Our study, for the first time, described the somatic mutation in the whole exome of a colorectal adenoma. The adenoma had a smaller number of somatic mutations but demonstrating a similar pattern of enrichment in nucleotide transitions and involving similar functional pathways as the adenocarcinoma from the same patient. Identification of these gene alterations and their associated pathways in the adenoma has provided new sights into the molecular process of developmental course from colorectal adenoma to colorectal adenocarcinoma.
We identified 12 somatic nonsynonymous SNVs in the adenoma. The APC gene was the only gene reportedly associated with colon cancer. It was found to be mutated in both adenoma and adenocarcinoma. Four other genes were reported as mutated genes in other types of cancer. First, a missense mutation in LAMA3 in adenoma changed from leucine to serine. LAMA3 is involved in cell adhesion, signal transduction and differentiation and its mutations were previously reported in brain cancer 
, ovary cancer 
and melanoma 
. Second, a missense SNV in CDH20 changed from arginine to glutamine. CDH20 encodes a type II classical cadherin which is involved in cell to cell adhesion and its mutation was previously reported in breast cancer 
. Third, a nonsense mutation was found in BIRC6 and would result in a truncated protein. The mutations in BIRC6 were previously reported in several kinds of cancer including melanoma 
, glioma 
, breast cancer 
and pancreatic cancer 
. Its gene product, also known as APOLLON, acts as an ubiquitin-conjugating enzyme (E2) and inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination. Fourth, a missense SNV was found in NMBR. NMBR encodes a Neuromedin B receptor, and its mutations were previously reported in gliomas 
There were 42 somatic nonsynonymous SNVs in the adenocarcinoma. Among them, APC and FBXW7 were reported as two mutated gene ‘mountains’ in colorectal carcinomas 
. In addition, 5 other mutated genes were previously reported in colon cancers including FAM181A, NRXN3, KIAA1409, TFR2, and COL4A6. The mutation of FAM181A was reported in colon cancers 
. But its function is not clear, so the further funcational study will be needed. NRXN3 functions in the vertebrate nervous system as cell adhesion molecules and receptors and was previously found to be mutated in colon cancer 
, breast cancer 
, glioma 
, squamous cell carcinoma of the head and neck 
and ovary cancer 
. The mutation of KIAA1409, which is an unknown protein, was previously reported in colon cancers 
, ovary cancer 
, and melanoma 
. TFR2 encodes a single-pass type II membrane protein involved in iron uptake and was previously found to be mutated in colon cancer 
and liver cancer 
. COL4A6 encodes one of the six subunits of type IV collagen likely involved in cell to cell adhesion and was found to be mutated in ovary cancer 
and colon cancer 
. We observed mutations in other 8 genes in the adenocarcinoma. Their mutations were only reported in non-CRC malignancies. Thus, they are newly discovered gene mutations in CRCs.
In addition to the APC/Wnt pathway known to be involved in the development of the colorectal adenoma, this study has identified a few new cellular pathways that are altered in the adenoma at the genetic level. These pathways are also altered at the genetic level in the adenocarcinoma, suggesting that they may functionally drive colorectal tumorigenesis. First, CDH20 and LAMA3, which are both involved in cell adhesion, were found to be mutated in the colorectal adenoma. This is quite interesting as the cell adhesion pathway is thought to be important for cancer cell invasion and metastasis, which are the characteristics of the later stage of cancer development. Our finding thus provides direct evidence supporting a recently proposed hypothesis that the capacity of metastasis may have been acquired by the cancer cells at the early stage of their development 
. Second, our result also showed that ubiquitin mediated proteolysis pathway is altered at the genetic level in the early stage of tumorigenesis. BIRC6 which encodes E2 ubiquitin-conjugating enzyme is involved in ubiquitin mediated proteolysis. Although we found that FBXW7 which encodes E3 ubiquitin-ligase enzyme is mutated only in colorectal adenocarcinomas 
, previous report has identified somatic mutations in FBXW7 in adenomas 
. Recently, whole-exome sequencing of premalignant lesions of pancreatic adenocarcinoma also revealed recurrent mutations in components of ubiquitin-dependent pathways 
. Our study thus suggested that the ubiquitin mediated proteolysis may play a role in the early stage of tumorigenesis in the CRC. Third, we found OR6X1 and NMBR, which are involved in olfactory transduction and neuroactive ligand-receptor interaction, respectively, are mutated in the adenoma. Many proteins involved in neuronal transduction are also involved in cell-cell communication, which again is important for cancer cell invasion and metastasis. The functions of the mutations of OR6X1 and NMBR in the early stage of colorectal tumorigenesis remain to be explored. Multiple genes involved in olfactory transduction and neuroactive ligand-receptor interaction including OR13J1, OR51E2, GNAL, and GRIK1 were also found by this study to be mutated in the adenocarcinoma, suggesting these two classes of genes warrant further investigation. Finally, although neither the remaining mutations found in the adenoma nor the genetic alterations in their involved pathways are observed in the adenocarcinoma, their importance in the development of colorectal adenoma cannot be excluded.
Although the host environmental factors were largely eliminated by analyzing the mutation profiles of the adenoma and the adenocarcinoma from the same patient, it is not surprising that mutations in the adenoma are not present in the adenocarcinoma from the same patient because they may have arisen from two independent tumorigenesis processes. Nevertheless, we found that mutations affecting the same cellular pathways were found in both the adenoma and the adenocarcinoma from the same patient. It is also not surprising that identical mutations identified in the adenoma from one patient were not found in adenomas from additional patients tested in this study. We anticipate that different adenomas harbor mutations in different regions on the same genes that were found to be mutated in one adenoma. If these genes are important for the development of adenoma, we may see them repeatedly altered in multiple adenomas by sequencing their entire exome. However, none of them except APC are anticipated to be frequently mutated in the adenoma. The same cellular pathways such as the cell adhesion and ubiquitin-dependent pathways may be altered in other components at the genetic level more frequently in the adenomas and therefore warrant further investigation.