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Homologous recombination deficiency real-time clinical assays, ready or not?

Published:September 20, 2020DOI:https://doi.org/10.1016/j.ygyno.2020.08.035

      Highlights

      • Homologous Recombination Repair is a central pathway for DNA damage repair.
      • Current methods for detection of homologous recombination deficiency (HRD) do not fully correlate with treatment response.
      • Absence of RAD51 foci formation has been used as a “functional assay” for HRD.
      • Replication fork degradation has been correlated with platinum-sensitvity in BRCA-deficient tumors.
      • BRCA1, BRCA2, and RAD51 have roles in both homologous recombination repair and replication fork protection.

      Abstract

      Cancers with deficiencies in homologous recombination-mediated DNA repair (HRR) demonstrate improved clinical outcomes and increased survival. Approximately 50% of high-grade serous ovarian cancers (HGSOC) exhibit homologous recombination deficiency (HRD). HRD can be caused by germline or somatic mutations of genes involved in the HR pathway. Given platinum-based chemotherapy and poly (ADP-ribose) polymerase inhibitors (PARPis) are used in HGSOC, double-strand breaks (DSBs) are common. Unrepaired DSBs are toxic to cells as genomic instability ensues and cells eventually die. Thus, tumor cells with DSBs utilize the high-fidelity HRR as one of the central pathways for repair. In tumors that have HRD, an alternate pathway such as non-homologous end-joining (NHEJ) is used and leads to error-prone repair. To date, methods for clinical detection of homologous recombination deficiency (HRD) are limited to genomic changes of HRR genes and genomic mutation patterns resulting from HRD genes involved in HR-mediated DNA repair. However, these tests detect genomic scars that might not always correlate well with PARP inhibitor or platinum sensitivity in the current state. Therefore, a functional HRD assay should be able to more accurately predict tumor response in real-time. RAD51 foci formation has been used as a functional assay to define HRD and closely correlates with chemotherapy and PARPi sensitivity. The inability to form RAD51 foci is a common feature of HRD. DNA damage can also cause transient slowing or stalling of replication forks defined as replication stress. Replication fork stalling can lead to fork degradation and decreased cell viability if forks do not resume DNA synthesis. Fork degradation has been found to lead to chemosensitivity in BRCA-deficient tumors. To determine this fork degradation phenotype, replication fork/DNA fiber assays are utilized. This review will highlight functional assays for HRD in the context of translating these to real-time clinical assays.

      Keywords

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      References

        • Vilenchik M.M.
        • Knudson A.G.
        Endogenous DNA double-strand breaks: production, fidelity of repair, and induction of cancer.
        Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 12871-12876
        • Whelan D.R.
        • Lee W.T.C.
        • Yin Y.
        • Ofri D.M.
        • Bermudez-Hernandez K.
        • Keegan S.
        • et al.
        Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks.
        Nat. Commun. 2018; 9: 3882
        • Byrum A.K.
        • Vindigni A.
        • Mosammaparast N.
        Defining and modulating ‘BRCAness’.
        Trends Cell Biol. 2019; 29: 740-751
        • Konstantinopoulos P.A.
        • Ceccaldi R.
        • Shapiro G.I.
        • D’Andrea A.D.
        Homologous recombination deficiency: exploiting the fundamental vulnerability of ovarian cancer.
        Cancer Discov. 2015; 5: 1137-1154
        • Walsh T.
        • Casadei S.
        • Lee M.K.
        • Pennil C.C.
        • Nord A.S.
        • Thornton A.M.
        • et al.
        Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing.
        Proc. Natl. Acad. Sci. U. S. A. 2011; 108: 18032-18037
        • Pennington K.P.
        • Walsh T.
        • Harrell M.I.
        • Lee M.K.
        • Pennil C.C.
        • Rendi M.H.
        • et al.
        Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian, fallopian tube, and peritoneal carcinomas.
        Clin. Cancer Res. 2014; 20: 764-775
        • Wagle N.
        • Berger M.F.
        • Davis M.J.
        • Blumenstiel B.
        • Defelice M.
        • Pochanard P.
        • et al.
        High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.
        Cancer Discov. 2012; 2: 82-93
        • Swisher E.M.
        • Lin K.K.
        • Oza A.M.
        • Scott C.L.
        • Giordano H.
        • Sun J.
        • et al.
        Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1): an international, multicentre, open-label, phase 2 trial.
        Lancet Oncol. 2017; 18: 75-87
        • Mirza M.R.
        • Monk B.J.
        • Herrstedt J.
        • Oza A.M.
        • Mahner S.
        • Redondo A.
        • et al.
        Niraparib maintenance therapy in platinum-sensitive, recurrent ovarian cancer.
        N. Engl. J. Med. 2016; 375: 2154-2164
        • Davies H.
        • Glodzik D.
        • Morganella S.
        • Yates L.R.
        • Staaf J.
        • Zou X.
        • et al.
        HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
        Nat. Med. 2017; 23: 517-525
        • Chopra N.
        • Tovey H.
        • Pearson A.
        • Cutts R.
        • Toms C.
        • Proszek P.
        • et al.
        Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer.
        Nat. Commun. 2020; 11: 2662
        • Zhao E.Y.
        • Shen Y.
        • Pleasance E.
        • Kasaian K.
        • Leelakumari S.
        • Jones M.
        • et al.
        Homologous recombination deficiency and platinum-based therapy outcomes in advanced breast cancer.
        Clin. Cancer Res. 2017; 23: 7521-7530
        • Edwards S.L.
        • Brough R.
        • Lord C.J.
        • Natrajan R.
        • Vatcheva R.
        • Levine D.A.
        • et al.
        Resistance to therapy caused by intragenic deletion in BRCA2.
        Nature. 2008; 451: 1111-1115
        • Kondrashova O.
        • Nguyen M.
        • Shield-Artin K.
        • Tinker A.V.
        • Teng N.N.H.
        • Harrell M.I.
        • et al.
        Secondary somatic mutations restoring RAD51C and RAD51D associated with acquired resistance to the PARP inhibitor rucaparib in high-grade ovarian carcinoma.
        Cancer Discov. 2017; 7: 984-998
        • Sakai W.
        • Swisher E.M.
        • Karlan B.Y.
        • Agarwal M.K.
        • Higgins J.
        • Friedman C.
        • et al.
        Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers.
        Nature. 2008; 451: 1116-1120
        • Norquist B.
        • Wurz K.A.
        • Pennil C.C.
        • Garcia R.
        • Gross J.
        • Sakai W.
        • et al.
        Secondary somatic mutations restoring BRCA1/2 predict chemotherapy resistance in hereditary ovarian carcinomas.
        J. Clin. Oncol. 2011; 29: 3008-3015
        • Swisher E.M.
        • Sakai W.
        • Karlan B.Y.
        • Wurz K.
        • Urban N.
        • Taniguchi T.
        Secondary BRCA1 mutations in BRCA1-mutated ovarian carcinomas with platinum resistance.
        Cancer Res. 2008; 68: 2581-2586
        • Drost R.
        • Dhillon K.K.
        • van der Gulden H.
        • van der Heijden I.
        • Brandsma I.
        • Cruz C.
        • et al.
        BRCA1185delAG tumors may acquire therapy resistance through expression of RING-less BRCA1.
        J. Clin. Invest. 2016; 126: 2903-2918
        • Johnson N.
        • Johnson S.F.
        • Yao W.
        • Li Y.C.
        • Choi Y.E.
        • Bernhardy A.J.
        • et al.
        Stabilization of mutant BRCA1 protein confers PARP inhibitor and platinum resistance.
        Proc. Natl. Acad. Sci. U. S. A. 2013; 110: 17041-17046
        • Wang Y.
        • Bernhardy A.J.
        • Cruz C.
        • Krais J.J.
        • Nacson J.
        • Nicolas E.
        • et al.
        The BRCA1-Delta11q alternative splice isoform bypasses germline mutations and promotes therapeutic resistance to PARP inhibition and cisplatin.
        Cancer Res. 2016; 76: 2778-2790
        • Burger H.
        • Loos W.J.
        • Eechoute K.
        • Verweij J.
        • Mathijssen R.H.
        • Wiemer E.A.
        Drug transporters of platinum-based anticancer agents and their clinical significance.
        Drug Resist. Updat. 2011; 14: 22-34
        • Chaudhuri A.R.
        • Callen E.
        • Ding X.
        • Gogola E.
        • Duarte A.A.
        • Lee J.E.
        • et al.
        Replication fork stability confers chemoresistance in BRCA-deficient cells.
        Nature. 2016; 535: 382
        • Jaspers J.E.
        • Kersbergen A.
        • Boon U.
        • Sol W.
        • van Deemter L.
        • Zander S.A.
        • et al.
        Loss of 53BP1 causes PARP inhibitor resistance in Brca1-mutated mouse mammary tumors.
        Cancer Discov. 2013; 3: 68-81
        • Rondinelli B.
        • Gogola E.
        • Yucel H.
        • Duarte A.A.
        • van de Ven M.
        • van der Sluijs R.
        • et al.
        EZH2 promotes degradation of stalled replication forks by recruiting MUS81 through histone H3 trimethylation.
        Nat. Cell Biol. 2017; 19: 1371-1378
        • Rottenberg S.
        • Jaspers J.E.
        • Kersbergen A.
        • van der Burg E.
        • Nygren A.O.
        • Zander S.A.
        • et al.
        High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs.
        Proc. Natl. Acad. Sci. U. S. A. 2008; 105: 17079-17084
        • Xu G.
        • Chapman J.R.
        • Brandsma I.
        • Yuan J.
        • Mistrik M.
        • Bouwman P.
        • et al.
        REV7 counteracts DNA double-strand break resection and affects PARP inhibition.
        Nature. 2015; 521: 541-544
        • Hill S.J.
        • Decker B.
        • Roberts E.A.
        • Horowitz N.S.
        • Muto M.G.
        • Worley Jr., M.J.
        • et al.
        Prediction of DNA repair inhibitor response in short-term patient-derived ovarian cancer organoids.
        Cancer Discov. 2018; 8: 1404-1421
        • Hurley R.M.
        • Wahner Hendrickson A.E.
        • Visscher D.W.
        • Ansell P.
        • Harrell M.I.
        • Wagner J.M.
        • et al.
        53BP1 as a potential predictor of response in PARP inhibitor-treated homologous recombination-deficient ovarian cancer.
        Gynecol. Oncol. 2019; 153: 127-134
        • Makvandi M.
        • Pantel A.
        • Schwartz L.
        • Schubert E.
        • Xu K.
        • Hsieh C.J.
        • et al.
        A PET imaging agent for evaluating PARP-1 expression in ovarian cancer.
        J. Clin. Invest. 2018; 128: 2116-2126
        • Del Campo J.M.
        • Matulonis U.A.
        • Malander S.
        • Provencher D.
        • Mahner S.
        • Follana P.
        • et al.
        Niraparib maintenance therapy in patients with recurrent ovarian cancer after a partial response to the last platinum-based chemotherapy in the ENGOT-OV16/NOVA trial.
        J. Clin. Oncol. 2019; 37: 2968-2973
        • Stover E.H.
        • Konstantinopoulos P.A.
        • Matulonis U.A.
        • Swisher E.M.
        Biomarkers of response and resistance to DNA repair targeted therapies.
        Clin. Cancer Res. 2016; 22: 5651-5660
        • Graeser M.
        • McCarthy A.
        • Lord C.J.
        • Savage K.
        • Hills M.
        • Salter J.
        • et al.
        A marker of homologous recombination predicts pathologic complete response to neoadjuvant chemotherapy in primary breast cancer.
        Clin. Cancer Res. 2010; 16: 6159-6168
        • Mukhopadhyay A.
        • Elattar A.
        • Cerbinskaite A.
        • Wilkinson S.J.
        • Drew Y.
        • Kyle S.
        • et al.
        Development of a functional assay for homologous recombination status in primary cultures of epithelial ovarian tumor and correlation with sensitivity to poly(ADP-ribose) polymerase inhibitors.
        Clin. Cancer Res. 2010; 16: 2344-2351
        • Naipal K.A.
        • Verkaik N.S.
        • Ameziane N.
        • van Deurzen C.H.
        • Ter Brugge P.
        • Meijers M.
        • et al.
        Functional ex vivo assay to select homologous recombination-deficient breast tumors for PARP inhibitor treatment.
        Clin. Cancer Res. 2014; 20: 4816-4826
        • Tumiati M.
        • Hietanen S.
        • Hynninen J.
        • Pietila E.
        • Farkkila A.
        • Kaipio K.
        • et al.
        A functional homologous recombination assay predicts primary chemotherapy response and long-term survival in ovarian cancer patients.
        Clin. Cancer Res. 2018; 24: 4482-4493
        • Mason J.M.
        • Chan Y.L.
        • Weichselbaum R.W.
        • Bishop D.K.
        Non-enzymatic roles of human RAD51 at stalled replication forks.
        Nat. Commun. 2019; 10: 4410
        • Ceccaldi R.
        • Rondinelli B.
        • D’Andrea A.D.
        Repair pathway choices and consequences at the double-strand break.
        Trends Cell Biol. 2016; 26: 52-64
        • Wilson A.J.
        • Stubbs M.
        • Liu P.
        • Ruggeri B.
        • Khabele D.
        The BET inhibitor INCB054329 reduces homologous recombination efficiency and augments PARP inhibitor activity in ovarian cancer.
        Gynecol. Oncol. 2018; 149: 575-584
        • Shah M.M.
        • Dobbin Z.C.
        • Nowsheen S.
        • Wielgos M.
        • Katre A.A.
        • Alvarez R.D.
        • et al.
        An ex vivo assay of XRT-induced Rad51 foci formation predicts response to PARP-inhibition in ovarian cancer.
        Gynecol. Oncol. 2014; 134: 331-337
        • Castroviejo-Bermejo M.
        • Cruz C.
        • Llop-Guevara A.
        • Gutierrez-Enriquez S.
        • Ducy M.
        • Ibrahim Y.H.
        • et al.
        A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation.
        EMBO Mol. Med. 2018; 10
        • Meijer T.G.
        • Verkaik N.S.
        • Sieuwerts A.M.
        • van Riet J.
        • Naipal K.A.T.
        • van Deurzen C.H.M.
        • et al.
        Functional ex vivo assay reveals homologous recombination deficiency in breast cancer beyond BRCA gene defects.
        Clin. Cancer Res. 2018; 24: 6277-6287
        • Meijer T.G.
        • Verkaik N.S.
        • van Deurzen C.H.
        • Dubbink H.J.
        • den Toom D.
        • Sleddens H.F.B.M.
        • De Hoop E.O.
        • Dinjens W.N.M.
        • Kanaar R.
        • van Gent D.C.
        • Jager A.
        Direct ex vivo observations of homologous recombination defect reversal after DNA-damaging chemotherapy in patients with metastatic breast cancer.
        JCO Precis. Oncol. 2019; 3: 1-12
        • Cruz C.
        • Castroviejo-Bermejo M.
        • Gutierrez-Enriquez S.
        • Llop-Guevara A.
        • Ibrahim Y.H.
        • Gris-Oliver A.
        • et al.
        RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA-mutated breast cancer.
        Ann. Oncol. 2018; 29: 1203-1210
        • Waks A.G.
        • Cohen O.
        • Kochupurakkal B.
        • Kim D.
        • Dunn C.E.
        • Buendia Buendia J.
        • et al.
        Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer.
        Ann. Oncol. 2020; 31: 590-598
        • San Filippo J.
        • Sung P.
        • Klein H.
        Mechanism of eukaryotic homologous recombination.
        Annu. Rev. Biochem. 2008; 77: 229-257
        • Kawamoto T.
        • Araki K.
        • Sonoda E.
        • Yamashita Y.M.
        • Harada K.
        • Kikuchi K.
        • et al.
        Dual roles for DNA polymerase eta in homologous DNA recombination and translesion DNA synthesis.
        Mol. Cell. 2005; 20: 793-799
        • Wiese C.
        • Dray E.
        • Groesser T.
        • San Filippo J.
        • Shi I.
        • Collins D.W.
        • et al.
        Promotion of homologous recombination and genomic stability by RAD51AP1 via RAD51 recombinase enhancement.
        Mol. Cell. 2007; 28: 482-490
        • Balmus G.
        • Pilger D.
        • Coates J.
        • Demir M.
        • Sczaniecka-Clift M.
        • Barros A.C.
        • et al.
        ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks.
        Nat. Commun. 2019; 10: 87
        • Gogola E.
        • Duarte A.A.
        • de Ruiter J.R.
        • Wiegant W.W.
        • Schmid J.A.
        • de Bruijn R.
        • et al.
        Selective loss of PARG restores PARylation and counteracts PARP inhibitor-mediated synthetic lethality.
        Cancer Cell. 2018; 33 (e12): 1078-1093
        • Guillemette S.
        • Serra R.W.
        • Peng M.
        • Hayes J.A.
        • Konstantinopoulos P.A.
        • Green M.R.
        • et al.
        Resistance to therapy in BRCA2 mutant cells due to loss of the nucleosome remodeling factor CHD4.
        Genes Dev. 2015; 29: 489-494
        • Kais Z.
        • Rondinelli B.
        • Holmes A.
        • O’Leary C.
        • Kozono D.
        • D’Andrea A.D.
        • et al.
        FANCD2 maintains fork stability in BRCA1/2-deficient tumors and promotes alternative end-joining DNA repair.
        Cell Rep. 2016; 15: 2488-2499
        • Ait Saada A.
        • Lambert S.A.E.
        • Carr A.M.
        Preserving replication fork integrity and competence via the homologous recombination pathway.
        DNA Repair (Amst). 2018; 71: 135-147
        • Yao N.Y.
        • O’Donnell M.
        Replisome structure and conformational dynamics underlie fork progression past obstacles.
        Curr. Opin. Cell Biol. 2009; 21: 336-343
        • Berti M.
        • Vindigni A.
        Replication stress: getting back on track.
        Nat. Struct. Mol. Biol. 2016; 23: 103-109
        • Zeman M.K.
        • Cimprich K.A.
        Causes and consequences of replication stress.
        Nat. Cell Biol. 2014; 16: 2-9
        • Cortez D.
        Preventing replication fork collapse to maintain genome integrity.
        DNA Repair (Amst.). 2015; 32: 149-157
        • Daza-Martin M.
        • Starowicz K.
        • Jamshad M.
        • Tye S.
        • Ronson G.E.
        • MacKay H.L.
        • et al.
        Isomerization of BRCA1-BARD1 promotes replication fork protection.
        Nature. 2019; 571: 521-527
        • Schlacher K.
        • Christ N.
        • Siaud N.
        • Egashira A.
        • Wu H.
        • Jasin M.
        Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11.
        Cell. 2011; 145: 529-542
        • Ying S.
        • Hamdy F.C.
        • Helleday T.
        Mre11-dependent degradation of stalled DNA replication forks is prevented by BRCA2 and PARP1.
        Cancer Res. 2012; 72: 2814-2821
        • Quinet A.
        • Tirman S.
        • Jackson J.
        • Šviković S.
        • Lemaçon D.
        • Carvajal-Maldonado D.
        • et al.
        PRIMPOL-mediated adaptive response suppresses replication fork reversal in BRCA-deficient cells.
        Mol Cell. 2020; 77 (e9): 461-474
        • Maya-Mendoza A.
        • Moudry P.
        • Merchut-Maya J.M.
        • Lee M.
        • Strauss R.
        • Bartek J.
        High speed of fork progression induces DNA replication stress and genomic instability.
        Nature. 2018; 559: 279-284
        • Helleday T.
        The underlying mechanism for the PARP and BRCA synthetic lethality: clearing up the misunderstandings.
        Mol. Oncol. 2011; 5: 387-393
        • Murai J.
        • Huang S.Y.
        • Das B.B.
        • Renaud A.
        • Zhang Y.
        • Doroshow J.H.
        • et al.
        Trapping of PARP1 and PARP2 by clinical PARP inhibitors.
        Cancer Res. 2012; 72: 5588-5599
        • Bensimon A.
        • Simon A.
        • Chiffaudel A.
        • Croquette V.
        • Heslot F.
        • Bensimon D.
        Alignment and sensitive detection of DNA by a moving interface.
        Science. 1994; 265: 2096-2098
        • Michalet X.
        • Ekong R.
        • Fougerousse F.
        • Rousseaux S.
        • Schurra C.
        • Hornigold N.
        • et al.
        Dynamic molecular combing: stretching the whole human genome for high-resolution studies.
        Science. 1997; 277: 1518-1523
        • Parra I.
        • Windle B.
        High resolution visual mapping of stretched DNA by fluorescent hybridization.
        Nat. Genet. 1993; 5: 17-21
        • Técher H.
        • Koundrioukoff S.
        • Azar D.
        • Wilhelm T.
        • Carignon S.
        • Brison O.
        • et al.
        Replication dynamics: biases and robustness of DNA fiber analysis.
        J. Mol. Biol. 2013; 425: 4845-4855
        • Quinet A.
        • Carvajal-Maldonado D.
        • Lemacon D.
        • Vindigni A.
        DNA fiber analysis: mind the gap!.
        Methods Enzymol. 2017; 591: 55-82
        • Schlacher K.
        • Wu H.
        • Jasin M.
        A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2.
        Cancer Cell. 2012; 22: 106-116
        • Nieminuszczy J.
        • Schwab R.A.
        • Niedzwiedz W.
        The DNA fiber technique - tracking helicases at work.
        Methods. 2016; 108: 92-98
        • Konstantinopoulos P.A.
        • Lheureux S.
        • Moore K.N.
        PARP inhibitors for ovarian cancer: current indications, future combinations, and novel assets in development to target DNA damage repair.
        Am. Soc. Clin. Oncol. Educ. Book. 2020; 40: 1-16