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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from healthy controls and early stage CRC patient's tumor

ABSTRACT: Metastasis is the major cause of cancer mortality. Up to 25% of early stage sporadic colorectal cancer (CRC) patients succumb to metastasis after curative surgery. We used microarrays to detail gene expression and identified a metastasis-prone signature for early stage CRC. Keywords: RNA expression Tumors from age- and ethnicity-matched 70 patients and biopsies from 12 healthy controls were used. We aimed to find a metastasis-prone signature for early stage CRC by genome-wide expression profiling of age- and ethnicity-matched patients and healthy controls using the Affymetrix U133 Plus 2 array.

ORGANISM(S): Homo sapiens

SUBMITTER: Yi Hong

PROVIDER: E-GEOD-9348 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A 'metastasis-prone' signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics.

Hong Yi Y Downey Thomas T Eu Kong Weng KW Koh Poh Koon PK Cheah Peh Yean PY

Clinical & experimental metastasis 20100209 2

Metastasis is the major cause of cancer mortality. We aimed to find a metastasis-prone signature for early stage mismatch-repair proficient sporadic colorectal cancer (CRC) patients for better prognosis and informed use of adjuvant chemotherapy. The genome-wide expression profiles of 82 age-, ethnicity- and tissue-matched patients and healthy controls were analyzed using the Affymetrix U133 Plus 2 array. Metastasis-negative patients have 5 years or more of follow-up. A 10 x 10 two-level nested c ...[more]

PMID: 20143136

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Expression data from healthy controls and early stage CRC patient's tumor

Project description:Metastasis is the major cause of cancer mortality. Up to 25% of early stage sporadic colorectal cancer (CRC) patients succumb to metastasis after curative surgery. We used microarrays to detail gene expression and identified a metastasis-prone signature for early stage CRC. Keywords: RNA expression

2010-02-15 | GSE9348 | GEO

Epigenetic memory of obesity predisposes to colorectal cancer

Project description:Colorectal cancer (CRC) is the third most common cancer worldwide. Obesity is a major risk factor with long-lasting effects on the predisposition to CRC even after weight loss; however, the mechanistic underpinnings remain poorly understood. Using a diet-induced obesity mouse model, we profiled cell-intrinsic alterations in colonic epithelium from young and aged obese mice compared with their age-matched controls, to gain insights into the progression of obesity-associated dysregulations in colonic cellular states. Cellular metabolic reprogramming occurred at early stage, boosting the number and function of stem/stem-like cells; while cell-intrinsic rewiring of signal transduction networks happened at later stage, promoting growth factor-independent proliferation. Strikingly, colonic DNA methylome was pre-programmed by obesity at young age priming for a tumor-prone gene signature after aging. Furthermore, obesity-related changes were substantially preserved after weight loss, potentially contributing to long-term predisposition to CRC. These findings broadened our perspectives on how obesity shapes the predisposition to CRC.

2017-12-19 | GSE100276 | GEO

Extracellular vesicle membrane protein profiling and targeted mass spectrometry unveil novel plasma biomarkers for detection of colorectal cancer

Project description:Extracellular vesicles (EVs) are valuable sources for the discovery of useful cancer biomarkers. This study explores the potential usefulness of tumor cell-derived EV membrane proteins as plasma biomarkers for early detection of colorectal cancer (CRC). EVs were isolated from the culture supernatants of four CRC cell lines by ultracentrifugation, and their protein profiles were analyzed by LC-MS/MS. Bioinformatics analysis of identified proteins revealed 518 EV membrane proteins in common among at least three CRC cell lines. We next used accurate in-clusion mass screening (AIMS) in parallel with iTRAQ-based quantitative proteomic analysis to highlight candidate proteins and validated their presence in pooled plasma-generated EVs from 30 healthy controls and 30 CRC patients. From these, we chose 14 potential EV-derived targets for further quantification by targeted MS assay in a separate individual cohort comprising of 73 CRC and 80 healthy subjects. Quantitative analyses revealed significant increases in ADAM10, CD59 and TSPAN9 levels (2.19- to 5.26-fold, p <0.0001) in plasma EVs from CRC patients, with AUC values of 0.83, 0.95 and 0.87, respectively. Higher EV CD59 levels were significantly corre-lated with distant metastasis (p = 0.0475), and higher EV TSPAN9 levels were significantly asso-ciated with lymph node metastasis (p = 0.0011), distant metastasis at diagnosis (p = 0.0104) and higher TNM stage (p = 0.0065). A two-marker panel consisting of CD59 and TSPAN9 outper-formed the conventional marker CEA in discriminating CRC and stage I/II CRC patients from healthy controls, with AUC values of 0.98 and 0.99, respectively. Our results identify EV mem-brane proteins in common among CRC cell lines and altered plasma EV protein profiles in CRC patients, and suggest plasma EV CD59 and TSPAN9 as a novel biomarker panel for detecting early-stage CRC.

2023-03-11 | PXD038871 | Pride

Stage II and stage III colorectal cancer

Project description:Distant metastasis is the major causes of death in colorectal cancer (CRC) patients. In order to identify genes influencing the prognosis of patients with CRC, we compared gene expression in primary tumors with and without distant metastasis using an oligonucleotide microarray. We also examined the expression of the candidate gene in 100 CRC patients by quantitative real-time reverse transcription PCR and studied the relationship between its expression and the prognosis of patients with CRC. As a result, we identified MUC12 as a candidate gene involved in metastasis processes by microarray analysis. Quantitative real-time reverse transcription PCR showed that MUC12 expression was significantly lower in cancer tissues than in adjacent normal tissues (P < 0.001). In stage II and stage III CRC, patients with low expression showed worse disease-free survival (P = 0.038). Multivariate analysis disclosed that MUC12 expression status was an independent prognostic factor in stage II and stage III CRC (relative risk, 9.532; 95% confidence interval, 2.303-41.905; P = 0.002). This study revealed the prognostic value of MUC12 expression in CRC patients. Moreover, our result suggests MUC12 expression is a possible candidate gene for assessing postoperative adjuvant therapy for CRC patients.

2010-02-04 | GSE18105 | GEO

Modeling Tumor Development and Metastasis using Paired Organoids Derived from Patients with Colorectal Cancer Liver Metastases

Project description:Tumor metastasis accounts for the majority of cancer-related deaths; it is therefore important to develop preclinical models that faithfully recapitulate disease progression. Here, we generated paired organoids derived from primary tumors and matched liver metastases in the same colorectal cancer patients (CRC). Despite the fact that paired organoids exhibit comparable gene expression and cell morphology. organoids from metastatic lesions demonstrate more aggressive phenotypes, tumorigenesis, and metastatic capacity than those from primary lesions. Transcriptional analyses of the paired organoids reveal signature genes and pathways altered during the progression of CRC. including SOX2, altered during the progression of CRC. Further study shows that inducible knockdown of SOX2 attenuated invasion, proliferation, and liver metastasis outgrowth. Taken together, we use patient-derived organoids to model cancer metastasis. Our data propose that SOX2 is not only a critical biomarker for the development and metastasis of CRC, but also a potent target for the disease treatment.

2020-10-05 | GSE148918 | GEO

Comparative profiling of primary colorectal carcinomas and liver metastases

Project description:PURPOSE: We sought to identify genes of clinical significance to predict survival and the risk for colorectal liver metastasis (CLM), the most common site of metastasis from colorectal cancer (CRC). PATIENTS AND METHODS: We profiled gene expression in 31 specimens from primary CRC and 32 unmatched specimens of CLM, and performed Significance Analysis of Microarrays (SAM) of the expressed genes between these two groups. To characterize the clinical relevance of two highly-ranked differentially expressed signature genes, we analyzed the expression of secreted phosphoprotein 1 (SPP1 or osteopontin) and lymphoid enhancer factor-1 (LEF1) by immunohistochemistry using a tissue microarray (TMA) representing an independent set of 154 patients with primary CRC. Supervised analysis using SAM identified 963 genes with significantly higher expression in CLM compared to primary CRC, with a false discovery rate of <0.5%. TMA analysis showed SPP1 and LEF1 protein overexpression in 60% and 44% of CRC cases, respectively. Subsequent occurrence of CLM was significantly correlated with the overexpression of LEF1 (chi-square p = 0.035), but not SPP1 (p = 0.14). Kaplan Meier analysis revealed significantly worse survival in patients with overexpression of LEF1 (p < 0.01), but not SPP1 (p = 0.11). Both univariate and multivariate analyses identified stage (p < 0.0001) and LEF1 overexpression (p < 0.05) as important prognostic markers, but not tumor grade or SPP1. CONCLUSION: Among signature genes differentially expressed between CLM and primary CRC, we demonstrate overexpression of LEF1 in primary CRC to be a prognostic factor for poor survival and increased risk for liver metastasis. cDNA microarrays from the Stanford Functional Genomics Facility were used to perform mRNA transcript profiling of 31 freshly-frozen primary colorectal cancer specimens, and compared to published profiles of 32 unmatched colorectal liver metastases and 12 normal liver specimens.

2011-03-22 | E-GEOD-22834 | biostudies-arrayexpress

Genomic profiles vary with race and subtype in young African American and European American breast cancer (SNP)

Project description:In the United States, African-American (AA) women are more likely to develop early-onset breast cancer and have historically poorer outcomes due to this disease compared to European-American (EA) women. Here, we analyzed genomic profiles of breast tumors from young women (<50 years old), matched by tumor subtype, histological grade, and ethnicity (African-American, AA, compared to European-American, EA). DNA copy number alterations (CNAs) were analyzed on the Affymetrix Human SNP Array v 6.0 platform. The study provides insight into the genetic component of ethnicity-related breast cancer health disparities. DNA copy number alterations (CNAs) and genotypes were analyzed using the Affymetrix SNP 6.0 platform. Breast tumor samples from young women (< 50 years old) were matched as follows: a matched pair consists of one AA and one EA sample, matched for tumor grade and tumor subtype (based on immunohistochemical analysis of ER, PR, and HER2 status). DNA from forty-four samples (22 AA, 22 EA) was analyzed on the Affymetrix SNP 6.0 array according to manufacturer’s directions.

2013-01-29 | E-GEOD-26232 | biostudies-arrayexpress

Homo sapiens

Project description:Expression data from early stage CRC patients' tumors [Affymetrix]

| PRJNA323569 | ENA

Homo sapiens

Project description:Expression data from early stage CRC patients' tumors [Agilent]

| PRJNA323568 | ENA

Comparing miRNA Signature of Colon Cancer Primary Tumors to Metastases Formed in the Liver

Project description:Genome wide miRNA expression profiling was performed using Affymetric miRNA v. 3.0 Array on 48 samples which included paired FFPE colon tuomor and metastisized liver and paired normal colon, normal liver). The data set was divided into two categories and identified by tissue source and patient demographics: Tissue (Colon, Liver), Source (Colon Tumor Liver Met, Colon Normal, Liver Normal), Sex (Male, Female), Patient Pair. microRNAs (miRs) are frequently dysregulated in colorectal cancer (CRC) and subsets are correlated with advanced tumor stage and metastasis. Despite this, the development of prognostic biomarkers that predict metastatic potential remain limited. Our study was designed to identify, validate, and elucidate underlying biology imposed by a miR signature that defines and predicts metastatic disease. Genome-wide miR expression profiling was performed on fourteen patient-matched stage IV primary CRC tumors and corresponding liver metastases using microRNA array technology. Based on these results, this miR panel was then validated and evaluated in normal colon tissue (N = 5), early stage (I & II, N = 11) and late stage (Stage III & IV, N = 14) colorectal primary tumors via qRT-PCR.

2017-05-02 | GSE98406 | GEO

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