Genetic heterogeneity of primary lesion and metastasis in small intestine neuroendocrine tumors

Dirk Walter,Oliver Waidmann,Christine Koch,Martin Leo Hansmann,Stefan Zeuzem,Florian Battke,Ria Winkelmann,Jan Peveling-Oberhag,Markus Schneider,Jörg Bojunga,Katharina Holzer,Patrick N Harter

doi:10.1038/s41598-018-22115-0

Abstract

Data on intratumoral heterogeneity of small intestine neuroendocrine tumors (SI-NETs) and related liver metastasis are limited. The aim of this study was to characterize genetic heterogeneity of 5 patients with SI-NETs. Therefore, formalin-fixed, paraffin-embedded tissue samples of primary and metastatic lesions as well as benign liver of five patients with synchronously metastasized, well differentiated SI-NETs were analyzed with whole exome sequencing. For one patient, chip based 850k whole DNA methylome analysis was performed of primary and metastatic tumor tissue as well as control tissue. Thereby, 156 single nucleotide variants (SNVs) in 150 genes were identified and amount of mutations per sample ranged from 9–34 (mean 22). The degree of common (0–94%) and private mutations per sample was strongly varying (6–100%). In all patients, copy number variations (CNV) were found and the degree of intratumoral heterogeneity of CNVs corresponded to SNV analysis. DNA methylation analysis of a patient without common SNVs revealed a large overlap of common methylated CpG sites. In conclusion, SI-NET primary and metastatic lesions show a highly varying degree of intratumoral heterogeneity. Driver events might not be detectable with exome analysis only, and further comprehensive studies including whole genome and epigenetic analyses are warranted.

Highlights

Neuroendocrine tumors of the small intestine (SI-NET) represent the most common small intestine neoplasm, occurring with an incidence of 1/100,0001
Estimated mean percentage of tumor cells was comparable for primary tumors and metastatic lesions (86%, 70–95%)
A comparable mean somatic mutation rate of 0.33/mega base (Mb) for primary and 0.41/Mb for metastatic lesions was observed which is within the range of previous large scale sequencing studies on SI-NET of Banck et al and Francis et al where a mean of 0.1/Mb and 0.77/Mb was reported, respectively[10,11]

Summary

Introduction

Neuroendocrine tumors of the small intestine (SI-NET) represent the most common small intestine neoplasm, occurring with an incidence of 1/100,0001 They originate from enterochromaffine cells of the digestive tract and frequently secrete neuroamines or peptide hormones which can lead to a variety of clinical syndromes. Data on variation of the mutational landscape between primary and metastatic lesions are limited and available exome data are highly diverse with the percentage of common mutations of primary lesion and metastasis ranging from 0–47%11. Further characterization of this intratumoral heterogeneity is of high importance to better understand tumorigenesis of SI-NETs and its possible implications on future therapy approaches. We thereby unveiled a profound genetic variability strongly suggesting presence of subclonality within SI-NETs

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Conclusion