Unstable Genome and Transcriptome Dynamics during Tumor Metastasis Contribute to Therapeutic Heterogeneity in Colorectal Cancers

Abstract

Purpose: Genomic and transcriptomic alterations during metastasis are considered to affect clinical outcome of colorectal cancers, but detailed clinical implications of metastatic alterations are not fully uncovered. We aimed to investigate the effect of metastatic evolution on in vivo treatment outcome, and identify genomic and transcriptomic alterations associated with drug responsiveness. Experimental Design: We developed and analyzed patientderived xenograft (PDX) models from 35 patients with colorectal cancer including 5 patients with multiple organ metastases (MOMs). We performed whole-exome, DNA methylation, and RNA sequencing for patient and PDX tumors. With samples from patients with MOMs, we conducted phylogenetic and subclonal analysis and in vivo drug efficacy test on the corresponding PDX models. Results: Phylogenetic analysis using mutation, expression, and DNA methylation data in patients with MOMs showed that mutational alterations were closely connected with transcriptomic and epigenomic changes during the tumor evolution. Subclonal analysis revealed that initial primary tumors with larger number of subclones exhibited more dynamic changes in subclonal architecture according to metastasis, and loco-regional and distant metastases occurred in a parallel or independent fashion. The PDX models from MOMs demonstrated therapeutic heterogeneity for targeted treatment, due to subclonal acquisition of additional mutations or transcriptomic activation of bypass signaling pathway during tumor evolution. Conclusions: This study demonstrated in vivo therapeutic heterogeneity of colorectal cancers using PDX models, and suggests that acquired subclonal alterations in mutations or gene expression profiles during tumor metastatic processes can be associated with the development of drug resistance and therapeutic heterogeneity of colorectal cancers.

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

“…A caveat to PDX models is that intratumoral evolution can occur during engraftment and passaging 11,22–25 . Such evolution could potentially modify treatment response of PDXs with respect to the patient tumors 23,26,27 , particularly if the evolution were to systematically alter cancer-related genes. This issue is related to multi-region comparisons of patient tumors 28–31 , for which local mutational and immune infiltration variations have suggested differential phenotypes among multi-region samples 32 .…”

Advanced technological tools to study multidrug resistance in cancer

“…Besides, RNA sequencing can be used to study associations between genomic and transcriptomic alterations during tumor development, drug response and clinical outcome of patients. These changes can be associated with the development of drug resistance and differences in therapy outcomes (Cho et al, 2019). Whole transcriptome RNA sequencing can reveal the role of transcript deregulation and alternative splicing in malignant transformation and chemoresistance (De Laere et al, 2017;Goff et al, 2013) as described in Table 1.…”

“…Other tools like next-generation sequencing (NGS) which has become irreplaceable in discovering mutations, gene expression and cancer biomarkers, offers a broad spectrum of possibilities for studying MDR (Chandana et al, 2019;Cho et al, 2019;Kyrochristos et al, 2019;Li et al, 2015aLi et al, , 2015b. In the last years, high throughput NGS technology revealed important findings regarding the genomic, epigenetic and transcriptomic diversity of cancers that otherwise would not be possible to acquire by standard histopathological analysis (Jiang et al, 2014;Teixeira et al, 2019;Turajlic et al, 2019).…”

Circulating Tumor DNA in Colorectal Cancer—From Concept to Clinic

“…26 Studies have now shown that tumor cells within the same tumor mass in an individual patient can also carry several different molecular alterations, referred to as intratumoral heterogeneity, contributing to drug resistance. 21,23,[27][28][29] Whole genome or exome sequencing of DNA from CRC has characterized a number of recurrent somatically mutated genes, such as APC, TP53, KRAS, NRAS, BRAF, and PIK3CA, 30,31 affording the ability to perform targeted panel sequencing for liquid biopsies. Several studies have demonstrated that ctDNA profiling can accurately reproduce the genomic landscape of tumor tissue, 21,[32][33][34] and more specifically the detection of RAS mutations by ctDNA analysis has also been validated, demonstrating it to be a viable alternative to tissue-based RAS testing.…”