title: Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency.
abstract: Whole-exome sequencing (Exome-seq) has been successfully applied in several recent studies. We here sequenced the exomes of 15 pancreatic tumor cell lines and their matched normal samples. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they showed a 10.5-fold increase in the rate of somatic indels, e.g., truncating indels in TP53 and TGFBR2, indicating MLH1 haploinsufficiency in the correction of DNA indel errors. We further analyzed the exomes of 15 renal cell carcinomas and confirmed MLH1 haploinsufficiency. We observed a much higher rate of indel mutations in the affected cases and identified recurrent truncating indels in several cancer genes such as VHL, PBRM1, and JARID1C. Together, our data suggest that MLH1 hemizygous deletion, through increasing the rate of indel mutations, could drive the development and progression of sporadic cancers.
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo 153-8904, Japan.
authors.forename: Linghua
authors.initials: L
authors.lastname: Wang
authors.forename: Shuichi
authors.initials: S
authors.lastname: Tsutsumi
authors.forename: Tokuichi
authors.initials: T
authors.lastname: Kawaguchi
authors.forename: Koichi
authors.initials: K
authors.lastname: Nagasaki
authors.forename: Kenji
authors.initials: K
authors.lastname: Tatsuno
authors.forename: Shogo
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Fei
authors.initials: F
authors.lastname: Sang
authors.forename: Kohtaro
authors.initials: K
authors.lastname: Sonoda
authors.forename: Minoru
authors.initials: M
authors.lastname: Sugawara
authors.forename: Akio
authors.initials: A
authors.lastname: Saiura
authors.forename: Seiko
authors.initials: S
authors.lastname: Hirono
authors.forename: Hiroki
authors.initials: H
authors.lastname: Yamaue
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Miki
authors.forename: Minoru
authors.initials: M
authors.lastname: Isomura
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Totoki
authors.forename: Genta
authors.initials: G
authors.lastname: Nagae
authors.forename: Takayuki
authors.initials: T
authors.lastname: Isagawa
authors.forename: Hiroki
authors.initials: H
authors.lastname: Ueda
authors.forename: Satsuki
authors.initials: S
authors.lastname: Murayama-Hosokawa
authors.forename: Tatsuhiro
authors.initials: T
authors.lastname: Shibata
authors.forename: Hiromi
authors.initials: H
authors.lastname: Sakamoto
authors.forename: Yae
authors.initials: Y
authors.lastname: Kanai
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kaneda
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Noda
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Aburatani
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics*; D000483:Alleles; D045744:Cell Line, Tumor; D059472:Exome; D042822:Genomic Instability; D057895:Haploinsufficiency; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019656:Loss of Heterozygosity; D000070957:MutL Protein Homolog 1; D009154:Mutation; D059645:Mutation Rate; D009687:Nuclear Proteins / Q000235:genetics*; D010190:Pancreatic Neoplasms / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C501486:MLH1 protein, human; D009687:Nuclear Proteins; D000070957:MutL Protein Homolog 1