CAT-seq: A Chemical Strategy for Subcellular-Resolved RNA Profiling and Synchronous Multi-omics Investigation
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ABSTRACT:
PROVIDER: PRJNA1073189 | ENA |
REPOSITORIES: ENA
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Project description:We evaluated the profile of miRNA and snoRNA expression in 5 synchronous CRC and matched normal colorectal tissues using the Affymetrix GeneChip miRNA 1.0 array. A total of 24 miRNA differential expressed transcripts which represent 27 mature miRNAs, including an oncogenic miR-17-92a and oncosuppressive miR-143-145 cluster, and a global up-regulation of snoRNAs were revealed in cancer tissues compared with matched normal tissues. Global miRNA expression could distinguish synchronous cancer from normal mucosa. Our findings represent the first comprehensive miRNA and snoRNA expression signatures for synchronous CRC, which increase the understanding of the molecular basis of synchronous CRC, and firstly implicate that dysregulation of snoRNAs and miRNA clusters may present therapeutic targets for synchronous CRC.
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Project description:In vertebrates, non-lens bg-crystallins are widely expressed in various tissues, but their functions are unknown. The molecular mechanisms of trefoil factors, initiators of mucosal healing and being greatly involved in tumorigenesis, have remained elusive.A naturally existing 72-kDa complex of non-lens bg-crystallin (a-subunit) and trefoil factor (b-subunit), named bg-CAT, was identified from frog Bombina maxima skin secretions. Its a-subunit and b-subunit (containing three trefoil factor domains), with a non-covalently linked form of ab2, show significant sequence homology to ep37 proteins, a group of non-lens bg-crystallins identified in newt Cynops pyrrhogaster and mammalian trefoil factors, respectively. The bg-CAT showed multiple cellular effects on human umbilical vein endothelial cells. Low dosages of bg-CAT (25-50 pM) were able to stimulate cell migration and wound healing. At high concentrations, it induced cell detachment (EC50 10 nM) and apoptosis. The bg-CAT was rapidly endocytosed via intracellular vacuole formation. Under confocal microscope, some of the vacuoles were translocated to nucleus and partially fused with nuclear membrane. However, what exactly target of bg-CAT act on HUVECs nuclear is still unknown. Primary cultured HUVECs treated with bg-CAT (25 nM, 2 h) were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genome wide level of significant differential gene expression induced by bg-CAT on HUVECs in order to get clues about bg-CAT action mechanisms. These findings illustrate novel cellular functions of non-lens bg-cyrstallins and action mechanism via association with trefoil factors, serving as clues for investigating the possible occurrence of similar molecules and action mechanisms in mammals.
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Project description:Purpose: Increasing genomics-based evidence suggests that synchronous endometrial and ovarian cancer (SEOC) represents clonally related primary and metastatic tumors. A systematic analysis of the global protein landscape of SEOCs, heretofore lacking, could reveal functional and disease-specific consequences of known genetic alterations, the directionality of metastasis, and accurate histological markers to distinguish SEOCs from single-site tumors. Experimental Design: We performed a systematic proteogenomic analysis of 29 patients diagnosed with SEOC at three international gynecologic oncology treatment centers (Chicago, Vancouver, Tübingen). For direct comparison to single-site tumors, we included 9 patients with single-site endometrioid ovarian and 26 patients with single-site endometrial endometrioid cancer. For all 64 patients, we performed sequencing of a 275-gene cancer panel combined with compartment-resolved mass spectrometry (MS) based proteomics of consecutive tissue sections to compare global (6,000+ proteins), tumor, and stromal proteomes. Results: DNA-based panel sequencing confirmed that most SEOCs are clonally related, suggesting primary and metastatic disease. These findings were further substantiated on the global proteome level, uncovering pronounced differences between SEOCs and single tumors and underscoring the importance of the stromal proteome in defining and identifying SEOCs. Our integrated proteogenomic approach confirmed that SEOCs more closely resemble endometrial endometrioid than endometrioid ovarian cancers. Conclusions: The integrated proteogenomic data show that SEOCs are distinguishable from endometrial endometrioid or endometrioid ovarian cancers. Based on their proteogenomic similarity to endometrial endometrioid cancers, we conclude that most synchronous endometrial and ovarian cancers represent primary endometrial endometrioid cancers that have metastasized to the ovary.
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