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December 9, 2025Open Access

Identification of Novel Susceptibility Genes for Early-Onset Colorectal Cancer Through Germline Rare Variant Burden Testing

RSRuocen SongUniversity of Florida RMReger R. MikaeelWashington University in St. Louis ZHZhongping HeUniversity of Florida

Key Points

This research aims to identify new susceptibility genes for early-onset colorectal cancer using genetic testing methods.
Analyzed 212 cases of early-onset colorectal cancer and polyps
Utilized exome sequencing and gene-based rare variant burden testing
Conducted independent validation in the UK Biobank
Identified MEIKIN as a novel susceptibility gene for early-onset colorectal cancer
Found other genes with borderline significance including STK25 and PGBD4
Supported the role of both gain-of-function and loss-of-function variants in CRC risk

Abstract

Background: Colorectal cancer (CRC) is a leading cause of cancer death, and the incidence and mortality rates among young adults are rising. Although a subset of CRC cases presents with a family history, suggesting a hereditary component, the specific genetic underpinnings remain incompletely understood, particularly in early-onset CRC (EOCRC). This study aimed to discover novel risk genes for EOCRC using exome sequencing and gene-based rare variant burden testing. Methods: Our cohort consisted of 212 European-ancestry cases (174 diagnosed with CRC and 38 with significant polyps) from the South Australian Young Onset Colorectal Polyp and Cancer Study (SAYO) and 31,699 unaffected controls from the Simons Foundation Powering Autism Research for Knowledge (SPARK) cohort. After filtering for ancestry, relatedness, variant quality, and population allele frequency, we performed gene-set and individual-gene burden tests using predicted deleterious missense and loss-of-function variants. Statistical significance was assessed using permutation-corrected binomial testing. An independent validation was conducted in the UK Biobank. Results: Loss-of-function variants in known CRC tumor suppressor genes were significantly enriched in SAYO cases. Gene-level analyses identified MEIKIN as a novel EOCRC susceptibility candidate (p value = 1.0 × 10−7), with supporting enrichment of deleterious missense and loss-of-function variants in distal colon cancer cases from the UK Biobank. Additional genes (STK25, PGBD4, DIRAS3, ATG3, RPS6KA4, and DDX42) demonstrated borderline significance, implicating pathways related to kinetochore assembly, autophagy regulation, and immune signaling. Both predicted gain-of-function and loss-of-function variants contributed to the EOCRC risk, supporting heterogeneous mechanisms of CRC pathogenesis. Conclusions: This study identified novel candidate risk genes for EOCRC, underscoring the role of rare variants and expanding our understanding of the genetic architecture of CRC. Future studies should include functional validation and replication studies on other ancestries to confirm and extend these results.

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