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Genetic, functional, and histopathological evaluation of two C-terminal BRCA1 missense variants
  1. P K Lovelock1,2,
  2. S Healey2,
  3. W Au3,
  4. E Y M Sum4,
  5. A Tesoriero5,
  6. E M Wong5,
  7. S Hinson6,
  8. R Brinkworth1,
  9. A Bekessy2,
  10. O Diez7,
  11. L Izatt8,
  12. E Solomon8,
  13. M Jenkins5,
  14. H Renard9,
  15. J Hopper5,
  16. P Waring10,
  17. kConFab Investigators10,
  18. S V Tavtigian9,
  19. D Goldgar9,
  20. G J Lindeman4,
  21. J E Visvader4,
  22. F J Couch6,
  23. B R Henderson3,
  24. M Southey5,9,
  25. G Chenevix-Trench2,
  26. A B Spurdle2,
  27. M A Brown1
  1. 1School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
  2. 2Queensland Institute of Medical Research, Brisbane, Australia
  3. 3Westmead Institute for Cancer Research, University of Sydney, Westmead Millennium Institute at Westmead Hospital, Sydney, Australia
  4. 4The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
  5. 5Department of Pathology, University of Melbourne, Melbourne, Australia
  6. 6Mayo Clinic College of Medicine, Rochester, MI, USA
  7. 7Servei de Genetica, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
  8. 8Division of Genetics and Molecular Medicine, King’s College, Guy’s Hospital, London, UK
  9. 9International Agency for Research on Cancer, Lyon, France
  10. 10Peter MacCallum Cancer Centre, Melbourne, Australia
  1. Correspondence to:
 Dr Georgia Chenevix-Trench
 Queensland Institute of Medical Research, Herston, Brisbane, Queensland 4000, Australia; Georgia.Trench{at}qimr.edu.au

Abstract

Background: The vast majority of BRCA1 missense sequence variants remain uncharacterised for their possible effect on protein expression and function, and therefore are unclassified in terms of their pathogenicity. BRCA1 plays diverse cellular roles and it is unlikely that any single functional assay will accurately reflect the total cellular implications of missense mutations in this gene.

Objective: To elucidate the effect of two BRCA1 variants, 5236G>C (G1706A) and 5242C>A (A1708E) on BRCA1 function, and to survey the relative usefulness of several assays to direct the characterisation of other unclassified variants in BRCA genes.

Methods and Results: Data from a range of bioinformatic, genetic, and histopathological analyses, and in vitro functional assays indicated that the 1708E variant was associated with the disruption of different cellular functions of BRCA1. In transient transfection experiments in T47D and 293T cells, the 1708E product was mislocalised to the cytoplasm and induced centrosome amplification in 293T cells. The 1708E variant also failed to transactivate transcription of reporter constructs in mammalian transcriptional transactivation assays. In contrast, the 1706A variant displayed a phenotype comparable to wildtype BRCA1 in these assays. Consistent with functional data, tumours from 1708E carriers showed typical BRCA1 pathology, while tumour material from 1706A carriers displayed few histopathological features associated with BRCA1 related tumours.

Conclusions: A comprehensive range of genetic, bioinformatic, and functional analyses have been combined for the characterisation of BRCA1 unclassified sequence variants. Consistent with the functional analyses, the combined odds of causality calculated for the 1706A variant after multifactorial likelihood analysis (1:142) indicates a definitive classification of this variant as “benign”. In contrast, functional assays of the 1708E variant indicate that it is pathogenic, possibly through subcellular mislocalisation. However, the combined odds of 262:1 in favour of causality of this variant does not meet the minimal ratio of 1000:1 for classification as pathogenic, and A1708E remains formally designated as unclassified. Our findings highlight the importance of comprehensive genetic information, together with detailed functional analysis for the definitive categorisation of unclassified sequence variants. This combination of analyses may have direct application to the characterisation of other unclassified variants in BRCA1 and BRCA2.

  • BIC, Breast Information Core
  • BRCT, BRCA1 C-terminal
  • DHPLC, denaturing high performance liquid chromatography
  • DMEM, Dulbecco’s modified Eagle’s medium
  • ER, estrogen receptor
  • FCS, fetal calf serum
  • LCL, lymphoblastoid cell line
  • LOH, loss of heterozygosity
  • LR, likelihood ratio
  • PR, progesterone receptor
  • SNP, single nucleotide polymorphism
  • SNuPE, single nucleotide primer extension
  • BRCA1
  • functional analysis
  • unclassified variants

https://doi.org/10.1136/jmg.2005.033258

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    Footnotes

    • Published Online First 2 June 2005

    • kConFab has been funded by the Kathleen Cuningham Foundation, National Breast Cancer Foundation, National Health and Medical Research Council (NHMRC), Cancer Council of Victoria, Cancer Council of South Australia, Queensland Cancer Fund, Cancer Council of New South Wales, Cancer Foundation of Western Australia, and Cancer Council of Tasmania. This research was supported by a grant from the Susan G. Komen Breast Cancer Foundation, the NHMRC, and the INHERIT BRCAs programme from the Canadian Institute for Health Research. ABS is funded by an NHMRC Career Development Award. JH, GC-T, and BRH are NHMRC Senior Principal, Principal, and Senior Research Fellows, and WA is funded by an NHMRC Dora Lush postgraduate scholarship. Collection of ABCFS control DNA was funded by the NHMRC

    • Competing interests: none declared