Homologous Recombination Deficiency: Genes, Repair, and Cancer

Cells rely on accurate DNA repair mechanisms to maintain genetic stability. Homologous recombination deficiency (HRD) occurs when this process is impaired, leading to an accumulation of mutations that drive disease, particularly cancer. Understanding HRD is crucial for identifying individuals at risk and developing targeted therapies.

Key Genes Involved

HRD arises from mutations in genes responsible for repairing double-strand DNA breaks. BRCA1 and BRCA2 are the most extensively studied due to their strong association with hereditary breast and ovarian cancers. BRCA1 orchestrates the recruitment of repair factors to sites of DNA damage, while BRCA2 facilitates RAD51 loading, essential for strand invasion and exchange. Loss-of-function mutations in either gene disrupt these processes, leading to genomic instability and increased tumorigenesis.

Beyond BRCA1 and BRCA2, other genes contribute to homologous recombination repair. PALB2 bridges BRCA1 and BRCA2, stabilizing their interaction and ensuring efficient RAD51 recruitment. PALB2 mutations confer a breast cancer risk comparable to BRCA2 mutations, underscoring its significance in maintaining genomic integrity. ATM and CHEK2 encode proteins involved in DNA damage sensing and checkpoint activation. ATM phosphorylates BRCA1 in response to DNA breaks, while CHEK2 amplifies the damage signal, ensuring repair mechanisms are engaged. Deficiencies in these genes compromise the cell’s ability to detect and respond to DNA damage, exacerbating HRD-related vulnerabilities.

Additional contributors to HRD include RAD51C and RAD51D, which assist in RAD51 filament formation, necessary for strand invasion and repair fidelity. Mutations in these genes increase the risk of ovarian and breast cancers. The Fanconi anemia (FA) pathway, particularly genes such as FANCA, FANCD2, and FANCI, intersects with homologous recombination by facilitating the repair of interstrand crosslinks. Defects in FA genes not only predispose individuals to bone marrow failure syndromes but also contribute to HRD-associated malignancies.

Role in DNA Repair

Homologous recombination (HR) is a precise mechanism for repairing double-strand breaks (DSBs), preventing genomic instability. Unlike error-prone pathways such as non-homologous end joining (NHEJ), HR utilizes an undamaged sister chromatid as a template, ensuring high-fidelity restoration of the DNA sequence. When HRD is present, cells lose this capability, leading to mutations, chromosomal rearrangements, and increased tumor susceptibility.

The process begins with damage detection, triggering activation of proteins such as ATM and ATR. These kinases phosphorylate BRCA1, which recruits nucleases and helicases to resect DNA ends, generating single-stranded DNA (ssDNA) overhangs. BRCA2 then facilitates RAD51 loading onto ssDNA, enabling homology search and strand invasion. Once the homologous sequence is located, DNA polymerases extend the broken strand using the intact sister chromatid as a guide before the repaired DNA is ligated.

HRD disrupts these steps depending on the genetic defect. BRCA1 mutations impair end resection, preventing ssDNA generation, while BRCA2 deficiencies halt RAD51 loading. PALB2 mutations compromise RAD51 recruitment, reducing repair efficiency. Defects in RAD51 paralogs such as RAD51C and RAD51D destabilize the recombinase complex, weakening repair. Without functional HR, cells rely on alternative pathways like NHEJ and microhomology-mediated end joining (MMEJ), which introduce deletions, insertions, and translocations that contribute to genomic instability.

Cancer Associations

HRD is strongly linked to cancer, as defective DNA repair drives genomic instability and tumor development. Cancers with HRD exhibit characteristic patterns of mutations and structural alterations due to the inability to accurately repair double-strand breaks. This deficiency is particularly evident in hereditary cancers, where germline mutations in BRCA1, BRCA2, and PALB2 elevate the risk of breast, ovarian, prostate, and pancreatic cancers. In sporadic cancers, somatic inactivation or epigenetic silencing of these genes further contributes to HRD-associated tumorigenesis.

Breast and ovarian cancers are among the most well-characterized HRD-linked malignancies. BRCA1 mutations increase the lifetime risk of breast cancer up to 72% and ovarian cancer up to 44%, while BRCA2 mutations confer risks of 69% and 17%, respectively. These tumors exhibit a distinct mutational signature, including large-scale chromosomal rearrangements and loss of heterozygosity. Beyond hereditary cases, sporadic high-grade serous ovarian cancers (HGSOCs) frequently display HRD due to somatic BRCA mutations or epigenetic silencing of HR-related genes.

HRD is also implicated in prostate and pancreatic cancers, particularly in cases with BRCA2 and ATM mutations. HRD-positive prostate cancers often exhibit aggressive features, including increased genomic instability and poor differentiation, making them more likely to progress to metastatic castration-resistant prostate cancer (mCRPC). In pancreatic cancer, BRCA1/2 mutations are found in approximately 5-7% of cases, with HRD-associated tumors showing heightened sensitivity to DNA-damaging agents such as platinum-based chemotherapy. These findings have important therapeutic implications, as tumors with HRD often respond differently to treatment.

Distinct Genomic Patterns

Cancers with HRD exhibit characteristic genomic alterations that distinguish them from tumors with intact DNA repair mechanisms. A high burden of structural variants, including large-scale deletions, duplications, and chromosomal rearrangements, arises because cells lacking functional HR rely on error-prone repair pathways. Whole-genome sequencing studies reveal that HRD-positive tumors frequently display loss of heterozygosity (LOH), where one copy of a gene is deleted or rendered nonfunctional, further exacerbating genomic instability. LOH scores quantify these deletions and serve as biomarkers for HRD identification.

Another defining feature of HRD-associated tumors is an increased prevalence of tandem duplications, particularly in BRCA1-mutant breast and ovarian cancers. These duplications, spanning 2 to 10 kilobases, result from faulty repair processes. Studies analyzing whole-genome sequencing data from The Cancer Genome Atlas (TCGA) show that tandem duplications strongly predict BRCA1 loss, making them a valuable genomic signature for identifying tumors with HR dysfunction. In contrast, BRCA2-deficient tumors accumulate more deletions with microhomology at breakpoints, a hallmark of alternative repair pathways like MMEJ.

Detection Methods

Identifying HRD in tumors is essential for guiding treatment decisions, particularly for therapies targeting DNA repair vulnerabilities. Several diagnostic approaches assess HRD status, ranging from genetic testing of homologous recombination-related genes to broader genomic signatures indicative of DNA repair dysfunction. Modern detection methods integrate multiple biomarkers to improve sensitivity and specificity in clinical applications.

Next-generation sequencing (NGS)-based genetic testing screens for mutations in key homologous recombination genes such as BRCA1, BRCA2, and PALB2. This method detects both germline and somatic mutations, providing a comprehensive assessment of HRD-related genetic defects. However, because HRD can also arise from epigenetic silencing or complex structural variations, additional genomic analyses are often required. HRD scoring systems incorporate measures such as LOH, large-scale state transitions (LSTs), and telomeric allelic imbalance (TAI). These genomic scars accumulate in tumors with defective homologous recombination, providing a quantitative measure of HRD even in cases without identifiable gene mutations. Commercial assays like Myriad’s MyChoice HRD test and FoundationOne CDx utilize these metrics to classify tumors as HRD-positive or HRD-negative, helping oncologists tailor treatment strategies.

Beyond genomic profiling, functional assays are emerging as a promising avenue for HRD detection. Unlike static genetic or genomic tests, functional assays assess a tumor’s real-time ability to repair DNA damage. One such method measures RAD51 foci formation following DNA damage induction, as RAD51 loading onto single-stranded DNA is a hallmark of homologous recombination activity. Tumors with HRD show impaired RAD51 foci formation, indicating defective repair function. Additionally, CRISPR-based screening techniques systematically disrupt DNA repair pathways and observe cellular responses. While these functional approaches are still being refined for clinical use, they offer the potential for more precise HRD assessments, particularly when genetic and genomic testing yield inconclusive results.