Are Homologous Recombination Deficiency Mutations Relevant in Colorectal Cancer?

The loss of functional DNA damage response (DDR) pathways increases genome mutability and instability and is a critical enabling characteristic underlying cancer development and invasion (1). The archetype of aberrant DDR is germline loss of BRCA1 or BRCA2, key tumor suppressors required for high-fidelity homologous recombination to repair DNA double-strand breaks (DSBs) arising because of replication stress (2). Loss of the wild-type BRCA1/2 allele in the course of carcinogenesis consequently causes homologous recombination deficiency (HRD), increasing vulnerability to therapies like platinum chemotherapeutics that crosslink DNA and cause DSBs, which overwhelms DNA damage repair capabilities (3). Additionally, HRD cells rely on more error-prone alternative DDR pathways, such as nonhomologous end joining, to repair DNA breaks sufficiently to avoid mitotic catastrophe and cell death, increasing mutagenesis and genomic instability. This causes HRD to have synthetic lethality with poly-ADP ribose polymerase (PARP) inhibitors, which impairs alternative DDR pathways requiring functional PARP and traps PARP1 at single-strand breaks, stalling replication forks and causing DSBs and genotoxicity (4). PARP inhibitor therapy is US Food and Drug Administration approved for multiple types of metastatic cancer in patients with germline BRCA1/2 mutations, including ovarian cancer, breast cancer, prostate cancer, and pancreatic cancer. Novel therapies targeting other DDR pathway components, such as ATM, ATR, DNA-PK, CHK1/2, and WEE1, are in clinical investigation for HRD cancers (5). Thus, identifying additional cancer types and biomarkers of HRD may expand the number of patients who could benefit from DDR inhibitors.

Indeed, many genomic aberrations beyond germline BRCA1/2 mutations can cause a HRD phenotype. Repair of DSBs via homologous recombination is a multistep process requiring multiple proteins besides BRCA1 and BRCA2 (6), and mutation or loss of a gene encoding any of these proteins could impair DSB repair and cause HRD. For example, tumor genomic sequencing detecting a mutation in at least 1 of 15 HRD genes (BRCA1, BRCA2, ATM, BRIP1, BARD1, CDK12, CHEK1, CHEK2, FANCL, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, and RAD54L) was validated and approved as a companion diagnostic to identify patients with castration-resistant prostate cancer who benefit from receiving the PARP inhibitor olaparib (7). Although mutations in any individual HRD-related gene have low prevalence in any given cancer type, the sum of HRD-related mutations is found in up to 10%-17.4% of cancers (depending on which genes are considered HRD related and varying by cancer type) (8). Colorectal cancer is not typically associated with germline BRCA1, BRCA2, or PALB2 mutations (9). However, composite somatic HRD mutations are found in 13.8% of colorectal cancer patients and are enriched in microsatellite unstable (MSI-high), right-sided, BRAF mutant cancers (10).

It has not been clear if the presence of mutations in HRD-associated genes is the optimal biomarker to predict for clinically relevant HRD causing particular susceptibility to platinum agents and PARP inhibitors. Epigenetic silencing of HRD genes may functionally cause HRD and enhanced mutagenesis and thus confer functional HRD, despite lacking mutations in HRD genes (11). In contrast, cancers that are heterozygous for defective BRCA1/2 and retain a normal allele do not have functional HRD (12), indicating that the presence of a mutation alone may not be the optimal biomarker. Cancers that truly have HRD are expected to have unique mutational signatures (13) and features of genomic instability reflecting HRD. Loss of heterozygosity (LOH) of intermediate size regions (more than 15 Mb but less than a whole chromosome) resulting from erroneous repair of sister chromatids in mitosis in HRD cells is associated with defective BRCA1/2 mutation (14). Telomeric allelic imbalance (15) and chromosomal large-scale state transitions (16) are additional measures of genomic instability that are detectable in HRD cancers. A genomic assay measuring LOH, telomeric allelic imbalance, and large-scale state transitions from tumor DNA specimens was developed and validated as a companion diagnostic to identify patients with ovarian cancer whose tumors had HRD who were more likely to benefit from receiving the PARP inhibitor niraparib (17,18) or from maintenance therapy with olaparib and bevacizumab (19). However, for the subset of colorectal cancers that harbor mutations in HRD genes, the functional and clinical impact of these mutations has not been well described previously.

In this issue, Moretto and colleagues (20) address this important gap in the literature by describing clinical and pathologic characteristics of colorectal cancers harboring mutations in 1 of 33 HRD-related genes. They perform their analysis in both a large retrospective cohort and in samples from the randomized phase III TRIBE2 trial in which all patients received doublet or triplet oxaliplatin-backbone chemotherapy regimens (21). HRD mutations were more commonly found in MSI-high cancers, with 73.4% of MSI-high tumors having at least 1 HRD mutation. However, none of the MSI-high cancers with HRD mutations displayed high LOH, suggesting that these HRD mutations did not functionally confer HRD and raising the possibility that the HRD mutations are passenger mutations rather than driver mutations in these tumors with high rates of mutations. Notably, MSI-high colorectal cancers have been recognized to have overall genome-wide hypermethylation and also lack LOH as compared with microsatellite stable (MSS) colorectal cancers (22). Further study is warranted to determine if HRD mutations confer a functional HRD mutation signature in MSI-high colorectal cancers.

Conversely, 9.5% of MSS cancers had HRD mutations and more cases that had high LOH (16.2% vs 9.5%), suggesting that unlike in MSI-high tumors, HRD mutations in MSS tumors are more likely to confer functional HRD. Nevertheless, the majority of the tumors with HRD mutations did not have high LOH and likely maintained some level of homologous recombination function, highlighting the need to better molecularly and functionally characterize tumors with clinically relevant HRD.

The analysis from TRIBE2 importantly demonstrates that patients with MSS tumors with HRD mutations had better outcomes with platinum-based therapy compared with patients who did not have HRD mutations, providing some of our first clinical evidence that the presence of HRD mutations indeed may be associated with greater platinum sensitivity in colorectal cancer. Indeed, greater sensitivity to platinum chemotherapy agents was associated with susceptibility to PARP inhibitors in a subset of colorectal cancer models preclinically, although this sensitivity was best measured by an in vitro functional DNA damage assay rather than by HRD mutations or HRD mutational signatures (23). Efforts to bring this work to the clinic will be limited by rarity of predicted functional HRD, with only 1.5% of MSS cancers with HRD mutations and associated LOH. This work clearly suggests that future studies targeting biomarker selected subsets of HRD tumors should incorporate LOH to identify the patient population most likely to benefit from predicted synergistic strategies. Thus, the totality of evidence increasingly indicates that DDR agents are likely to be active in at least a subset of molecularly defined colorectal cancers, which are also defined clinically by platinum sensitivity; although the optimal biomarker remains to be defined, HRD mutations and signatures certainly merit further study in colorectal cancer.

Funding

SK is supported by R10CA218230, 5P50CA221707, and P30CA016772

Notes

Role of the funders: The funders had no role in the writing of this editorial or the decision to submit it for publication.

Disclosures: Lee (Research funding: Amgen, Exelixis, Bristol-Myers Squibb, Pfizer, Rafael Pharmaceuticals, EMD Serono, Genentech/Roche to my institution. Consulting: Pfizer). Kopetz (Research funding: Sanofi, Biocartis, Guardant Health, Array BioPharma, Genentech/Roche, EMD Serono, MedImmune, Novartis, Amgen, Lilly, Daiichi Sankyo. Consulting: Roche, Genentech, EMD Serono, Merck, Karyopharm Therapeutics, Amal Therapeutics, Navire Pharma, Symphogen, Holy Stone, Biocartis, Amgen, Novartis, Lilly, Boehringer Ingelheim, Boston Biomedical, AstraZeneca/MedImmune, Bayer Health, Pierre Fabre, Redx Pharma, Ipsen, Daiichi Sankyo, Natera, HalioDx, Lutris, Jacobio, Pfizer, Repare Therapeutics, Inivata).

Author contributions: Writing, original draft—MSL, SK; writing, editing and revisions—MSL, SK.

Data Availability

Not applicable.