Elucidating the Multi-omics of Early-Onset Colorectal Cancer

Author

Jumanah AlshenaifiFollow

Date of Graduation

5-2025

Document Type

Dissertation (PhD)

Program Affiliation

Quantitative Sciences

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Scott Kopetz

Committee Member

Andy Futreal

Committee Member

Eduardo Vilar-Sanchez

Committee Member

John Paul Shen

Committee Member

Wenyi Wang

Abstract

The incidence and mortality rates of sporadic early-onset colorectal cancer have increased in recent decades, but there is no clear etiological basis for this trend. EOCRC is commonly defined as colon and rectal cancers diagnosed before the age of 50 years. The rising incidence of EOCRC has made it the second most common cancer and the third leading cause of cancer death in this age group. The rising incidence of EOCRC is also documented internationally in more than 20 countries across different continents. Clinically, EOCRC has a distinct, more aggressive clinical profile than LOCRC. While approximately 15% of EOCRC cases are hereditary, the remaining ~85% is largely unknown.

Exposomes are human environmental risk factors that can be external or internal, such as obesity, lifestyle, antibiotics, or gut microbiota. In epidemiological studies, exposomes have been linked to EOCRC. The impact of the exposome on the biological mechanisms and development of EOCRC remains predominantly unidentified.

To better understand this alarming trend and identify potential causes, we investigated the multi-omics of the EOCRC. Mutational signatures are the footprints of endogenous or exogenous exposomal exposures.

In the first study, we focused on early-onset rectal cancer (EORC) where the epidemiologic changes are the most concerning. Using whole-genome and RNA sequencing cohorts, we studied 1,255 microsatellite-stable treatment-naïve rectal cancer tumors across age groups. While the spectrum of mutated genes in early-onset rectal cancer only modestly varies from later onset patients, there are distinctive mutational patterns and signatures, along with transcriptomic profiles, distinguishing early-onset from late-onset. EORC was specifically linked to SBS88 and ID18 (indicating DNA damage caused by colibactin-producing pks+ E. coli) and SBS17b (related to DNA damage caused by reactive oxygen species (ROS)) mutational signatures. Further metagenomics and transcriptomic analysis validated the mutational signatures and EORC. These signatures suggest a role of exposure to pks+ E. coli with EORC tumorigenesis.

Although KRAS mutations and the MAPK/ERK pathway have a major influence on colorectal cancer, their role in EOCRC is not fully understood. Therefore, we focused in the second study on investigating the role of the RAS signaling, specifically the MAPK pathway in EOCRC. Hallmark GSEA enrichment analysis revealed that KRAS signaling was consistently enriched in both cohorts. However, using the novel KRAS-ERK gene signature, which better captures pathway functionality, we found consistent upregulation of the MAPK pathway in EOCRC tumors, irrespective of KRAS mutational status, in both cohorts (p < 0.0001). This study not only elucidates the unique molecular attributes of EOCRC but also lays the groundwork for exploring KRAS-targeted therapies in this aggressive cancer subtype. Given the rising incidence of EOCRC, our research carries substantial implications for its early detection, prevention, and the development of precision therapeutic strategies.

The Mutational landscape of EOCRC patients has been reported to differ from the late-onset groups. Using a cohort of 10,000 patients, this study investigates the clinical, mutational, and co-mutational features of colorectal cancer in early-onset (< 50 years) compared to late-onset (LOCRC, ≥ 50 years). EOCRC was associated with a higher prevalence of Asian and Hispanic patients, rectal or left-sided tumors (72% vs. 59%), and advanced-stage disease. Molecular analyses revealed differences in mutation patterns, with EOCRC having higher frequencies of TP53 (74% vs. 68%, P < 0.01) and SMAD4 (17% vs. 14%, P = 0.015), while BRAF (5% vs. 11%, P < 0.001) and NOTCH1 (2.7% vs. 4.1%, P = 0.01) mutations were more prevalent in LOCRC. Stratification by tumor site and MSI status highlighted significant location- and age-specific molecular differences, such as increased KRAS and CTNNB1 mutations in right-sided EOCRC and higher BRAF prevalence in MSI-H LOCRC (47% vs. 6.7%, P < 0.001). Additionally, co-occurrence analysis revealed unique mutational networks in EOCRC MSS, including significant co-occurrences of FBXW7 with NOTCH3, RB1, and PIK3R1. This study highlights the significance of age-specific molecular profiling, offering insights into the unique biology of EOCRC and potential clinical applications.

Keywords

Early-Onset Colorectal Cancer, Early-Onset rectal Cancer, Multi-omics, Mutational Signatures, Pks+ E. coli, Colibactin, MAPK pathway, KRAS, Genomics, Transcriptomics, Proteomics