title: Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing.
abstract: The acute cellular response to stress generates a subpopulation of reversibly stress-tolerant cells under conditions that are lethal to the majority of the population. Stress tolerance is attributed to heterogeneity of gene expression within the population to ensure survival of a minority. We performed whole transcriptome sequencing analyses of metastatic human breast cancer cells subjected to the chemotherapeutic agent paclitaxel at the single-cell and population levels. Here we show that specific transcriptional programs are enacted within untreated, stressed, and drug-tolerant cell groups while generating high heterogeneity between single cells within and between groups. We further demonstrate that drug-tolerant cells contain specific RNA variants residing in genes involved in microtubule organization and stabilization, as well as cell adhesion and cell surface signaling. In addition, the gene expression profile of drug-tolerant cells is similar to that of untreated cells within a few doublings. Thus, single-cell analyses reveal the dynamics of the stress response in terms of cell-specific RNA variants driving heterogeneity, the survival of a minority population through generation of specific RNA variants, and the efficient reconversion of stress-tolerant cells back to normalcy.
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, CA 95064;
authors.forename: Mei-Chong Wendy
authors.initials: MC
authors.lastname: Lee
authors.affiliation: Laboratory of Regulatory Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: Lopez-Diaz
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, CA 95064;
authors.forename: Shahid Yar
authors.initials: SY
authors.lastname: Khan
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, CA 95064;
authors.forename: Muhammad Akram
authors.initials: MA
authors.lastname: Tariq
authors.affiliation: Transgenic Core Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; and.
authors.forename: Yelena
authors.initials: Y
authors.lastname: Dayn
authors.affiliation: Five3 Genomics, LLC, Santa Cruz, CA 95060.
authors.forename: Charles Joseph
authors.initials: CJ
authors.lastname: Vaske
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, CA 95064;
authors.forename: Amie J
authors.initials: AJ
authors.lastname: Radenbaugh
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, CA 95064;
authors.forename: Hyunsung John
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Laboratory of Regulatory Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037; pourmand@soe.ucsc.edu emerson@salk.edu.
authors.forename: Beverly M
authors.initials: BM
authors.lastname: Emerson
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, CA 95064; pourmand@soe.ucsc.edu emerson@salk.edu.
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
mesh_terms: D000972:Antineoplastic Agents, Phytogenic / Q000494:pharmacology*; D001943:Breast Neoplasms / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D019008:Drug Resistance, Neoplasm / Q000187:drug effects / Q000235:genetics; D005260:Female; D006801:Humans; D017239:Paclitaxel / Q000494:pharmacology*; D012334:RNA, Neoplasm / Q000096:biosynthesis / Q000235:genetics; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic / Q000187:drug effects / Q000235:genetics
chemical_list: D000972:Antineoplastic Agents, Phytogenic; D012334:RNA, Neoplasm; D017239:Paclitaxel
keywords: RNA-Seq; drug resistance; paclitaxel; single cell; tumor heterogeniety