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Assessment of PARP4 as a candidate breast cancer susceptibility gene

  • Epidemiology
  • Published:
Breast Cancer Research and Treatment Aims and scope Submit manuscript

Abstract

Purpose

PARP4 has been proposed as a candidate breast cancer susceptibility gene. However, its function and involvement in breast carcinogenesis is unclear. We sought to determine the variant frequency of PARP4 in BRCA-negative women referred for genetic testing from Singapore and to perform functional analyses of PARP4.

Methods

Next-generation sequencing of PARP4 was conducted for 198 BRCA-negative cases from Singapore. Three independent case–control association analyses of PARP4 were performed for (1) our Singaporean cohort, (2) three dbGaP datasets, and (3) cases from TCGA, with controls from the Exome Aggregation Consortium (ExAC). PARP4 knockout cells were generated utilizing the CRISPR-Cas9 approach in MDA-MB-231 (breast cancer) and MCF10A (normal breast) cell lines, and colony formation, cell proliferation, and migration assays carried out.

Results

Candidate variants in PARP4 were identified in 5.5% (11/198) of our Singapore cohort. Case–control association studies for our cases and the dbGaP datasets showed no significant association. However, a significant association was observed for PARP4 variants when comparing 988 breast cancer cases from the TCGA provisional data and 53,105 controls from ExAC (ALL) (OR 0.249, 95% CI 0.139–0.414, P = 2.86 × 10−11). PARP4 knockout did not affect the clonogenicity, proliferation rate, and migration of normal breast cells, but appeared to decrease the proliferation rate and clonogenicity of breast cancer cells.

Conclusions

Taken together, our results do not support that PARP4 functions as a cancer susceptibility gene. This study highlights the importance of performing functional analyses for candidate cancer predisposition genes.

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Data availability

Additional data are available from the corresponding author on reasonable request.

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Acknowledgements

The authors are grateful to the volunteers who have participated in this study and colleagues who have referred patients. This study utilized datasets retrieved from dbGaP through the following accession numbers: phs001050.v1.p1 (BEAUTY), phs000822.v1.p1, and phs000601.v1.p1 (FAVR). The BEAUTY study was supported by Mayo Clinic Center for Individualized Medicine, Nadia’s Gift Foundation, John P. Guider, The Pharmacogenomics Research Network (U10GM 61388-15), Mayo Clinic Cancer Center (CA15083-40A2), and Mayo Clinic Breast SPORE P50CA 116201-9 (Goetz, Ingle, Kalari, Suman). The phs000822.v1.p1 study was supported by the NHGRI Grant fund U54 HG003067, and the FAVR study was supported by NIH (R01CA155767), National Health and Medical Research Council, Australia (APP1025145), Cancer Council Victoria (Grant #628774), and Susan G Komen for the Cure (KG111155). We thank all the study participants, submitters, and all funding bodies of these studies.

Funding

This work was supported by a grant from the National Medical Research Council (NMRC) of Singapore (NMRC/CBRG/0034/2013) awarded to A.S.G. Lee and by Centre Grant NMRC support to the National Cancer Centre of Singapore.

Author information

Author notes

  1. Aldo Prawira and Prabhakaran Munusamy have contributed equally to this work.

Authors and Affiliations

  1. Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Singapore

    Aldo Prawira, Prabhakaran Munusamy, Jimin Yuan, Claire Hian Tzer Chan, Geok Ling Koh, Jiancheng Hu & Ann Siew Gek Lee

  2. Department of Medical Oncology, National Cancer Centre, Singapore, Singapore

    Timothy Wai Ho Shuen, Yoon Sim Yap, Min Han Tan & Peter Ang

  3. Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore

    Jiancheng Hu

  4. Institute of Bioengineering and Nanotechnology, Singapore, Singapore

    Min Han Tan

  5. Lucence Diagnostics Pte Ltd, Singapore, Singapore

    Min Han Tan

  6. Oncocare Cancer Centre, Gleneagles Medical Centre, Singapore, Singapore

    Peter Ang

  7. Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Ann Siew Gek Lee

  8. Office of Clinical and Academic Faculty Affairs, Duke-NUS Medical School, Singapore, Singapore

    Ann Siew Gek Lee

Authors
  1. Aldo Prawira
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Contributions

Conception and design: ASGL, PM, AP. Development of methodology: AP, JY, JCH, TWHS. Acquisition of material (including recruitment of patients): YSY, MHT, PA. Acquisition of data (conducted experiments and tests): AP, CHTC, GKL. Analysis and interpretation of data (e.g., statistical analysis, biostatistics, computational analysis): AP, PM, ASGL. Writing, review, and/or revision of the manuscript: AP, PM, ASGL. Study support and supervision: ASGL. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ann Siew Gek Lee.

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Conflict of interest

MHT has executive responsibilities at and is a shareholder of Lucence Diagnostics Pte. Ltd. No potential conflicts of interest were disclosed by the other authors.

Ethical approval

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.

Informed consent

Written informed consent was obtained from all study participants.

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Supplementary material 1 (DOCX 17 kb)

10549_2019_5286_MOESM2_ESM.tiff

Supplementary Fig. 1 Visual representation of missense variants within the PARP4 gene identified in our patient cohort. BRCT, BRCA1 C-terminus domain; PARP, Poly(ADP-ribose) polymerase catalytic domain; VIT, Vault protein inter-alpha-trypsin domain; VWA, von-Willebrand Factor Type A domain. Supplementary material 2 (TIFF 11959 kb)

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Prawira, A., Munusamy, P., Yuan, J. et al. Assessment of PARP4 as a candidate breast cancer susceptibility gene. Breast Cancer Res Treat 177, 145–153 (2019). https://doi.org/10.1007/s10549-019-05286-w

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  • DOI: https://doi.org/10.1007/s10549-019-05286-w

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