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Araiza-Olivera D, Prudnikova TY, Uribe-Alvarez C, Cai KQ, Franco-Barraza J, Dones JM, Raines RT, Chernoff J. Identifying and Targeting Key Driver Genes for Collagen Production within the 11q13/14 Breast Cancer Amplicon. Mol Cancer Res 2025; 23:405-415. [PMID: 39836438 PMCID: PMC12048276 DOI: 10.1158/1541-7786.mcr-24-0331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 11/22/2024] [Accepted: 01/16/2025] [Indexed: 01/22/2025]
Abstract
Breast cancers of the Integrative Cluster 2 (IntClust-2) type, characterized by amplification of a small portion of chromosome 11, have a median survival of only 5 years. Several cancer-relevant genes occupy this portion of chromosome 11, and it is thought that overexpression of a combination of driver genes in this region is responsible for the poor outcome of women in this group. In this study, we used a gene editing method to knock out, one by one, each of the 198 genes that are located within the amplified region of chromosome 11 and determined how much each of these genes contributed to the survival of breast cancer cells. In addition to well-known drivers such as CCND1 and PAK1, we identified two different genes (SERPINH1 and P4HA3) that encode proteins involved in collagen synthesis and organization. Using both in vitro and in vivo functional analyses, we determined that P4HA3 and/or SERPINH1 provide a critical driver function for IntClust-2 basic processes, such as viability, proliferation, and migration. Inhibiting these enzymes via genetic or pharmacologic means reduced collagen synthesis and impeded oncogenic signaling transduction in cell culture models, and a small-molecule inhibitor of P4HA3 was effective in treating 11q13 tumor growth in an animal model. As collagen has a well-known association with tissue stiffness and aggressive forms of breast cancer, we believe that the two genes we identified provide an opportunity for a new therapeutic strategy in IntClust-2 breast cancers. Implications: Breast cancers with 11q13/14 chromosomal amplifications may be vulnerable to inhibitors of collagen synthesis.
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Affiliation(s)
- Daniela Araiza-Olivera
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Tatiana Y. Prudnikova
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Cristina Uribe-Alvarez
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kathy Q. Cai
- Histopathology Facility, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Janusz Franco-Barraza
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Marvin and Concetta Greenberg Pancreatic Cancer Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jesús M. Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
| | - Jonathan Chernoff
- Cancer Signaling and Microenvironment Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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2
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Araiza-Olivera D, Prudnikova TY, Uribe-Alvarez C, Cai KQ, Franco-Barraza J, Dones JM, Raines RT, Chernoff J. Identifying and targeting key driver genes for collagen production within the 11q13/14 breast cancer amplicon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587019. [PMID: 38586042 PMCID: PMC10996585 DOI: 10.1101/2024.03.27.587019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Genetic studies indicate that breast cancer can be divided into several basic molecular groups. One of these groups, termed IntClust-2, is characterized by amplification of a small portion of chromosome 11 and has a median survival of only five years. Several cancer-relevant genes occupy this portion of chromosome 11, and it is thought that overexpression of a combination of driver genes in this region is responsible for the poor outcome of women in this group. In this study we used a gene editing method to knock out, one by one, each of 198 genes that are located within the amplified region of chromosome 11 and determined how much each of these genes contributed to the survival of breast cancer cells. In addition to well-known drivers such as CCND1 and PAK1 , we identified two different genes ( SERPINH1 and P4HA3 ), that encode proteins involved in collagen synthesis and organization. Using both in vitro and in vivo functional analyses, we determined that P4HA3 and/or SERPINH1 provide a critical driver function on IntClust-2 basic processes, such as viability, proliferation, and migration. Inhibiting these enzymes via genetic or pharmacologic means reduced collagen synthesis and impeded oncogenic signaling transduction in cell culture models, and a small-molecule inhibitor of P4HA3 was effective in treating 11q13 tumor growth in an animal model. As collagen has a well-known association with tissue stiffness and aggressive forms of breast cancer, we believe that the two genes we identified provide an opportunity for a new therapeutic strategy in IntClust-2 breast cancers.
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3
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Martins FC, Couturier DL, de Santiago I, Sauer CM, Vias M, Angelova M, Sanders D, Piskorz A, Hall J, Hosking K, Amirthanayagam A, Cosulich S, Carnevalli L, Davies B, Watkins TBK, Funingana IG, Bolton H, Haldar K, Latimer J, Baldwin P, Crawford R, Eldridge M, Basu B, Jimenez-Linan M, Mcpherson AW, McGranahan N, Litchfield K, Shah SP, McNeish I, Caldas C, Evan G, Swanton C, Brenton JD. Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer. Nat Commun 2022; 13:6360. [PMID: 36289203 PMCID: PMC9606297 DOI: 10.1038/s41467-022-33870-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 10/06/2022] [Indexed: 01/12/2023] Open
Abstract
Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we show that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and methylation status. We identify five prevalent clonal driver SCNAs (chromosomal amplifications encompassing MYC, PIK3CA, CCNE1, KRAS and TERT) from multi-regional HGSOC data and reason that their strong selection should prioritise them as key biomarkers for targeted therapies. We use primary HGSOC spheroid models to test interactions between in vitro targeted therapy and SCNAs. MYC chromosomal copy number is associated with in-vitro and clinical response to paclitaxel and in-vitro response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context of MYC-amplified HGSOC is statistically associated with increased prevalence of SCNAs in genes from the PI3K pathway. Co-occurrence of amplifications in MYC and genes from the PI3K pathway is independently observed in squamous lung cancer and triple negative breast cancer. In this work, we show that identifying co-occurrence of clonal driver SCNA genes could be used to tailor therapeutics for precision medicine.
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Affiliation(s)
- Filipe Correia Martins
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK.
- Experimental Medicine Initiative, University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Gynaecological Oncology, Cambridge University Hospitals, Cambridge, UK.
| | - Dominique-Laurent Couturier
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Ines de Santiago
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Maria Vias
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Deborah Sanders
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - James Hall
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ionut G Funingana
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Helen Bolton
- Department of Gynaecological Oncology, Cambridge University Hospitals, Cambridge, UK
| | - Krishnayan Haldar
- Department of Gynaecological Oncology, Cambridge University Hospitals, Cambridge, UK
| | - John Latimer
- Department of Gynaecological Oncology, Cambridge University Hospitals, Cambridge, UK
| | - Peter Baldwin
- Department of Gynaecological Oncology, Cambridge University Hospitals, Cambridge, UK
| | - Robin Crawford
- Department of Gynaecological Oncology, Cambridge University Hospitals, Cambridge, UK
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Bristi Basu
- Cambridge University Hospitals, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Andrew W Mcpherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Centre, NYC, USA
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Centre, NYC, USA
| | - Iain McNeish
- Department of Surgery and Cancer, Imperial College of London, London, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Gerard Evan
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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4
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Broit N, Johansson PA, Rodgers CB, Walpole S, Hayward NK, Pritchard AL. Systematic review and meta-analysis of genomic alterations in acral melanoma. Pigment Cell Melanoma Res 2022; 35:369-386. [PMID: 35229492 PMCID: PMC9540316 DOI: 10.1111/pcmr.13034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/15/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
Acral melanoma (AM) tumors arise on the palms, soles, fingers, toes, and nailbeds. A comprehensive systematic meta-analysis of AM genomic aberrations has not been conducted to date. A literature review was carried out to identify studies sequencing AM. Whole-genome/exome data from 181 samples were identified. Targeted panel sequencing data from MSK-IMPACT were included as a validation cohort (n = 92), and studies using targeted hot spot sequencing were also collated for BRAF (n = 26 studies), NRAS (n = 21), and KIT (n = 32). Statistical analysis indicated BRAF, NRAS, PTEN, TYRP1, and KIT as significantly mutated genes. Frequent copy-number aberrations were also found for important cancer genes, such as CDKN2A, KIT, MDM2, CCND1, CDK4, and PAK1, among others. Mapping genomic alterations within the context of the hallmarks of cancer identified four components frequently altered, including (i) sustained proliferative signaling and (ii) evading growth suppression, (iii) genome instability and mutation, and (iv) enabling replicative immortality. This analysis provides the largest analysis of genomic aberrations in AM in the literature to date and highlights pathways that may be therapeutically targetable.
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Affiliation(s)
- Natasa Broit
- Oncogenomics GroupQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
- Faculty of MedicineUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Peter A. Johansson
- Oncogenomics GroupQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Chloe B. Rodgers
- Genetics and Immunology GroupUniversity of the Highlands and IslandsInvernessUK
| | - Sebastian T. Walpole
- Oncogenomics GroupQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Nicholas K. Hayward
- Oncogenomics GroupQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Antonia L. Pritchard
- Oncogenomics GroupQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
- Genetics and Immunology GroupUniversity of the Highlands and IslandsInvernessUK
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5
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Nelfinavir Induces Cytotoxicity towards High-Grade Serous Ovarian Cancer Cells, Involving Induction of the Unfolded Protein Response, Modulation of Protein Synthesis, DNA Damage, Lysosomal Impairment, and Potentiation of Toxicity Caused by Proteasome Inhibition. Cancers (Basel) 2021; 14:cancers14010099. [PMID: 35008264 PMCID: PMC8750028 DOI: 10.3390/cancers14010099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary High-grade serous ovarian cancer (HGSOC) accounts for 70% of all ovarian-cancer-related deaths. Mainstay treatment with platinum-based drugs following surgery results in favorable outcomes in the majority of patients; however, in >80% of cases, the disease relapses with eventual drug resistance. As such, urgent development of improved alternative therapies is necessary for HGSOC patients with lower life expectancy. Rapid repurposing of market available drugs for cancer therapy is a cost-effective alternative to bypass the decade-long traditional drug development pipeline. Among potential drug-repurposing candidates, nelfinavir (NFV)—an anti-infective agent to treat acquired immunodeficiency syndrome (AIDS)—has shown anti-cancer effects against diverse cancers; however, its remedial benefits against HGSOC are unknown. In this study, we explored how NFV targets HGSOC cells obtained from patients at platinum-sensitive and -resistant stages. We observed beneficial efficacy elicited by NFV against HGSOC in both disease conditions through multiple mechanistic avenues, suggesting positive drug-repurposing prospects. Abstract High-grade serous ovarian cancer (HGSOC) is a significant cause of mortality among women worldwide. Traditional treatment consists of platinum-based therapy; however, rapid development of platinum resistance contributes to lower life expectancy, warranting newer therapies to supplement the current platinum-based protocol. Repurposing market-available drugs as cancer therapeutics is a cost- and time-effective way to avail new therapies to drug-resistant patients. The anti-HIV agent nelfinavir (NFV) has shown promising toxicity against various cancers; however, its role against HGSOC is unknown. Here, we studied the effect of NFV against HGSOC cells obtained from patients along disease progression and carrying different sensitivities to platinum. NFV triggered, independently of platinum sensitivity, a dose-dependent reduction in the HGSOC cell number and viability, and a parallel increase in hypo-diploid DNA content. Moreover, a dose-dependent reduction in clonogenic survival of cells escaping the acute toxicity was indicative of long-term residual damage. In addition, dose- and time-dependent phosphorylation of H2AX indicated NFV-mediated DNA damage, which was associated with decreased survival and proliferation signals driven by the AKT and ERK pathways. NFV also mediated a dose-dependent increase in endoplasmic reticulum stress-related molecules associated with long-term inhibition of protein synthesis and concurrent cell death; such events were accompanied by a proapoptotic environment, signaled by increased phospho-eIF2α, ATF4, and CHOP, increased Bax/Bcl-2 ratio, and cleaved executer caspase-7. Finally, we show that NFV potentiates the short-term cell cycle arrest and long-term toxicity caused by the proteasome inhibitor bortezomib. Overall, our in vitro study demonstrates that NFV can therapeutically target HGSOC cells of differential platinum sensitivities via several mechanisms, suggesting its prospective repurposing benefit considering its good safety profile.
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6
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Manasa P, Sidhanth C, Krishnapriya S, Vasudevan S, Ganesan TS. Oncogenes in high grade serous adenocarcinoma of the ovary. Genes Cancer 2020; 11:122-136. [PMID: 33488950 PMCID: PMC7805537 DOI: 10.18632/genesandcancer.206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022] Open
Abstract
High grade serous ovarian cancer is characterized by relatively few mutations occurring at low frequency, except in TP53. However other genetic aberrations such as copy number variation alter numerous oncogenes and tumor suppressor genes. Oncogenes are positive regulators of tumorigenesis and play a critical role in cancer cell growth, proliferation, and survival. Accumulating evidence suggests that they are crucial for the development and the progression of high grade serous ovarian carcinoma (HGSOC). Though many oncogenes have been identified, no successful inhibitors targeting these molecules and their associated pathways are available. This review discusses oncogenes that have been identified recently in HGSOC using different screening strategies. All the genes discussed in this review have been functionally characterized both in vitro and in vivo and some of them are able to transform immortalized ovarian surface epithelial and fallopian tube cells upon overexpression. However, it is necessary to delineate the molecular pathways affected by these oncogenes for the development of therapeutic strategies.
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Affiliation(s)
- Pacharla Manasa
- Laboratory for Cancer Biology, Department of Medical Oncology and Clinical Research Cancer Institute (WIA), Chennai, India
| | - Chirukandath Sidhanth
- Laboratory for Cancer Biology, Department of Medical Oncology and Clinical Research Cancer Institute (WIA), Chennai, India
| | - Syama Krishnapriya
- Laboratory for Cancer Biology, Department of Medical Oncology and Clinical Research Cancer Institute (WIA), Chennai, India
| | - Sekar Vasudevan
- Laboratory for Cancer Biology, Department of Medical Oncology and Clinical Research Cancer Institute (WIA), Chennai, India
| | - Trivadi S Ganesan
- Laboratory for Cancer Biology, Department of Medical Oncology and Clinical Research Cancer Institute (WIA), Chennai, India
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7
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GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer. J Cell Commun Signal 2020; 15:57-70. [PMID: 32888136 DOI: 10.1007/s12079-020-00582-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is the most lethal gynecological malignancy and molecular mechanisms of its progression and metastasis are not completely understood. Some members of GAB (GRB2-associated binding) protein family have been reported to be involved in tumor cell proliferation and metastasis in various cancer types. In the present study, we analyzed the expression of GAB proteins (GAB1, GAB2 and GAB3) in ovarian cancer compared to normal ovarian tissue, in terms of tumor stage, tumor grade and histological type. Differential expression analyses performed in R programming environment using multiple transcriptome datasets (n = 1449) showed that GAB1 expression is decreased in ovarian cancer independently of tumor stage, grade and histotype. Unlike GAB1, expression of GAB2 and GAB3 are increased from early stage to late stage and from low grade to high grade in epithelial ovarian cancer. GAB2 and GAB3 also showed histotype-dependent expression. GAB3 was computed as a top gene whose expression most significantly changed between tumor cells from primary tumor, metastases and ascites. High expression of GAB2 and GAB3 was shown to be associated with shorter progression-free survival in ovarian cancer. This study shows that GAB2 and GAB3 can be important regulators of tumor progression and metastasis in ovarian cancer.
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8
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GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors. Sci Rep 2020; 10:9027. [PMID: 32493985 PMCID: PMC7271235 DOI: 10.1038/s41598-020-65915-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/08/2020] [Indexed: 02/06/2023] Open
Abstract
Encouraging clinical results using immune checkpoint therapies to target the PD-1 axis in a variety of cancer types have paved the way for new immune therapy trials in brain tumor patients. However, the molecular mechanisms that regulate expression of the PD-1 pathway ligands, PD-L1 and PD-L2, remain poorly understood. To address this, we explored the cell-intrinsic mechanisms of constitutive PD-L1 and PD-L2 expression in brain tumors. PD-L1 and PD-L2 expression was assessed by flow cytometry and qRT-PCR in brain tumor cell lines and patient tumor-derived brain tumor-initiating cells (BTICs). Immunologic effects of PD-L2 overexpression were evaluated by IFN-γ ELISPOT. CD274 and PDCD1LG2 cis-regulatory regions were cloned from genomic DNA and assessed in full or by mutating and/or deleting regulatory elements by luciferase assays. Correlations between clinical responses and PD-L1 and PD-L2 expression status were evaluated in TCGA datasets in LGG and GBM patients. We found that a subset of brain tumor cell lines and BTICs expressed high constitutive levels of PD-L1 and PD-L2 and that PD-L2 overexpression inhibited neoantigen specific T cell IFN-γ production. Characterization of novel cis-regulatory regions in CD274 and PDCD1LG2 lead us to identify that GATA2 is sufficient to drive PD-L1 and PD-L2 expression and is necessary for PD-L2 expression. Importantly, in TCGA datasets, PD-L2 correlated with worse clinical outcomes in glioma patients.. By perturbing GATA2 biology, targeted therapies may be useful to decrease inhibitory effects of PD-L2 in the microenvironment.
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9
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Abildgaard C, Do Canto LM, Steffensen KD, Rogatto SR. Long Non-coding RNAs Involved in Resistance to Chemotherapy in Ovarian Cancer. Front Oncol 2020; 9:1549. [PMID: 32039022 PMCID: PMC6985280 DOI: 10.3389/fonc.2019.01549] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022] Open
Abstract
Ovarian cancer (OC) accounts for more than 150,000 deaths worldwide every year. Patients are often diagnosed at an advanced stage with metastatic dissemination. Although platinum- and taxane-based chemotherapies are effective treatment options, they are rarely curative and eventually, the disease will progress due to acquired resistance. Emerging evidence suggests a crucial role of long non-coding RNAs (lncRNAs) in the response to therapy in OC. Transcriptome profiling studies using high throughput approaches have identified differential expression patterns of lncRNAs associated with disease recurrence. Furthermore, several aberrantly expressed lncRNAs in resistant OC cells have been related to increased cell division, improved DNA repair, up-regulation of drug transporters or reduced susceptibility to apoptotic stimuli, supporting their involvement in acquired resistance. In this review, we will discuss the key aspects of lncRNAs associated with the development of resistance to platinum- and taxane-based chemotherapy in OC. The molecular landscape of OC will be introduced, to provide a background for understanding the role of lncRNAs in the acquisition of malignant properties. We will focus on the interplay between lncRNAs and molecular pathways affecting drug response to evaluate their impact on treatment resistance. Additionally, we will discuss the prospects of using lncRNAs as biomarkers or targets for precision medicine in OC. Although there is still plenty to learn about lncRNAs and technical challenges to be solved, the evidence of their involvement in OC and the development of acquired resistance are compelling and warrant further investigation for clinical applications.
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Affiliation(s)
- Cecilie Abildgaard
- Department of Clinical Genetics, Lillebaelt Hospital-University Hospital of Southern Denmark, Vejle, Denmark.,Department of Clinical Oncology, Lillebaelt Hospital-University Hospital of Southern Denmark, Vejle, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Luisa M Do Canto
- Department of Clinical Genetics, Lillebaelt Hospital-University Hospital of Southern Denmark, Vejle, Denmark
| | - Karina D Steffensen
- Department of Clinical Oncology, Lillebaelt Hospital-University Hospital of Southern Denmark, Vejle, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Silvia R Rogatto
- Department of Clinical Genetics, Lillebaelt Hospital-University Hospital of Southern Denmark, Vejle, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
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10
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Perez-Juarez CE, Arechavaleta-Velasco F, Zeferino-Toquero M, Alvarez-Arellano L, Estrada-Moscoso I, Diaz-Cueto L. Inhibition of PI3K/AKT/mTOR and MAPK signaling pathways decreases progranulin expression in ovarian clear cell carcinoma (OCCC) cell line: a potential biomarker for therapy response to signaling pathway inhibitors. Med Oncol 2019; 37:4. [PMID: 31713081 DOI: 10.1007/s12032-019-1326-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/22/2019] [Indexed: 12/24/2022]
Abstract
Patients with advanced stage ovarian clear cell carcinoma (OCCC) have a poor prognosis due to resistance to conventional platinum chemotherapy. Recent studies have demonstrated that PI3K/AKT/mTOR and ERK1/2 signaling pathways are involved in this chemoresistance. Progranulin (PGRN) overexpression contributes to cisplatin resistance of epithelial ovarian cancer cell lines. Also, PGRN expression is regulated by AKT/mTOR and ERK1/2 signaling pathways in different cell types. Thus, the present study was designed to identify if PGRN expression is regulated by AKT, mTOR, and ERK1/2 signaling pathways in the OCCC cell line TOV-21G. Cultured TOV-21G cells were incubated with different concentrations of pharmacological cell signaling inhibitors. PGRN expression and phosphorylation of ERK1/2, AKT, and mTOR were assessed by Western blotting. Inhibition of AKT, mTOR, and ERK1/2 significantly reduced PGRN expression. Cell viability was not affected, while cell proliferation significantly decreased with all inhibitors used in this study. These observations demonstrated that inhibition of PI3K/AKT/mTOR and ERK1/2 signaling pathways reduces PGRN expression in TOV-21G cells. Thus, PGRN could be considered as a candidate for explaining the high resistance to platinum-based treatment and a potential biomarker for therapy response to cell signaling inhibitors in patients with OCCC.
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Affiliation(s)
- Carlos Eduardo Perez-Juarez
- Unidad de Investigacion Medica en Medicina Reproductiva, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Av. Rio Magdalena No. 289, Sexto piso, Tizapan San Angel, 01090, Ciudad de Mexico, Mexico.,Posgrado en Ciencias Biologicas, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Fabian Arechavaleta-Velasco
- Unidad de Investigacion Medica en Medicina Reproductiva, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Av. Rio Magdalena No. 289, Sexto piso, Tizapan San Angel, 01090, Ciudad de Mexico, Mexico
| | - Moises Zeferino-Toquero
- Departamento de Oncologia Ginecologica, UMAE Hospital de Gineco-Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico.,Departamento de Cirugia Oncologica, Hospital de Gineco-Obstetricia No.3, Centro Medico Nacional La Raza, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | | | - Isaias Estrada-Moscoso
- Departamento de Patologia, UMAE Hospital de Gineco-Obstetricia No. 4 "Luis Castelazo Ayala", IMSS, Ciudad de Mexico, Mexico
| | - Laura Diaz-Cueto
- Unidad de Investigacion Medica en Medicina Reproductiva, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social, Av. Rio Magdalena No. 289, Sexto piso, Tizapan San Angel, 01090, Ciudad de Mexico, Mexico.
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11
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Das MK, Kleppa L, Haugen TB. Functions of genes related to testicular germ cell tumour development. Andrology 2019; 7:527-535. [DOI: 10.1111/andr.12663] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/05/2019] [Accepted: 05/12/2019] [Indexed: 12/15/2022]
Affiliation(s)
- M. K. Das
- Faculty of Health Sciences; OsloMet - Oslo Metropolitan University; Oslo Norway
- Department of Molecular Medicine, Faculty of Medicine; University of Oslo; Oslo Norway
| | - L. Kleppa
- Faculty of Health Sciences; OsloMet - Oslo Metropolitan University; Oslo Norway
| | - T. B. Haugen
- Faculty of Health Sciences; OsloMet - Oslo Metropolitan University; Oslo Norway
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12
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Fang Z, Li T, Chen W, Wu D, Qin Y, Liu M, Wu G, He L, Li H, Gu H. Gab2 promotes cancer stem cell like properties and metastatic growth of ovarian cancer via downregulation of miR-200c. Exp Cell Res 2019; 382:111462. [PMID: 31194976 DOI: 10.1016/j.yexcr.2019.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 11/24/2022]
Abstract
Scaffolding adaptor Gab2 is overexpressed in a subset of high-grade ovarian cancer. Our published work shows that Gab2 via PI3K enhances migratory behaviors and epithelial to mesenchymal transition (EMT) features of ovarian cancer cells in vitro. However, it is still unclear how Gab2/PI3K pathway reuglates EMT characteristics and whether Gab2 promotes the growth of ovarian cancer stem cell (CSC)-like population and metastatic growth. In this study, we examined the effects of Gab2 expression on CSC-like cell growth using Aldefluor and tumorshpere assays commonly used for assessing ovarian cancer cells with CSC properties. Gab2 overexpression increased the number of ALDH+ cells and tumorsphere formation in two different ovarian cancer cell lines OVCAR5 and OVCAR8, whereas knockdown of Gab2 decreased the number of ALDH+ cells and tumorsphere formation in Caov-3 cells. Furthermore, Gab2 promoted metastatic tumor growth of OVCAR5 in nude mice. Mechanistically, we uncovered that Gab2 via PI3K specifically inhibited miR-200c expression. miR-200c downregulation contributed to the Gab2-enhanced cell migratory behaviors, EMT properties, and the expansion of ALDH+ cells and tumorspheres. Furthermore, Gab2 promoted CD44 expression and cell migration/invasion through miR-200c downregulation. Our findings support a model that Gab2-PI3K pathway via miR-200c downregulation promotes CD44 expression, EMT characteristics, and CSC-like cell growth. Therapies involving miR-200c or targeting CD44 should help treat ovarian cancer with high Gab2 expression.
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Affiliation(s)
- Zenghui Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Tong Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Wanzhou Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Du Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yaqian Qin
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Min Liu
- Department of Orthopedics, Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325200, China
| | - Guang Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Licai He
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hongzhi Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.
| | - Haihua Gu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.
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13
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High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019. [PMID: 30813239 DOI: 10.3390/ijms20040952] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
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14
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High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019. [PMID: 30813239 DOI: 10.3390/ijms20040952]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
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15
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High-Grade Serous Ovarian Cancer: Basic Sciences, Clinical and Therapeutic Standpoints. Int J Mol Sci 2019; 20:ijms20040952. [PMID: 30813239 PMCID: PMC6412907 DOI: 10.3390/ijms20040952] [Citation(s) in RCA: 397] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Among a litany of malignancies affecting the female reproductive tract, that of the ovary is the most frequently fatal. Moreover, while the steady pace of scientific discovery has fuelled recent ameliorations in the outcomes of many other cancers, the rates of mortality for ovarian cancer have been stagnant since around 1980. Yet despite the grim outlook, progress is being made towards better understanding the fundamental biology of this disease and how its biology in turn influences clinical behaviour. It has long been evident that ovarian cancer is not a unitary disease but rather a multiplicity of distinct malignancies that share a common anatomical site upon presentation. Of these, the high-grade serous subtype predominates in the clinical setting and is responsible for a disproportionate share of the fatalities from all forms of ovarian cancer. This review aims to provide a detailed overview of the clinical-pathological features of ovarian cancer with a particular focus on the high-grade serous subtype. Along with a description of the relevant clinical aspects of this disease, including novel trends in treatment strategies, this text will inform the reader of recent updates to the scientific literature regarding the origin, aetiology and molecular-genetic basis of high-grade serous ovarian cancer (HGSOC).
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16
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Sun B, Jensen NR, Chung D, Yang M, LaRue AC, Cheung HW, Wang Q. Synergistic effects of SHP2 and PI3K pathway inhibitors in GAB2-overexpressing ovarian cancer. Am J Cancer Res 2019; 9:145-159. [PMID: 30755818 PMCID: PMC6356928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023] Open
Abstract
The scaffold/adaptor growth factor receptor bound 2 (GRB2)-associated binding protein 2 (GAB2) is frequently amplified and/or overexpressed in primary high-grade serous ovarian cancers (HGSOCs). Here we investigate a novel treatment strategy by targeting SHP2 and PI3K signaling in HGSOCs with GAB2 amplification/overexpression (GAB2High). The expression of GAB2 was analyzed in primary HGSOCs and ovarian cancer cell lines. In vitro and in vivo assays were performed to demonstrate the effect of SHP2 and PI3K-mediated GAB2High HGSOC progression. Analysis of gene expression data reveals that primary GAB2High HGSOCs are associated with increased ERBB, RAS, and MAPK activity signatures. Inhibition of SHP2 by an allosteric inhibitor SHP099 selectively inhibits ERK1/2 activity, proliferation, and survival of GAB2High ovarian cancer cell lines. Treatment with SHP099 has a synergistic effect with BKM120, a pan-class I PI3K inhibitor, at suppressing proliferation and survival of GAB2High ovarian cancer cells in vitro and in vivo by more effectively activating both BIM and BAD and inhibiting c-MYC compared with individual inhibitor. Our findings identify an important role of SHP2 in promoting proliferation and survival of GAB2High ovarian cancer cells, and combinatorial SHP2 and PI3K inhibition may be a promising therapeutic approach for such cancer.
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Affiliation(s)
- Bowen Sun
- The First Affiliate Hospital, Biomedical Translational Research Institute, Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan UniversityGuangzhou 510632, China
- Department of Pathology and Laboratory Medicine, Medical University of South CarolinaCharleston, SC 29425, USA
| | - Nathaniel R Jensen
- Department of Pathology and Laboratory Medicine, Medical University of South CarolinaCharleston, SC 29425, USA
- Ralph H. Johnson VAMC, Department of Veterans AffairsCharleston, SC 29401, USA
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South CarolinaCharleston, SC 29425, USA
| | - Meixiang Yang
- The First Affiliate Hospital, Biomedical Translational Research Institute, Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan UniversityGuangzhou 510632, China
| | - Amanda C LaRue
- Department of Pathology and Laboratory Medicine, Medical University of South CarolinaCharleston, SC 29425, USA
- Ralph H. Johnson VAMC, Department of Veterans AffairsCharleston, SC 29401, USA
| | - Hiu Wing Cheung
- Department of Pathology and Laboratory Medicine, Medical University of South CarolinaCharleston, SC 29425, USA
| | - Qi Wang
- Department of Pathology and Laboratory Medicine, Medical University of South CarolinaCharleston, SC 29425, USA
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17
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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18
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Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A. BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation. J Proteome Res 2018; 17:759-769. [PMID: 29249144 PMCID: PMC6092923 DOI: 10.1021/acs.jproteome.7b00775] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biotin-based labeling strategies are widely employed to study protein-protein interactions, subcellular proteomes and post-translational modifications, as well as, used in drug discovery. While the high affinity of streptavidin for biotin greatly facilitates the capture of biotinylated proteins, it still presents a challenge, as currently employed, for the recovery of biotinylated peptides. Here we describe a strategy designated Biotinylation Site Identification Technology (BioSITe) for the capture of biotinylated peptides for LC-MS/MS analyses. We demonstrate the utility of BioSITe when applied to proximity-dependent labeling methods, APEX and BioID, as well as biotin-based click chemistry strategies for identifying O-GlcNAc-modified sites. We demonstrate the use of isotopically labeled biotin for quantitative BioSITe experiments that simplify differential interactome analysis and obviate the need for metabolic labeling strategies such as SILAC. Our data also highlight the potential value of site-specific biotinylation in providing spatial and topological information about proteins and protein complexes. Overall, we anticipate that BioSITe will replace the conventional methods in studies where detection of biotinylation sites is important.
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Affiliation(s)
- Dae In Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jevon A. Cutler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Pre-Doctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sina Reckel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Anil K. Madugundu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Raiha Tahir
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Hana L. Goldschmidt
- Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Karen L. Reddy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Richard L. Huganir
- Solomon H. Snyder Department of Neuroscience, Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Natasha E. Zachara
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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19
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Ovarian Cancers: Genetic Abnormalities, Tumor Heterogeneity and Progression, Clonal Evolution and Cancer Stem Cells. MEDICINES 2018; 5:medicines5010016. [PMID: 29389895 PMCID: PMC5874581 DOI: 10.3390/medicines5010016] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 02/07/2023]
Abstract
Four main histological subtypes of ovarian cancer exist: serous (the most frequent), endometrioid, mucinous and clear cell; in each subtype, low and high grade. The large majority of ovarian cancers are diagnosed as high-grade serous ovarian cancers (HGS-OvCas). TP53 is the most frequently mutated gene in HGS-OvCas; about 50% of these tumors displayed defective homologous recombination due to germline and somatic BRCA mutations, epigenetic inactivation of BRCA and abnormalities of DNA repair genes; somatic copy number alterations are frequent in these tumors and some of them are associated with prognosis; defective NOTCH, RAS/MEK, PI3K and FOXM1 pathway signaling is frequent. Other histological subtypes were characterized by a different mutational spectrum: LGS-OvCas have increased frequency of BRAF and RAS mutations; mucinous cancers have mutation in ARID1A, PIK3CA, PTEN, CTNNB1 and RAS. Intensive research was focused to characterize ovarian cancer stem cells, based on positivity for some markers, including CD133, CD44, CD117, CD24, EpCAM, LY6A, ALDH1. Ovarian cancer cells have an intrinsic plasticity, thus explaining that in a single tumor more than one cell subpopulation, may exhibit tumor-initiating capacity. The improvements in our understanding of the molecular and cellular basis of ovarian cancers should lead to more efficacious treatments.
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20
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Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K. NetSig: network-based discovery from cancer genomes. Nat Methods 2018; 15:61-66. [PMID: 29200198 PMCID: PMC5985961 DOI: 10.1038/nmeth.4514] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/19/2017] [Indexed: 12/21/2022]
Abstract
Methods that integrate molecular network information and tumor genome data could complement gene-based statistical tests to identify likely new cancer genes; but such approaches are challenging to validate at scale, and their predictive value remains unclear. We developed a robust statistic (NetSig) that integrates protein interaction networks with data from 4,742 tumor exomes. NetSig can accurately classify known driver genes in 60% of tested tumor types and predicts 62 new driver candidates. Using a quantitative experimental framework to determine in vivo tumorigenic potential in mice, we found that NetSig candidates induce tumors at rates that are comparable to those of known oncogenes and are ten-fold higher than those of random genes. By reanalyzing nine tumor-inducing NetSig candidates in 242 patients with oncogene-negative lung adenocarcinomas, we find that two (AKT2 and TFDP2) are significantly amplified. Our study presents a scalable integrated computational and experimental workflow to expand discovery from cancer genomes.
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Affiliation(s)
- Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Michael S. Lawrence
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Candace R. Chouinard
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Yashaswi Shrestha
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Jessica Xin Hu
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Elizabeth Worstell
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Emily Shea
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Nina Ilic
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alireza Kashani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - William C. Hahn
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joshua D. Campbell
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Jesse S. Boehm
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, Cancer Program, Cambridge, MA 02142, USA
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21
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Park YR, Bae SH, Ji W, Seo EJ, Lee JC, Kim HR, Jang SJ, Choi CM. GAB2 Amplification in Squamous Cell Lung Cancer of Non-Smokers. J Korean Med Sci 2017; 32:1784-1791. [PMID: 28960030 PMCID: PMC5639058 DOI: 10.3346/jkms.2017.32.11.1784] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 08/04/2017] [Indexed: 01/12/2023] Open
Abstract
Lung squamous cell cancer (SCC) is typically found in smokers and has a very low incidence in non-smokers, indicating differences in the tumor biology of lung SCC in smokers and non-smokers. However, the specific mutations that drive tumor growth in non-smokers have not been identified. To identify mutations in lung SCC of non-smokers, we performed a genetic analysis using arrays comparative genomic hybridization (ArrayCGH). We analyzed 19 patients with lung SCC who underwent surgical treatment between April 2005 and April 2015. Clinical characteristics were reviewed, and DNA was extracted from fresh frozen lung cancer specimens. All of copy number alterations from ArrayCGH were validated using The Cancer Genome Atlas (TCGA) copy number variation (CNV) data of lung SCC. We examined the frequency of copy number changes according to the smoking status (non-smoker [n = 8] or smoker [n = 11]). We identified 16 significantly altered regions from ArrayCGH data, three gain and four loss regions overlapped with the TCGA lung squamous cell carcinoma (LUSC) patients. Within these overlapped significant regions, we detected 15 genes that have been reported in the Cancer Gene census. We also found that the proto-oncogene GAB2 (11q14.1) was significantly amplified in non-smokers patients and vice versa in both ArrayCGH and TCGA data. Immunohistochemical analyses showed that GAB2 protein was relatively upregulated in non-smoker than smoker tissues (37.5% vs. 9.0%, P = 0.007). GAB2 amplification may have an important role in the development of lung SCC in non-smokers. GAB2 may represent a potential biomarker for lung SCC in non-smokers.
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Affiliation(s)
- Yu Rang Park
- Clinical Research Center, Asan Institute of Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
- Department of Biomedical Informatics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Soo Hyeon Bae
- Department of Pulmonology and Critical Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Wonjun Ji
- Department of Pulmonology and Critical Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Eul Ju Seo
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jae Cheol Lee
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Hyeong Ryul Kim
- Department of Thoracic Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Chang Min Choi
- Department of Pulmonology and Critical Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
- Office of Clinical Research Information, Asan Institute of Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea.
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22
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Bai S, Ingram P, Chen YC, Deng N, Pearson A, Niknafs YS, O'Hayer P, Wang Y, Zhang ZY, Boscolo E, Bischoff J, Yoon E, Buckanovich RJ. EGFL6 Regulates the Asymmetric Division, Maintenance, and Metastasis of ALDH+ Ovarian Cancer Cells. Cancer Res 2017; 76:6396-6409. [PMID: 27803106 DOI: 10.1158/0008-5472.can-16-0225] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/25/2016] [Indexed: 01/12/2023]
Abstract
Little is known about the factors that regulate the asymmetric division of cancer stem-like cells (CSC). Here, we demonstrate that EGFL6, a stem cell regulatory factor expressed in ovarian tumor cells and vasculature, regulates ALDH+ ovarian CSC. EGFL6 signaled at least in part via the oncoprotein SHP2 with concomitant activation of ERK. EGFL6 signaling promoted the migration and asymmetric division of ALDH+ ovarian CSC. As such, EGFL6 increased not only tumor growth but also metastasis. Silencing of EGFL6 or SHP2 limited numbers of ALDH+ cells and reduced tumor growth, supporting a critical role for EGFL6/SHP2 in ALDH+ cell maintenance. Notably, systemic administration of an EGFL6-neutralizing antibody we generated restricted tumor growth and metastasis, specifically blocking ovarian cancer cell recruitment to the ovary. Together, our results offer a preclinical proof of concept for EGFL6 as a novel therapeutic target for the treatment of ovarian cancer. Cancer Res; 76(21); 6396-409. ©2016 AACR.
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Affiliation(s)
- Shoumei Bai
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Patrick Ingram
- Department of Electrical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Yu-Chih Chen
- Department of Electrical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Ning Deng
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Alex Pearson
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Yashar S Niknafs
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Patrick O'Hayer
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Yun Wang
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Elisa Boscolo
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joyce Bischoff
- Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Euisik Yoon
- Department of Electrical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Ronald J Buckanovich
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan. .,Division of Gynecologic-Oncology, Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan
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23
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Wang L, Lu J, Wu H, Wang L, Liang X, Liang Z, Liu T. Expression of signaling adaptor proteins predicts poor prognosis in pancreatic ductal adenocarcinoma. Diagn Pathol 2017; 12:42. [PMID: 28558797 PMCID: PMC5450263 DOI: 10.1186/s13000-017-0633-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 05/12/2017] [Indexed: 11/17/2022] Open
Abstract
Background Adaptor proteins bridge the gap between cell surface receptors and their downstream signaling elements. The clinicopathological and prognostic values of adaptor proteins remain poorly understood. The purpose of the present study was to explore the expression and prognostic value of three adaptor proteins: GRB2-associated binding protein 2 (GAB2), CRK-like protein (CRKL) and fibroblast growth factor receptor substrate 2 (FRS2) in pancreatic ductal adenocarcinoma (PDAC). Methods The expression of GAB2, CRKL, and FRS2 in 77 formalin fixed paraffin embedded (FFPE) samples from 77 PDAC patients, along with three paired fresh PDAC and matched normal tissues from 3 PDAC patients was analyzed by immunohistochemistry and western blot, respectively. The association between the expression of the three proteins and the clinicopathological factors of PDAC was assessed by χ2 test. The correlation between the expression levels of the three proteins was analyzed by Spearman rank correlation analyses; Kaplan-Meier survival analyses were also performed. Results IHC was successful in 75, 76, and 77 cases for GAB2, CRKL, and FRS2, respectively. Of which, the positive rate of GAB2, CRKL, and FRS2 protein expression was 40.00% (30/75), 53.95% (41/76) and 35.06% (27/77), respectively. The positive rate of GAB2, CRKL and FRS2 co-expression was 16.88% (13/77). Though there was no association between GAB2 expression, CRKL expression, FRS2 expression, GAB2/CRKL/FRS2 co-expression and the clinicopathological parameters of PDAC, positive correlations were observed between the expressions of the three proteins. Further, univariate survival analysis showed that positive expression of GAB2, CRKL and FRS2 and co-expression of GAB2/CRKL/FRS2 of PDAC predicted poor clinical outcomes, and multivariate survival analysis suggested that positive expression of GAB2 and positive co-expression of GAB2/CRKL/FRS2 were independent prognostic factors for disease-free survival (DFS) and overall survival (OS), respectively. Conclusion In conclusion, GAB2, CRKL, and FRS2 may be potential prognosticators and therapeutic targets for PDAC patients.
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Affiliation(s)
- Lili Wang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junliang Lu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huanwen Wu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Li Wang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaolong Liang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhiyong Liang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Tonghua Liu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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24
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25
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Howard TP, Vazquez F, Tsherniak A, Hong AL, Rinne M, Aguirre AJ, Boehm JS, Hahn WC. Functional Genomic Characterization of Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 81:237-246. [PMID: 27815544 DOI: 10.1101/sqb.2016.81.031070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
International efforts to sequence cancer genomes now provide an overview of the major genetic alterations that occur in most human cancers. These studies have identified many highly recurrent alterations in specific cancer subtypes but have also identified mutations that occur at lower frequency and unstudied variants of known cancer-associated genes. To elucidate the function of such cancer alleles, we have developed several approaches to systematically interrogate genomic changes found in human tumors. In general, we have taken two complementary approaches. In the first approach, we focus on perturbing genes identified as mutated, amplified, or deleted by cancer genome annotation efforts, whereas in the second, we have taken an unbiased approach to identify genes that are essential for cancer cell proliferation or survival in cell lines that are extensively annotated to identify context-specific essential genes. These studies begin to allow us to define a cancer dependencies map.
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Affiliation(s)
- Thomas P Howard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Francisca Vazquez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Aviad Tsherniak
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Andrew L Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142.,Boston Children's Hospital, Boston, Massachusetts 02115
| | - Mik Rinne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Jesse S Boehm
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
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26
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Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell 2016; 30:214-228. [PMID: 27478040 PMCID: PMC5003022 DOI: 10.1016/j.ccell.2016.06.022] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/27/2016] [Accepted: 06/29/2016] [Indexed: 01/19/2023]
Abstract
Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas. We present an expression-based variant-impact phenotyping (eVIP) method that uses gene expression changes to distinguish impactful from neutral somatic mutations. eVIP identified 69% of mutations analyzed as impactful and 31% as functionally neutral. A subset of the impactful mutations induces xenograft tumor formation in mice and/or confers resistance to cellular EGFR inhibition. Among these impactful variants are rare somatic, clinically actionable variants including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and multiple BRAF variants, demonstrating that rare mutations can be functionally important in cancer.
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Affiliation(s)
- Alice H. Berger
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Angela N. Brooks
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
| | - Marcin Imielinski
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | | | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Sasha Pantel
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Jacqueline Watson
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Joshua D. Campbell
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
| | | | | | | | - Ted Natoli
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
| | - Bang Wong
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Todd R. Golub
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Address correspondence to M.M. () or J.S.B. ()
| | - Jesse S. Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA
- Address correspondence to M.M. () or J.S.B. ()
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27
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Abstract
The complexity of genomic alterations in cancer has made it difficult to identify oncogenic drivers for the development of targeted therapies. The study by Berger et al. in this issue of Cancer Cell demonstrates that high-throughput functional profiling can uncover impactful mutations and oncogenic driver alleles.
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Affiliation(s)
- Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Scott Powers
- Department of Pathology, Stony Brook University, One Nichols Drive, Stony Brook, NY 11794, USA.
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28
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Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles. Cancer Discov 2016; 6:714-26. [PMID: 27147599 PMCID: PMC4930723 DOI: 10.1158/2159-8290.cd-16-0160] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/26/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies. SIGNIFICANCE Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Eejung Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nina Ilic
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Lihua Zou
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Atanas Kamburov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Xiaoping Yang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Rakela Lubonja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Cindy Nguyen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Xiaoyun Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Larson Hogstrom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ted Natoli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medicine, University of California, San Diego, La Jolla, California
| | - Heiko Horn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven M Corsello
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kasper Lage
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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29
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Zhang Z, Huang K, Gu C, Zhao L, Wang N, Wang X, Zhao D, Zhang C, Lu Y, Meng Y. Molecular Subtyping of Serous Ovarian Cancer Based on Multi-omics Data. Sci Rep 2016; 6:26001. [PMID: 27184229 PMCID: PMC4868982 DOI: 10.1038/srep26001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/25/2016] [Indexed: 01/22/2023] Open
Abstract
Classification of ovarian cancer by morphologic features has a limited effect on serous ovarian cancer (SOC) treatment and prognosis. Here, we proposed a new system for SOC subtyping based on the molecular categories from the Cancer Genome Atlas project. We analyzed the DNA methylation, protein, microRNA, and gene expression of 1203 samples from 599 serous ovarian cancer patients. These samples were divided into nine subtypes based on RNA-seq data, and each subtype was found to be associated with the activation and/or suppression of the following four biological processes: immunoactivity, hormone metabolic, mesenchymal development and the MAPK signaling pathway. We also identified four DNA methylation, two protein expression, six microRNA sequencing and four pathway subtypes. By integrating the subtyping results across different omics platforms, we found that most RNA-seq subtypes overlapped with one or two subtypes from other omics data. Our study sheds light on the molecular mechanisms of SOC and provides a new perspective for the more accurate stratification of its subtypes.
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Affiliation(s)
- Zhe Zhang
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Ke Huang
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Chenglei Gu
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Luyang Zhao
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Nan Wang
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaolei Wang
- Beijing Institute of Health Service and Medical Information, Beijing 100850, China
| | - Dongsheng Zhao
- Beijing Institute of Health Service and Medical Information, Beijing 100850, China
| | - Chenggang Zhang
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing 100850, China
| | - Yiming Lu
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing 100850, China
| | - Yuanguang Meng
- Department of Gynecologic Oncology, Chinese PLA General Hospital, Beijing 100853, China
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30
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Shull AY, Noonepalle SK, Awan FT, Liu J, Pei L, Bollag RJ, Salman H, Ding Z, Shi H. RPPA-based protein profiling reveals eIF4G overexpression and 4E-BP1 serine 65 phosphorylation as molecular events that correspond with a pro-survival phenotype in chronic lymphocytic leukemia. Oncotarget 2016; 6:14632-45. [PMID: 25999352 PMCID: PMC4546493 DOI: 10.18632/oncotarget.4104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/08/2015] [Indexed: 12/22/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL), the most common adult leukemia, remains incurable despite advancements in treatment regimens over the past decade. Several expression profile studies have been pursued to better understand CLL pathogenesis. However, these large-scale studies only provide information at the transcriptional level. To better comprehend the differential protein changes that take place in CLL, we performed a reverse-phase protein array (RPPA) analysis using 167 different antibodies on B-cell lysates from 18 CLL patients and 6 normal donors. From our analysis, we discovered an enrichment of protein alterations involved with mRNA translation, specifically upregulation of the translation initiator eIF4G and phosphorylation of the cap-dependent translation inhibitor 4E-BP1 at serine 65. Interestingly, 4E-BP1 phosphorylation occurred independently of AKT phosphorylation, suggesting a disconnect between PI3K/AKT pathway activation and 4E-BP1 phosphorylation. Based on these results, we treated primary CLL samples with NVP-BEZ235, a PI3K/mTOR dual inhibitor, and compared its apoptotic-inducing potential against the BTK inhibitor Ibrutinib and the PI3Kδ inhibitor Idelalisib. We demonstrated that treatment with NVP-BEZ235 caused greater apoptosis, greater apoptotic cleavage of eIF4G, and greater dephosphorylation of 4E-BP1 in primary CLL cells. Taken together, these results highlight the potential dependence of eIF4G overexpression and 4E-BP1 phosphorylation in CLL survival.
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Affiliation(s)
- Austin Y Shull
- Department of Biochemistry & Molecular Biology, Georgia Regents University, Augusta, Georgia, USA.,GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Satish K Noonepalle
- Department of Biochemistry & Molecular Biology, Georgia Regents University, Augusta, Georgia, USA.,GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Farrukh T Awan
- The Ohio State Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Jimei Liu
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Lirong Pei
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Roni J Bollag
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA.,Department of Pathology, Georgia Regents University, Augusta, Georgia, USA
| | - Huda Salman
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA.,Deparment of Medicine, Georgia Regents University, Augusta, Georgia, USA
| | - Zhiyong Ding
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Huidong Shi
- Department of Biochemistry & Molecular Biology, Georgia Regents University, Augusta, Georgia, USA.,GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
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31
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Tsang YH, Dogruluk T, Tedeschi PM, Wardwell-Ozgo J, Lu H, Espitia M, Nair N, Minelli R, Chong Z, Chen F, Chang QE, Dennison JB, Dogruluk A, Li M, Ying H, Bertino JR, Gingras MC, Ittmann M, Kerrigan J, Chen K, Creighton CJ, Eterovic K, Mills GB, Scott KL. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nat Commun 2016; 7:10500. [PMID: 26806015 PMCID: PMC4737758 DOI: 10.1038/ncomms10500] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/21/2015] [Indexed: 12/16/2022] Open
Abstract
As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC). This approach reveals oncogenic activity for rare gene aberrations in genes including NAD Kinase (NADK), which regulates NADP(H) homeostasis and cellular redox state. We further validate mutant NADK, whose expression provides gain-of-function enzymatic activity leading to a reduction in cellular reactive oxygen species and tumorigenesis, and show that depletion of wild-type NADK in PDAC cell lines attenuates cancer cell growth in vitro and in vivo. These data indicate that annotating rare aberrations can reveal important cancer signalling pathways representing additional therapeutic targets.
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Affiliation(s)
- Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Philip M. Tedeschi
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, New Jersey 08903, USA
| | - Joanna Wardwell-Ozgo
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Maribel Espitia
- Department of Systems Biology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Nikitha Nair
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Rosalba Minelli
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Zechen Chong
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Fengju Chen
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Qing Edward Chang
- Department of Genomics Medicine, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Jennifer B. Dennison
- Department of Systems Biology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Armel Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Min Li
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Haoqiang Ying
- Department of Genomics Medicine, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Joseph R. Bertino
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, New Jersey 08903, USA
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - John Kerrigan
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, New Jersey 08903, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Chad J. Creighton
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Karina Eterovic
- Department of Systems Biology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Gordon B. Mills
- Department of Systems Biology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Kenneth L. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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32
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Distinct GAB2 signaling pathways are essential for myeloid and lymphoid transformation and leukemogenesis by BCR-ABL1. Blood 2016; 127:1803-13. [PMID: 26773044 DOI: 10.1182/blood-2015-06-653006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 01/04/2016] [Indexed: 11/20/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) directed against BCR-ABL1, the product of the Philadelphia (Ph) chromosome, have revolutionized treatment of patients with chronic myeloid leukemia (CML). However, acquired resistance to TKIs is a significant clinical problem in CML, and TKI therapy is much less effective against Ph(+)B-cell acute lymphoblastic leukemia (B-ALL). BCR-ABL1, via phosphorylated Tyr177, recruits the adapter GRB2-associated binding protein 2 (GAB2) as part of a GRB2/GAB2 complex. We showed previously that GAB2 is essential for BCR-ABL1-evoked myeloid transformation in vitro. Using a genetic strategy and mouse models of CML and B-ALL, we show here that GAB2 is essential for myeloid and lymphoid leukemogenesis by BCR-ABL1. In the mouse model, recipients of BCR-ABL1-transducedGab2(-/-)bone marrow failed to develop CML-like myeloproliferative neoplasia. Leukemogenesis was restored by expression of GAB2 but not by GAB2 mutants lacking binding sites for its effectors phosphatidylinositol 3-kinase (PI3K) or SRC homology 2-containing phosphotyrosine phosphatase 2 (SHP2). GAB2 deficiency also attenuated BCR-ABL1-induced B-ALL, but only the SHP2 binding site was required. The SHP2 and PI3K binding sites were differentially required for signaling downstream of GAB2. Hence, GAB2 transmits critical transforming signals from Tyr177 to PI3K and SHP2 for CML pathogenesis, whereas only the GAB2-SHP2 pathway is essential for lymphoid leukemogenesis. Given that GAB2 is dispensable for normal hematopoiesis, GAB2 and its effectors PI3K and SHP2 represent promising targets for therapy in Ph(+)hematologic neoplasms.
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Perets R, Drapkin R. It's Totally Tubular....Riding The New Wave of Ovarian Cancer Research. Cancer Res 2015; 76:10-7. [PMID: 26669862 DOI: 10.1158/0008-5472.can-15-1382] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/10/2015] [Indexed: 12/28/2022]
Abstract
Hereditary breast and ovarian cancer syndrome carries significant mortality for young women if effective preventive and screening measures are not taken. Preventive salpingo-oophorectomy is currently the only method known to reduce the risk of ovarian cancer-related death. Histopathological analyses of these surgical specimens indicate that a high proportion of ovarian cancers in women at high risk and in the general population arise from the fallopian tube. This paradigm shift concerning the cell of origin for the most common subtype of ovarian cancer, high-grade serous carcinoma, has sparked a major effort within the research community to develop new and robust model systems to study the fallopian tube epithelium as the cell of origin of "ovarian" cancer. In this review, evidence supporting the fallopian tube as the origin of ovarian cancer is presented as are novel experimental model systems for studying the fallopian tube epithelium in high-risk women as well as in the general population. This review also addresses the clinical implications of the newly proposed cell of origin, the clinical questions that arise, and novel strategies for ovarian cancer prevention.
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Affiliation(s)
- Ruth Perets
- Division of Oncology, Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa, Israel.
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Overexpression of GAB2 in ovarian cancer cells promotes tumor growth and angiogenesis by upregulating chemokine expression. Oncogene 2015; 35:4036-47. [PMID: 26657155 PMCID: PMC4977484 DOI: 10.1038/onc.2015.472] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 11/12/2015] [Accepted: 11/14/2015] [Indexed: 01/29/2023]
Abstract
We previously found that the scaffold adapter GRB2-associated binding protein 2 (GAB2) is amplified and overexpressed in a subset of primary high-grade serous ovarian cancers and cell lines. Ovarian cancer cells overexpressing GAB2 are dependent on GAB2 for activation of the phosphatidylinositol 3-kinase (PI3K) pathway and are sensitive to PI3K inhibition. In this study, we show an important role of GAB2 overexpression in promoting tumor angiogenesis by upregulating expression of multiple chemokines. Specifically, we found that suppression of GAB2 by inducible small hairpin RNA in ovarian cancer cells inhibited tumor cell proliferation, angiogenesis and peritoneal tumor growth in immunodeficient mice. Overexpression of GAB2 upregulated the secretion of several chemokines from ovarian cancer cells, including CXCL1, CXCL2 and CXCL8. The secreted chemokines not only signal through endothelial CXCR2 receptor in a paracrine manner to promote endothelial tube formation, but also act as autocrine growth factors for GAB2-induced transformation of fallopian tube secretory epithelial cells and clonogenic growth of ovarian cancer cells overexpressing GAB2. Pharmacological inhibition of inhibitor of nuclear factor kappa-B kinase subunit β (IKKβ), but not PI3K, mechanistic target of rapamycin (mTOR) or mitogen-activated protein kinase (MEK), could effectively suppress GAB2-induced chemokine expression. Inhibition of IKKβ augmented the efficacy of PI3K/mTOR inhibition in suppressing clonogenic growth of ovarian cancer cells with GAB2 overexpression. Taken together, these findings suggest that overexpression of GAB2 in ovarian cancer cells promotes tumor growth and angiogenesis by upregulating expression of CXCL1, CXCL2 and CXCL8 that is IKKβ-dependent. Co-targeting IKKβ and PI3K pathways downstream of GAB2 might be a promising therapeutic strategy for ovarian cancer that overexpresses GAB2.
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Luo LY, Hahn WC. Oncogenic Signaling Adaptor Proteins. J Genet Genomics 2015; 42:521-529. [PMID: 26554907 PMCID: PMC4643408 DOI: 10.1016/j.jgg.2015.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 02/08/2023]
Abstract
Signal transduction pathways activated by receptor tyrosine kinases (RTK) play a critical role in many aspects of cell function. Adaptor proteins serve an important scaffolding function that facilitates key signaling transduction events downstream of RTKs. Recent work integrating both structural and functional genomic approaches has identified several adaptor proteins as new oncogenes. In this review, we focus on the discovery, structure and function, and therapeutic implication of three of these adaptor oncogenes, CRKL, GAB2, and FRS2. Each of the three genes is recurrently amplified in lung adenocarcinoma or ovarian cancer, and is essential to cancer cell lines that harbor such amplification. Overexpression of each gene is able to transform immortalized human cell lines in in vitro or in vivo models. These observations identify adaptor protein as a distinct class of oncogenes and potential therapeutic targets.
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Affiliation(s)
- Leo Y Luo
- Health Sciences and Technology Program, Harvard Medical School, Boston, MA 02115, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.
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Ding CB, Yu WN, Feng JH, Luo JM. Structure and function of Gab2 and its role in cancer (Review). Mol Med Rep 2015; 12:4007-4014. [PMID: 26095858 PMCID: PMC4526075 DOI: 10.3892/mmr.2015.3951] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 05/19/2015] [Indexed: 12/30/2022] Open
Abstract
The docking proteins of the Grb-associated binder (Gab) family transduce cellular signals between receptors and intracellular downstream effectors, and provide a platform for protein-protein interactions. Gab2, a key member of the Gab family of proteins, is involved in the amplification and integration of signal transduction, evoked by a variety of extracellular stimuli, including growth factors, cytokines and antigen receptors. Gab2 protein lacks intrinsic catalytic activity; however, when phosphorylated by protein-tyrosine kinases (PTKs), Gab2 recruits several Src homology-2 (SH2) domain-containing proteins, including the SH2-containing protein tyrosine phosphatase 2 (SHP2), the p85 subunit of phosphoinositide-3 kinase (PI3K), phospholipase C-γ (PLCγ)1, Crk, and GC-GAP. Through these interactions, the Gab2 protein triggers various downstream signal effectors, including SHP2/rat sarcoma viral oncogene/RAF/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase and PI3K/AKT, involved in cell growth, differentiation, migration and apoptosis. It has been previously reported that aberrant Gab2 and/or Gab2 signaling is closely associated with human tumorigenesis, particularly in breast cancer, leukemia and melanoma. The present review aimed to focus on the structure and effector function of Gab2, its role in cancer and its potential for use as an effective therapeutic target.
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Affiliation(s)
- Chen-Bo Ding
- Department of Immunology and Immunology Innovation Base for Postgraduate Education in Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
| | - Wei-Na Yu
- Department of Immunology and Immunology Innovation Base for Postgraduate Education in Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
| | - Ji-Hong Feng
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
| | - Jun-Min Luo
- Department of Immunology and Immunology Innovation Base for Postgraduate Education in Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563099, P.R. China
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Davis SJ, Sheppard KE, Anglesio MS, George J, Traficante N, Fereday S, Intermaggio MP, Menon U, Gentry-Maharaj A, Lubinski J, Gronwald J, Pearce CL, Pike MC, Wu A, Kommoss S, Pfisterer J, du Bois A, Hilpert F, Ramus SJ, Bowtell DDL, Huntsman DG, Pearson RB, Simpson KJ, Campbell IG, Gorringe KL. Enhanced GAB2 Expression Is Associated with Improved Survival in High-Grade Serous Ovarian Cancer and Sensitivity to PI3K Inhibition. Mol Cancer Ther 2015; 14:1495-503. [PMID: 25852062 DOI: 10.1158/1535-7163.mct-15-0039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/19/2015] [Indexed: 11/16/2022]
Abstract
Identification of genomic alterations defining ovarian carcinoma subtypes may aid the stratification of patients to receive targeted therapies. We characterized high-grade serous ovarian carcinoma (HGSC) for the association of amplified and overexpressed genes with clinical outcome using gene expression data from 499 HGSC patients in the Ovarian Tumor Tissue Analysis cohort for 11 copy number amplified genes: ATP13A4, BMP8B, CACNA1C, CCNE1, DYRK1B, GAB2, PAK4, RAD21, TPX2, ZFP36, and URI. The Australian Ovarian Cancer Study and The Cancer Genome Atlas datasets were also used to assess the correlation between gene expression, patient survival, and tumor classification. In a multivariate analysis, high GAB2 expression was associated with improved overall and progression-free survival (P = 0.03 and 0.02), whereas high BMP8B and ATP13A4 were associated with improved progression-free survival (P = 0.004 and P = 0.02). GAB2 overexpression and copy number gain were enriched in the AOCS C4 subgroup. High GAB2 expression correlated with enhanced sensitivity in vitro to the dual PI3K/mTOR inhibitor PF-04691502 and could be used as a genomic marker for identifying patients who will respond to treatments inhibiting PI3K signaling.
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Affiliation(s)
- Sally J Davis
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Karen E Sheppard
- Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joshy George
- Cancer Genetics and Genomics Laboratory and Australian Ovarian Cancer Study, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Nadia Traficante
- Cancer Genetics and Genomics Laboratory and Australian Ovarian Cancer Study, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Sian Fereday
- Cancer Genetics and Genomics Laboratory and Australian Ovarian Cancer Study, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Maria P Intermaggio
- Department of Preventive Medicine, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Usha Menon
- Gynaecological Cancer Research Centre, Women's Cancer, University College London, Institute for Women's Health, London, United Kingdom
| | - Aleksandra Gentry-Maharaj
- Gynaecological Cancer Research Centre, Women's Cancer, University College London, Institute for Women's Health, London, United Kingdom
| | - Jan Lubinski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | | | - Malcolm C Pike
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Anna Wu
- Department of Preventive Medicine, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Stefan Kommoss
- Department of Gynecology and Obstetrics, Tuebingen University, Tuebingen, Germany
| | - Jacobus Pfisterer
- Department of Gynecology and Obstetrics, Kiel University, Kiel, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Klinik (HSK), Essen, Germany
| | - Felix Hilpert
- University Hospital Schleswig-Holstein, Kiel, Germany
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - David D L Bowtell
- Cancer Genetics and Genomics Laboratory and Australian Ovarian Cancer Study, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard B Pearson
- Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kaylene J Simpson
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia. Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kylie L Gorringe
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
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Ding C, Luo J, Yu W, Gao S, Yang L, Chen C, Feng J. Gab2 is a novel prognostic factor for colorectal cancer patients. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:2779-2786. [PMID: 26045784 PMCID: PMC4440093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 06/04/2023]
Abstract
Gab2 (Grb2-associated binder 2), a member of the DOS/Gab family of scaffolding adapters, serves as a critical signal amplifier downstream of various growth factor receptors. Recent studies have identified that Gab2 is overexpressed in several cancer types and that increased Gab2 expression promotes cell proliferation, cell transformation, and tumor progression. Here, we show for the first time that Gab2 protein is overexpressed in clinical colorectal cancer (CRC) specimens. Elevated mRNA (P=0.014) expression and protein (P=0.003) expression of Gab2 were found in most CRC tissues compared with the matched adjacent non-tumor tissues using real-time quantitative reverse transcription PCR (qRT-PCR) and western blotting, respectively. Immunohistochemical analyses showed that Gab2 protein was upregulated in CRC tissues relative to adjacent normal tissues (P<0.001), and this overexpression was significantly correlated with lymph node metastasis (P=0.007), distant metastasis (P<0.001) and TNM stage (P=0.002). According to Kaplan-Meier model, CRC patients with Gab2-positive had a significantly poorer prognosis compared to those with Gab2-negative (P=0.007). Multivariate analysis suggested that the positive expression of Gab2 protein was an independent prognostic factor for CRC patients. In conclusion, our data demonstrated that Gab2 expression may play an important role in the progression of CRC, and underscored that Gab2 has the potential value as a prognostic predictor for CRC patients.
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Affiliation(s)
- Chenbo Ding
- Department of Immunology, Zunyi Medical College, Immunology Innovation Base of Postgraduate Education in Guizhou ProvinceZunyi, China
| | - Junmin Luo
- Department of Immunology, Zunyi Medical College, Immunology Innovation Base of Postgraduate Education in Guizhou ProvinceZunyi, China
| | - Weina Yu
- Department of Immunology, Zunyi Medical College, Immunology Innovation Base of Postgraduate Education in Guizhou ProvinceZunyi, China
| | - Shaoying Gao
- Department of Immunology, Zunyi Medical College, Immunology Innovation Base of Postgraduate Education in Guizhou ProvinceZunyi, China
| | - Liwen Yang
- Department of Immunology, Zunyi Medical College, Immunology Innovation Base of Postgraduate Education in Guizhou ProvinceZunyi, China
| | - Chao Chen
- Department of Immunology, Zunyi Medical College, Immunology Innovation Base of Postgraduate Education in Guizhou ProvinceZunyi, China
| | - Jihong Feng
- Department of Oncology, Affiliated Hospital of Zunyi Medical CollegeZunyi, China
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Luo LY, Kim E, Cheung HW, Weir BA, Dunn GP, Shen RR, Hahn WC. The Tyrosine Kinase Adaptor Protein FRS2 Is Oncogenic and Amplified in High-Grade Serous Ovarian Cancer. Mol Cancer Res 2015; 13:502-9. [PMID: 25368431 PMCID: PMC4369154 DOI: 10.1158/1541-7786.mcr-14-0407] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
UNLABELLED High-grade serous ovarian cancers (HGSOC) are characterized by widespread recurrent regions of copy-number gain and loss. Here, we interrogated 50 genes that are recurrently amplified in HGSOC and essential for cancer proliferation and survival in ovarian cancer cell lines. FRS2 is one of the 50 genes located on chromosomal region 12q15 that is focally amplified in 12.5% of HGSOC. We found that FRS2-amplified cancer cell lines are dependent on FRS2 expression, and that FRS2 overexpression in immortalized human cell lines conferred the ability to grow in an anchorage-independent manner and as tumors in immunodeficient mice. FRS2, an adaptor protein in the FGFR pathway, induces downstream activation of the Ras-MAPK pathway. These observations identify FRS2 as an oncogene in a subset of HGSOC that harbor FRS2 amplifications. IMPLICATIONS These studies identify FRS2 as an amplified oncogene in a subset of HGSOC. FRS2 expression is essential to ovarian cancer cells that harbor 12q15 amplification.
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Affiliation(s)
- Leo Y Luo
- Health Sciences and Technology Program, Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eejung Kim
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hiu Wing Cheung
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Barbara A Weir
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gavin P Dunn
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Rhine R Shen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Astellas Pharma U.S. Inc., Santa Monica, California
| | - William C Hahn
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
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