Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA profiling in rectus abdominis muscle from patients with upper GI cancer

ABSTRACT: 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)

ORGANISM(S): Homo sapiens

SUBMITTER: Iain Gallagher

PROVIDER: E-GEOD-18832 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia.

Stephens Nathan A NA Gallagher Iain J IJ Rooyackers Olav O Skipworth Richard J RJ Tan Ben H BH Marstrand Troels T Ross James A JA Guttridge Denis C DC Lundell Lars L Fearon Kenneth C KC Timmons James A JA

Genome medicine 20100115 1

<h4>Background</h4>Cancer cachexia is a multi-organ tissue wasting syndrome that contributes to morbidity and mortality in many cancer patients. Skeletal muscle loss represents an established key feature yet there is no molecular understanding of the disease process. In fact, the postulated molecular regulators of cancer cachexia originate largely from pre-clinical models and it is unclear how these translate to the clinical environment.<h4>Methods</h4>Rectus abdominis muscle biopsies were obtai ...[more]

PMID: 20193046

Similar Datasets

mRNA profiling in rectus abdominis muscle from patients with upper GI cancer

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.

2010-01-19 | GSE18832 | GEO

Skeletal Muscle Fibrosis in Pancreatic Cancer Patients with Respect to Survival

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

Genome-Wide Association Studies in Upper Gastrointestinal Cancers (Asian)

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

Homo sapiens

Project description:mRNA profiling in rectus abdominis muscle from patients with upper GI cancer

| PRJNA121169 | ENA

Transcription profiling of Rhesus monkey extraocular muscle and its layers

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

Gene expression profiling of Rhesus monkey extraocular muscle and its layers (Porter lab)

2004-04-01 | GSE907 | GEO

Genome-Wide Association Studies in Upper Gastrointestinal Cancers (Asian)

| phs000361.v1.p1 | EGA

Impact of the non-muscle cutting periumbilical transverse incision on the risk of incisional hernia compared to the midline incision during laparoscopic colorectal cancer surgery: A randomized controlled multi-center trial

Project description:Interventions: Procedure/Surgery : Incision for removal or anastomosis of colon tissue is performed by extending the laparoscopic incision horizontally. A transverse incision is made in the anterior fascia of the rectus muscle. The abdominal rectus muscle is not incised, but the muscles are lateralized out to find the posterior fascia and peritoneum and incise horizontally. Primary outcome(s): Incisional hernia incidence rate of 1 year (12 months) from the date of surgery Primary Purpose : Other(To demonstrate that transverse incision after laparoscopic colorectal cancer surgery reduces the incidence of incisional hernia compared to vertical incision around the umbilicus), Intervention Model : Parallel, Blinding/Masking : , Blinding Target : , Allocation : RCT

| 2513939 | ecrin-mdr-crc

Stereotactic Body Radiation Therapy in the Management of Upper GI Malignancies.

Project description:The role of external beam radiation therapy (EBRT) in the management of upper gastrointestinal malignancies is constantly evolving. As radiation therapy techniques improve and are able to deliver more ablative doses of radiotherapy while sparing healthy tissue, radiation can be applied to a wider range of clinical scenarios. Stereotactic body radiation therapy (SBRT) allows a high dose of radiation to be delivered to a highly conformal treatment volume in a short amount of time. Another potential advantage of SBRT is its ability to increase tumor immunogenicity, while also having less of an immunosuppressive effect on the patient, as compared to conventionally fractionated radiation therapy. In so doing, SBRT may potentiate the effects of immune therapy when the two treatments are combined, thus improving therapeutic outcomes. This article provides an overview of the role of SBRT in the management of upper gastrointestinal GI malignancies and the emerging data on immune biomarkers and SBRT, with a focus on pancreatic and liver cancer.

| S-EPMC5874664 | biostudies-literature

Differential isoform expression and selective muscle involvement in muscular dystrophies

Project description:To test the hypothesis that different muscles may express variable amounts of different isoforms of muscle genes, we applied a custom-designed exon microarray containing probes for 57 muscle-specific genes to assay the transcriptional profiles in sets of human adult, lower limb skeletal muscles. Muscle biopsies from 15 individuals were selected for analysis dissected from 21 anatomically different muscles collected from eight men and seven women, ranging from 61 to 91 years The muscle tissue samples collected included samples from 11 different thigh muscles––vastus medialis, vastus lateralis, vastus intermedialis, sartorius, gracilis, semimembranosus, semitendinosus, biceps femoris, adductor magnus, adductor longus, and rectus femoris––and 10 lower leg muscles––flexor digitorum longus, extensor digitorum longus, tibialis posterior, tibialis anterior, peroneus longus/brevis, extensor hallucis longus, gastrocnemius lateralis, gastrocnemius medialis, flexor hallucis longus, and soleus. Approximately five to seven muscle pieces were collected from each individual muscle sampled. The muscle sample pieces obtained for histological analysis measured roughly 10 mm x 5 mm, and the pieces for RNA isolation 5 mm x 5 mm. The samples were obtained directly from the proximal vital parts of the amputated limbs and processed immediately following their removal to avoid tissue degradation.To test the hypothesis that different muscles may express variable amounts of different isoforms of muscle genes, we applied a custom-designed Agilent exon microarray containing probes for 57 muscle-specific genes to assay the transcriptional profiles in sets of human adult, lower limb skeletal muscles

2015-06-17 | E-GEOD-69938 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data