Project description:Transcriptional profiling of early-onset sporadic rectal adenocarcinoma, comparing Wnt- and Wnt+ rectal tumor. Goal was to determine differentially expressed genes between them based on global gene expression.
Project description:Copy number profiling of early-onset sporadic rectal adenocarcinoma, comparing Wnt- and Wnt+ rectal tumor. Goal was to determine differentially altered genes between them based on global copy no.
Project description:Early-onset sporadic rectal cancer (EOSRC) is a unique and predominant colorectal cancer
(CRC) subtype in India. To identify molecular alterations underlying rectal adenocarcinoma, we performed whole-exome sequencing analysis of 47 carefully selected well-annotated microsatellite stable (MSS) rectal tumor and matched normal sample pairs (EOSRC-IN).
Project description:The incidence of sporadic early-onset colon cancer (EOCC) has increased worldwide. The molecular mechanisms in the tumor and the tumor microenvironment in EOCC are not fully understood. The aim of this study is to unravel unique spatial transcriptomic and proteomic profiles in tumor epithelial cells and cancer-associated fibroblasts (CAFs). Sporadic colon cancer FFPE tissue samples were divided into patients diagnosed with EOCC (<50 yrs) and late-onset colon cancer (LOCC, ≥50 yrs). A total of 13 LOCC and 13 EOCC patients that were analyzed using HTG EdgeSeq Precision Immuno-Oncology Panel. The data generated was combined with in silico analysis and functional assays to characterize FAP(+) CAFs at the EOCC tumor invasive margin.
Project description:The incidence of sporadic early-onset colon cancer (EOCC) has increased worldwide. The molecular mechanisms in the tumor and the tumor microenvironment in EOCC are not fully understood. The aim of this study is to unravel unique spatial transcriptomic and proteomic profiles in tumor epithelial cells and cancer-associated fibroblasts (CAFs). Sporadic colon cancer FFPE tissue samples were divided into patients diagnosed with EOCC (<50 yrs) and late-onset colon cancer (LOCC, ≥50 yrs). Spatial transcriptomic analysis of 112 areas of interest (AOIs) were performed using Nanostring GeoMx digital spatial profiling. The data generated was combined with in silico analysis and functional assays to characterize FAP(+) CAFs at the EOCC tumor invasive margin.
Project description:Gene fusions (GFs) represent a distinct class of structural variants identified consistently in cancer genomes across multiple cancer types. Several GFs exhibit gain of oncogenic function, and thus, have been the focus for development of efficient targeted therapies. Here, we present a comprehensive landscape of GFs in early-onset sporadic rectal cancer (EOSRC), a poorly studied colorectal cancer (CRC) subtype prevalent in developing countries from the transcriptome analysis of 37 EOSRC samples. Gene Ontology analysis revealed enrichment of unique biological process terms associated with 5’- and 3’- fusion partner genes. An extensive network analysis highlighted several promiscuous genes participating in GF formation. Further, an in-depth evaluation revealed significant association of these promiscuous genes with chromosome fragile sites.
