title: Whole genome and normalized mRNA sequencing reveal genetic status of TK6, WTK1, and NH32 human B-lymphoblastoid cell lines.
abstract: Closely related TK6, WTK1, and NH32 human B-lymphoblastoid cell lines differ in their p53 functional status. These lines are used frequently in genotoxicity studies and in studies aimed at understanding the role of p53 in DNA repair. Despite their routine use, little is known about the genetic status of these cells. To provide insight into their genetic composition, we sequenced and analyzed the entire genome of TK6 cells, as well as the normalized transcriptomes of TK6, WTK1, and NH32 cells. Whole genome sequencing (WGS) identified 21,561 genes and 5.17×10(6) small variants. Within the small variants, 50.54% were naturally occurring single nucleotide polymorphisms (SNPs) and 49.46% were mutations. The mutations were comprised of 92.97% single base-pair substitutions and 7.03% insertions or deletions (indels). The number of predicted genes, SNPs, and small mutations are similar to frequencies observed in the human population in general. Normalized mRNA-seq analysis identified the expression of transcripts bearing SNPs or mutations for TK6, WTK1, and NH32 as 2.88%, 2.04%, and 1.71%, respectively, and several of the variant transcripts identified appear to have important implications in genetic toxicology. These include a single base deletion mutation in the ferritin heavy chain gene (FTH1) resulting in a frame shift and protein truncation in TK6 that impairs iron metabolism. SNPs in the thiopurine S-methyltransferase (TPMT) gene (TPMT*3A SNP), and in the xenobiotic metabolizing enzyme, NADPH quinine oxidoreductase 1 (NQO1) gene (NQO1*2 SNP), are both associated with decreased enzyme activity. The clinically relevant TPMT*3A and NQO1*2 SNPs can make these cell lines useful in pharmacogenetic studies aimed at improving or tailoring drug treatment regimens that minimize toxicity and enhance efficacy.
authors.affiliation: Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States.
authors.forename: Javier
authors.initials: J
authors.lastname: Revollo
authors.affiliation: Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States. Electronic address: Dayton.petibone@fda.hhs.gov.
authors.forename: Dayton M
authors.initials: DM
authors.lastname: Petibone
authors.affiliation: Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States.
authors.forename: Page
authors.initials: P
authors.lastname: McKinzie
authors.affiliation: Division of Systems Biology, FDA/NCTR, Jefferson, AR 72079, United States.
authors.forename: Bridgett
authors.initials: B
authors.lastname: Knox
authors.affiliation: Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States.
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Morris
authors.affiliation: Division of Systems Biology, FDA/NCTR, Jefferson, AR 72079, United States.
authors.forename: Baitang
authors.initials: B
authors.lastname: Ning
authors.affiliation: Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States.
authors.forename: Vasily N
authors.initials: VN
authors.lastname: Dobrovolsky
mesh_terms: D000483:Alleles; D001402:B-Lymphocytes / Q000187:drug effects* / Q000378:metabolism; D002460:Cell Line; D049109:Cell Proliferation / Q000187:drug effects; D004249:DNA Damage / Q000187:drug effects; D004260:DNA Repair / Q000187:drug effects; D005290:Ferric Compounds / Q000633:toxicity; D005293:Ferritins / Q000235:genetics / Q000378:metabolism; D016368:Frameshift Mutation; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019189:Iron Metabolism Disorders / Q000139:chemically induced / Q000235:genetics; D008780:Methyltransferases / Q000378:metabolism; D009154:Mutation; D016660:NAD(P)H Dehydrogenase (Quinone) / Q000235:genetics / Q000378:metabolism; D010088:Oxidoreductases; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013866:Thioguanine / Q000633:toxicity; D059467:Transcriptome; D016159:Tumor Suppressor Protein p53 / Q000235:genetics / Q000378:metabolism
chemical_list: D005290:Ferric Compounds; D012333:RNA, Messenger; D016159:Tumor Suppressor Protein p53; C025314:ferric citrate; D005293:Ferritins; C454461:FTH1 protein, human; D010088:Oxidoreductases; D016660:NAD(P)H Dehydrogenase (Quinone); C447479:NQO1 protein, human; D008780:Methyltransferases; C022745:thiopurine methyltransferase; D013866:Thioguanine
keywords: FTH1; Human B-lymphoblastoid cells; NQO1*2; Next generation sequencing (NGS); TPMT*3A; p53