Cell-Based Models to Identify Genetic Variants Contributing to Anticancer Drug Response

Summary

A goal of pharmacogenetics is the design of individualized therapy based on a patient’s genomic sequence to maximize response and minimize toxicity. Current chemotherapy is associated with serious, at times life-threatening, toxicity. Identifying heritable genetic variants responsible for chemotherapeutic toxicities is challenging because of its multigenic nature and the difficulty of studying chemotherapeutic toxicity using traditional genetic screening strategies, such as unaffected families.

Cell-based models using lymphoblastoid cell lines from individuals comprising large pedigrees are a means to overcome these limitations. Several investigators within the NIH Pharmacogenetics Research Network have used cell-based models, genome-wide mapping strategies including linkage, and association studies to search for genes responsible for toxicities and for responses associated with chemotherapy. By comparing the variations in chemotherapy-induced cytotoxicity in cell lines from within and among families, the extent to which genetics contributes to human variation in susceptibility to such cytotoxicity can be evaluated.

Centre d’ Etude du Polymorphisme Humain (CEPH) pedigrees have genetic information in the form of SNPs and microsatellites in the public domain, which allows for linkage analysis to identify genetic regions harboring genes contributing to cytotoxicity. Another cell-based model utilizes International HapMap cell lines to identify genetic variants and gene expression associated with chemotherapeutic agent–induced cytotoxicity. With extensive genotypic information and gene expression levels available for these cell lines, associations can be made between genotype and cytotoxicity, and between genotype and gene expression; and correlations can be made between gene expression and cytotoxicity. These studies enable the determination of genetic variants contributing to sensitivity to cytotoxicity through the modulation of gene expression.

There are a number of advantages to the use of CEPH cell lines for evaluating toxicities associated with chemotherapy. Use of cell lines avoids giving toxic chemotherapy to healthy volunteers; cells can be grown under identical conditions; and extensive genotype data for CEPH cell lines are publicly available, allowing investigators to utilize classical mapping techniques (e.g., linkage analysis, association) to study the genetic influence of human variation in drug sensitivity.

Despite the advantages of this cell-based system, limitations include that LCLs represent only one specific tissue type from unaffected individuals, which may or may not be appropriate when assessing a phenotypic effect that occurs in a different tissue (e.g., peripheral neuropathy, diarrhea). Another limitation is that most cell lines do not express cytochrome P450 genes and thus the contribution of metabolism and pharmacokinetics on drug affect is not taken into account. In spite of these limitations, these cell lines provide an opportunity for initial identification of important genes and variants that can be validated in further studies. This comprehensive approach can be broadly applied to other phenotypes that are measurable in cell lines, and for the first time allows the application of familial genetic analysis in the search for genes important in chemotherapeutic response and toxicity.