Assessment of MYC Gene and WNT Pathway Alterations in Early-Onset Colorectal Cancer Among Hispanic/Latino Patients Using Integrated Multi-Omics Approaches

Abstract

Colorectal cancer (CRC) has increased at an alarming rate amongst younger (< 50 years) individuals. Such early-onset colorectal cancer (EOCRC) has been particularly notable within the Hispanic/Latino population. Yet, this population has not been sufficiently profiled in terms of two critical elements of CRC -- the MYC proto-oncogene and WNT signaling pathway. Here, we performed a comprehensive multi-omics analysis on 30 early-onset and 37 late-onset CRC (≥ 50 years) samples from Hispanic/Latino patients. Our analysis included DNA exome sequencing for somatic mutations, somatic copy number alterations, and global and local genetic similarity. Using RNA sequencing, we also assessed differential gene expression, cellular pathways, and gene fusions. We then compared our findings from early-onset Hispanic/Latino patient samples with publicly available data from Non-Hispanic White cohorts. Across all early-onset patients, which had a median 1000 Genomes Project Peruvian-in-Lima-like (1KG-PEL-like) genetic similarity proportion of 60%, we identified 41 WNT pathway genes with significant mutations. Six important examples were APC, TCF7L2, DKK1, DKK2, FZD10, and LRP5. Notably, patients with mutations in DKK1 and DKK2 had the highest 1KG-PEL-like proportion (79%). When we compared the Hispanic/Latino cohort to the Non-Hispanic White cohorts, four of these key genes -- DKK1, DKK2, FZD10, and LRP5 -- were significant in both risk association analyses and differential gene expression. Interestingly, early-onset tumors (vs. late-onset) exhibited distinct somatic copy number alterations and gene expression profiles; the differences included MYC and drug-targetable WNT pathway genes. We also identified a novel WNT gene fusion, RSPO3, in early-onset tumors; it was associated with enhanced WNT signaling. This integrative analysis underscores the distinct molecular features of EOCRC cancer in the Hispanic/Latino population; reveals potential avenues for tailored precision medicine therapies; and emphasizes the importance of multi-omics approaches in studying colorectal carcinogenesis. We expect this data to help contribute towards reducing cancer health disparities.

Significance: This study offers multi-omics profiling analysis of early-onset colorectal cancer (EOCRC) in an underserved community, explores the implications of MYC gene and WNT pathway alterations, and provides critical insights into cancer health disparities.

Figure 1:. Global Ancestry and Chromosome-Level Admixture Patterns.

a) Global ancestry principal component analysis (PCA) plot. This PCA plot illustrates the global ancestry of our Hispanic/Latino colorectal cancer cohort of 67 individuals, represented by black points, in the context of five super populations: African (1KG-AFR-like, blue), Peruvian-Lima (1KG-PEL-like, red), East Asian (1KG-EAS-like, yellow), European (1KG-EUR-like, green), and South Asian (1KG-SAS-like, purple). The plot displays the distribution of these samples along two principal components, PC1 and PC2, which captures the majority of variance in the genetic data. This visualization helps to contextualize the ancestry composition of our cohort relative to these major global populations. b) This figure illustrates the similarity frequencies in each tumor sample from a cohort of 67 Hispanic/Latino (H/L) colorectal cancer (CRC) patients. The genomes are categorized into five super populations, same as section a. Samples are stratified by age of diagnosis into two groups, early-onset and late-onset, with the proportion of 1KG-PEL-like and 1KG-EUR-like ancestry included.

Figure 2:. Mutation Frequencies in CRC Tumors from H/L Patients.

a) This panel shows the mutation frequencies in each of the tumor samples from 67 Hispanic/Latino colorectal cancer patients. The samples are categorized as early-onset or late-onset. The color codes represent different attributes: dark orange for early-onset samples with an 1KG-PEL-like similarity proportion less than or equal to the median, light orange for early-onset samples with an 1KG-PEL-like similarity proportion greater than the median, light blue for late-onset samples with an 1KG-PEL-like similarity proportion less than or equal to the median, dark blue for late-onset samples with an 1KG-PEL-like similarity proportion greater than the median, light green for hypermutated, dark green for non-hypermutated, dark yellow for MSI, and light yellow for MSS. The inset highlights mutations in genes apart of the Wnt pathway among the early-onset and late-onset groups, with the sample order consistent with the main graph. b) This panel depicts the significantly mutated genes in early-onset and late-onset tumors.

Figure 3:. Somatic Copy Number Alterations (SCNAs) Analysis of Genomic Changes in 30 Early-Onset and 37 Late-Onset Hispanic/Latino Colorectal Cancer Patients.

a) Heatmap of SCNAs: This panel displays SCNAs at both chromosomal and sub-chromosomal levels across 30 early-onset tumor samples from Hispanic/Latino colorectal cancer patients. Deletions (losses) are indicated in blue, while insertions (gains) are shown in red. b) Focal Deletions: This figure highlights the focal deletions identified across 30 early-onset tumor samples. c) Focal Amplifications: This figure presents the focal amplifications observed in the same set of tumor samples. d) Heatmap of SCNAs: This panel displays SCNAs at both chromosomal and sub-chromosomal levels across 37 late-onset tumor samples from Hispanic/Latino colorectal cancer patients. Deletions (losses) are indicated in blue, while insertions (gains) are shown in red. e) Focal Deletions: This figure highlights the focal deletions identified across 37 late-onset tumor samples. f) Focal Amplifications: This figure presents the focal amplifications observed in the same set of tumor samples.

Figure 4:. Differential gene expression (DGE) Analysis and Gene Fusion Analysis among CRC tumors from 30 Early-Onset and 37 Late-Onset Hispanic/Latino patients.

a) Differentially expressed-related genes: This table shows the genes that are differentially expressed when comparing early-onset and late-onset CRC cases. b) Mean-Average (MA) plot: This scatter plot shows the upregulated and downregulated Wnt/β-catenin pathway genes according to the log2 fold change. c) These circle plots illustrate the gene fusions detected across 30 early-onset and 37 late-onset samples from our Hispanic/Latino (H/L) colorectal cancer (CRC) cohort. Clinically actionable gene fusions are highlighted in red, providing insights into potential therapeutic targets for this patient population.

Figure 5:. Integrative Genomic Alteration Patterns in Wnt/β-catenin Pathways Among CRC Tumors from 67 Hispanic/Latino Patients.

a) The Wnt/β-catenin signaling pathway: Panel A: In the absence of Wnt signaling, β-catenin is degraded by a destruction complex. TCF/Lef proteins in the nucleus, along with the TLE co-repressor, suppress Wnt/β-catenin target genes. Panel B: Upon Wnt ligand binding to the FZD and LRP5/6 co-receptors, the destruction complex is inactivated, allowing β-catenin to accumulate and enter the nucleus. There, it binds TCF/Lef and recruits co-activators to activate target genes. Panel C: In colorectal cancers, APC truncations prevent β-catenin degradation, leading to its accumulation in the nucleus. This results in aberrant activation of Wnt/β-catenin target genes. Abbreviations: WRE: Wnt-responsive element; TCF/Lef: T-cell factor/Lymphoid enhancer factor; TLE: Transducin-like enhancer; FZD: Frizzled; LRP5/6: Lipoprotein receptor-related protein 5 or 6; AXIN1/2: Axis inhibition proteins 1 and/or 2; CRC: Colorectal cancer; APC: Adenomatous polyposis coli; GSK3: Glycogen synthase kinase 3; CK1: Casein kinase 1. b) This grid represents integrative genomic alteration patterns in the Wnt/β-catenin pathway among colorectal cancer (CRC) tumors from 67 Hispanic/Latino patients. Each column corresponds to an individual case, and each row represents a gene. The grid is divided into early-onset and late-onset. The color codes represent different attributes: red for amplifications, blue for deletions, an orange border for 1KG-PEL-like similarity proportion greater than the median, a light blue border for 1KG-PEL-like similarity proportion less than or equal to the median, and a bright green dot for somatic mutations. Genes are labeled in red for up-regulated and blue for down-regulated.