Uncovering colorectal cancer etiology and biology by integrating proteomics with other omics data

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PROJECT SUMMARY Genetic factors play a significant role in the etiology of colorectal cancer (CRC). To date, approximately 180 genetic susceptibility loci have been identified for CRC through genome-wide association studies (GWAS). However, causal genes for the large majority of these loci remain unknown, hindering the translation of GWAS findings into disease prevention and treatment. Recently, we and others have identified many putative CRC susceptibility genes using transcriptome-wide association studies (TWAS) that focus exclusively on mRNAs. However, it is the proteins not mRNAs that primarily perform cellular functions. Furthermore, cellular proteins are only moderately correlated with their corresponding mRNAs, and for many proteins, correlation is poor as many factors affect protein synthesis and post-translation stability. Herein, we propose a well-powered proteome-wide association study (PWAS) to systematically search the proteome to identify proteins associated with CRC risk and further characterize their roles in colorectal tumor progression and cellular functions. Specifically, we propose the following aims. Aim 1: To conduct a well-powered PWAS to identify proteins for CRC risk. We will generate proteomics (~10,000 proteins) and genomics data in normal colon tissues from 300 subjects to build genetic models to predict protein expression across the proteome. These models will be applied to the GWAS data of 125,487 individuals (58,131 cases) of European descent to evaluate associations of genetically predicted proteins with CRC risk. We will integrate PWAS findings, along with results from GWAS/TWAS to assess inter-relationships of genes, mRNAs and proteins in the pathogenesis of CRC. Aim 2: To investigate potential roles of PWAS-identified proteins in the adenoma-carcinoma sequence. We will analyze spatial expression of 30 selected PWAS-identified proteins in FFPE samples from 150 early-, late- stage adenoma, and invasive carcinoma from white patients (N= 50 for each group) to investigate if these proteins affect the adenoma-carcinoma sequence. Aim 3: To conduct a nested case-control study to evaluate associations of CRC risk with promising blood proteins uncovered in Aims 1/2: We will analyze circulating levels of 21 proteins selected from Aims 1 and 2 in pre-diagnostic blood samples collected from 1,000 and their matched 1,200 controls of Asian, African and European ancestry. Aim 4: To investigate effects of up to 10 selected PWAS-identified proteins on cellular functions using CRISPRi/a perturbation experiments in multiple normal colon epithelial, and CRC cell lines. We will also assess their potential roles in regulating known CRC signaling, and newly identified CRC pathways uncovered from our study by performing RNA-sequencing and further in vitro verification in both treated and vehicle cells. Given the rigorous study design, the unique resources, and the methodological strengths, we expect that this proposed study will greatly advance our understanding of CRC biology to accelerate the translation of genetic findings in CRC prevention and the development of therapeutic targets.