Exome Capture Sequencing of Adenoma Reveals Genetic Alterations in Multiple Cellular Pathways at the Early Stage of Colorectal Tumorigenesis

<div><p>Most of colorectal adenocarcinomas are believed to arise from adenomas, which are premalignant lesions. Sequencing the whole exome of the adenoma will help identifying molecular biomarkers that can predict the occurrence of adenocarcinoma more precisely and help understanding the molecular pathways underlying the initial stage of colorectal tumorigenesis. We performed the exome capture sequencing of the normal mucosa, adenoma and adenocarcinoma tissues from the same patient and sequenced the identified mutations in additional 73 adenomas and 288 adenocarcinomas. Somatic single nucleotide variations (SNVs) were identified in both the adenoma and adenocarcinoma by comparing with the normal control from the same patient. We identified 12 nonsynonymous somatic SNVs in the adenoma and 42 nonsynonymous somatic SNVs in the adenocarcinoma. Most of these mutations including OR6X1, SLC15A3, KRTHB4, RBFOX1, LAMA3, CDH20, BIRC6, NMBR, GLCCI1, EFR3A, and FTHL17 were newly reported in colorectal adenomas. Functional annotation of these mutated genes showed that multiple cellular pathways including Wnt, cell adhesion and ubiquitin mediated proteolysis pathways were altered genetically in the adenoma and that the genetic alterations in the same pathways persist in the adenocarcinoma. CDH20 and LAMA3 were mutated in the adenoma while NRXN3 and COL4A6 were mutated in the adenocarcinoma from the same patient, suggesting for the first time that genetic alterations in the cell adhesion pathway occur as early as in the adenoma. Thus, the comparison of genomic mutations between adenoma and adenocarcinoma provides us a new insight into the molecular events governing the early step of colorectal tumorigenesis.</p> </div

Validated somatic mutation in the colorectal adenoma.

<p>Validated somatic mutation in the colorectal adenoma.</p

Summary of sequencing coverage of the normal mucosa, adenoma and adenocarcinoma from the same patient.

<p>Summary of sequencing coverage of the normal mucosa, adenoma and adenocarcinoma from the same patient.</p

Validated somatic mutation in the colorectal adenocarcinoma.

<p>Validated somatic mutation in the colorectal adenocarcinoma.</p

Mutated pathways in adenoma and adenocarcinoma.

<p>Mutated pathways in adenoma and adenocarcinoma.</p

Somatic SNVs pattern in the adenoma and the adenocarcinoma.

<p>(A) Somatic mutation spectrum in adenoma and adenocarcinoma, similar with 11 colorectal cancers previously reported <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053310#pone.0053310-Sjoblom1" target="_blank">[10]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053310#pone.0053310-Wood1" target="_blank">[11]</a>. (B) Fractions of guanine mutations at 5′-CpG-3′ dinucleotides in the exome of adenoma and adenocarcinoma. (C) Prevalence of somatic SNVs in the coding region and non-coding region of the exome of the adenoma and the adenocarcinoma.</p

Recurrent mutations in 288 additional cases of colorectal tumors.

<p>Recurrent mutations in 288 additional cases of colorectal tumors.</p

Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines

Under the guidance of the Chromosome-centric Human Proteome Project (C-HPP),, we conducted a systematic survey of the expression status of genes located at human chromosome 20 (Chr.20) in three cancer tissues, gastric, colon, and liver carcinoma, and their representative cell lines. We have globally profiled proteomes in these samples with combined technology of LC–MS/MS and acquired the corresponding mRNA information upon RNA-seq and RNAchip. In total, 323 unique proteins were identified, covering 60% of the coding genes (323/547) in Chr.20. With regards to qualitative information of proteomics, we overall evaluated the correlation of the identified Chr.20 proteins with target genes of transcription factors or of microRNA, conserved genes and cancer-related genes. As for quantitative information, the expression abundances of Chr.20 genes were found to be almost consistent in both tissues and cell lines of mRNA in all individual chromosome regions, whereas those of Chr.20 proteins in cells are different from tissues, especially in the region of 20q13.33. Furthermore, the abundances of Chr.20 proteins were hierarchically evaluated according to tissue- or cancer-related distribution. The analysis revealed several cancer-related proteins in Chr.20 are tissue- or cell-type dependent. With integration of all the acquired data, for the first time we established a solid database of the Chr.20 proteome