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Missense PALB2 germline variant disrupts nuclear localization of PALB2 in a patient with breast cancer

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Abstract

The PALB2 protein is essential to RAD51-mediated homologous recombination (HR) repair. Germline monoallelic PALB2 pathogenic variants confer significant risks for breast cancer. However, the majority of PALB2 variants remain classified as variants of unknown significance (VUS). We aim to functionally and mechanistically evaluate three novel PALB2 VUS. Patient-derived lymphoblastoid cell lines containing the VUS were analyzed for nuclear localization and foci formation of RAD51 as a measure of HR efficiency. To understand the mechanism underlying the HR deficiency, PALB2 nuclear localization was assessed using immunofluorescence studies. Among these VUS, c.3251C>T (p.Ser1084Leu) occurred in a patient with metastatic breast cancer while c.1054G>C (p.Glu352Gln) and c.1057A>G (p.Lys353Glu) were seen in patients with squamous cell carcinoma of skin and renal cell carcinoma respectively. Variant c.3251C>T was located within the WD40 domain which normally masked the nuclear export signal sequence responsible for nuclear delocalization of PALB2. Correspondingly, c.3251C>T displayed aberrant cytoplasmic localization of PALB2 which led to an impaired RAD51 nuclear localization and foci formation. On the other hand, both c.1054G>C and c.1057A>G showed intact HR functions and nuclear localization of PALB2, consistent with their locations within domains of no known function. Additionally, the prevalence of c.1054G>C was similar among healthy controls and patients with breast cancer (as seen in other studies), suggestive of its non-pathogenicity. In conclusion, our studies provided the functional evidence showing the deleterious effect of c.3251C>T, and non-deleterious effects of c.1054G>C and c.1057A>G. Using the ClinGen Pathogenicity calculator, c.3251C>T remains a VUS while c.1054G>C and c.1057A>G may be classified as likely benign variants.

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Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We would like to thank the patients and research participants for their contribution to the study. We would like to acknowledge St Jude PeCan Data Portal for the web application in generating Fig. 1e.

Funding

We thank our sources of support: National Medical Research Council (CSA) (NMRC/CSA-INV/0017/2017) and Singhealth Foundation Research Grant (SHF/PRISM002/2015) to JN and SingHealth (SMSTDA-Project FY2018) to MR. JYM is a FRQS chair in genome stability and was supported by a CIHR Foundation grant.

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Authors and Affiliations

  1. Duke-NUS Medical School, Singapore, 169857, Singapore

    Ming Ren Toh & Joanne Ngeow

  2. Cancer Genetics Service, Division of Medical Oncology, National Cancer Center, Singapore, 169610, Singapore

    Chen Ee Low, Siao Ting Chong, Sock Hoai Chan, Nur Diana Binte Ishak, Eliza Courtney, Arun Mouli Kolinjivadi & Joanne Ngeow

  3. CHU de Québec Research Center, Oncology Division, HDQ Pavilion, 9 McMahon, Québec City, QC, G1R 3S3, Canada

    Amélie Rodrigue & Jean-Yves Masson

  4. Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada

    Amélie Rodrigue & Jean-Yves Masson

  5. Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore

    Arun Mouli Kolinjivadi & Joanne Ngeow

  6. Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673, Singapore

    Joanne Ngeow

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  1. Ming Ren Toh
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Contributions

CE, MR, ST, SH, ND, EC and AMK made substantial contributions to the design, administration and conceptualization of the study, interpretation of data and critically revising and drafting the manuscript. AR and JYM provided expertise and reagents. JN provided funding, acquisition of data, conception and design of the study, manuscript review and editing. All authors approved the submission of the final manuscript and agreed to be accountable for all aspects of the work.

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Correspondence to Joanne Ngeow.

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The authors declare that they have no conflict of interest.

Ethical approval

This study was approved by the Singhealth Centralized Institutional Review Board (IRB 2010/426/B) with signed inform consent from participants.

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Toh, M.R., Low, C.E., Chong, S.T. et al. Missense PALB2 germline variant disrupts nuclear localization of PALB2 in a patient with breast cancer. Familial Cancer 19, 123–131 (2020). https://doi.org/10.1007/s10689-020-00163-8

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