Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

Bii, Victor M.; Trobridge, Grant D.

doi:10.3390/cancers8110099

Cited by 4 publications

(7 citation statements)

References 105 publications

(170 reference statements)

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“…As a consequence, vector integration can influence expression of cellular genes, which in the worst case may result in malignant transformation as seen in mouse models [ 7 , 8 , 35 ], but also in clinical gene therapy [ 36 , 37 ]. Based thereon, insertional mutagenesis with replication-defective retroviral vectors has become a powerful tool to identify genes involved in various processes of malignant transformation and tumor outgrowth in different tissues [ 38 ]. At the same time, IM-mediated malignant transformation represents a rare event [ 39 ], and its probability depends on the respective cell type.…”

Section: Discussionmentioning

confidence: 99%

Multi-color RGB marking enables clonality assessment of liver tumors in a murine xenograft model

et al. 2017

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We recently introduced red-green-blue (RGB) marking for clonal cell tracking based on individual color-coding. Here, we applied RGB marking to study clonal development of liver tumors. Immortalized, non-tumorigenic human fetal hepatocytes expressing the human telomerase reverse transcriptase (FH-hTERT) were RGB-marked by simultaneous transduction with lentiviral vectors encoding mCherry, Venus, and Cerulean. Multi-color fluorescence microscopy was used to analyze growth characteristics of RGB-marked FH-hTERT in vitro and in vivo after transplantation into livers of immunodeficient mice with endogenous liver damage (uPA/SCID). After initially polyclonal engraftment we observed oligoclonal regenerative nodules derived from transplanted RGB-marked FH-hTERT. Some mice developed monochromatic invasive liver tumors; their clonal origin was confirmed both on the molecular level, based on specific lentiviral-vector insertion sites, and by serial transplantation of one tumor. Vector insertions in proximity to the proto-oncogene MCF2 and the transcription factor MITF resulted in strong upregulation of mRNA expression in the respective tumors. Notably, upregulated MCF2 and MITF expression was also observed in 21% and 33% of 24 human hepatocellular carcinomas analyzed. In conclusion, liver repopulation with RGB-marked FH-hTERT is a useful tool to study clonal progression of liver tumors caused by insertional mutagenesis in vivo and will help identifying genes involved in liver cancer.

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Section: Discussionmentioning

confidence: 99%

Multi-color RGB marking enables clonality assessment of liver tumors in a murine xenograft model

et al. 2017

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“…Although other vector-mediated mechanisms of genotoxicity have been reported [ 5 , 6 ], enhancer-mediated activation of gene promoters is the most common [ 7 , 8 ]. Following these studies replication-incompetent retroviral vectors have been developed as a powerful tool to identify driver genes [ 9 – 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…Replication-incompetent retroviral vectors have the ability to stably infect many mammalian cell types without causing secondary integrations that may impede the identification of the primary retroviral integration sites (RISs). This makes them a powerful tool to identify driver genes in different human cancers [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…To map RISs in mutagenesis screens, PCR and non-PCR based approaches have been used to identify the junctions between the retroviral LTR and chromosomal DNA [ 10 , 20 – 22 ]. Shuttle vector rescue, a non-PCR based approach, generates LTR-chromosome junctions that are typically longer than those produced by PCR and can improve the detection of RIS in repetitive regions, whereas modified genomic sequencing PCR (MGS-PCR) is more sensitive [ 14 ]. The sequence reads obtained from these approaches are mapped to the genome and nearby candidate driver genes can be rapidly identified using bioinformatics tools such the vector integration site analysis (VISA) webserver [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

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Replication-incompetent gammaretroviral and lentiviral vector-based insertional mutagenesis screens identify prostate cancer progression genes

et al. 2018

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Replication-incompetent gammaretroviral (γRV) and lentiviral (LV) vectors have both been used in insertional mutagenesis screens to identify cancer drivers. In this approach the vectors stably integrate in the host cell genome and induce cancers by dysregulating nearby genes. The cells that contain a retroviral vector provirus in or near a proto-oncogene or tumor suppressor are preferentially enriched in a tumor. γRV and LV vectors have different integration profiles and genotoxic potential, making them potentially complementary tools for insertional mutagenesis screens. We performed screens using both γRV and LV vectors to identify driver genes that mediate progression of androgen-independent prostate cancer (AIPC) using a xenotransplant mouse model. Vector transduced LNCaP cells were injected orthotopically into the prostate gland of immunodeficient mice. Mice that developed tumors were castrated to create an androgen-deficient environment and metastatic tumors that developed were analyzed. A high-throughput modified genomic sequencing PCR (MGS-PCR) approach identified the positions of vector integrations in these metastatic tumors. OR2A14, FER1L6, TAOK3, MAN1A2, MBNL2, SERBP1, PLEKHA2, SPTAN1, ADAMTS1, SLC30A5, ABCC1, SLC7A1 and SLC25A24 were identified as candidate prostate cancer (PC) progression genes. TAOK3 and ABCC1 expression in PC patients predicted the risk of recurrence after androgen deprivation therapy. Our data shows that γRV and LV vectors are complementary approaches to identify cancer driver genes which may be promising potential biomarkers and therapeutic targets.

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“…Recent studies revealed that TP53 and OBSCN genes are highly mutated among 189 candidate genes in breast and colorectal cancers [ 13 , 17 ]. However, scientific background on OBSCN mutation and its impacts are limited in comparison to the other key genes involved in breast cancer [ 18 , 19 ]. Mutations in OBSCN gene (> 15%) are observed in breast cancer patient samples published by TCGA.…”

Section: Introductionmentioning

confidence: 99%

A comprehensive genomic meta-analysis identifies confirmatory role ofOBSCNgene in breast tumorigenesis

Rajendran¹,

Deng²

2017

Oncotarget

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The giant multifunctional protein “OBSCURIN” is encoded by OBSCN gene and is mostly expressed in cardiac and other skeletal muscles responsible for myofibrils organization. Loss of OBSCURIN affects the entire downstream pathway proteins vital for various cellular functions including cell integration and cell adhesion. The OBSCN gene mutations are more frequently observed in various muscular diseases, and cancers. Nevertheless, the direct role of OBSCN in tumorigenesis remains elusive. Interestingly, in clinical breast cancer samples a significant number of function changing mutations have been identified in OBSCN gene. In this study, we identified a significant role of OBSCN by conducting an integrative analysis of copy number alterations, functional mutations, gene methylation and expression data from various BRCA cancer projects data available on cBioPortal and TCGA firebrowse portal. Finally, we carried out genetic network analysis, which revealed that OBSCN gene plays a significant role in GPCR, RAS, p75 or Wnt signaling pathways. Similarly, OBSCN gene interacts with many cancer-associated genes involved in breast tumorigenesis. The OBSCN gene probably regulates breast cancer progression and metastasis and the prognostic molecular signatures such as copy number alterations and gene expression of OBSCN may serve as a tool to identify breast tumorigenesis and metastasis.

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Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

Cited by 4 publications

References 105 publications

Multi-color RGB marking enables clonality assessment of liver tumors in a murine xenograft model

Multi-color RGB marking enables clonality assessment of liver tumors in a murine xenograft model

Replication-incompetent gammaretroviral and lentiviral vector-based insertional mutagenesis screens identify prostate cancer progression genes

A comprehensive genomic meta-analysis identifies confirmatory role ofOBSCNgene in breast tumorigenesis

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