Colorectal Cancer Genetic Heterogeneity Delineated by Multi-Region Sequencing

Abstract

Intratumor heterogeneity (ITH) leads to an underestimation of the mutational landscape portrayed by a single needle biopsy and consequently affects treatment precision. The extent of colorectal cancer (CRC) genetic ITH is not well understood in Chinese patients. Thus, we conducted deep sequencing by using the OncoGxOne™ Plus panel, targeting 333 cancer-specific genes in multi-region biopsies of primary and liver metastatic tumors from three Chinese CRC patients. We determined that the extent of ITH varied among the three cases. On average, 65% of all the mutations detected were common within individual tumors. KMT2C aberrations and the NCOR1 mutation were the only ubiquitous events. Subsequent phylogenetic analysis showed that the tumors evolved in a branched manner. Comparison of the primary and metastatic tumors revealed that PPP2R1A (E370X), SETD2 (I1608V), SMAD4 (G382T), and AR splicing site mutations may be specific to liver metastatic cancer. These mutations might contribute to the initiation and progression of distant metastasis. Collectively, our analysis identified a substantial level of genetic ITH in CRC, which should be considered for personalized therapeutic strategies.

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

“…We obtained: (a) a clonal group of 34 mutations detected in all samples (b) a subclonal group of 3 mutations private to the metastatic regions, and (c) 8 mutations with distinct mutational profiles. The clonal group contains mutations in key colorectal driver genes such as APC, KRAS, PIK3CA and TP53 [15], Edmonds's model predicts branching evolution and high levels of ITH among the subclonal populations, consistently with the original phylogenetic analysis by Lu et al [40] ( Figure 5B). In particular, the subclonal trajectory that characterizes the primary regions is initiated by a stopgain SNV in the DNA damage repair gene ATM, whereas the subclonal metastatic expansion seems to originate by a stopgain SNV in GNAQ, a gene reponsible for diffusion in many tumour types [41].…”

“…Multi-region P3 ( Figure 5: A. Multi-region sequencing data for a MSI-high colorectal cancer from [40], with three regions of the primary cancer: p3-1, p3-2 and p3-3, and two of one metastasis: L-1 and L-2.…”

Proteome Heterogeneity in Colorectal Cancer

“…ITH complicates biomarkers discovery and therapeutic intervention given to the patient. Previous genomic studies have shown that biopsy from a single tumor and multiple tumors failed to give a comprehensive picture of a tumor's genomic mutational landscape . This holds true for proteomics analysis as well where single regional biopsy or a small chunk of a tumor may underestimate the proteome landscape of heterogeneous tumors.…”

“…CRC tumor heterogeneity has been reported at the genetic and protein levels . Numerous researches based on genomic and transcriptomic profiles have been done to reveal the extensive intertumor heterogeneity in CRC .…”

“…Multi‐region sequencing of biopsies from the primary tumors and liver metastases showed 30–40% of identified somatic mutations failed to be detected in every sequenced region . Recent findings reported genomic profiling of 349 individual glands obtained from 15 colorectal tumors showed uniformly high intratumor heterogeneity (ITH) and subclone mixing in distant regions .…”