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Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T

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Abstract

Purpose

Disruption of splicing motifs by genetic variants can affect the correct generation of mature mRNA molecules leading to aberrant transcripts. In some cases, variants may alter the physiological transcription profile composed of several transcripts, and an accurate in vitro evaluation is crucial to establish their pathogenicity. In this study, we have characterized a novel PALB2 variant c.3201+5G>T identified in a breast cancer family.

Methods

Peripheral blood RNA was analyzed in two carriers and ten controls by RT-PCR and Sanger sequencing. The splicing profile was also characterized by semi-quantitative capillary electrophoresis and quantitative PCR. RAD51 foci formation and PALB2 LOH status were evaluated in primary breast tumor samples from the carriers.

Results

PALB2 c.3201+5G>T disrupts intron 11 donor splice site and modifies the abundance of several alternative transcripts (∆11, ∆12, and ∆11,12), also present in control samples. All transcripts are predicted to encode for non-functional proteins. Semi-quantitative and quantitative analysis of PALB2 full-length transcript indicated haploinsufficiency in carriers. One tumor exhibited PALB2 LOH and RAD51 assay indicated homologous recombination deficiency in both tumors.

Conclusions

Our results support a pathogenic classification for PALB2 c.3201+5G>T, highlighting the impact of variants causing an imbalanced expression of natural RNA isoforms in cancer susceptibility.

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References

  1. Scotti MM, Swanson MS (2016) RNA mis-splicing in disease. Nat Rev Genet 17:19–32. https://doi.org/10.1038/nrg.2015.3

    Article  CAS  PubMed  Google Scholar 

  2. Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3:285–298. https://doi.org/10.1038/nrg775

    Article  CAS  PubMed  Google Scholar 

  3. de la Hoya M, Soukarieh O, López-Perolio I et al (2016) Combined genetic and splicing analysis of BRCA1 c.[594-2A> C; 641A> G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Hum Mol Genet 25:2256–2268. https://doi.org/10.1093/hmg/ddw094

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bonnet C, Krieger S, Vezain M et al (2008) Screening BRCA1 and BRCA2 unclassified variants for splicing mutations using reverse transcription PCR on patient RNA and an ex vivo assay based on a splicing reporter minigene. J Med Genet 45:438–446. https://doi.org/10.1136/jmg.2007.056895

    Article  CAS  PubMed  Google Scholar 

  5. Baralle D, Buratti E (2017) RNA splicing in human disease and in the clinic. Clin Sci 131:355–368. https://doi.org/10.1042/CS20160211

    Article  CAS  Google Scholar 

  6. Zhang F, Ma J, Wu J et al (2009) PALB2 Links BRCA1 and BRCA2 in the DNA-Damage Response. Curr Biol 19:524–529. https://doi.org/10.1016/j.cub.2009.02.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Xia B, Sheng Q, Nakanishi K et al (2006) Control of BRCA2 cellular and clinical functions by a nuclear partner, PALB2. Mol Cell 22:719–729. https://doi.org/10.1016/j.molcel.2006.05.022

    Article  CAS  PubMed  Google Scholar 

  8. Park JY, Zhang F, Andreassen PR (2014) PALB2: The hub of a network of tumor suppressors involved in DNA damage responses. Biochim Biophys Acta 1846:263–275. https://doi.org/10.1016/j.bbcan.2014.06.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Tung N, Domchek SM, Stadler Z et al (2016) Counselling framework for moderate-penetrance cancer-susceptibility mutations. Nat Rev Clin Oncol 13:581–588. https://doi.org/10.1038/nrclinonc.2016.90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Antoniou AC, Casadei S, Heikkinen T et al (2014) Breast-cancer risk in families with mutations in PALB2. N Engl J Med 371:497–506. https://doi.org/10.1056/NEJMoa1400382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Pritzlaff M, Summerour P, McFarland R et al (2017) Male breast cancer in a multi-gene panel testing cohort: insights and unexpected results. Breast Cancer Res Treat 161:575–586. https://doi.org/10.1007/s10549-016-4085-4

    Article  PubMed  Google Scholar 

  12. Zhen DB, Rabe KG, Gallinger S et al (2015) BRCA1, BRCA2, PALB2, and CDKN2A mutations in familial pancreatic cancer: A PACGENE study. Genet Med 17:569–577. https://doi.org/10.1038/gim.2014.153

    Article  CAS  PubMed  Google Scholar 

  13. AlDubayan SH, Giannakis M, Moore ND et al (2018) Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet 102:401–414. https://doi.org/10.1016/j.ajhg.2018.01.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bonache S, Esteban I, Moles-Fernández A et al (2018) Multigene panel testing beyond BRCA1/2 in breast/ovarian cancer Spanish families and clinical actionability of findings. J Cancer Res Clin Oncol 144:2495–2513

    Article  CAS  PubMed  Google Scholar 

  15. Cruz C, Castroviejo-Bermejo M, Gutiérrez-Enríquez S et al (2018) RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA-mutated breast cancer. Ann Oncol 29:1203–1210. https://doi.org/10.1093/annonc/mdy099

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Castroviejo‐Bermejo M, Cruz C, Llop‐Guevara A et al (2018) A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation. EMBO Mol Med 10:e9172

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Davy G, Rousselin A, Goardon N et al (2017) Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer. Eur J Hum Genet 25:1147–1154. https://doi.org/10.1038/ejhg.2017.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Oliver AW, Swift S, Lord CJ et al (2009) Structural basis for recruitment of BRCA2 by PALB2. EMBO Rep 10:990–996. https://doi.org/10.1038/embor.2009.126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Buisson R, Niraj J, Pauty J et al (2014) Breast cancer proteins PALB2 and BRCA2 stimulate polymerase η in recombination-associated DNA Synthesis At Blocked Replication Forks. Cell Rep 6:553–564. https://doi.org/10.1016/j.celrep.2014.01.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Park JY, Singh TR, Nassar N et al (2014) Breast cancer-associated missense mutants of the PALB2 WD40 domain, which directly binds RAD51C, RAD51 and BRCA2, disrupt DNA repair. Oncogene 33:4803–4812. https://doi.org/10.1038/onc.2013.421

    Article  CAS  PubMed  Google Scholar 

  21. Pauty J, Couturier AM, Rodrigue A et al (2017) Cancer-causing mutations in the tumor suppressor PALB2 reveal a novel cancer mechanism using a hidden nuclear export signal in the WD40 repeat motif. Nucleic Acids Res 45:2644–2657. https://doi.org/10.1093/nar/gkx011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Lee J, Li N, Rowley S et al (2018) Molecular analysis of PALB2 associated breast cancers. J Pathol 245:53–60. https://doi.org/10.1111/peps.12055

    Article  CAS  PubMed  Google Scholar 

  23. Buisson R, Masson J-Y (2012) PALB2 self-interaction controls homologous recombination. Nucleic Acids Res 40:10312–10323. https://doi.org/10.1093/nar/gks807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Naipal KAT, Verkaik NS, Ameziane N et al (2014) Functional ex vivo assay to select homologous recombination-deficient breast tumors for PARP inhibitor treatment. Clin Cancer Res 20:4816–4826. https://doi.org/10.1158/1078-0432.CCR-14-0571

    Article  CAS  PubMed  Google Scholar 

  25. Buisson R, Dion-Côté A-M, Coulombe Y et al (2010) Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination. Nat Struct Mol Biol 17:1247–1254. https://doi.org/10.1038/nsmb.1915

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Southey MC, Winship I, Nguyen-Dumont T (2016) PALB2: research reaching to clinical outcomes for women with breast cancer. Hered Cancer Clin Pract 14:9. https://doi.org/10.1186/s13053-016-0049-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Nepomuceno TC, De Gregoriis G, de Oliveira FMB et al (2017) The role of PALB2 in the DNA Damage response and cancer predisposition. Int J Mol Sci. https://doi.org/10.3390/ijms18091886

    Article  PubMed  PubMed Central  Google Scholar 

  28. Richards S, Aziz N, Bale S et al (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17:405–423. https://doi.org/10.1038/gim.2015.30

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors thank Cristina Cruz and Violeta Serra from the Experimental Therapeutics Group at VHIO for kindly providing immunofluorescence protocols and helpful discussions. The authors also acknowledge the Cellex Foundation for providing research facilities and equipment, and Leo Judkins for English language editing.

Funding

This work was supported by Spanish Instituto de Salud Carlos III (ISCIII) funding, an initiative of the Spanish Ministry of Economy and Innovation partially supported by European Regional Development FEDER Funds: FIS PI12/02585 and PI15/00355 (to O Diez), PI13/01711 and PI16/01218 (to S. Gutiérrez-Enríquez). S. Gutiérrez-Enríquez is supported by a Miguel Servet contract (CP10/00617). M. Castroviejo-Bermejo is awarded with a Junta Provincial de Barcelona, Fundación Científica Asociación Española Contra el Cáncer (AECC) fellowship. S. Bonache is recipient of an Asociación Española Contra el Cáncer (AECC) contract.

Author information

Author notes

  1. Laura Duran-Lozano and Gemma Montalban have contributed equally to this work.

Authors and Affiliations

  1. Oncogenetics Group, Vall d’Hebron Institute of Oncology, VHIO, 08035, Barcelona, Spain

    Laura Duran-Lozano, Gemma Montalban, Sandra Bonache, Alejandro Moles-Fernández, Sara Gutiérrez-Enríquez & Orland Diez

  2. Area of Clinical and Molecular Genetics, University Hospital of Vall d’Hebron, 08035, Barcelona, Spain

    Anna Tenés & Orland Diez

  3. Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, VHIO, 08035, Barcelona, Spain

    Marta Castroviejo-Bermejo

  4. High Risk and Cancer Prevention Group, VHIO, 08035, Barcelona, Spain

    Estela Carrasco, Adrià López-Fernández, Sara Torres-Esquius, Neus Gadea, Neda Stjepanovic & Judith Balmaña

  5. Medical Oncology Department, University Hospital of Vall d’Hebron, 08035, Barcelona, Spain

    Neus Gadea, Neda Stjepanovic & Judith Balmaña

Authors
  1. Laura Duran-Lozano
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  2. Gemma Montalban
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  3. Sandra Bonache
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Corresponding authors

Correspondence to Sara Gutiérrez-Enríquez or Orland Diez.

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The authors declare that they have no conflict of interest.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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informed consent was obtained from all individual participants included in the study.

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Duran-Lozano, L., Montalban, G., Bonache, S. et al. Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T. Breast Cancer Res Treat 174, 543–550 (2019). https://doi.org/10.1007/s10549-018-05094-8

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  • DOI: https://doi.org/10.1007/s10549-018-05094-8

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