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Small intestinal neuroendocrine tumors (SI-NETs) are the most common malignancy of the small intestine. They are typically slow-growing, often presenting with multiple primary tumors and, in many cases, metastases at diagnosis. Radical surgery remains the only curative option, yielding a five-year survival rate of approximately 67%. However, the lack of comprehensive molecular understanding limits the availability of personalized treatment strategies. The aim of this thesis was to further characterize the molecular landscape of SI-NETs using state-of-the-art genomic and transcriptomic tools.

In Paper I, long-read whole-genome sequencing revealed few recurrent structural variants across samples. The most notable consistency was found in the frequency of deletions and insertions between tumors. In the chromosome 18 methylation subgroup analysis, we identified a general hypomethylation trend across the genome, but with contrasting hypermethylation patterns in genes located on the chromosome 18.

In Paper II, we explored alternative splicing differences between primary tumors and liver metastases using full-length transcript analysis. Only a small number of recurrent differences emerged across analytical approaches, and their functional consequences were difficult to predict. A comparative analysis using corresponding short-read transcriptomes did not reveal consistent splicing alterations, highlighting the lack of or complexity of splicing variation in SI-NETs.

Building on our earlier in vitro experiments of metformin’s anti-tumor effects in SI-NET cell lines, Paper III reports an in vivo follow-up in which oral metformin administration to tumor xenografted mice significantly inhibited tumor growth. Analysis of mRNA and miRNA expression patterns identified potential treatment-induced miRNA biomarkers. External single-cell RNA sequencing data further validated a subset of genes particularly relevant to SI-NET biology.

In Paper IV, we applied single-cell RNA sequencing to distinguish molecular differences between SI-NET tumor cells and their presumed cell of origin, the rare enterochromaffin (EC) cell. A clear distinction between SI-NET tumor cells and EC cells revealed 373 significantly altered genes; among these, 26 exhibited tumor-specific activation or silencing. While some of these changes corroborated previous findings, several novel gene expression shifts were identified, offering new insight into tumor initiation and progression.