DNA Repair Pathway Gene Expression Score Correlates with Repair Proficiency and Tumor Sensitivity to Chemotherapy (original) (raw)

Navigating Tumor Therapy with an RPS

For cancer patients, DNA damage is a double-edged sword. Mutations can contribute to carcinogenesis, but the cancer cell can’t survive with too much DNA damage. Indeed, many cancer therapies aim at increasing DNA damage, but selecting the correct therapies for individual patients can be hit-or-miss. Pitroda et al. proposed that mechanisms of double-strand DNA break repair could correlate with cancer prognosis and could guide choices in cancer therapy.

The authors devised a recombination proficiency score (RPS) based on the expression levels for four genes involved in DNA repair pathway preference. They then validated the RPS in patients with either breast or non–small cell lung cancer. Tumors with low RPS—suppressed homologous recombination (HR)—were associated with greater mutagenesis and decreased likelihood of patient survival. This prognosis could be counteracted with platinum-based adjuvant chemotherapy—patients with suppressed HR were more sensitive to this treatment. These data suggest that RPS can help determine treatment course for cancer patients.

Abstract

Mutagenesis is a hallmark of malignancy, and many oncologic treatments function by generating additional DNA damage. Therefore, DNA damage repair is centrally important in both carcinogenesis and cancer treatment. Homologous recombination (HR) and nonhomologous end joining are alternative pathways of double-strand DNA break repair. We developed a method to quantify the efficiency of DNA repair pathways in the context of cancer therapy. The recombination proficiency score (RPS) is based on the expression levels for four genes involved in DNA repair pathway preference (Rif1, PARI, RAD51, and Ku80), such that high expression of these genes yields a low RPS. Carcinoma cells with low RPS exhibit HR suppression and frequent DNA copy number alterations, which are characteristic of error-prone repair processes that arise in HR-deficient backgrounds. The RPS system was clinically validated in patients with breast or non–small cell lung carcinomas (NSCLCs). Tumors with low RPS were associated with greater mutagenesis, adverse clinical features, and inferior patient survival rates, suggesting that HR suppression contributes to the genomic instability that fuels malignant progression. This adverse prognosis associated with low RPS was diminished if NSCLC patients received adjuvant chemotherapy, suggesting that HR suppression and associated sensitivity to platinum-based drugs counteract the adverse prognosis associated with low RPS. Therefore, RPS may help oncologists select which therapies will be effective for individual patients, thereby enabling more personalized care.

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Supplementary Material

Summary

Fig. S1. Most of the drug sensitivity values mined from the CCLE database were generated in the same cell lines.

Fig. S2. A representative panel of cancer cell lines exhibit expected levels of drug resistance.

Fig. S3. Measurements of mRNA by real-time qRT-PCR for six representative cell lines generated RPS values that were comparable to RPS values calculated from array-based mRNA levels reported in the CCLE database.

Table S1. DNA repair genes that significantly associate with topotecan sensitivity.

Table S2. Correlation coefficients resulting from combinations of genes.

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REFERENCES AND NOTES

Thompson L. H., Schild D., Homologous recombinational repair of DNA ensures mammalian chromosome stability. Mutat. Res. 477, 131–153 (2001).

Lieber M. R., Ma Y., Pannicke U., Schwarz K., The mechanism of vertebrate nonhomologous DNA end joining and its role in V(D)J recombination. DNA Repair 3, 817–826 (2004).

Chapman J. R., Sossick A. J., Boulton S. J., Jackson S. P., BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J. Cell Sci. 125, 3529–3534 (2013).

Zimmermann M., Lottersberger F., Buonomo S. B., Sfeir A., de Lange T., 53BP1 regulates DSB repair using Rif1 to control 5′ end resection. Science 339, 700–704 (2013).

Chapman J. R., Barral P., Vannier J. B., Borel V., Steger M., Tomas-Loba A., Sartori A. A., Adams I. R., Batista F. D., Boulton S. J., RIF1 is essential for 53BP1-dependent nonhomologous end joining and suppression of DNA double-strand break resection. Mol. Cell 49, 858–871 (2013).

Buis J., Stoneham T., Spehalski E., Ferguson D. O., Mre11 regulates CtIP-dependent double-strand break repair by interaction with CDK2. Nat. Struct. Mol. Biol. 19, 246–252 (2012).

Arlt M. F., Rajendran S., Birkeland S. R., Wilson T. E., Glover T. W., De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining. PLOS Genet. 8, e1002981 (2012).

Guirouilh-Barbat J., Huck S., Bertrand P., Pirzio L., Desmaze C., Sabatier L., Lopez B. S., Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. Mol. Cell 14, 611–623 (2004).

Bennardo N., Cheng A., Huang N., Stark J. M., Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLOS Genet. 4, e1000110 (2008).

Malkova A., Haber J. E., Mutations arising during repair of chromosome breaks. Annu. Rev. Genet. 46, 455–473 (2012).

Bryant H. E., Schultz N., Thomas H. D., Parker K. M., Flower D., Lopez E., Kyle S., Meuth M., Curtin N. J., Helleday T., Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature 434, 913–917 (2005).

Farmer H., McCabe N., Lord C. J., Tutt A. N., Johnson D. A., Richardson T. B., Santarosa M., Dillon K. J., Hickson I., Knights C., Martin N. M., Jackson S. P., Smith G. C., Ashworth A., Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434, 917–921 (2005).

O’Shaughnessy J., Osborne C., Pippen J. E., Yoffe M., Patt D., Rocha C., Koo I. C., Sherman B. M., Bradley C., Iniparib plus chemotherapy in metastatic triple-negative breast cancer. N. Engl. J. Med. 364, 205–214 (2011).

Edwards S. L., Brough R., Lord C. J., Natrajan R., Vatcheva R., Levine D. A., Boyd J., Reis-Filho J. S., Ashworth A., Resistance to therapy caused by intragenic deletion in BRCA2. Nature 451, 1111–1115 (2008).

Sakai W., Swisher E. M., Karlan B. Y., Agarwal M. K., Higgins J., Friedman C., Villegas E., Jacquemont C., Farrugia D. J., Couch F. J., Urban N., Taniguchi T., Secondary mutations as a mechanism of cisplatin resistance in _BRCA2_-mutated cancers. Nature 451, 1116–1120 (2008).

Willers H., Taghian A. G., Luo C. M., Treszezamsky A., Sgroi D. C., Powell S. N., Utility of DNA repair protein foci for the detection of putative BRCA1 pathway defects in breast cancer biopsies. Mol. Cancer Res. 7, 1304–1309 (2009).

Birkelbach M., Ferraiolo N., Gheorghiu L., Pfäffle H. N., Daly B., Ebright M. I., Spencer C., O’Hara C., Whetstine J. R., Benes C. H., Sequist L. V., Zou L., Dahm-Daphi J., Kachnic L. A., Willers H., Detection of impaired homologous recombination repair in NSCLC cells and tissues. J. Thorac. Oncol. 8, 279–286 (2013).

Redon C. E., Weyemi U., Parekh P. R., Huang D., Burrell A. S., Bonner W. M., γ-H2AX and other histone post-translational modifications in the clinic. Biochim. Biophys. Acta 1819, 743–756 (2012).

Barretina J., Caponigro G., Stransky N., Venkatesan K., Margolin A. A., Kim S., Wilson C. J., Lehár J., Kryukov G. V., Sonkin D., Reddy A., Liu M., Murray L., Berger M. F., Monahan J. E., Morais P., Meltzer J., Korejwa A., Jané-Valbuena J., Mapa F. A., Thibault J., Bric-Furlong E., Raman P., Shipway A., Engels I. H., Cheng J., Yu G. K., Yu J., Aspesi P., de Silva M., Jagtap K., Jones M. D., Wang L., Hatton C., Palescandolo E., Gupta S., Mahan S., Sougnez C., Onofrio R. C., Liefeld T., MacConaill L., Winckler W., Reich M., Li N., Mesirov J. P., Gabriel S. B., Getz G., Ardlie K., Chan V., Myer V. E., Weber B. L., Porter J., Warmuth M., Finan P., Harris J. L., Meyerson M., Golub T. R., Morrissey M. P., Sellers W. R., Schlegel R., Garraway L. A., The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).

Nitiss J., Wang J. C., DNA topoisomerase-targeting antitumor drugs can be studied in yeast. Proc. Natl. Acad. Sci. U.S.A. 85, 7501–7505 (1988).

Arnaudeau C., Lundin C., Helleday T., DNA double-strand breaks associated with replication forks are predominantly repaired by homologous recombination involving an exchange mechanism in mammalian cells. J. Mol. Biol. 307, 1235–1245 (2001).

Moldovan G. L., Dejsuphong D., Petalcorin M. I., Hofmann K., Takeda S., Boulton S. J., D’Andrea A. D., Inhibition of homologous recombination by the PCNA-interacting protein PARI. Mol. Cell 45, 75–86 (2012).

Martin R. W., Orelli B. J., Yamazoe M., Minn A. J., Takeda S., Bishop D. K., RAD51 up-regulation bypasses BRCA1 function and is a common feature of _BRCA1_-deficient breast tumors. Cancer Res. 67, 9658–9665 (2007).

Honrado E., Osorio A., Palacios J., Milne R. L., Sánchez L., Díez O., Cazorla A., Syrjakoski K., Huntsman D., Heikkilä P., Lerma E., Kallioniemi A., Rivas C., Foulkes W. D., Nevanlinna H., Benítez J., Immunohistochemical expression of DNA repair proteins in familial breast cancer differentiate _BRCA2_-associated tumors. J. Clin. Oncol. 23, 7503–7511 (2005).

Sartori A. A., Lukas C., Coates J., Mistrik M., Fu S., Bartek J., Baer R., Lukas J., Jackson S. P., Human CtIP promotes DNA end resection. Nature 450, 509–514 (2007).

Yata K., Lloyd J., Maslen S., Bleuyard J. Y., Skehel M., Smerdon S. J., Esashi F., Plk1 and CK2 act in concert to regulate Rad51 during DNA double strand break repair. Mol. Cell 45, 371–383 (2012).

van Vugt M. A., Gardino A. K., Linding R., Ostheimer G. J., Reinhardt H. C., Ong S. E., Tan C. S., Miao H., Keezer S. M., Li J., Pawson T., Lewis T. A., Carr S. A., Smerdon S. J., Brummelkamp T. R., Yaffe M. B., A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G2/M DNA damage checkpoint. PLOS Biol. 8, e1000287 (2010).

Thompson L. H., Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: The molecular choreography. Mutat. Res. 751, 158–246 (2012).

Takata M., Sasaki M. S., Tachiiri S., Fukushima T., Sonoda E., Schild D., Thompson L. H., Takeda S., Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs. Mol. Cell. Biol. 21, 2858–2866 (2001).

Fang M., Xia F., Mahalingam M., Virbasius C. M., Wajapeyee N., Green M. R., MEN1 is a melanoma tumor suppressor that preserves genomic integrity by stimulating transcription of genes that promote homologous recombination-directed DNA repair. Mol. Cell. Biol. 33, 2635–2647 (2013).

Pierce A. J., Johnson R. D., Thompson L. H., Jasin M., XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev. 13, 2633–2638 (1999).

Hinz J. M., Tebbs R. S., Wilson P. F., Nham P. B., Salazar E. P., Nagasawa H., Urbin S. S., Bedford J. S., Thompson L. H., Repression of mutagenesis by Rad51D-mediated homologous recombination. Nucleic Acids Res. 34, 1358–1368 (2006).

Payen C., Koszul R., Dujon B., Fischer G., Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms. PLOS Genet. 4, e1000175 (2008).

Linke S. P., Sengupta S., Khabie N., Jeffries B. A., Buchhop S., Miska S., Henning W., Pedeux R., Wang X. W., Hofseth L. J., Yang Q., Garfield S. H., Stürzbecher H. W., Harris C. C., p53 interacts with hRAD51 and hRAD54, and directly modulates homologous recombination. Cancer Res. 63, 2596–2 605 (2003).

Sirbu B. M., Lachmayer S. J., Wülfing V., Marten L. M., Clarkson K. E., Lee L. W., Gheorghiu L., Zou L., Powell S. N., Dahm-Daphi J., Willers H., ATR-p53 restricts homologous recombination in response to replicative stress but does not limit DNA interstrand crosslink repair in lung cancer cells. PLOS One 6, e23053 (2011).

Gebow D., Miselis N., Liber H. L., Homologous and nonhomologous recombination resulting in deletion: Effects of p53 status, microhomology, and repetitive DNA length and orientation. Mol. Cell. Biol. 20, 4028–4035 (2000).

Zhu C. Q., Ding K., Strumpf D., Weir B. A., Meyerson M., Pennell N., Thomas R. K., Naoki K., Ladd-Acosta C., Liu N., Pintilie M., Der S., Seymour L., Jurisica I., Shepherd F. A., Tsao M. S., Prognostic and predictive gene signature for adjuvant chemotherapy in resected non–small-cell lung cancer. J. Clin. Oncol. 28, 4417–4424 (2010).

Okayama H., Kohno T., Ishii Y., Shimada Y., Shiraishi K., Iwakawa R., Furuta K., Tsuta K., Shibata T., Yamamoto S., Watanabe S., Sakamoto H., Kumamoto K., Takenoshita S., Gotoh N., Mizuno H., Sarai A., Kawano S., Yamaguchi R., Miyano S., Yokota J., Identification of genes upregulated in _ALK_-positive and _EGFR/KRAS/ALK_-negative lung adenocarcinomas. Cancer Res. 72, 100–111 (2012).

Tang H., Xiao G., Behrens C., Schiller J., Allen J., Chow C. W., Suraokar M., Corvalan A., Mao J., White M. A., Wistuba I. I., Minna J. D., Xie Y., A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small cell lung cancer patients. Clin. Cancer Res. 19, 1577–1586 (2013).

Director’s Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma, Shedden K., Taylor J. M., Enkemann S. A., Tsao M. S., Yeatman T. J., Gerald W. L., Eschrich S., Jurisica I., Giordano T. J., Misek D. E., Chang A. C., Zhu C. Q., Strumpf D., Hanash S., Shepherd F. A., Ding K., Seymour L., Naoki K., Pennell N., Weir B., Verhaak R., Ladd-Acosta C., Golub T., Gruidl M., Sharma A., Szoke J., Zakowski M., Rusch V., Kris M., Viale A., Motoi N., Travis W., Conley B., Seshan V. E., Meyerson M., Kuick R., Dobbin K. K., Lively T., Jacobson J. W., Beer D. G., Gene expression–based survival prediction in lung adenocarcinoma: A multi-site, blinded validation study. Nat. Med. 14, 822–827 (2008).

Neyeloff J. L., Fuchs S. C., Moreira L. B., Meta-analyses and Forest plots using a Microsoft Excel spreadsheet: Step-by-step guide focusing on descriptive data analysis. BMC Res. Notes 5, 52 (2012).

Steensma D. P., The beginning of the end of the beginning in cancer genomics. N. Engl. J. Med. 368, 2138–2140 (2013).

Winnepenninckx V., Lazar V., Michiels S., Dessen P., Stas M., Alonso S. R., Avril M. F., Ortiz Romero P. L., Robert T., Balacescu O., Eggermont A. M., Lenoir G., Sarasin A., Tursz T., van den Oord J. J., Spatz A.; Melanoma Group of the European Organization for Research and Treatment of Cancer, Gene expression profiling of primary cutaneous melanoma and clinical outcome. J. Natl. Cancer Inst. 98, 472–482 (2006).

Sarasin A., Kauffmann A., Overexpression of DNA repair genes is associated with metastasis: A new hypothesis. Mutat. Res. 659, 49–55 (2008).

Swisher E. M., Taniguchi T., Karlan B. Y., Molecular scores to predict ovarian cancer outcomes: A worthy goal, but not ready for prime time. J. Natl. Cancer Inst. 104, 642–645 (2012).

Kang J., D’Andrea A. D., Kozono D., A DNA repair pathway–focused score for prediction of outcomes in ovarian cancer treated with platinum-based chemotherapy. J. Natl. Cancer Inst. 104, 670–681 (2012).

Bindra R. S., Glazer P. M., Repression of RAD51 gene expression by E2F4/p130 complexes in hypoxia. Oncogene 26, 2048–2057 (2007).

Kim P. M., Allen C., Wagener B. M., Shen Z., Nickoloff J. A., Overexpression of human RAD51 and RAD52 reduces double-strand break-induced homologous recombination in mammalian cells. Nucleic Acids Res. 29, 4352–4360 (2001).

Flygare J., Fält S., Ottervald J., Castro J., Dackland A. L., Hellgren D., Wennborg A., Effects of HsRad51 overexpression on cell proliferation, cell cycle progression, and apoptosis. Exp. Cell Res. 268, 61–69 (2001).

Raderschall E., Stout K., Freier S., Suckow V., Schweiger S., Haaf T., Elevated levels of Rad51 recombination protein in tumor cells. Cancer Res. 62, 219–225 (2002).

Shah P. P., Zheng X., Epshtein A., Carey J. N., Bishop D. K., Klein H. L., Swi2/Snf2-related translocases prevent accumulation of toxic Rad51 complexes during mitotic growth. Mol. Cell 39, 862–872 (2010).

Wahba L., Gore S. K., Koshland D., The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability. eLIFE 2, e00505 (2013).

Richardson C., Stark J. M., Ommundsen M., Jasin M., Rad51 overexpression promotes alternative double-strand break repair pathways and genome instability. Oncogene 23, 546–553 (2004).

Mortensen U. H., Bendixen C., Sunjevaric I., Rothstein R., DNA strand annealing is promoted by the yeast Rad52 protein. Proc. Natl. Acad. Sci. U.S.A. 93, 10729–10734 (1996).

Carter S. L., Eklund A. C., Kohane I. S., Harris L. N., Szallasi Z., A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat. Genet. 38, 1043–1048 (2006).

Galanty Y., Belotserkovskaya R., Coates J., Polo S., Miller K. M., Jackson S. P., Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks. Nature 462, 935–939 (2009).

Galanty Y., Belotserkovskaya R., Coates J., Jackson S. P., RNF4, a SUMO-targeted ubiquitin E3 ligase, promotes DNA double-strand break repair. Genes Dev. 26, 1179–1195 (2012).

Wang Z. C., Birkbak N. J., Culhane A. C., Drapkin R., Fatima A., Tian R., Schwede M., Alsop K., Daniels K. E., Piao H., Liu J., Etemadmoghadam D., Miron A., Salvesen H. B., Mitchell G., DeFazio A., Quackenbush J., Berkowitz R. S., Iglehart J. D., Bowtell D. D.; Australian Ovarian Cancer Study Group;, Matulonis U. A., Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clin. Cancer Res. 18, 5806–5815 (2012).

Joosse S. A., Brandwijk K. I., Devilee P., Wesseling J., Hogervorst F. B., Verhoef S., Nederlof P. M., Prediction of _BRCA2_-association in hereditary breast carcinomas using array-CGH. Breast Cancer Res. Treat. 132, 379–389 (2012).

Joosse S. A., van Beers E. H., Tielen I. H., Horlings H., Peterse J. L., Hoogerbrugge N., Ligtenberg M. J., Wessels L. F., Axwijk P., Verhoef S., Hogervorst F. B., Nederlof P. M., Prediction of _BRCA1_-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res. Treat. 116, 479–489 (2009).

Liauw S. L., Connell P. P., Weichselbaum R. R., New paradigms and future challenges in radiation oncology: An update of biological targets and technology. Sci. Transl. Med. 5, 173sr2 (2013).

**Correction:**The original heading on page 4, "Cell lines with high RPS have elevated genomic instability,' was incorrect. The word â€œhighâ€ should have been â€œlow.â€ This has been corrected