Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model

Bard-Chapeau, Emilie A.; Nguyễn, Anh Tuấn; Rust, Alistair G.; Sayadi, Ahmed; Lee, Philip; Chua, Belinda Q.; New, Lee Sun; Jong, Johann de; Ward, Jerrold M.; Chin, Christopher K Y; Chew, Valerie; Toh, Han Chong; Abastado, Jean Pierre; Benoukraf, Touati; Soong, Richie; Bard, Frédéric; Dupuy, Adam J.; Johnson, Randy L.; Radda, George K.; Chan, Eric Chun Yong; Wessels, Lodewyk F.A.; Adams, David J.; Jenkins, Nancy A.; Copeland, Neal G.

doi:10.1038/ng.2847

Cited by 105 publications

(120 citation statements)

References 87 publications

(143 reference statements)

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“…Transposon insertion sites were sequenced using splinkerette PCR to produce barcoded PCR products, which were then pooled and sequenced (22)(23)(24). To obtain the maximum amount of sequencing reads and avoid PCR bias (29), we used Illumina sequencing and acoustic shearing of genomic DNA (gDNA).…”

Section: Discussionmentioning

confidence: 99%

“…Using the gene-centric common integration site (CIS) calling method (gCIS) (30), we identified 61 CCGs from IHBC/SB lines and 233 CCGs from IHBC/SB-derived tumors (P < 0.05, χ 2 test followed by Bonferroni correction) (Tables S1 and S2). CISs are genomic regions that contain more transposon insertions than predicted by chance and thus are likely to mark the location of CCGs (22). Only one CCG overlapped between these two datasets ( Fig.…”

Section: Identification Of Ccgs Driving the Development Of Mesenchymalmentioning

confidence: 93%

“…Our laboratory has successfully modeled more than 20 different types of human cancers in mice using Sleeping Beauty (SB) transposon mutagenesis and has identified hundreds of candidate cancer genes (CCGs), which show striking overlaps with genes mutated or deregulated in human cancers (22)(23)(24). We also have developed in vitro cell-based SB mutagenesis screens that have made it possible to identify genes involved in the malignant transformation of neural stem cells into glioma-initiating Significance Epithelial-mesenchymal transition (EMT) contributes to metastasis and chemoresistance in patients with hepatocellular carcinoma (HCC), but the genes driving EMT are poorly understood.…”

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confidence: 99%

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Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma

Kodama

Newberg

Kodama

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Epithelial-mesenchymal transition (EMT) is thought to contribute to metastasis and chemoresistance in patients with hepatocellular carcinoma (HCC), leading to their poor prognosis. The genes driving EMT in HCC are not yet fully understood, however. Here, we show that mobilization of Sleeping Beauty (SB) transposons in immortalized mouse hepatoblasts induces mesenchymal liver tumors on transplantation to nude mice. These tumors show significant down-regulation of epithelial markers, along with up-regulation of mesenchymal markers and EMT-related transcription factors (EMTTFs). Sequencing of transposon insertion sites from tumors identified 233 candidate cancer genes (CCGs) that were enriched for genes and cellular processes driving EMT. Subsequent trunk driver analysis identified 23 CCGs that are predicted to function early in tumorigenesis and whose mutation or alteration in patients with HCC is correlated with poor patient survival. Validation of the top trunk drivers identified in the screen, including MET (MET proto-oncogene, receptor tyrosine kinase), GRB2-associated binding protein 1 (GAB1), HECT, UBA, and WWE domain containing 1 (HUWE1), lysine-specific demethylase 6A (KDM6A), and protein-tyrosine phosphatase, nonreceptor-type 12 (PTPN12), showed that deregulation of these genes activates an EMT program in human HCC cells that enhances tumor cell migration. Finally, deregulation of these genes in human HCC was found to confer sorafenib resistance through apoptotic tolerance and reduced proliferation, consistent with recent studies showing that EMT contributes to the chemoresistance of tumor cells. Our unique cell-based transposon mutagenesis screen appears to be an excellent resource for discovering genes involved in EMT in human HCC and potentially for identifying new drug targets.H CC is the sixth most common cancer and the third-leading cause of cancer-related deaths worldwide (1). In the United States, the incidence of HCC is increasing, and overall 5-y survival is now <12%, despite recent progress in diagnostic and therapeutic modalities (2). This high mortality rate is related mainly to a high recurrence rate and associated intrahepatic or extrahepatic metastases (1). Patients with HCC who develop metastasis are no longer eligible for liver transplantation therapy and have very limited therapeutic options. Currently, sorafenib is the sole systemic antineoplastic agent for HCC described in the National Comprehensive Cancer Network (NCCN) guideline (3); however, its clinical benefit is limited (4), and alternative effective treatments are needed for these patients.Epithelial-mesenchymal transition (EMT) is a complex differentiation process whereby epithelial cells lose their identity and acquire mesenchymal characteristics (5). EMT is observed routinely in developmental processes, but is also believed to play an important role in the migration, invasion, and metastasis of various cancers (6-9). It also promotes the generation of cancer stem cells, thereby contributing to tumor recurrence and metastasis...

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Section: Discussionmentioning

confidence: 99%

Section: Identification Of Ccgs Driving the Development Of Mesenchymalmentioning

confidence: 93%

mentioning

confidence: 99%

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Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma

Kodama

Newberg

Kodama

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…To identify genes that cooperate with PTEN in the progression of breast cancer, we crossed Pten fl/fl mice with K5-Cre transgenic mice to generate K5-Cre Tg/+ ;Pten fl/+ mice. The mice were then crossed to mice carrying one of two conditional SB transposition systems (SB11 fl/fl ;T2/Onc2 Tg/Tg ) (18) or (SB11 fl/fl ;T2/Onc3 Tg/Tg ) (27) to generate K5-Cre Tg/+ ;Pten fl/+ ;SB11 fl/+ ;T2/Onc2 Tg/+ (SB/Pten-Onc2) or K5-Cre Tg/+ ;Pten fl/+ ;SB11 fl/+ ;T2/Onc3 Tg/+ (SB/Pten-Onc3) mice. SB/ Pten-Onc2 mice carry 350 copies of T2/Onc2, all linked together at a single site on chromosome 1, whereas SB/Pten-Onc3 mice carry a 30-copy T2/Onc3 transposon concatamer located on chromosome 9 (20,27).…”

Section: Sb Mutagenesis Promotes the Development Of Multiple Breast Cmentioning

confidence: 99%

“…New technologies that would provide a more complete understanding of the genetics of TNBC are still needed to deconvolute the complexity of this deadly cancer. Our laboratory and others have pioneered the use of transposon mutagenesis in mice as a tool for cancer gene discovery (18)(19)(20)(21)(22)(23)(24)(25)(26). Transposons induce cancer by randomly inserting into the mouse genome, mutating, and disrupting potential cancer genes.…”

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Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression

Rangel

Lee

Ban

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Triple-negative breast cancer (TNBC) has the worst prognosis of any breast cancer subtype. To better understand the genetic forces driving TNBC, we performed a transposon mutagenesis screen in a phosphatase and tensin homolog (Pten) mutant mice and identified 12 candidate trunk drivers and a much larger number of progression genes. Validation studies identified eight TNBC tumor suppressor genes, including the GATA-like transcriptional repressor TRPS1. Down-regulation of TRPS1 in TNBC cells promoted epithelial-to-mesenchymal transition (EMT) by deregulating multiple EMT pathway genes, in addition to increasing the expression of SERPINE1 and SERPINB2 and the subsequent migration, invasion, and metastasis of tumor cells. Transposon mutagenesis has thus provided a better understanding of the genetic forces driving TNBC and discovered genes with potential clinical importance in TNBC.Sleeping Beauty | breast cancer | TRPS1 | metastasis | tumor suppressors B reast cancer is the second leading cause of cancer-related deaths in the United States. The Cancer Genome Atlas (TCGA) network has classified breast cancer into four main subtypes: luminal A, luminal B, HER2+, and basal-like (1-5). Basal-like or triplenegative breast cancer (TNBC) constitutes 10-20% of all breast cancers and has a higher rate of distal recurrence and a poorer prognosis than other breast cancer subtypes. Less than 30% of women with metastatic TNBC survive 5 y and almost all die from their disease despite adjuvant chemotherapy (1, 3-5). Mutations, rearrangements, or deletions in highly penetrant genes such as BRCA1, BRCA2, TP53, CDH1, STK11, and PTEN are important drivers of TNBC (6-8). PTEN is a dual-specificity phosphatase that antagonizes the PI3K/AKT pathway through its lipid phosphatase activity and negatively regulates the MAPK pathway through its protein phosphatase activity (9, 10). Mutations in PTEN drive epithelial-mesenchymal transition (EMT) and promote metastasis in TNBC (11-13). Similarly, in mice, heterozygous deletion of Pten induces mammary tumors with basal-like characteristics (14)(15)(16)(17).Despite all of the cancer genome-sequencing efforts, there is still an incomplete understanding of the genes and genetic networks driving TNBC. New technologies that would provide a more complete understanding of the genetics of TNBC are still needed to deconvolute the complexity of this deadly cancer. Our laboratory and others have pioneered the use of transposon mutagenesis in mice as a tool for cancer gene discovery (18-26). Transposons induce cancer by randomly inserting into the mouse genome, mutating, and disrupting potential cancer genes. Transposon insertions in tumors thus serve as molecular tags for the high-throughput cloning and identification of cancer genes. In addition, because transposon insertions are PCR-amplified before they are sequenced, insertional mutations in cancer genes that are present in only a small fraction of tumor cells can be identified. Transposon mutagenesis can thus identify genes that are functioning at th...

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Generation of Mouse Models of Cancer Using Transposon‐Mediated Approaches

Bermejo-Rodríguez

Pérez–Mancera

2017

Encyclopedia of Life Sciences

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Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model

Cited by 105 publications

References 87 publications

Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma

Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma

Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression

Generation of Mouse Models of Cancer Using Transposon‐Mediated Approaches

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