Patient-derived conditionally reprogrammed cells maintain intra-tumor genetic heterogeneity

Joanna Hu,Bruna R S Correa,Richard Schlegel,Pedro A F Galante,Luiz O F Penalva,David L Rimm,Seema Agarwal

doi:10.1038/s41598-018-22427-1

Abstract

Preclinical in vitro models provide an essential tool to study cancer cell biology as well as aid in translational research, including drug target identification and drug discovery efforts. For any model to be clinically relevant, it needs to recapitulate the biology and cell heterogeneity of the primary tumor. We recently developed and described a conditional reprogramming (CR) cell technology that addresses many of these needs and avoids the deficiencies of most current cancer cell lines, which are usually clonal in origin. Here, we used the CR cell method to generate a collection of patient-derived cell cultures from non-small cell lung cancers (NSCLC). Whole exome sequencing and copy number variations are used for the first time to address the capability of CR cells to keep their tumor-derived heterogeneity. Our results indicated that these primary cultures largely maintained the molecular characteristics of the original tumors. Using a mutant-allele tumor heterogeneity (MATH) score, we showed that CR cells are able to keep and maintain most of the intra-tumoral heterogeneity, suggesting oligoclonality of these cultures. CR cultures therefore represent a pre-clinical lung cancer model for future basic and translational studies.

Highlights

Intra-tumor heterogeneity (ITH), defined by the coexistence of genetically distinct sub-clonal populations of cells within the same tumor, is the most relevant feature of all cancers and defines the response to a given therapy, cellular dissemination and progression of primary tumor[1,2,3,4]
conditional reprogramming (CR) Lung cancer cultures were established directly from tissue samples from ten individual patients (Table 1) who were diagnosed with non-small cell lung cancer
Based on the Jaccard similarity (1 – Jaccard distance), we found that all CR cells are located in the upper quadrant suggesting that they are more similar in term of their single nucleotide variations (SNVs) to tumors than to normal (Fig. 1A)

Summary

Introduction

Intra-tumor heterogeneity (ITH), defined by the coexistence of genetically distinct sub-clonal populations of cells within the same tumor, is the most relevant feature of all cancers and defines the response to a given therapy, cellular dissemination and progression of primary tumor[1,2,3,4]. Patient derived tumor xenografts (PDXs) are able to capture the intra-tumor heterogeneity[7,8,9,10], but the success rate of establishing these models is not very high and it is not very cost-effective, especially for drug discovery studies[8,9,11,12,13,14]. We established 10 individual primary cell lung cancer cultures directly from patient’s tissue samples using conditionally reprogram (CR) technology. Whole exome sequencing (WES) and copy number variations (CNVs) were used to assess the level of ITH in cell cultures when compared with primary tumor and normal tissue materials from each patient. Our results indicate that patient-derived cell model system using CR technology is able to capture intra-tumor heterogeneity in addition to maintaining the morphological features

Methods

Results

Conclusion