Dataset Information

[HPP-2.0] The Comparable Microenvironment Shared by Colorectal Adenoma and Carcinoma: An Evidence of Stromal Proteomics

ABSTRACT: we initiated a proteomic project to survey stromal proteins responsive to adenoma and carcinoma of colorectal tissues. Most tissues of adjacent, adenoma, and carcinoma were individually sampled from CRC patients using LCM, after which tissue samples were subjected to proteomic analysis using high-resolution mass spectrometry and individual quantification in data-independent acquisition (DIA) mode. By integrating various datasets and bioinformatic algorithms, the analysis concluded that the epithelial proteomics were CRC stage-dependent, whereas the stromal proteomics in adenoma was comparable with that in carcinoma.

ORGANISM(S): Homo Sapiens

SUBMITTER: Jin Zi

PROVIDER: PXD046176 | iProX | Tue Oct 17 00:00:00 BST 2023

REPOSITORIES: iProX

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The Comparable Microenvironment Shared by Colorectal Adenoma and Carcinoma: An Evidence of Stromal Proteomics.

Yan Keqiang K Bai Bin B Ren Yan Y Cheng Benliang B Zhang Xia X Zhou Haichao H Liang Yuting Y Chen Lingyun L Zi Jin J Yang Qinghai Q Zhao Qingchuan Q Liu Siqi S

Frontiers in oncology 20220401

Tumor microenvironment (TME) is a key factor involved in cancer development and metastasis. In the TME of colorectal cancer (CRC), the gene expression status of stromal tissues could influence the CRC process from normal to adenoma then carcinoma; however, the expression status at the protein level has not yet been well evaluated. A total of 22 CRC patients were recruited for this study, and the tissue regions corresponding with adjacent, adenoma, and carcinoma were carefully excised by laser ca ...[more]

PMID: 35433435

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Project description:Background. Most colorectal cancers (CRC) arise in a progression through adenoma to carcinoma phenotypes as a consequence of altered genetic information. Clinical progression of CRC may occur in parallel with distinctive signaling alterations. We designed multidirectional analyses integrating microarray-based data with biostatistics and bioinformatics to elucidate the signaling and metabolic alterations underlying CRC development in the adenoma-carcinoma sequence. Methodology/Principal Findings. Studies were performed on normal mucosa, adenoma, and CRC samples obtained during surgery or colonoscopy. Collections of cryostat sections prepared from the tissue samples were evaluated by a pathologist to control the relative cell type content. RNA was isolated from 105 macro- and 40 microdissected specimens. The measurements were done using Affymetrix GeneChip HG-U133plus2, and probe set data were generated using two normalization algorithms: MAS5 and GCRMA with LVS. The data were evaluated using pair-wise comparisons and data decomposition into SVD modes. The method selected for the functional analysis used the Kolmogorov-Smirnov test. Based on a consensus of the results obtained by two tissue handling procedures, two normalization algorithms, and two probe set sorting criteria, we identified six KEGG signaling and metabolic pathways (cell cycle, DNA replication, p53 signaling pathway, purine metabolism, pyrimidine metabolism, and RNA polymerase) that are significantly altered in both macro- and microdissected tumor samples compared to normal colon. On the other hand, pathways altered between benign and malignant tumors were identified only in the macrodissected tissues. Conclusion/Significance. Multidirectional analyses of microarray data allow the identification of essential signaling alterations underlying CRC development. Although the proposed strategy is computationally complex and labor–intensive, it may reduce the number of false results. Gene expression profiles of 40 tissue samples representing distant full-thickness normal colon, normal colon mucosa dissected from tumor, adenoma, and carcinoma. Gene expression profiles of 105 tissue samples representing colon carcinomas, adenocarcinomas, and normal colon samples.

Dataset Information

[HPP-2.0] The Comparable Microenvironment Shared by Colorectal Adenoma and Carcinoma: An Evidence of Stromal Proteomics

Publications

The Comparable Microenvironment Shared by Colorectal Adenoma and Carcinoma: An Evidence of Stromal Proteomics.

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