Organoid cultures of early-onset colorectal cancers reveal distinct and rare genetic profiles

Gut. 2020 Dec;69(12):2165-2179. doi: 10.1136/gutjnl-2019-320019. Epub 2020 Mar 26.

Abstract

Objective: Sporadic early-onset colorectal cancer (EOCRC) has bad prognosis, yet is poorly represented by cell line models. We examine the key mutational and transcriptomic alterations in an organoid biobank enriched in EOCRCs.

Design: We established paired cancer (n=32) and normal organoids (n=18) from 20 patients enriched in microsatellite-stable EOCRC. Exome and transcriptome analysis was performed.

Results: We observed a striking diversity of molecular phenotypes, including PTPRK-RSPO3 fusions. Transcriptionally, RSPO fusion organoids resembled normal colon organoids and were distinct from APC mutant organoids, with high BMP2 and low PTK7 expression. Single cell transcriptome analysis confirmed the similarity between RSPO fusion organoids and normal organoids, with a propensity for maturation on Wnt withdrawal, whereas the APC mutant organoids were locked in progenitor stages. CRISPR/Cas9 engineered mutation of APC in normal human colon organoids led to upregulation of PTK7 protein and suppression of BMP2, but less so with an engineered RNF43 mutation. The frequent co-occurrence of RSPO fusions with SMAD4 or BMPR1A mutation was confirmed in TCGA database searches. RNF43 mutation was found in organoid from a leukaemia survivor with a novel mutational signature; and organoids with POLE proofreading mutation displayed ultramutation. The cancer organoid genomes were stable over long culture periods, while normal human colon organoids tended to be subject to clonal dominance over time.

Conclusions: These organoid models enriched in EOCRCs with linked genomic data fill a gap in existing CRC models and reveal distinct genetic profiles and novel pathway cooperativity.

Keywords: Early-onset colon cancer; R-spondin fusion; RNF43; colon carcinogenesis; colorectal cancer; colorectal cancer genes; gene expression; organoid models; serrated neoplasia.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenomatous Polyposis Coli Protein / genetics
  • Bone Morphogenetic Protein 2 / genetics
  • Bone Morphogenetic Protein Receptors, Type I / genetics
  • CRISPR-Cas Systems
  • Cell Adhesion Molecules / genetics
  • Colorectal Neoplasms / genetics*
  • Gene Expression Profiling
  • Gene Fusion
  • Genetic Profile*
  • Humans
  • Models, Genetic
  • Mutation
  • Organoids / pathology*
  • Receptor Protein-Tyrosine Kinases / genetics
  • Receptor-Like Protein Tyrosine Phosphatases, Class 2 / genetics
  • Smad4 Protein / genetics
  • Thrombospondins / genetics
  • Tissue Banks
  • Ubiquitin-Protein Ligases / genetics
  • Up-Regulation
  • Whole Exome Sequencing

Substances

  • APC protein, human
  • Adenomatous Polyposis Coli Protein
  • BMP2 protein, human
  • Bone Morphogenetic Protein 2
  • Cell Adhesion Molecules
  • RSPO3 protein, human
  • SMAD4 protein, human
  • Smad4 Protein
  • Thrombospondins
  • RNF43 protein, human
  • Ubiquitin-Protein Ligases
  • PTK7 protein, human
  • Receptor Protein-Tyrosine Kinases
  • BMPR1A protein, human
  • Bone Morphogenetic Protein Receptors, Type I
  • PTPRK protein, human
  • Receptor-Like Protein Tyrosine Phosphatases, Class 2