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Lack of evidence for germline RNF43 mutations in patients with serrated polyposis syndrome from a large multinational study
  1. Daniel D Buchanan1,2,
  2. Mark Clendenning1,
  3. Li Zhuoer1,
  4. Jenna R Stewart1,
  5. Sharelle Joseland2,
  6. Sonja Woodall3,
  7. Julie Arnold3,
  8. Kara Semotiuk4,
  9. Melyssa Aronson4,
  10. Spring Holter4,
  11. Steven Gallinger5,
  12. Mark A Jenkins2,
  13. Kevin Sweet6,
  14. Finlay A Macrae7,8,9,
  15. Ingrid M Winship7,8,
  16. Susan Parry3,
  17. Christophe Rosty1,10,11
  18. on behalf of the Genetics of Colonic Polyposis Study
  1. 1Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
  2. 2Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
  3. 3New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand
  4. 4Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mt Sinai Hospital, Toronto, Ontario, Canada
  5. 5Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada 
  6. 6Division of Human Genetics, Ohio State University Medical Centre, Columbus, Ohio, USA
  7. 7Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
  8. 8Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia
  9. 9Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
  10. 10Envoi Specialist Pathologists, Herston, Queensland, Australia
  11. 11School of Medicine, The University of Queensland, Herston, Queensland, Australia
  1. Correspondence to Dr Daniel D Buchanan, Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology and Centre for Epidemiology and Biostatistics, University of Melbourne, Parkville, VIC 3010, Australia; daniel.buchanan{at}unimelb.edu.au

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Serrated polyposis syndrome (SPS) is characterised by the occurrence of multiple serrated polyps in the large bowel. Defined clinically by the 2010 revised WHO, SPS is associated with an increased risk of colorectal cancer (CRC) for affected individuals and their first-degree relatives. Yan et al1 recently reported their findings from whole-exome sequencing (WES) of six individuals with SPS from four families, identifying a single family carrying a germline likely pathogenic variant in RNF43 (c.953-1 G>A, c.953_954delAG, p.E318fs). In this family, six carriers were identified, five of whom met the WHO criteria for SPS. This adds to two previous reports of germline mutations within RNF43 in individuals with SPS or who developed multiple serrated polyps.2 ,3 The current study by Yan et al1 also importantly showed loss of second wildtype allele in 16 serrated polyps, five adenomatous polyps, and in the rectal adenocarcinoma from carriers through somatic single nucleotide variants or loss of heterozygosity, adding further weight to a potential role of RNF43 in the development of colonic serrated neoplasia.

We present here our results from two genetic screens of a large cohort of individuals with SPS recruited to the Genetics of Colorectal Polyposis Study (GCPS). The GCPS has recruited 422 families with at least one SPS-affected individual from Family Cancer Clinics within Australia, Toronto Canada, Ohio, USA and from the New Zealand Familial Gastrointestinal Cancer Service. The first screen comprised 74 individuals with SPS selected based on early age at diagnosis, high numbers of serrated polyps throughout the colon and having a first-degree relative with SPS or CRC (table 1) and consisted of WES (n=58; Agilent XT SureSelect_V4 52 Mb capture, 100 bp paired-end sequencing on a HiSeq2500 to a mean depth of 100×) and whole-genome sequencing (WGS; n=16; 150 bp paired-end reads using Illumina Hi-Seq X Ten sequencer to average 30× coverage). For the RNF43 gene, we filtered for variants with a minor allele frequency of <1% in reference databases and that were (1) likely to cause loss of function (LoF) via a non-sense/stop gain, frameshift or splice site or (2) were non-synonymous variants predicted to be damaging by ≥2 out of four in silico programmes (PolyPhen2, SIFT, FATHMM, CADD). No LoF variants were identified; however, two rare non-synonymous variants predicted to be damaging by both PolyPhen2 and CADD were detected in a single carrier each (table 2).

Table 1

Characteristics of the individuals with SPS tested in this study, comprising 74 SPS cases who underwent whole genome or whole-exome sequencing and 221 who were tested for the two RNF43 loss-of-function mutations p.R113* and p.R132* using HRM assays

Table 2

Two non-synonymous likely pathogenic variants in RNF43 identified from whole-genome sequencing and whole-exome sequencing of 74 individuals with serrated polyposis syndrome

A second targeted genetic screen was performed specifically testing for the RNF43 p.R113*2 and p.R132*3 variants to determine their prevalence in individuals with SPS. We tested blood-derived DNA from 221 SPS cases from the GCPS, a subset of which have been previously described,4 using a high-resolution melt (HRM) assay for each mutation where samples with aberrant melting profiles were Sanger sequenced to confirm genotype sequence (primers and PCR conditions in online supplementary table). None of the tested individuals with SPS were carriers of either of these two RNF43 germline LoF variants. However, we cannot exclude the possibility that other variants within RNF43 could exist within a proportion of the 221 patients with SPS who were tested.

Supplementary table

Primers and PCR conditions used in the HRM assay for RNF43 variants p.R113* and p.R132*.

The study by Yan et al1 adds to the reported number of SPS families with germline mutations in RNF43, now totalling four. The paucity of RNF43 germline LoF variants in 295 patients with SPS from the GCPS suggests that mutations in RNF43 may account for only a small proportion of SPS suggesting that additional genetic risk factors for SPS are yet to be identified. In conclusion, our findings do not support the need for routine germline testing of RNF43 in individuals who meet the criteria for SPS.

Acknowledgments

Participants of the GCPS, staff from the FCCs from across Australia, New Zealand, Canada and Ohio USA who contributed to patient recruitment and the Biorepository staff from the Genetic Epidemiology Laboratory.

References

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Footnotes

  • Contributors All authors of this research paper have directly participated in the planning, execution or analysis of the study, and have approved the final version submitted. We would like to acknowledge the contributions of the participants of the Genetics of Colonic Polyposis Study, staff from the FCCs from across Australia, New Zealand, Canada and Ohio, USA who contributed to patient recruitment and the Biorepository staff from the Genetic Epidemiology Laboratory.

  • Funding This work was supported by Cancer Council Queensland project grant (GNT1006290). CR is the Jeremy Jass Pathology Fellow, MAJ is an NHMRC Senior Research Fellow and DDB is a University of Melbourne Research at Melbourne Accelerator Program Senior Research Fellow.

  • Disclaimer Authors had full responsibility for the design of the study, the collection of the data, the analysis and interpretation of the data, the decision to submit the manuscript for publication and the writing of the manuscript.

  • Competing interests None declared.

  • Ethics approval University of Melbourne Human Research Ethics Committee.

  • Provenance and peer review Not commissioned; internally peer reviewed.

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