Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency

Linghua Wang, Shuichi Tsutsumi, Tokuichi Kawaguchi, Koichi Nagasaki, Kenji Tatsuno, Shogo Yamamoto, Fei Sang, Kohtaro Sonoda, Minoru Sugawara, Akio Saiura, Seiko Hirono, Hiroki Yamaue, Yoshio Miki, Minoru Isomura, Yasushi Totoki, Genta Nagae, Takayuki Isagawa, Hiroki Ueda, Satsuki Murayama-Hosokawa, Tatsuhiro Shibata & 5 others Hiromi Sakamoto, Yae Kanai, Atsushi Kaneda, Tetsuo Noda, Hiroyuki Aburatani

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Pages (from-to)208-219
Number of pages12
JournalGenome Research
Volume22
Issue number2
DOIs
Publication statusPublished - 2012 Feb
Externally publishedYes

Fingerprint

Exome
Haploinsufficiency
Genomic Instability
Mutation Rate
Pancreatic Neoplasms
Cell Line
Mutation
Microsatellite Instability
Loss of Heterozygosity
Neoplasm Genes
Tumor Cell Line
Transcriptome
Renal Cell Carcinoma
Microsatellite Repeats
Genes
Exons
DNA
Neoplasms

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency. / Wang, Linghua; Tsutsumi, Shuichi; Kawaguchi, Tokuichi; Nagasaki, Koichi; Tatsuno, Kenji; Yamamoto, Shogo; Sang, Fei; Sonoda, Kohtaro; Sugawara, Minoru; Saiura, Akio; Hirono, Seiko; Yamaue, Hiroki; Miki, Yoshio; Isomura, Minoru; Totoki, Yasushi; Nagae, Genta; Isagawa, Takayuki; Ueda, Hiroki; Murayama-Hosokawa, Satsuki; Shibata, Tatsuhiro; Sakamoto, Hiromi; Kanai, Yae; Kaneda, Atsushi; Noda, Tetsuo; Aburatani, Hiroyuki.

In: Genome Research, Vol. 22, No. 2, 02.2012, p. 208-219.

Research output: Contribution to journalArticle

Wang, L, Tsutsumi, S, Kawaguchi, T, Nagasaki, K, Tatsuno, K, Yamamoto, S, Sang, F, Sonoda, K, Sugawara, M, Saiura, A, Hirono, S, Yamaue, H, Miki, Y, Isomura, M, Totoki, Y, Nagae, G, Isagawa, T, Ueda, H, Murayama-Hosokawa, S, Shibata, T, Sakamoto, H, Kanai, Y, Kaneda, A, Noda, T & Aburatani, H 2012, 'Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency', Genome Research, vol. 22, no. 2, pp. 208-219. https://doi.org/10.1101/gr.123109.111
Wang, Linghua ; Tsutsumi, Shuichi ; Kawaguchi, Tokuichi ; Nagasaki, Koichi ; Tatsuno, Kenji ; Yamamoto, Shogo ; Sang, Fei ; Sonoda, Kohtaro ; Sugawara, Minoru ; Saiura, Akio ; Hirono, Seiko ; Yamaue, Hiroki ; Miki, Yoshio ; Isomura, Minoru ; Totoki, Yasushi ; Nagae, Genta ; Isagawa, Takayuki ; Ueda, Hiroki ; Murayama-Hosokawa, Satsuki ; Shibata, Tatsuhiro ; Sakamoto, Hiromi ; Kanai, Yae ; Kaneda, Atsushi ; Noda, Tetsuo ; Aburatani, Hiroyuki. / Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency. In: Genome Research. 2012 ; Vol. 22, No. 2. pp. 208-219.
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AU - Wang, Linghua

AU - Tsutsumi, Shuichi

AU - Kawaguchi, Tokuichi

AU - Nagasaki, Koichi

AU - Tatsuno, Kenji

AU - Yamamoto, Shogo

AU - Sang, Fei

AU - Sonoda, Kohtaro

AU - Sugawara, Minoru

AU - Saiura, Akio

AU - Hirono, Seiko

AU - Yamaue, Hiroki

AU - Miki, Yoshio

AU - Isomura, Minoru

AU - Totoki, Yasushi

AU - Nagae, Genta

AU - Isagawa, Takayuki

AU - Ueda, Hiroki

AU - Murayama-Hosokawa, Satsuki

AU - Shibata, Tatsuhiro

AU - Sakamoto, Hiromi

AU - Kanai, Yae

AU - Kaneda, Atsushi

AU - Noda, Tetsuo

AU - Aburatani, Hiroyuki

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N2 - 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.

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