title: Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms.
abstract: Although targeted therapies are initially effective, resistance inevitably emerges. Several methods, such as genetic analysis of resistant clinical specimens, have been applied to uncover these resistance mechanisms to facilitate follow-up care. Although these approaches have led to clinically relevant discoveries, difficulties in attaining the relevant patient material or in deconvoluting the genomic data collected from these specimens have severely hampered the path towards a cure. To this end, we here describe a tool for expeditious discovery that may guide improvement in first-line therapies and alternative clinical management strategies. By coupling preclinical in vitro or in vivo drug selection with next-generation sequencing, it is possible to identify genomic structural variations and/or gene expression alterations that may serve as functional drivers of resistance. This approach facilitates the spontaneous emergence of alterations, enhancing the probability that these mechanisms may be observed in the patients. In this protocol we provide guidelines to maximize the potential for uncovering single nucleotide variants that drive resistance using adherent lines.
authors.affiliation: H3 Biomedicine.
authors.forename: Manav
authors.initials: M
authors.lastname: Korpal
authors.affiliation: H3 Biomedicine.
authors.forename: Jacob
authors.initials: J
authors.lastname: Feala
authors.affiliation: H3 Biomedicine.
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Puyang
authors.affiliation: H3 Biomedicine.
authors.forename: Jian
authors.initials: J
authors.lastname: Zou
authors.affiliation: Massachusetts General Hospital.
authors.forename: Alex H
authors.initials: AH
authors.lastname: Ramos
authors.affiliation: H3 Biomedicine.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Wu
authors.affiliation: H3 Biomedicine.
authors.forename: Timm
authors.initials: T
authors.lastname: Baumeister
authors.affiliation: H3 Biomedicine.
authors.forename: Lihua
authors.initials: L
authors.lastname: Yu
authors.affiliation: H3 Biomedicine.
authors.forename: Markus
authors.initials: M
authors.lastname: Warmuth
authors.affiliation: H3 Biomedicine; ping_zhu@h3biomedicine.com.
authors.forename: Ping
authors.initials: P
authors.lastname: Zhu
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D004351:Drug Resistance / Q000235:genetics*; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D045325:HCT116 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D066298:In Vitro Techniques; D058990:Molecular Targeted Therapy
chemical_list: D000970:Antineoplastic Agents