Changes in gene expression in small bowel neuroendocrine tumors associated with progression to metastases

Abstract

Background: Small bowel neuroendocrine tumors (SBNETs) present frequently with metastases, yet little is known about the molecular basis of this progression. This study sought to identify the serial differential expression of genes between normal small bowel, primary small bowel neuroendocrine tumors, and liver metastases.

Methods: RNA isolated from matched normal small bowel tissue, primary small bowel neuroendocrine tumors, and liver metastases in 12 patients was analyzed with whole transcriptome expression microarrays and RNA-Seq. Changes in gene expression between primary small bowel neuroendocrine tumors and normal small bowels, and liver metastases versus primary small bowel neuroendocrine tumors were calculated. Common genes that were differentially expressed serially (increasing or decreasing from normal small bowel to primary small bowel neuroendocrine tumors to liver metastases) were identified, and 10 were validated using qPCR.

Results: Use of 2 transcriptome platforms allowed for a robust discrimination of genes important in small bowel neuroendocrine tumors progression. Serial differential expression was validated in 7/10 genes, all of which had been described previously in abdominal cancers, and with several interacting with members of the AKT, MYC, or MAPK3 pathways. Liver metastases had consistent underexpression of PMP22, while high expression of SERPINA10 and SYT13 was characteristic of both pSBTs and liver metastases.

Conclusion: Identification of the serial differential expression of genes from normal tissues to primary tumors to metastases lends insight into important pathways for SBNETs progression. Differential expression of various genes, including PMP22, SYT13 and SERPINA10, are associated with the progression of SBNETs and warrant further investigation.

Figure 1

Box plot of expression levels of candidate genes. N = Normal Small Bowel; P = Primary Tumor; L = Liver Metastasis.

Figure 2

Plot of gene expression for each individual patient. Dotted line represents gene expression of a single patient who had discordant expression for multiple genes. N = Normal Small Bowel; P = Primary Tumor; L = Liver Metastasis.

Figure 3

Classification tree for differentiation of primary tumors from liver metastases using expression levels of PMP22 and SYT13. Cutoff limits expressed as −dCt values. Dark grey= Liver metastasis. Light Grey = Primary tumor.

Figure 4

Gene network constructed from candidate genes using IPA. Red boxes = Increased expression in our data set. Blue boxes= Decreased expression in our data set.