Testing for homologous repair genes (HRR+)

WHAT IS HRR?

Homologous recombination repair genes are involved in the repair of damaged DNA.

Less than 1 in 1000 DNA lesions are persistent. This fact is explained by the functioning of a number of enzymatic repair systems that recognize and repair DNA damage. Disturbance of these systems functioning leads to an uncontrolled increase in the number of mutations that occur in the cell.

< 1 in 1000

of DNA lesions are persistent

One of such systems is the homologous recombination repair (HRR) system, which is aimed at repairing double-strand breaks in the DNA molecule using the genetic material of the homologous chromosome. HRR uses sister chromatids as a template for DNA repair; thus, this mechanism is only available during the late phase of the S/G2 cell cycle.

During HRR, part of the DNA sequence around the double-strand break is removed (resection), exposing regions of single-stranded DNA. DNA recombinase RAD51 binds these regions and enters the DNA sequence on the homologous sister chromatid, using it as a template for the synthesis of new DNA at the double-strand break.

HRR is a complex molecular process that depends on a complex set of proteins.

The BRCA1 and BRCA2 genes play an important role in the HRR pathway, and their dysfunction is the most studied mechanism in tumor cells. Germline and somatic mutations, epigenetic modifications of BRCA1 and BRCA2, as well as genetic changes in some other HRR pathway genes, such as CDK12, CHEK1, CHEK2, RAD51, RAD51B, RAD51C, RAD51D, PALB2, are associated with breast, ovarian, pancreatic, prostate and endometrial cancers.

Mutations in the HRR genes can be divided into two different categories:

germline mutations (germinal),
somatic mutations.

Pathogenic variants in these genes can lead to a deficiency in DNA damage repair and sensitivity to PARP inhibitor therapy.

PARP inhibitors (PARPi) and HRR:

PARP plays a vital role in the repair of DNA single-strand breaks by repairing the gap after removal of the damaged base.

Mechanism of Action of PARP Inhibitors

Inhibition of PARP at the sites of single-stranded DNA breaks results in double-stranded DNA breaks when attempting to replicate the DNA. Double-stranded DNA breaks are usually repaired using the process of homologous recombinational repair (HRR). HRR-deficient tumors cannot accurately repair DNA damage, and if the PARP protein also fails to function properly, both base excision repair (another type of single-strand damage repair) and HRR are disrupted.

In these tumors, DNA repair by low-fidelity repair mechanisms such as non-homologous end joining can cause accumulation of genomic instability, eventually leading to cell death (synthetic lethality).

If PARP is inhibited in cells without HRR deficiency, it does not adversely affect the viability of the tumor cell and the ability to repair single-stranded DNA damage due to the function of other repair pathways.

In addition, preclinical data suggests that PARPi may also benefit patients whose tumors are sensitive to platinum-based chemotherapy and who have got Homologous Recombination Deficiency due to genes other than BRCA1/2.

PARP inhibitors are indicated for various types of cancer, while for breast and pancreatic cancer, germinal mutations in the BRCA1/2 genes are an indication for appointment, and genetic testing for germinal or somatic mutations in the HRR genes by NGS is recommended for all patients with metastatic prostate cancer, as well as ovarian cancer (HRD status).

A figure from de Bono J et al. Annals Oncol. 2019

HRR testing is indicated in those types of cancer, when hereditary tumor syndromes associated with germinal pathogenic variants of mismatched nucleotide repair (MMR) genes are often found, so the study includes the MLH1, MSH2, MSH6, PMS2 genes as well.

Genetic testing based on tumor tissue can both detect somatic variants and suspect germline variants. It is cost-effective and time saving as only one test is to be performed to identify all patients with pathogenic variants who can benefit from PARPi.

Analysis of tumor material allows clinicians to identify an additional approximately 7% of ovarian cancer patients with pathogenic BRCA variants that would be missed if the study was performed from peripheral blood.

According to the clinical guidelines of the Ministry of Health of the Russian Federation, genetic testing for germline mutations in genes involved in DNA repair by homologous recombination (HRR) is recommended for all patients with locally advanced prostate cancer (PC) and metastases in regional lymph nodes. Tumor testing for somatic mutations in the HRR genes by NGS is recommended for all patients with metastatic PC.

What is the HRR+ testing used for?

The detection of Homologous Recombination Deficiency in a tumor applies:

As a prognostic marker
As a predictive marker that determines

the effectiveness of platinum-based chemotherapy drugs;

The presence of HRR mutations leads to persistent DNA damage by platinum-based drugs, which causes cell death.
as a marker of sensitivity to PARP inhibitor therapy.
Deficiency in repair by homologous DNA recombination is associated with susceptibility to poly(ADP-ribose) polymerase inhibition in several types of cancer, including breast, ovarian, pancreatic, and prostate cancer.

Who needs the HRR+ testing?

Patients with:

locally advanced or metastatic prostate cancer;
ovarian cancer who may benefit from PARPi maintenance therapy or who are resistant to platinum-based therapy;
breast cancer and suspected pathogenic BRCA1/2 variant;
epithelial ovarian, fallopian tube and peritoneal cancers all (SGO recommendations);
pancreatic cancer, if BRCA1/2 mutations are suspected.