Multi-omics Analysis reveals novel therapeutic vulnerabilities in lung cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE159857 | GEO | 2022/05/04
REPOSITORIES: GEO
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Project description:WES sequencing of multiple regions per tumor from 8 lung cancer patients (LUSC, LCNEC and LUAD) and adjacent healthy lung tissue for each patient.
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Project description:<p><a href="https://cptac-data-portal.georgetown.edu/study-summary/S056" target="_blank">Proteogenomics of Lung Adenocarcinoma, Gillette et al., 2020 publication is here</a><br><br>Lung cancer is a leading cause of cancer death in the United States and in 2019 it is estimated that there will be over 228,000 new cases (<a href="https://www.cancer.org/cancer/non-small-cell-lung-cancer/about/key-statistics.html" target="_blank">American Cancer Society</a>). There are two main types, small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). A majority of patients (85%) have NSCLC, with a significant portion of those individuals having a histological subtype lung adenocarcinoma (LUAD) <a href="https://www.ncbi.nlm.nih.gov/pubmed/29364287" target="_blank">Herbst et al., 2018 Nature</a>. To advance the proteogenomic understanding of LUAD, the CPTAC program has investigated 111 tumors, (with 102 tumors paired with normal adjacent tissue samples) and subjected these samples to global proteome and phosphoproteome analysis. An optimized workflow for mass spectrometry of tissues using isobaric tags (TMT (tandem mass tags)-10) was used (<a href="https://www.ncbi.nlm.nih.gov/pubmed/29988108" target="_blank">Mertins et al., Nature Protocols 2018</a>). Proteome and phosphoproteome data from the LUAD discovery cohort is available below along with peptide spectrum matches (PSMs) and protein summary reports from the CPTAC common data analysis pipeline (CDAP).</p><p><em>Clinical Data</em> for LUAD tumors are provided below. Updates will be available as the LUAD cohort characterization proceeds.<br><em>Genomic Data</em> for LUAD tumors is available from the NCI Genomic Data Commons (GDC), <a href="https://portal.gdc.cancer.gov/projects/CPTAC-3" target="_blank">here</a><br><em>Imaging Data</em> for LUAD tumors is available from NCI, The Cancer Imaging Archive (TCIA), <a href="https://wiki.cancerimagingarchive.net/display/Public/CPTAC-LUAD" target="_blank">here</a><br>This release includes over 4500 files and 914 GB of data.</p>
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Project description:The aim of this project was to identify microRNAs associated with the expression subtypes in patients diagnosed with non-small cell lung cancer. Based on mRNA expression data the samples were assign to a gene expression subtype based on 506 gene centroid classifier. The patients enrolled in this study underwent curatively intended surgical resection. Subtype-specific microRNA expression was correlated to gene set enrichment scores in order to identify associated pathways that the microRNAs may be regulating, characterizing the expression subtypes. In order to assess if the subtype-specific microRNA signal originate from the lung cancer cells or from infiltrating immune cells, we compared our subtype-specific microRNAs with the results from a study investigating human cell-specific microRNA expression. In this project the authors sequenced microRNAs from 46 primary cell types, 42 cancer cell lines and tissues (McCall MN, Kim MS, Adil M, Patil AH, Lu Y, Mitchell CJ, Leal-Rojas P, Xu J, Kumar M, Dawson VL et al: Toward the human cellular microRNAome. Genome Res 2017, 27(10):1769-1781). The results were further validated in independent NSCLC cohorts (LUAD and LUSC) from The Cancer Genome Atlas (TCGA). In this study we identified subtype specific microRNAs associated with essential processes characterizing the expression subtypes of ADs and SCCs.
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