MRNA profiling in rectus abdominis muscle from patients with upper GI cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE18832 | GEO | 2010/01/19
SECONDARY ACCESSION(S): PRJNA121169
REPOSITORIES: GEO
Similar Datasets
Project description:Rectus abdominis muscle biopsies were obtained from 65 upper gastrointestinal (UGI) cancer patients during open surgery and RNA profiling was performed on a subset of this cohort (n=21) using the Affymetrix U133+2 platform with the aim of identifying biomarkers of cancer related muscle wasting. N = 21 (18 UGI cancer; 3 non cancer surgery)
2010-05-15 | E-GEOD-18832 | biostudies-arrayexpress
Project description:Skeletal muscle wasting is a devastating consequence of cancer that may be responsible for nearly 30% of cancer-related deaths. In addition to muscle atrophy, we have identified significant muscle fiber damage and replacement of muscle with fibrotic tissue in rectus abdominis muscle biopsies from cachectic pancreatic ductal adenocarcinoma (PDAC) patients that associates with poor survival. Transcriptional profiling of muscle harvested from these same patients supported these findings by identifying gene clusters related to wounding, inflammation and cellular response to TGF-B upregulated in cachectic PDAC patients compared with non-cancer controls. In this dataset, we include the expression data obtained from rectus abdominis muscle biopsies fron non-cancer controls patients undergoing abdominal surgery for benign reasons and from PDAC patients undergoing tumor-resection surgery. PDAC patients were further classified as non-cachectic or cachectic. Cachexia was defined as a body weight loss of >5% during the 6 months prior to surgery. The purpose of this study was to identify the broader transcriptional networks changed in cachectic PDAC patients versus non-cancer controls, that may be associated with the histological changes observed in muscle biopsies harvested from these same patients.
2019-12-03 | GSE130563 | GEO
Project description:mRNA profiling in rectus abdominis muscle from patients with upper GI cancer
| PRJNA121169 | ENA
Project description:Cancer-associated muscle wasting associates with poor clinical outcomes1, but its underlying biology is largely uncharted in humans2. Unbiased RNAome analysis (coding and non-coding RNAs) with unsupervised clustering using Integrative Non-negative Matrix Factorization (intNMF)3 provides an avenue to identify distinct molecular subtypes, here applied to muscle of patients with colorectal or pancreatic cancer. Rectus abdominis biopsies from 84 patients was profiled using high-throughput next generation sequencing. Here we show that intNMF with stringent quality metrics of clustering identifies 2 highly coherent molecular subtypes within muscle of patients with cancer. Patients in Subtype 1 (vs Subtype 2) showed clinical manifestations of cachexia: high-grade weight loss, low muscle mass, atrophy of Type IIA and Type IIX muscle fibres and reduced survival. Based on differential expression between the subtypes, our results indicate biological processes that may contribute to cancer-associated loss of muscle mass and function, including altered post-transcriptional regulation, and perturbation of neuronal systems, cytokine storm/cellular immune response, extracellular matrix, and metabolic abnormalities spanning xenobiotic metabolism, hemostasis, signal transduction, embryonic/pluripotent stem cells, and amino acid metabolism. Differential expression between subtypes indicates involvement of multiple, intertwined higher-order gene regulatory networks, suggesting potential for interacting (hub)lncRNA-miRNA-mRNA interaction networks as targets for future research.
2025-07-17 | GSE254878 | GEO
Project description:Cancer-associated muscle wasting associates with poor clinical outcomes1, but its underlying biology is largely uncharted in humans2. Unbiased RNAome analysis (coding and non-coding RNAs) with unsupervised clustering using Integrative Non-negative Matrix Factorization (intNMF)3 provides an avenue to identify distinct molecular subtypes, here applied to muscle of patients with colorectal or pancreatic cancer. Rectus abdominis biopsies from 84 patients was profiled using high-throughput next generation sequencing. Here we show that intNMF with stringent quality metrics of clustering identifies 2 highly coherent molecular subtypes within muscle of patients with cancer. Patients in Subtype 1 (vs Subtype 2) showed clinical manifestations of cachexia: high-grade weight loss, low muscle mass, atrophy of Type IIA and Type IIX muscle fibres and reduced survival. Based on differential expression between the subtypes, our results indicate biological processes that may contribute to cancer-associated loss of muscle mass and function, including altered post-transcriptional regulation, and perturbation of neuronal systems, cytokine storm/cellular immune response, extracellular matrix, and metabolic abnormalities spanning xenobiotic metabolism, hemostasis, signal transduction, embryonic/pluripotent stem cells, and amino acid metabolism. Differential expression between subtypes indicates involvement of multiple, intertwined higher-order gene regulatory networks, suggesting potential for interacting (hub)lncRNA-miRNA-mRNA interaction networks as targets for future research.
2025-07-17 | GSE254877 | GEO
Project description:Cancer-associated muscle wasting associates with poor clinical outcomes1, but its underlying biology is largely uncharted in humans2. Unbiased RNAome analysis (coding and non-coding RNAs) with unsupervised clustering using Integrative Non-negative Matrix Factorization (intNMF)3 provides an avenue to identify distinct molecular subtypes, here applied to muscle of patients with colorectal or pancreatic cancer. Rectus abdominis biopsies from 84 patients was profiled using high-throughput next generation sequencing. Here we show that intNMF with stringent quality metrics of clustering identifies 2 highly coherent molecular subtypes within muscle of patients with cancer. Patients in Subtype 1 (vs Subtype 2) showed clinical manifestations of cachexia: high-grade weight loss, low muscle mass, atrophy of Type IIA and Type IIX muscle fibres and reduced survival. Based on differential expression between the subtypes, our results indicate biological processes that may contribute to cancer-associated loss of muscle mass and function, including altered post-transcriptional regulation, and perturbation of neuronal systems, cytokine storm/cellular immune response, extracellular matrix, and metabolic abnormalities spanning xenobiotic metabolism, hemostasis, signal transduction, embryonic/pluripotent stem cells, and amino acid metabolism. Differential expression between subtypes indicates involvement of multiple, intertwined higher-order gene regulatory networks, suggesting potential for interacting (hub)lncRNA-miRNA-mRNA interaction networks as targets for future research.
2025-07-17 | GSE292052 | GEO
Project description:Rhesus monkey extraocular muscle. Data set includes: (a) whole medial and lateral rectus muscle and (b) global and orbital muscle layers separately microdissected using a Leica LSM. All samples were expression profiled here using the Affymetrix human U133 A&B arrays. Data form part of publication: Investigative Ophthalmology and Visual Science 45, 2004. Keywords = skeletal muscle Keywords = microarray Keywords = orbital layer Keywords = global layer Keywords: ordered
2004-04-01 | GSE907 | GEO
Project description:Cancer cachexia is a multifactorial condition characterized by skeletal muscle loss that impairs longevity and quality of life of the vast majority of cancer patients. However, the ability to develop therapeutic strategies to counter cachexia is impeded by the limited understanding of the underlying mechanisms of cachexia in human cancer patients. The purpose of this study was therefore to characterize the proteomic signature of skeletal muscle obtained from cachectic pancreatic ductal adenocarcinoma (PDAC) patients, who exhibit one of the highest rates of cachexia. Muscle biopsies (rectus abdominis) were obtained from PDAC patients (n=8; 70±10yr; BMI: 26.8±5.9kg･m-2) undergoing tumor resection surgery as well as age and sex-matched non-cancer controls (n=6; 66±9yr; BMI: 30.8±5.2kg･m-2). PDAC patients were cachectic (6 month body weight loss > 5%; mean: 15.7±7.9%) and did not undergo neoadjuvant therapy.
2025-06-23 | PXD047838 | Pride
Project description:Rhesus monkey extraocular muscle. Data set includes: (a) whole medial and lateral rectus muscle and (b) global and orbital muscle layers separately microdissected using a Leica LSM. All samples were expression profiled here using the Affymetrix human U133 A&B arrays. Data form part of publication: Investigative Ophthalmology and Visual Science 45 (in press), 2004.
2007-07-22 | E-GEOD-907 | biostudies-arrayexpress
Project description:<p>This project aims to conduct genome-wide association studies (GWAS) in two anatomically different upper gastrointestinal (UGI) cancer sites in two populations with distinctly different disease rates and genetic profiles. One population has very high rates for both esophageal squamous cell carcinomas (ESCCs) and gastric cancers (GCs) and is comprised of Asians (<b>the "Asian UGI GWAS"</b>), while the other population has low rates of ESCC and GC and includes non-Asians from the Americas, Europe, and Australia (<b>the "Non-Asian UGI GWAS"</b>).</p> <p>Study participants for the Asian UGI GWAS reported here (Illumina 660W Quad chip) were drawn from 2 studies, the Shanxi Upper Gastrointestinal Cancer Genetics Project (Shanxi) and the Linxian Nutrition Intervention Trial (NIT), a prospective cohort, and included a total of 1898 ESCCs, 1625 GCs, and 2100 controls. For the 2nd phase (8 TaqMan SNPs), additional subjects from Shanxi and NIT as well as subjects from the Shanghai Men's Health Study (SMHS), the Shanghai Women's Health Study (SWHS), and the Singapore Chinese Health Study (SCHS) were also included (217 ESCCs, 615 GCs, 1202 controls). Altogether 2115 ESCCs, 2240 GCs, and 3302 controls were genotyped in this study.</p>
| phs000361 | dbGaP