PIGA mutations and glycosylphosphatidylinositol anchor dysregulation in polyposis-associated duodenal tumorigenesis

The pathogenesis of duodenal tumours in the inherited tumour syndromes Familial Adenomatous Polyposis (FAP) and MUTYH-associated Polyposis (MAP) is poorly understood. This study aimed to identify genes that are significantly mutated in these tumours and to explore the effects of these mutations. Whole exome and whole transcriptome sequencing identified recurrent somatic coding variants of PIGA in 19/70 (27%) FAP and MAP duodenal adenomas, and further confirmed the established driver roles for APC and KRAS. PIGA catalyses the first step in glycosylphosphatidylinositol (GPI) anchor biosynthesis. Flow cytometry of PIGA-mutant adenoma-derived and CRISPR-edited duodenal organoids confirmed loss of GPI anchors in duodenal epithelial cells and transcriptional profiling of duodenal adenomas revealed transcriptional signatures associated with loss of PIGA. Implications: PIGA somatic mutation in duodenal tumours from patients with FAP and MAP and loss of membrane GPI-anchors may present new opportunities for understanding and intervention in duodenal tumorigenesis.

Optimisation of robust singleplex and multiplex droplet digital PCR assays for high confidence mutation detection in circulating tumour DNA

Liquid biopsies offer the potential to monitor cancer response and resistance to therapeutics in near real-time. However, the plasma cell free DNA (cfDNA) level can be low and the fraction of circulating tumour DNA (ctDNA) bearing a mutation - lower still. Detection of tumour-derived mutations in ctDNA is thus challenging and requires highly sensitive and specific assays. Droplet digital PCR (ddPCR) is a technique that enables exquisitely sensitive detection and quantification of DNA/RNA markers from very limiting clinical samples, including plasma. The Bio-Rad QX200 ddPCR system provides absolute quantitation of target DNA molecules using fluorescent dual-labelled probes. Critical to accurate sample analysis are validated assays that are highly specific, reproducible, and with known performance characteristics, especially with respect to false positives. We present a systematic approach to the development and optimisation of singleplex and multiplex ddPCR assays for the detection of point mutations with a focus on ensuring extremely low false positives whilst retaining high sensitivity. We also present a refined method to determine cfDNA extraction efficiency allowing for more accurate extrapolation of mutational levels in source samples. We have applied these approaches to successfully analyse many ctDNA samples from multiple clinical studies and generated exploratory data of high quality.

Burden and Profile of Somatic Mutation in Duodenal Adenomas from Patients with Familial Adenomatous- and MUTYH-associated Polyposis

Purpose: Duodenal polyposis and cancer are important causes of morbidity and mortality in familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP). This study aimed to comprehensively characterize somatic genetic changes in FAP and MAP duodenal adenomas to better understand duodenal tumorigenesis in these disorders.Experimental Design: Sixty-nine adenomas were biopsied during endoscopy in 16 FAP and 10 MAP patients with duodenal polyposis. Ten FAP and 10 MAP adenomas and matched blood DNA samples were exome sequenced, 42 further adenomas underwent targeted sequencing, and 47 were studied by array comparative genomic hybridization. Findings in FAP and MAP duodenal adenomas were compared with each other and to the reported mutational landscape in FAP and MAP colorectal adenomas.Results: MAP duodenal adenomas had significantly more protein-changing somatic mutations (P = 0.018), truncating mutations (P = 0.006), and copy number variants (P = 0.005) than FAP duodenal adenomas, even though MAP patients had lower Spigelman stage duodenal polyposis. Fifteen genes were significantly recurrently mutated. Targeted sequencing of APC, KRAS, PTCHD2, and PLCL1 identified further mutations in each of these genes in additional duodenal adenomas. In contrast to MAP and FAP colorectal adenomas, neither exome nor targeted sequencing identified WTX mutations (P = 0.0017).Conclusions: The mutational landscapes in FAP and MAP duodenal adenomas overlapped with, but had significant differences to those reported in colorectal adenomas. The significantly higher burden of somatic mutations in MAP than FAP duodenal adenomas despite lower Spigelman stage disease could increase cancer risk in the context of apparently less severe benign disease. Clin Cancer Res; 23(21); 6721-32. ©2017 AACR.

Abstract 2646: Targeting cancer stem cell pathways with cell-permeable peptide inhibitors

Direct targeting of several important cancer pathways has so far proved challenging, owing to the lack of pathway-specific targets that can be accessed by conventional small molecule drugs or therapeutic antibodies. Nexigen develops and advances peptide-based cancer therapeutics, a new class of drugs that functionally modulate currently undruggable pathways by targeting intracellular protein-protein-interactions.

One of these undruggable pathways, the Wnt signaling cascade, has been identified as a key pathway in cancer stem cells maintenance. Targeting oncongenic Wnt signaling therefore holds great promise for tackling not only tumor growth but also disease relapse, metastasis and drug resistance. Using our proprietary next generation peptide screening system, we could identify cell-permeable peptides that efficiently inhibit the Wnt pathway through a specific interaction with a key component of intracellular signaling. Our most advanced preclinical candidate has nanomolar target affinity and significantly reduces the expression of Wnt target genes in triple-negative MDA-MB-231 breast cancer cells. The further functional analysis of the peptide in various cancer cell lines revealed a dose-dependent inhibition of cell migration, invasion, proliferation, and the cancer stem cell phenotype. The siRNA-mediated knock-down of the target protein or the inhibition of the Wnt pathway recapitulated the inhibitory peptide effect in these assays. Most importantly, we observed a significant suppression of primary tumor growth, tumor cell self-renewal and a reduction of metastatic potential after treatment in different xenograft models.

In summary, our data suggest that our Wnt pathway peptide inhibitor could be a promising new drug candidate for the treatment of cancer stem cells in a broad diversity of cancers.

Citation Format: Verena Arndt, Annette Friebe, Elena Meuser, Katharina Ross, Franziska Agerer, Carmen Schulten-Schulz, Jens Waak, Daniel Friedrich, Hanjo Hennemann, Jörg Vollmer. Targeting cancer stem cell pathways with cell-permeable peptide inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2646. doi:10.1158/1538-7445.AM2015-2646