growth factor (HGF) receptor and alpha 6 beta 4 integrin signalling, indicating an active angiogenic response. The involvement of HGF receptor signalling was further validated by quantitative polymerase chain reaction (qPCR), confirming its role in pathological remodelling after SCI. Subsequently, we identified paxillin (Pxn) as a candidate gene that promotes endothelial cell migration via HGF receptor signalling. Immunohistochemistry demonstrated the role of Pxn in mediating endothelial cell migration and proliferation post-SCI. In summary, our findings indicate that Pxn is a key mediator of endothelial cell proliferation and migration in response to angiogenic factors, such as HGF, following SCI. However, further mechanistic studies are required to fully establish the role of Pxn in endothelial cell migration and proliferation after SCI.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201796","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

Identification of metabolomic signatures of diabetic kidney disease in urine and plasma using untargeted gas chromatography-mass spectrometry. 使用非靶向气相色谱-质谱法鉴定尿和血浆中糖尿病肾病的代谢组学特征。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-16 DOI: 10.1093/molecular-omics/aaiag001

Benlian Wang, Emilia Marin Quintero, Margaret Sojka, Katharyn Wallis, Danu Perumalla, Arisbeth Camarillo Reyes, Elimelda M Ongeri, Robert H Newman, Kip Zimmerman, Michael Olivier

{"title":"Identification of metabolomic signatures of diabetic kidney disease in urine and plasma using untargeted gas chromatography-mass spectrometry.","authors":"Benlian Wang, Emilia Marin Quintero, Margaret Sojka, Katharyn Wallis, Danu Perumalla, Arisbeth Camarillo Reyes, Elimelda M Ongeri, Robert H Newman, Kip Zimmerman, Michael Olivier","doi":"10.1093/molecular-omics/aaiag001","DOIUrl":"10.1093/molecular-omics/aaiag001","url":null,"abstract":"Diabetic kidney disease (DKD) is a complication of diabetes and the leading cause of kidney failure among diabetic patients. Unfortunately, it is typically diagnosed after normal kidney function is already significantly impaired. We used gas chromatography-mass spectrometry (GC-MS) of urine and plasma to explore whether metabolites can serve as potential biomarkers for the early diagnosis of DKD. Urine and plasma samples were obtained from 41 individuals [11 healthy controls, 20 patients with diabetes (diabetes mellitus or DM) and microalbuminuria, 10 patients with DKD]. A total of 342 metabolites were identified in urine samples and 252 metabolites were identified in plasma samples, with 182 metabolites overlapping between the two sample types. Among these, 58 metabolites from urine and 22 metabolites from plasma showed suggestive evidence (P-value < .05) of differences between samples from patients with DKD and samples from healthy control individuals. Sparse partial least squares discriminant analysis (sPLS-DA) was applied to identify metabolomics profiles (in urine, plasma, or both) that maximize separation between DKD patients and controls. A set of four metabolites in plasma, including tyrosine and threo-hydroxyaspartic acid, shows promise as an early-stage biomarker signature that will need to be validated in a larger study. Using this set of metabolites, we estimated the probability of DKD for each of the DM patients, based on their metabolomic profiles, and found a significant correlation with DM designation (low, medium, and high) and estimated glomerular filtration rate. Further validation in larger cohorts is needed to confirm their clinical utility and the ability to predict individuals at risk for DKD.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146202278","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

Integrative transcriptomics and metabolomics reveal distinct metabolic reprogramming in luminal and triple-negative breast cancer cells. 整合转录组学和代谢组学揭示了乳腺细胞和三阴性乳腺癌细胞中不同的代谢重编程。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-16 DOI: 10.1093/momics/aaiaf003

Preeti Ranawade, Babasaheb Sonwane, Ganesh Bose, Revati Jadhav, Rakesh Joshi, Smriti Mittal

{"title":"Integrative transcriptomics and metabolomics reveal distinct metabolic reprogramming in luminal and triple-negative breast cancer cells.","authors":"Preeti Ranawade, Babasaheb Sonwane, Ganesh Bose, Revati Jadhav, Rakesh Joshi, Smriti Mittal","doi":"10.1093/momics/aaiaf003","DOIUrl":"10.1093/momics/aaiaf003","url":null,"abstract":"Breast cancer subtypes exhibit significant molecular and metabolic heterogeneity, influencing their aggressiveness and therapeutic responses. Among them, triple-negative breast cancer (TNBC) is highly aggressive and often resistant to conventional therapies. To investigate the metabolic programming of this aggressiveness, we conducted an integrated transcriptomics and metabolomics analysis comparing the MCF-7 (luminal A, ER+/PR+) and MDA-MB-231 (TNBC) breast cancer cell lines. Transcriptome analysis of MCF-7 and MDA-MB-231 revealed the differential expression of genes involved in key metabolic pathways. Metabolomics data, further corroborated by transcriptomics, suggest pathway enrichment in beta-alanine, histidine, glutathione, nucleotide metabolism, and the tricarboxylic acid cycle. MDA-MB-231 cells displayed a metabolically aggressive phenotype with enhanced oxidative phosphorylation, redox adaptation, and nucleotide turnover. In contrast, MCF-7 cells showed a more regulated amino acid and redox metabolism profile. The integration of transcriptomic and metabolite profiles highlighted potential metabolic vulnerabilities in TNBC, offering insights into subtype-specific differences at the molecular level.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146202249","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

Urine metabolomics for seronegative rheumatoid arthritis: an exploratory dual-platform analysis. 血清阴性类风湿性关节炎的尿液代谢组学：一项探索性双平台分析。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-16 DOI: 10.1093/momics/aaiaf004

Koteswari Peddi, Satyanarayana Swamy Cheekatla, Usharajeswari Davulury, Prathyash Ushus M J, Satish Mutyam, Siva Kumar Kandula, Vishnu Vardhan Reddy Munagala, Sivakumar Vallabhapurapu

{"title":"Urine metabolomics for seronegative rheumatoid arthritis: an exploratory dual-platform analysis.","authors":"Koteswari Peddi, Satyanarayana Swamy Cheekatla, Usharajeswari Davulury, Prathyash Ushus M J, Satish Mutyam, Siva Kumar Kandula, Vishnu Vardhan Reddy Munagala, Sivakumar Vallabhapurapu","doi":"10.1093/momics/aaiaf004","DOIUrl":"10.1093/momics/aaiaf004","url":null,"abstract":"Seronegative rheumatoid arthritis (negRA) is difficult to diagnose due to the absence of rheumatoid factor and anticitrullinated peptide antibodies. This observational case-control study analysed urine samples from 35 negRA patients and 25 healthy controls using integrated liquid chromatography-quadrupole time-of-flight mass spectrometry and gas chromatography-mass spectrometry. Data were processed using mass spectrometry-data independent analysis and evaluated with multivariate approaches, including orthogonal partial least squares discriminant analysis and receiver operating characteristic curve analysis. We identified distinct urinary metabolic alterations in negRA, with four metabolites showing moderate-to-excellent diagnostic accuracy (area under the curve: 0.78-0.91). Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes indicated the involvement of redox regulation and nucleotide/cofactor metabolism. These findings support the potential of urine metabolomics as a non-invasive tool for biomarker discovery in negRA and warrant validation in larger cohorts.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146201756","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

Development of an immobilized system for RNA modification analysis. 用于RNA修饰分析的固定化系统的研制。

IF 2.4 4区生物学

Molecular omics Pub Date : 2026-01-10 DOI: 10.1093/momics/aaiaf005

Zhiyan Li, Luyao Yu, Xingyu Liu, Liangle Deng, Zongtao Lin, Zhuocheng Liu, Benjamin A Garcia, Yixuan Xie

{"title":"Development of an immobilized system for RNA modification analysis.","authors":"Zhiyan Li, Luyao Yu, Xingyu Liu, Liangle Deng, Zongtao Lin, Zhuocheng Liu, Benjamin A Garcia, Yixuan Xie","doi":"10.1093/momics/aaiaf005","DOIUrl":"10.1093/momics/aaiaf005","url":null,"abstract":"Characterizing RNA modifications is crucial for understanding fundamental biological processes, such as RNA folding, stability, translation, and splicing. However, current systems for ribonucleoside sample preparation are limited to the solution phase. In this study, we employed the click reaction between methyltetrazine and trans-cyclooctene to immobilize RNases, including nuclease P1, phosphodiesterase I, and shrimp alkaline phosphatase, on agarose beads. Using this digestion method, RNA was fully converted to ribonucleosides within 30 min. Importantly, integrating these immobilized RNases with a microspin tube modified with porous graphitic carbon enabled direct downstream MS analysis, constituting a streamlined system. We applied this system to monitor RNA modification dynamics during transforming growth factor-β (TGF-β)-induced epithelial-mesenchymal transition in lung cancer cells and observed significant changes in several RNA modifications (e.g. m6A and m5U), which is consistent with the indispensable role of RNA modifications in tumour metastasis. Overall, our results demonstrate the efficiency and robustness of our method and highlight a promising direction for RNA modification analysis, supporting the development of automated, high-throughput workflows for future large-cohort studies.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":"22 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12851623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146202198","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}

引用次数: 0

STUB1 (CHIP) – a prognostic marker in cancer 肿瘤预后标志物STUB1 （CHIP）

IF 2.4 4区生物学

Molecular omics Pub Date : 2025-11-19 DOI: 10.1039/D5MO00205B

Subhajit Karmakar, Mouli Chatterjee, Malini Basu and Mrinal K Ghosh

{"title":"STUB1 (CHIP) – a prognostic marker in cancer","authors":"Subhajit Karmakar, Mouli Chatterjee, Malini Basu and Mrinal K Ghosh","doi":"10.1039/D5MO00205B","DOIUrl":"10.1039/D5MO00205B","url":null,"abstract":" STUB1, also known as CHIP (C-terminus of Hsc70-Interacting Protein), plays a vital role in cellular protein homeostasis through its E3 ubiquitin ligase activity. Recent evidence suggests that STUB1 (CHIP) is implicated in various cancer types, influencing tumorigenesis by regulating the degradation of oncogenic and tumor suppressor proteins, viz., c-Myc, PTEN, p53 etc. This study investigates the prognostic value of STUB1 across multiple cancers through a comprehensive pan-cancer analysis utilizing large public databases, including The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) and further validation of results in multiple cancer cell lines. Our analysis reveals distinct expression patterns of STUB1 (CHIP) across different cancer types and highlights its correlation with clinical outcomes. In certain cancers, high STUB1 (CHIP) expression is associated with worse prognosis, likely due to its role in degrading tumor suppressor proteins. Conversely, in other cancer types, low STUB1 (CHIP) expression correlates with poor survival, possibly due to impaired degradation of oncogenic factors. The study provides crucial insights into the dual roles of STUB1 (CHIP) in several cancer types, establishing it as a potential prognostic marker. Our investigation into the contextual role of STUB1 (CHIP) within human tissue samples, employing immunoblotting and complementary assays, highlights its potential as a therapeutic target for restoring protein homeostasis and modulating cancer progression. Nonetheless, further research is necessary to comprehensively elucidate the mechanisms by which STUB1 (CHIP) regulates tumorigenesis across various cancer types.","PeriodicalId":19065,"journal":{"name":"Molecular omics","volume":" 6","pages":" 768-793"},"PeriodicalIF":2.4,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145549942","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