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Discrimination of low- and high-grade appendiceal mucinous neoplasms by targeted sequencing of cancer-related variants

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Abstract

DNA was obtained from matching micro-dissected, primary tumor cells, paired metastases, and peripheral blood mononuclear cells (germline) from patients with appendiceal mucinous neoplasms. We compared specimens from patient cohorts comprising low-grade adenomucinous neoplasm versus high-grade mucinous adenocarcinoma using a targeted, amplicon sequencing panel of 409 cancer related genes (Ion Torrent Comprehensive Cancer Panel, Thermo-Fisher, Waltham, MA). Copy number variants, single nucleotide variants and small insertions/deletions were identified using a multiplex algorithm pipeline (GATK, VarScan2, MuTect2, SIFT, SIFT-INDEL, PolyPhen-2, Provean). There were significantly more damaging variants in high-grade versus low-grade tumor cohorts. Both cohorts contained damaging, heterozygous germline variants (catenin β1; notch receptor 1 and 4) in pathways associated with cell-lineage specification (WNT, NOTCH). Damaging, somatic KRAS proto-oncogene, GTPase mutations were present in both cohorts, while somatic GNAS complex locus mutations were confined to low-grade neoplasms. Variants predominantly affected transcription factors, kinases, and stem cell signaling molecules in canonical pathways including epithelial to mesenchymal transition, stem cell pluripotency, p53, PTEN, and NF-қB signaling pathways. High-grade tumors demonstrated MYC proto-oncogene, bHLH transcription factor (MYC) and death domain associated protein (DAXX) amplification and damaging somatic variants in tumor protein p53 (TP53), likely to amplify an aggressive phenotype. Damaging APC, WNT signaling pathway regulator (APC) deletions were identified in metastatic tissue of both cohorts suggesting a role in invasive disease. Our data suggest that germline dysregulation of WNT and/or NOTCH pathways predisposes patients toward a secretory cell phenotype (i.e., goblet-like cells) upon acquisition of somatic KRAS mutations. Additional somatically acquired variants activating oncogenes MYC and DAXX and inhibiting the critical tumor suppressor, tumor protein TP53, were consistent with manifestation of a high-grade phenotype. These additional changes within the epithelial to mesenchymal transition signaling network (WNT, NOTCH, RAS/ERK/PI3K, PTEN, NF-қB), produce aggressive high-grade tumor characteristics by actively driving cells towards dedifferentiation, proliferation, and migration.

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Acknowledgements

We express our sincere gratitude to Clinton Miller from GenomOncology (Cleveland, OH) for providing access to the GenomAnalytics application which was instrumental in sorting and characterizing all variants in this study. Also, we appreciate the considerable efforts of James Hirmas, Christopher Dresher and Matthew Porter of GenomeNext (Columbus, OH) who performed an independent parallel variant analysis from the raw files using the Olympus platform to validate and extend the results of this study. We greatly appreciate the support of David Eaves and Cathy Valley from Bio-Rad Laboratories for their help in performing digital droplet PCR analysis of the copy number variant results obtained in this study. This project utilized the University of Pittsburgh Hillman Cancer Center shared resource facility (Cancer Genomics Facility) supported in part by award P30CA047904 (Dr. LaFramboise).

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Conflict of interest

The authors declare that they have no conflict of interest.

Correspondence to William A. LaFramboise or Haroon A. Choudry.

Supplementary information

  1. SUPPLEMENT TABLE 1: Canonical Pathways

  2. SUPPLEMENT 1: APC Deletions

  3. SUPPLEMENT 2: Digital Droplet PCR

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