Colorectal cancer (CRC) represents a complex and heterogeneous malignancy, affecting the large intestine and rectum, and remains among the most lethal cancers worldwide. Despite extensive research delineating its mutational landscape, significant gaps persist in understanding the mechanisms driving certain subtypes of this disease. Researchers at Fujita Health University in Japan have now shed light on the intricate genetic underpinnings of colorectal tumors characterized by a high tumor mutation burden (TMB), particularly those lacking mutations in canonical oncogenes such as APC, TP53, and KRAS. Their findings, recently published in Cancer Science, provide critical insights into alternative carcinogenic pathways and suggest promising avenues for precision oncology interventions.

Colorectal carcinogenesis has traditionally been viewed as a sequential process, where normal colonic epithelial cells accrue genetic alterations, transitioning into benign adenomas before progressing to malignant carcinomas. This stepwise model highlights the central role of mutations in four key genes: APC, TP53, KRAS, and PIK3CA. Mutations in these genes disrupt critical cellular processes such as cell cycle regulation, apoptosis, and signal transduction, thereby promoting tumor initiation and progression. It is well documented that the prevalence of these mutations varies depending on the tumor location within the colon; for instance, APC and TP53 variants predominate in left-sided colon cancers, whereas KRAS mutations more frequently occur in right-sided tumors. This anatomical specificity further extends to factors such as tumor morphology, immune microenvironment, metastatic potential, and therapeutic responsiveness, indicating distinct biological behaviors influenced by tumor site.

In recent years, a subset of CRC tumors has come into focus that diverges from the classical path of mutations involving APC, TP53, KRAS, and PIK3CA. Notably, BRAF mutations have surfaced as drivers in tumors characterized by a low frequency of these conventional alterations. These tumors typically evolve through an alternate molecular pathway termed the ‘serrated pathway,’ which is associated with distinct genetic and epigenetic changes, including high levels of microsatellite instability (MSI) and a CpG island methylator phenotype (CIMP). However, despite recognition of these molecular features, the specific mechanisms linking BRAF mutations to tumorigenesis via the serrated pathway have remained unclear.

Addressing this knowledge gap, the team led by Dr. Hideyuki Saya at Fujita Health University undertook an extensive genetic analysis of CRC tumors classified by their tumor mutation burden. Employing targeted exome sequencing on samples from 150 CRC patients, their research aimed to elucidate the mutation spectra of TMB-high tumors and explore the relationship between these mutations, MSI status, and tumor location. Their proprietary cancer genome analysis platform allowed for a comprehensive assessment of the mutational profiles, revealing that fourteen tumors exhibited a high TMB, with the overwhelming majority localized in the right colon.

Strikingly, these TMB-high right-sided tumors demonstrated a significant enrichment of BRAF mutations alongside MSI-high status, underscoring the interplay between genomic instability and oncogenic signaling in this subset. Further analysis uncovered frequent mutations in DNA damage response transducers such as ATM and POLE, as well as in mismatch repair genes including MSH2 and MSH6. These alterations are pivotal in maintaining genomic fidelity, and their disruption likely contributes to the elevated mutation rates observed. Importantly, mutational signature profiling suggested that defects in DNA repair pathways may precede the acquisition of BRAF mutations, positioning these genomic aberrations as early events in serrated pathway carcinogenesis.

Interestingly, despite lacking mutations in the canonical driver genes APC, TP53, and KRAS, TMB-high tumors harbored diverse mutations across other oncogenic pathways. These include aberrations in receptor tyrosine kinase-RAS signaling components, phosphatidylinositol 3-kinase (PI3K) pathway constituents such as PTEN, and genes involved in Notch signaling. The collective impact of these mutations likely supports tumor survival, proliferation, and immune evasion, painting a complex molecular portrait distinct from the classical colorectal tumorigenesis model. This heterogeneity highlights the necessity of moving beyond archetypal mutational landmarks to fully capture the genomic diversity of CRC.

The clinical implications of these discoveries are profound. Tumors with high TMB are increasingly recognized as potential candidates for immunotherapies due to their elevated neoantigen load, which may enhance immune system recognition. Moreover, the identification of alternate oncogenic drivers in TMB-high CRC suggests that targeted therapies, specifically tailored to these unique genetic alterations, could offer therapeutic benefit where conventional treatments falter. Dr. Saya emphasizes this point, noting the divergent biological characteristics and oncogenic mechanisms between right- and left-sided CRCs, which call for distinct treatment paradigms guided by precise genomic profiling.

Currently, the application of comprehensive cancer genome analyses remains limited to certain subgroups of patients, often dictated by availability and cost. However, this research advocates for broader adoption of such genomic diagnostics in routine clinical practice. By integrating techniques like targeted exome sequencing with advanced bioinformatics platforms, clinicians can gain invaluable insights into the mutational architecture of individual tumors. This precision approach not only informs optimal therapeutic strategies but also potentially improves prognostic accuracy and patient outcomes.

Looking forward, the Fujita Health University team is refining their in-house cancer genome analysis system to enhance its clinical utility specifically for CRC. Their goal is to develop a robust diagnostic tool capable of seamlessly integrating genetic data into clinical decision-making pathways, facilitating personalized treatments based on tumor genomics. Such advancements herald a new era in colorectal cancer management, shifting the paradigm from one-size-fits-all protocols toward nuanced, mutation-informed therapies.

This landmark study exemplifies the ongoing evolution of cancer genomics and its transformative potential in oncology. By unraveling the molecular complexities of CRC subsets with high TMB, the researchers illuminate the path for future investigations into tumor heterogeneity and therapeutic vulnerabilities. The elucidation of early DNA repair defects and alternate oncogenic pathways not only deepens our understanding of colorectal tumor biology but also underscores the critical importance of comprehensive mutation profiling in contemporary cancer care.

In the broader context of precision medicine, these findings resonate with a growing consensus: that successful cancer treatment increasingly hinges on the granular understanding of each tumor’s unique genomic landscape. As Dr. Saya aptly concludes, the universal implementation of cancer genome analysis could revolutionize standard care practices, empowering clinicians with the information necessary to tailor interventions with unprecedented precision. This vision portends a future where genetic insights drive the design of more effective, individualized therapies, thereby enhancing survival and quality of life for patients facing colorectal cancer.

In summary, the pioneering work from Fujita Health University significantly advances the molecular characterization of TMB-high colorectal cancers, revealing the prominence of BRAF mutations, DNA repair gene defects, and divergent oncogenic pathways in right-sided tumors. These discoveries not only challenge existing paradigms but also spotlight promising targets for emerging therapies, setting the stage for future translational research and clinical innovation in gastrointestinal oncology.

Subject of Research: Human tissue samples

Article Title: Mutation Analysis of TMB-High Colorectal Cancer: Insights Into Molecular Pathways and Clinical Implications

News Publication Date: 16-Jan-2025

References:
DOI: 10.1111/cas.16455

Image Credits: Wikimedia Commons

Keywords: colorectal cancer, tumor mutation burden, BRAF mutations, microsatellite instability, DNA damage response, targeted exome sequencing, precision oncology, serrated pathway, cancer genomics, right-sided colon cancer, molecular pathways, immunotherapy

Tags: alternative carcinogenic pathways in CRCAPC TP53 KRAS mutation analysiscolorectal cancer heterogeneity and subtypescolorectal cancer mutational landscapeFujita Health University colorectal researchgenetic underpinnings of colorectal tumorshigh tumor mutation burden in CRCinsights into colorectal cancer treatment strategiesmechanisms driving colorectal carcinogenesisprecision oncology for colorectal cancerstepwise model of colorectal cancer progressiontumor location-specific mutations in colon cancer

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• Source: https://bioengineer.org/mapping-the-mutational-landscape-of-colorectal-cancer/