Fanconi-BRCA pathway mutations in childhood T-cell acute lymphoblastic leukemia

Autoři: Gayle P. Pouliot aff001;  James Degar aff001;  Laura Hinze aff001;  Bose Kochupurakkal aff003;  Chau D. Vo aff001;  Melissa A. Burns aff001;  Lisa Moreau aff001;  Chirag Ganesa aff003;  Justine Roderick aff004;  Sofie Peirs aff005;  Bjorn Menten aff005;  Mignon L. Loh aff006;  Stephen P. Hunger aff007;  Lewis B. Silverman aff001;  Marian H. Harris aff008;  Kristen E. Stevenson aff009;  David M. Weinstock aff010;  Andrew P. Weng aff011;  Pieter Van Vlierberghe aff005;  Alan D. D’Andrea aff001;  Alejandro Gutierrez aff001
Působiště autorů: Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America aff001;  Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America aff002;  Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America aff003;  Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America aff004;  Department of Biomolecular Medicine, Ghent University, Ghent, Belgium aff005;  Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America aff006;  Division of Oncology and the Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America aff007;  Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, United States of America aff008;  Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America aff009;  Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America aff010;  Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada aff011
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0221288


BRCA2 (also known as FANCD1) is a core component of the Fanconi pathway and suppresses transformation of immature T-cells in mice. However, the contribution of Fanconi-BRCA pathway deficiency to human T-cell acute lymphoblastic leukemia (T-ALL) remains undefined. We identified point mutations in 9 (23%) of 40 human T-ALL cases analyzed, with variant allele fractions consistent with heterozygous mutations early in tumor evolution. Two of these mutations were present in remission bone marrow specimens, suggesting germline alterations. BRCA2 was the most commonly mutated gene. The identified Fanconi-BRCA mutations encode hypomorphic or null alleles, as evidenced by their inability to fully rescue Fanconi-deficient cells from chromosome breakage, cytotoxicity and/or G2/M arrest upon treatment with DNA cross-linking agents. Disabling the tumor suppressor activity of the Fanconi-BRCA pathway is generally thought to require biallelic gene mutations. However, all mutations identified were monoallelic, and most cases appeared to retain expression of the wild-type allele. Using isogenic T-ALL cells, we found that BRCA2 haploinsufficiency induces selective hypersensitivity to ATR inhibition, in vitro and in vivo. These findings implicate Fanconi-BRCA pathway haploinsufficiency in the molecular pathogenesis of T-ALL, and provide a therapeutic rationale for inhibition of ATR or other druggable effectors of homologous recombination.

Klíčová slova:

Gene sequencing – Genetic causes of cancer – Mutation – Point mutation – Polymerase chain reaction – Haploinsufficiency – Dideoxy DNA sequencing


1. Ceccaldi R, Sarangi P, D’Andrea AD. The Fanconi anaemia pathway: new players and new functions. Nature reviews Molecular cell biology. 2016;17(6):337–49. doi: 10.1038/nrm.2016.48 27145721

2. NCBI OMIM: Online Mendelian Inheritance in Man. MIM Number: 175100. Accessed December 12, 2018. [Internet].

3. Nishisho I, Nakamura Y, Miyoshi Y, Miki Y, Ando H, Horii A, et al. Mutations of chromosome 5q21 genes in FAP and colorectal cancer patients. Science. 1991;253(5020):665–9. doi: 10.1126/science.1651563 1651563

4. Groden J, Thliveris A, Samowitz W, Carlson M, Gelbert L, Albertsen H, et al. Identification and characterization of the familial adenomatous polyposis coli gene. Cell. 1991;66(3):589–600. doi: 10.1016/0092-8674(81)90021-0 1651174

5. Kinzler KW, Nilbert MC, Su LK, Vogelstein B, Bryan TM, Levy DB, et al. Identification of FAP locus genes from chromosome 5q21. Science. 1991;253(5020):661–5. doi: 10.1126/science.1651562 1651562

6. Yaeger R, Chatila WK, Lipsyc MD, Hechtman JF, Cercek A, Sanchez-Vega F, et al. Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer. Cancer Cell. 2018;33(1):125–36 e3. doi: 10.1016/j.ccell.2017.12.004 29316426

7. Wooster R, Neuhausen SL, Mangion J, Quirk Y, Ford D, Collins N, et al. Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science. 1994;265(5181):2088–90. doi: 10.1126/science.8091231 8091231

8. Friedman LS, Ostermeyer EA, Szabo CI, Dowd P, Lynch ED, Rowell SE, et al. Confirmation of BRCA1 by analysis of germline mutations linked to breast and ovarian cancer in ten families. Nat Genet. 1994;8(4):399–404. doi: 10.1038/ng1294-399 7894493

9. Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature. 2016;534(7605):47–54. doi: 10.1038/nature17676 27135926

10. Cancer Genome Atlas Research N. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609–15. doi: 10.1038/nature10166 21720365

11. Struewing JP, Hartge P, Wacholder S, Baker SM, Berlin M, McAdams M, et al. The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among Ashkenazi Jews. N Engl J Med. 1997;336(20):1401–8. doi: 10.1056/NEJM199705153362001 9145676

12. Breast Cancer Linkage C. Cancer risks in BRCA2 mutation carriers. Journal of the National Cancer Institute. 1999;91(15):1310–6. doi: 10.1093/jnci/91.15.1310 10433620

13. Waddell N, Pajic M, Patch AM, Chang DK, Kassahn KS, Bailey P, et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature. 2015;518(7540):495–501. doi: 10.1038/nature14169 25719666

14. Neidhardt G, Hauke J, Ramser J, Gross E, Gehrig A, Muller CR, et al. Association Between Loss-of-Function Mutations Within the FANCM Gene and Early-Onset Familial Breast Cancer. JAMA Oncol. 2017;3(9):1245–8. doi: 10.1001/jamaoncol.2016.5592 28033443

15. Kiiski JI, Pelttari LM, Khan S, Freysteinsdottir ES, Reynisdottir I, Hart SN, et al. Exome sequencing identifies FANCM as a susceptibility gene for triple-negative breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(42):15172–7. doi: 10.1073/pnas.1407909111 25288723

16. Alter BP. Fanconi anemia and the development of leukemia. Best Pract Res Clin Haematol. 2014;27(3–4):214–21. doi: 10.1016/j.beha.2014.10.002 25455269

17. Connor F, Bertwistle D, Mee PJ, Ross GM, Swift S, Grigorieva E, et al. Tumorigenesis and a DNA repair defect in mice with a truncating Brca2 mutation. Nat Genet. 1997;17(4):423–30. doi: 10.1038/ng1297-423 9398843

18. Friedman LS, Thistlethwaite FC, Patel KJ, Yu VP, Lee H, Venkitaraman AR, et al. Thymic lymphomas in mice with a truncating mutation in Brca2. Cancer Res. 1998;58(7):1338–43. 9537225

19. Cerabona D, Sun Z, Nalepa G. Leukemia and chromosomal instability in aged Fancc-/- mice. Exp Hematol. 2016;44(5):352–7. doi: 10.1016/j.exphem.2016.01.009 26860989

20. Smetsers S, Muter J, Bristow C, Patel L, Chandler K, Bonney D, et al. Heterozygote FANCD2 mutations associated with childhood T Cell ALL and testicular seminoma. Familial cancer. 2012;11(4):661–5. doi: 10.1007/s10689-012-9553-3 22829014

21. Rischewski JR, Clausen H, Leber V, Niemeyer C, Ritter J, Schindler D, et al. A heterozygous frameshift mutation in the Fanconi anemia C gene in familial T-ALL and secondary malignancy. Klin Padiatr. 2000;212(4):174–6. doi: 10.1055/s-2000-9673 10994546

22. Borriello A, Locasciulli A, Bianco AM, Criscuolo M, Conti V, Grammatico P, et al. A novel Leu153Ser mutation of the Fanconi anemia FANCD2 gene is associated with severe chemotherapy toxicity in a pediatric T-cell acute lymphoblastic leukemia. Leukemia. 2007;21(1):72–8. doi: 10.1038/sj.leu.2404468 17096012

23. Goldsby RE, Perkins SL, Virshup DM, Brothman AR, Bruggers CS. Lymphoblastic lymphoma and excessive toxicity from chemotherapy: an unusual presentation for Fanconi anemia. J Pediatr Hematol Oncol. 1999;21(3):240–3. 10363859

24. Svojgr K, Sumerauer D, Puchmajerova A, Vicha A, Hrusak O, Michalova K, et al. Fanconi anemia with biallelic FANCD1/BRCA2 mutations—Case report of a family with three affected children. Eur J Med Genet. 2016;59(3):152–7. doi: 10.1016/j.ejmg.2015.11.013 26657402

25. Fong PC, Boss DS, Yap TA, Tutt A, Wu P, Mergui-Roelvink M, et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med. 2009;361(2):123–34. doi: 10.1056/NEJMoa0900212 19553641

26. Tutt A, Robson M, Garber JE, Domchek SM, Audeh MW, Weitzel JN, et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and advanced breast cancer: a proof-of-concept trial. Lancet. 2010;376(9737):235–44. doi: 10.1016/S0140-6736(10)60892-6 20609467

27. Farmer H, McCabe N, Lord CJ, Tutt AN, Johnson DA, Richardson TB, et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature. 2005;434(7035):917–21. doi: 10.1038/nature03445 15829967

28. Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, et al. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight. 2016;1(19):e87062. doi: 10.1172/jci.insight.87062 27882345

29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. doi: 10.1101/gr.107524.110 20644199

30. Sawyer SL, Tian L, Kahkonen M, Schwartzentruber J, Kircher M, University of Washington Centre for Mendelian G, et al. Biallelic mutations in BRCA1 cause a new Fanconi anemia subtype. Cancer discovery. 2015;5(2):135–42. doi: 10.1158/2159-8290.CD-14-1156 25472942

31. Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, et al. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics. 2005;6:124. doi: 10.1186/1471-2105-6-124 15910681

32. Gutierrez A, Sanda T, Ma W, Zhang J, Grebliunaite R, Dahlberg S, et al. Inactivation of LEF1 in T-cell acute lymphoblastic leukemia. Blood. 2010;115(14):2845–51. doi: 10.1182/blood-2009-07-234377 20124220

33. Townsend EC, Murakami MA, Christodoulou A, Christie AL, Koster J, DeSouza TA, et al. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell. 2016;29(4):574–86. doi: 10.1016/j.ccell.2016.03.008 27070704

34. Howlett NG, Taniguchi T, Olson S, Cox B, Waisfisz Q, De Die-Smulders C, et al. Biallelic inactivation of BRCA2 in Fanconi anemia. Science. 2002;297(5581):606–9. doi: 10.1126/science.1073834 12065746

35. Timmers C, Taniguchi T, Hejna J, Reifsteck C, Lucas L, Bruun D, et al. Positional cloning of a novel Fanconi anemia gene, FANCD2. Mol Cell. 2001;7(2):241–8. 11239453

36. Naf D, Kupfer GM, Suliman A, Lambert K, D’Andrea AD. Functional activity of the fanconi anemia protein FAA requires FAC binding and nuclear localization. Mol Cell Biol. 1998;18(10):5952–60. doi: 10.1128/mcb.18.10.5952 9742112

37. Hirano S, Yamamoto K, Ishiai M, Yamazoe M, Seki M, Matsushita N, et al. Functional relationships of FANCC to homologous recombination, translesion synthesis, and BLM. EMBO J. 2005;24(2):418–27. doi: 10.1038/sj.emboj.7600534 15616572

38. de Winter JP, Rooimans MA, van Der Weel L, van Berkel CG, Alon N, Bosnoyan-Collins L, et al. The Fanconi anaemia gene FANCF encodes a novel protein with homology to ROM. Nat Genet. 2000;24(1):15–6. doi: 10.1038/71626 10615118

39. Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2018.

40. Aries IM, Bodaar K, Karim SA, Chonghaile TN, Hinze L, Burns MA, et al. PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia. J Exp Med. 2018;215(12):3094–114. doi: 10.1084/jem.20180570 30404791

41. Girardi T, Vicente C, Cools J, De Keersmaecker K. The genetics and molecular biology of T-ALL. Blood. 2017;129(9):1113–23. doi: 10.1182/blood-2016-10-706465 28115373

42. Sanchez-Martin M, Ferrando A. The NOTCH1-MYC highway toward T-cell acute lymphoblastic leukemia. Blood. 2017;129(9):1124–33. doi: 10.1182/blood-2016-09-692582 28115368

43. Strathdee CA, Gavish H, Shannon WR, Buchwald M. Cloning of cDNAs for Fanconi’s anaemia by functional complementation. Nature. 1992;356(6372):763–7. doi: 10.1038/356763a0 1574115

44. Pulsipher M, Kupfer GM, Naf D, Suliman A, Lee JS, Jakobs P, et al. Subtyping analysis of Fanconi anemia by immunoblotting and retroviral gene transfer. Molecular medicine. 1998;4(7):468–79. 9713825

45. Chandra S, Levran O, Jurickova I, Maas C, Kapur R, Schindler D, et al. A rapid method for retrovirus-mediated identification of complementation groups in Fanconi anemia patients. Mol Ther. 2005;12(5):976–84. doi: 10.1016/j.ymthe.2005.04.021 16084127

46. Auerbach AD, Wolman SR. Susceptibility of Fanconi’s anaemia fibroblasts to chromosome damage by carcinogens. Nature. 1976;261(5560):494–6. doi: 10.1038/261494a0 934283

47. McCabe N, Turner NC, Lord CJ, Kluzek K, Bialkowska A, Swift S, et al. Deficiency in the repair of DNA damage by homologous recombination and sensitivity to poly(ADP-ribose) polymerase inhibition. Cancer Res. 2006;66(16):8109–15. doi: 10.1158/0008-5472.CAN-06-0140 16912188

48. Bryant HE, Schultz N, Thomas HD, Parker KM, Flower D, Lopez E, et al. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature. 2005;434(7035):913–7. doi: 10.1038/nature03443 15829966

49. Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–25. doi: 10.1016/j.cels.2015.12.004 26771021

50. Tubbs A, Nussenzweig A. Endogenous DNA Damage as a Source of Genomic Instability in Cancer. Cell. 2017;168(4):644–56. doi: 10.1016/j.cell.2017.01.002 28187286

51. Dunn J, Potter M, Rees A, Runger TM. Activation of the Fanconi anemia/BRCA pathway and recombination repair in the cellular response to solar ultraviolet light. Cancer Res. 2006;66(23):11140–7. doi: 10.1158/0008-5472.CAN-06-0563 17145857

52. Federico MB, Vallerga MB, Radl A, Paviolo NS, Bocco JL, Di Giorgio M, et al. Chromosomal Integrity after UV Irradiation Requires FANCD2-Mediated Repair of Double Strand Breaks. PLoS Genet. 2016;12(1):e1005792. doi: 10.1371/journal.pgen.1005792 26765540

53. Reaper PM, Griffiths MR, Long JM, Charrier JD, Maccormick S, Charlton PA, et al. Selective killing of ATM- or p53-deficient cancer cells through inhibition of ATR. Nat Chem Biol. 2011;7(7):428–30. doi: 10.1038/nchembio.573 21490603

54. Foote KM, Nissink JWM, McGuire T, Turner P, Guichard S, Yates JWT, et al. Discovery and Characterization of AZD6738, a Potent Inhibitor of Ataxia Telangiectasia Mutated and Rad3 Related (ATR) Kinase with Application as an Anticancer Agent. J Med Chem. 2018;61(22):9889–907. doi: 10.1021/acs.jmedchem.8b01187 30346772

55. Pathania S, Bade S, Le Guillou M, Burke K, Reed R, Bowman-Colin C, et al. BRCA1 haploinsufficiency for replication stress suppression in primary cells. Nature communications. 2014;5:5496. doi: 10.1038/ncomms6496 25400221

56. Obermeier K, Sachsenweger J, Friedl TW, Pospiech H, Winqvist R, Wiesmuller L. Heterozygous PALB2 c.1592delT mutation channels DNA double-strand break repair into error-prone pathways in breast cancer patients. Oncogene. 2016;35(29):3796–806. doi: 10.1038/onc.2015.448 26640152

57. Strasser A, Harris AW, Cory S. bcl-2 transgene inhibits T cell death and perturbs thymic self-censorship. Cell. 1991;67(5):889–99. doi: 10.1016/0092-8674(91)90362-3 1959134

58. Skoulidis F, Cassidy LD, Pisupati V, Jonasson JG, Bjarnason H, Eyfjord JE, et al. Germline Brca2 heterozygosity promotes Kras(G12D) -driven carcinogenesis in a murine model of familial pancreatic cancer. Cancer Cell. 2010;18(5):499–509. doi: 10.1016/j.ccr.2010.10.015 21056012

59. Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, et al. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet. 2017;49(8):1211–8. doi: 10.1038/ng.3909 28671688

60. Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011;32(4):358–68. doi: 10.1002/humu.21445 21412949

61. Frousios K, Iliopoulos CS, Schlitt T, Simpson MA. Predicting the functional consequences of non-synonymous DNA sequence variants—evaluation of bioinformatics tools and development of a consensus strategy. Genomics. 2013;102(4):223–8. doi: 10.1016/j.ygeno.2013.06.005 23831115

62. Madubata CJ, Roshan-Ghias A, Chu T, Resnick S, Zhao J, Arnes L, et al. Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas. NPJ Genom Med. 2017;2:29. doi: 10.1038/s41525-017-0032-5 29263839

63. Cancer Genome Atlas Research N. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014;507(7492):315–22. doi: 10.1038/nature12965 24476821

64. Maung KZY, Leo PJ, Bassal M, Casolari DA, Gray JX, Bray SC, et al. Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia. Blood Cancer J. 2018;8(6):50. doi: 10.1038/s41408-018-0090-7 29891941

Článek vyšel v časopise


2019 Číslo 11