Why do universal HRD testing in ovarian cancer?

The rationale, and the test options for homologous recombination deficiency

Charna Albert

September 2020—Genetic testing in ovarian cancer has a therapeutic implication that will aid in developing a treatment plan, and it is pathologists who should take the lead in creating the testing protocol, said Samuel Caughron, MD, pathologist, president, and CEO of MAWD Pathology Group, in a recent CAP TODAY webinar.

Dr. Caughron explained the rationale for universal homologous recombination deficiency testing in patients with advanced ovarian cancer. The webinar, made possible by a medical sponsorship from AstraZeneca, is at www.captodayonline.com.

Homologous recombination deficiency, or HRD, is comparable to microsatellite instability, said Dr. Caughron, who is also chair of pathology and medical director of the clinical laboratory at AdventHealth Kansas City. Homologous recombination repair, or HRR, is comparable to mismatch repair. “But it’s fixing a different kind of damage,” he said. Mismatch repair fixes single base mismatches. HRR fixes double-strand breaks. In individuals with HRD, the HRR pathway is compromised.

While BRCA1 and BRCA2 are the most prominent molecules involved in HRR, others—RAD51, ATR/ATM, and MRN complex—“combine to give you homologous recombination repair.” When that functionality is lost, there are two possible outcomes: The double-strand breaks persist and cause a complete fracturing of DNA at that site, or the breaks may be repaired by non-homologous end joining, a non-high-fidelity repair pathway that introduces inversions and other genomic aberrations.

Both outcomes result in genomic instability, manifested as a cell’s ability to survive despite DNA damage. “This is the profile of tumors that have BRCA1 and/or BRCA2 proteins that are defective due to mutations, as well as mutations in the other HRR proteins.”

HRD can be caused by a range of specific genomic mutations or alterations in the HRR genes, including ones in BRCA1/2. But altered HRR gene expression, such as promoter methylation, can also cause HRD. And in a percentage of HRD cases the causes are unknown.

There are two core testing strategies for identifying HRD. The first is to test for the presence of specific mutations within BRCA1/2 and other HRR genes by looking at a single gene or panel of genes. “This is a complex problem,” Dr. Caughron said, because BRCA1 and BRCA2 are large genes with thousands of documented mutations, and identifying and interpreting them isn’t straightforward.

The other strategy is to test for the phenotypic effects of HRD within the genome of the tumor. One is loss of heterozygosity, or the presence of a single allele, a cross-chromosomal event that results in the loss of entire genes and the surrounding chromosomal region. In LOH, “There’s a stretch of DNA where, when we look at the genomic analysis, we see only one set of sequences.”

Another is telomeric allelic imbalance, or the accumulation of a discrepancy in the 1:1 allele ratio in the telomere of the chromosome. TAI, which is caused by reciprocal translocations, is “a signature you find in tumors that have genomic instability or HRD.” And the third aberration is chromosomal rearrangements, such as large chromosomal breaks. These are transition points between regions of abnormal and normal DNA, or between two different regions of abnormality.

“By identifying these features, we can find tumors that have homologous recombination deficiency without having to identify specific gene mutations or determine whether the mutation is deleterious,” Dr. Caughron said. There are commercially available assays that can assess one or more of these HRD phenotypes, and other assays that can detect related genes. “And there’s value in looking for genes,” he noted, because of the familial implications.

About 70 percent of patients with epithelial ovarian cancer have high-grade serous histology, and more than half of all high-grade serous ovarian cancers have an HRD phenotype (Konstantinopoulos PA, et al. Cancer Discov. 2015;5[11]:1137–1154; Frey MK, et al. Gynecol Oncol Res Pract. 2017;4:4). A little less than a quarter of women with advanced ovarian cancer have BRCA mutations, the “largest single cause of that type of biology to the tumor.” But a significant portion of HRD tumor cases are due to promoter methylation, and another portion is caused by gene mutations associated with other HRR system proteins. And for another segment, “we know the patient has an HRD phenotype, but we can’t identify the specific cause.”

Thus, about one in four women with advanced ovarian cancer has a BRCA mutation, and about one in two has HRD. “And an important point here is women without a BRCA mutation may still have tumors with HRD,” Dr. Caughron said.