Lack of APC somatic mutation is associated with early-onset colorectal cancer in African Americans

Carcinogenesis. 2018 Dec 13;39(11):1331-1341. doi: 10.1093/carcin/bgy122.

Abstract

African Americans (AAs) have higher incidence and mortality rates of colorectal cancer (CRC) compared with other US populations. They present with more right-sided, microsatellite stable disease and are diagnosed at earlier ages compared with non-Hispanic Whites (NHWs). To gain insight into these trends, we conducted exome sequencing (n = 45), copy number (n = 33) and methylation analysis (n = 11) of microsatellite stable AA CRCs. Results were compared with data from The Cancer Genome Atlas (TCGA). Two of the 45 tumors contained POLE mutations. In the remaining 43 tumors, only 27 (63%) contained loss-of-function mutations in APC compared with 80% of TCGA NHW CRCs. APC-mutation-negative CRCs were associated with an earlier onset of CRC (P = 0.01). They were also associated with lower overall mutation burden, fewer copy number variants and a DNA methylation signature that was distinct from the CpG island methylator phenotype characterized in microsatellite unstable disease. Three of the APC-mutation-negative CRCs had loss-of-function mutations in BCL9L. Mutations in driver genes identified by TCGA exome analysis were less frequent in AA CRC cases than TCGA NHWs. Genes that regulate the WNT signaling pathway, including SOX9, GATA6, TET1, GLIS1 and FAT1, were differentially hypermethylated in APC-mutation-negative CRCs, suggesting a novel mechanism for cancer development in these tumors. In summary, we have identified a subtype of CRC that is associated with younger age of diagnosis, lack of APC mutation, microsatellite and chromosome stability, lower mutation burden and distinctive methylation changes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenomatous Polyposis Coli Protein / genetics*
  • Black or African American / genetics*
  • Black or African American / statistics & numerical data*
  • Cadherins / genetics
  • Colorectal Neoplasms / epidemiology*
  • Colorectal Neoplasms / genetics*
  • Colorectal Neoplasms / pathology
  • DNA Copy Number Variations / genetics
  • DNA Methylation / genetics*
  • DNA-Binding Proteins / genetics
  • Exome Sequencing
  • Female
  • GATA6 Transcription Factor / genetics
  • Humans
  • Male
  • Microsatellite Instability
  • Microsatellite Repeats / genetics*
  • Middle Aged
  • Mixed Function Oxygenases / genetics
  • Proto-Oncogene Proteins / genetics
  • SOX9 Transcription Factor / genetics
  • Transcription Factors / genetics
  • Wnt Signaling Pathway / genetics

Substances

  • APC protein, human
  • Adenomatous Polyposis Coli Protein
  • BCL9L protein, human
  • Cadherins
  • DNA-Binding Proteins
  • FAT1 protein, human
  • GATA6 Transcription Factor
  • GATA6 protein, human
  • GLIS1 protein, human
  • Proto-Oncogene Proteins
  • SOX9 Transcription Factor
  • SOX9 protein, human
  • Transcription Factors
  • Mixed Function Oxygenases
  • TET1 protein, human