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Wen RM, Qiu Z, Marti GEW, Peterson EE, Marques FJG, Bermudez A, Wei Y, Nolley R, Lam N, Polasko AL, Chiu CL, Zhang D, Cho S, Karageorgos GM, McDonough E, Chadwick C, Ginty F, Jung KJ, Machiraju R, Mallick P, Crowley L, Pollack JR, Zhao H, Pitteri SJ, Brooks JD. AZGP1 deficiency promotes angiogenesis in prostate cancer. J Transl Med 2024; 22:383. [PMID: 38659028 PMCID: PMC11044612 DOI: 10.1186/s12967-024-05183-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Loss of AZGP1 expression is a biomarker associated with progression to castration resistance, development of metastasis, and poor disease-specific survival in prostate cancer. However, high expression of AZGP1 cells in prostate cancer has been reported to increase proliferation and invasion. The exact role of AZGP1 in prostate cancer progression remains elusive. METHOD AZGP1 knockout and overexpressing prostate cancer cells were generated using a lentiviral system. The effects of AZGP1 under- or over-expression in prostate cancer cells were evaluated by in vitro cell proliferation, migration, and invasion assays. Heterozygous AZGP1± mice were obtained from European Mouse Mutant Archive (EMMA), and prostate tissues from homozygous knockout male mice were collected at 2, 6 and 10 months for histological analysis. In vivo xenografts generated from AZGP1 under- or over-expressing prostate cancer cells were used to determine the role of AZGP1 in prostate cancer tumor growth, and subsequent proteomics analysis was conducted to elucidate the mechanisms of AZGP1 action in prostate cancer progression. AZGP1 expression and microvessel density were measured in human prostate cancer samples on a tissue microarray of 215 independent patient samples. RESULT Neither the knockout nor overexpression of AZGP1 exhibited significant effects on prostate cancer cell proliferation, clonal growth, migration, or invasion in vitro. The prostates of AZGP1-/- mice initially appeared to have grossly normal morphology; however, we observed fibrosis in the periglandular stroma and higher blood vessel density in the mouse prostate by 6 months. In PC3 and DU145 mouse xenografts, over-expression of AZGP1 did not affect tumor growth. Instead, these tumors displayed decreased microvessel density compared to xenografts derived from PC3 and DU145 control cells, suggesting that AZGP1 functions to inhibit angiogenesis in prostate cancer. Proteomics profiling further indicated that, compared to control xenografts, AZGP1 overexpressing PC3 xenografts are enriched with angiogenesis pathway proteins, including YWHAZ, EPHA2, SERPINE1, and PDCD6, MMP9, GPX1, HSPB1, COL18A1, RNH1, and ANXA1. In vitro functional studies show that AZGP1 inhibits human umbilical vein endothelial cell proliferation, migration, tubular formation and branching. Additionally, tumor microarray analysis shows that AZGP1 expression is negatively correlated with blood vessel density in human prostate cancer tissues. CONCLUSION AZGP1 is a negative regulator of angiogenesis, such that loss of AZGP1 promotes angiogenesis in prostate cancer. AZGP1 likely exerts heterotypical effects on cells in the tumor microenvironment, such as stromal and endothelial cells. This study sheds light on the anti-angiogenic characteristics of AZGP1 in the prostate and provides a rationale to target AZGP1 to inhibit prostate cancer progression.
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Affiliation(s)
- Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Zhengyuan Qiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - G Edward W Marti
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Eric E Peterson
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Fernando Jose Garcia Marques
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Abel Bermudez
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yi Wei
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rosalie Nolley
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nathan Lam
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alex LaPat Polasko
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chun-Lung Chiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dalin Zhang
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sanghee Cho
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | | | | | - Chrystal Chadwick
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Fiona Ginty
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Kyeong Joo Jung
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura Crowley
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sharon J Pitteri
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Pollack AS, Kunder CA, Brazer N, Shen Z, Varma S, West RB, Cunha GR, Baskin LS, Brooks JD, Pollack JR. Spatial transcriptomics identifies candidate stromal drivers of benign prostatic hyperplasia. JCI Insight 2024; 9:e176479. [PMID: 37971878 PMCID: PMC10906230 DOI: 10.1172/jci.insight.176479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Benign prostatic hyperplasia (BPH) is the nodular proliferation of the prostate transition zone in older men, leading to urinary storage and voiding problems that can be recalcitrant to therapy. Decades ago, John McNeal proposed that BPH originates with the "reawakening" of embryonic inductive activity by adult prostate stroma, which spurs new ductal proliferation and branching morphogenesis. Here, by laser microdissection and transcriptional profiling of the BPH stroma adjacent to hyperplastic branching ducts, we identified secreted factors likely mediating stromal induction of prostate glandular epithelium and coinciding processes. The top stromal factors were insulin-like growth factor 1 (IGF1) and CXC chemokine ligand 13 (CXCL13), which we verified by RNA in situ hybridization to be coexpressed in BPH fibroblasts, along with their cognate receptors (IGF1R and CXCR5) on adjacent epithelium. In contrast, IGF1 but not CXCL13 was expressed in human embryonic prostate stroma. Finally, we demonstrated that IGF1 is necessary for the generation of BPH-1 cell spheroids and patient-derived BPH cell organoids in 3D culture. Our findings partially support historic speculations on the etiology of BPH and provide what we believe to be new molecular targets for rational therapies directed against the underlying processes driving BPH.
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Affiliation(s)
- Anna S. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Christian A. Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Noah Brazer
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Zhewei Shen
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Gerald R. Cunha
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Laurence S. Baskin
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, California, USA
| | - James D. Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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Mitr R, Pollack JR. RE: Lower Exome Sequencing Coverage of Ancestrally African Patients in the Cancer Genome Atlas. J Natl Cancer Inst 2022; 114:1728. [PMID: 35801943 PMCID: PMC9745426 DOI: 10.1093/jnci/djac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 01/11/2023] Open
Affiliation(s)
- Rhea Mitr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan R Pollack
- Correspondence to: Jonathan R. Pollack, MD, PhD, Department of Pathology, Stanford University School of Medicine, 269 Campus Dr, CCSR-3245A, Stanford, CA, USA (e-mail: )
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4
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Grasedieck S, Cabantog A, MacPhee L, Im J, Ruess C, Demir B, Sperb N, Rücker FG, Döhner K, Herold T, Pollack JR, Bullinger L, Rouhi A, Kuchenbauer F. The retinoic acid receptor co-factor NRIP1 is uniquely upregulated and represents a therapeutic target in acute myeloid leukemia with chromosome 3q rearrangements. Haematologica 2021; 107. [PMID: 34854277 PMCID: PMC9335095 DOI: 10.3324/haematol.2020.276048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Aberrant expression of Ecotropic Viral Integration Site 1 (EVI1) is a hallmark of acute myeloid leukemia (AML) with inv(3) or t(3;3), which is a disease subtype with especially poor outcome. In studying transcriptomes from AML patients with chromosome 3q rearrangements, we identified a significant upregulation of the Nuclear Receptor Interacting Protein 1 (NRIP1) as well as its adjacent non-coding RNA LOC101927745. Utilizing transcriptomic and epigenomic data from over 900 primary samples from patients as well as genetic and transcriptional engineering approaches, we have identified several mechanisms that can lead to upregulation of NRIP1 in AML. We hypothesize that the LOC101927745 transcription start site harbors a context-dependent enhancer that is bound by EVI1, causing upregulation of NRIP1 in AML with chromosome 3 abnormalities. Furthermore, we showed that NRIP1 knockdown negatively affects the proliferation and survival of 3qrearranged AML cells and increases their sensitivity to all-trans retinoic acid, suggesting that NRIP1 is relevant for the pathogenesis of inv(3)/t(3;3) AML and could serve as a novel therapeutic target in myeloid malignancies with 3q abnormalities.
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Affiliation(s)
- Sarah Grasedieck
- University of British Columbia, Department of Microbiology & Immunology, Vancouver, British Columbia, Canada
| | - Ariene Cabantog
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Liam MacPhee
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Junbum Im
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christoph Ruess
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Burcu Demir
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Nadine Sperb
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Frank G. Rücker
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Konstanze Döhner
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Arefeh Rouhi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada,AR and FK contributed equally as co-senior authors
| | - Florian Kuchenbauer
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada,AR and FK contributed equally as co-senior authors
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5
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Grasedieck S, Cabantog A, MacPhee L, Im J, Ruess C, Demir B, Sperb N, Rücker FG, Döhner K, Herold T, Pollack JR, Bullinger L, Rouhi A, Kuchenbauer F. The retinoic acid receptor co-factor NRIP1 is uniquely upregulated and represents a therapeutic target in acute myeloid leukemia with chromosome 3q rearrangements. Haematologica 2021; 107:1758-1772. [PMID: 34854277 DOI: 10.3324/haematol.2021.276048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 11/09/2022] Open
Abstract
Aberrant expression of Ecotropic Viral Integration Site 1 (EVI1) is a hallmark of acute myeloid leukemia (AML) with inv(3) or t(3;3), which is a disease subtype with especially poor outcome. In studying transcriptomes from AML patients with chromosome 3q rearrangements, we identified a significant upregulation of the Nuclear Receptor Interacting Protein 1 (NRIP1) as well as its adjacent non-coding RNA LOC101927745. Utilizing transcriptomic and epigenomic data from over 900 primary patient samples as well as genetic and transcriptional engineering approaches, we have identified several mechanisms that can lead to upregulation of NRIP1 in AML. We hypothesize that the LOC101927745 transcription start site harbors a context-dependent enhancer that is bound by EVI1, causing upregulation of NRIP1 in AML with chr3 abnormalities. Furthermore, we show that NRIP1 knockdown negatively affects the proliferation and survival of 3q-rearranged AML cells and increases their sensitivity towards ATRA, suggesting that NRIP1 is relevant for the pathogenesis of inv(3)/t(3;3) AML and could serve as a novel therapeutic target in myeloid malignancies with 3q abnormalities.
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Affiliation(s)
- Sarah Grasedieck
- University of British Columbia, Dept. of Microbiology and Immunology, MSL Building, 2125 East Mall Vancouver, BC.
| | - Ariene Cabantog
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC
| | - Liam MacPhee
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC
| | - Junbum Im
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC
| | - Christoph Ruess
- Ulm University Hospital, Dept of Internal Medicine III, Albert-Einstein-Allee 23, Ulm
| | - Burcu Demir
- Ulm University Hospital, Dept of Internal Medicine III, Albert-Einstein-Allee 23, Ulm
| | - Nadine Sperb
- Ulm University Hospital, Dept of Internal Medicine III, Albert-Einstein-Allee 23, Ulm
| | - Frank G Rücker
- Ulm University Hospital, Dept of Internal Medicine III, Albert-Einstein-Allee 23, Ulm
| | - Konstanze Döhner
- Ulm University Hospital, Dept of Internal Medicine III, Albert-Einstein-Allee 23, Ulm
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr. 15, Munich
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Berlin
| | - Arefeh Rouhi
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC
| | - Florian Kuchenbauer
- Terry Fox Laboratory, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC.
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6
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Grasedieck S, Ruess C, Krowiorz K, Lux S, Pochert N, Schwarzer A, Klusmann JH, Jongen-Lavrencic M, Herold T, Bullinger L, Pollack JR, Rouhi A, Kuchenbauer F. The long non-coding RNA <i>Cancer Susceptibility 15</i> (<i>CASC15</i>) is induced by isocitrate dehydrogenase (IDH) mutations and maintains an immature phenotype in adult acute myeloid leukemia. Haematologica 2020; 105:e448-453. [PMID: 33054061 PMCID: PMC7556616 DOI: 10.3324/haematol.2019.235291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Sarah Grasedieck
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Christoph Ruess
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Kathrin Krowiorz
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Susanne Lux
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | - Nicole Pochert
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany
| | | | - Jan-Henning Klusmann
- Medizinische Hochschule Hannover (MHH), Hannover, Germany; Universitätsklinik und Poliklinik für Pädiatrie I, Halle (Saale), Germany
| | | | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Center for Environmental Health (HGMU), Munich, Germany
| | | | - Jonathan R Pollack
- Stanford University School of Medicine, Department of Pathology, Stanford, CA, USA
| | - Arefeh Rouhi
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany; Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Florian Kuchenbauer
- Ulm University Hospital, Department of Internal Medicine III, Ulm, Germany; Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.
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7
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Li Q, Hao Q, Cao W, Li J, Wu K, Elshimali Y, Zhu D, Chen QH, Chen G, Pollack JR, Vadgama J, Wu Y. PP2Cδ inhibits p300-mediated p53 acetylation via ATM/BRCA1 pathway to impede DNA damage response in breast cancer. Sci Adv 2019; 5:eaaw8417. [PMID: 31663018 PMCID: PMC6795508 DOI: 10.1126/sciadv.aaw8417] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Although nuclear type 2C protein phosphatase (PP2Cδ) has been demonstrated to be pro-oncogenic with an important role in tumorigenesis, the underlying mechanisms that link aberrant PP2Cδ levels with cancer development remain elusive. Here, we found that aberrant PP2Cδ activity decreases p53 acetylation and its transcriptional activity and suppresses doxorubicin-induced cell apoptosis. Mechanistically, we show that BRCA1 facilitates p300-mediated p53 acetylation by complexing with these two proteins and that S1423/1524 phosphorylation is indispensable for this regulatory process. PP2Cδ, via dephosphorylation of ATM, suppresses DNA damage-induced BRCA1 phosphorylation, leading to inhibition of p300-mediated p53 acetylation. Furthermore, PP2Cδ levels correlate with histological grade and are inversely associated with BRCA1 phosphorylation and p53 acetylation in breast cancer specimens. C23, our newly developed PP2Cδ inhibitor, promotes the anticancer effect of doxorubicin in MCF-7 xenograft-bearing nude mice. Together, our data indicate that PP2Cδ impairs p53 acetylation and DNA damage response by compromising BRCA1 function.
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Affiliation(s)
- Qun Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Department of Oncology, Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qiongyu Hao
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
| | - Wei Cao
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
| | - Jieqing Li
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
| | - Ke Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
| | - Yahya Elshimali
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
| | - Donghui Zhu
- University of North Texas, Denton, TX 76203, USA
| | - Qiao-Hong Chen
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA 93740, USA
| | - Guanglin Chen
- Department of Chemistry, California State University, Fresno, 2555 E. San Ramon Avenue, M/S SB70, Fresno, CA 93740, USA
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jay Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90059, USA
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Middleton LW, Shen Z, Varma S, Pollack AS, Gong X, Zhu S, Zhu C, Foley JW, Vennam S, Sweeney RT, Tu K, Biscocho J, Eminaga O, Nolley R, Tibshirani R, Brooks JD, West RB, Pollack JR. Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis. JCI Insight 2019; 5:129749. [PMID: 31094703 DOI: 10.1172/jci.insight.129749] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Benign prostatic hyperplasia (BPH) is the most common cause of lower urinary tract symptoms in men. Current treatments target prostate physiology rather than BPH pathophysiology and are only partially effective. Here, we applied next-generation sequencing to gain new insight into BPH. By RNAseq, we uncovered transcriptional heterogeneity among BPH cases, where a 65-gene BPH stromal signature correlated with symptom severity. Stromal signaling molecules BMP5 and CXCL13 were enriched in BPH while estrogen regulated pathways were depleted. Notably, BMP5 addition to cultured prostatic myofibroblasts altered their expression profile towards a BPH profile that included the BPH stromal signature. RNAseq also suggested an altered cellular milieu in BPH, which we verified by immunohistochemistry and single-cell RNAseq. In particular, BPH tissues exhibited enrichment of myofibroblast subsets, whilst depletion of neuroendocrine cells and an estrogen receptor (ESR1)-positive fibroblast cell type residing near epithelium. By whole-exome sequencing, we uncovered somatic single-nucleotide variants (SNVs) in BPH, of uncertain pathogenic significance but indicative of clonal cell expansions. Thus, genomic characterization of BPH has identified a clinically-relevant stromal signature and new candidate disease pathways (including a likely role for BMP5 signaling), and reveals BPH to be not merely a hyperplasia, but rather a fundamental re-landscaping of cell types.
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Affiliation(s)
| | | | | | | | - Xue Gong
- Department of Pathology.,Department of Urology
| | | | | | | | | | | | | | | | | | | | - Robert Tibshirani
- Department of Biomedical Data Science, and.,Department of Statistics, Stanford University School of Medicine, Stanford, California, USA
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Kumar R, Naz A, Kotapalli V, Gowrishankar S, Rao S, Pollack JR, Bashyam MD. Abstract 5438: XPNPEP3: A novel transcriptional target of canonical Wnt/β-catenin signalling. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Canonical Wnt/β-catenin signalling plays pivotal roles during embryonic development and adult tissue regeneration. Its aberrant activation however drives expression of a panoply of genes to facilitate colorectal tumorigenesis. Hence, it is imperative to delineate the complete β-catenin transcriptome. We performed genome-wide mRNA profiling of sporadic rectal cancer samples stratified by Wnt status. Results revealed significant up-regulation of XPNPEP3 transcript levels along with that of canonical Wnt targets AXIN2 and EPHB2 in Wnt+ samples. The differential expression of XPNPEP3 was further validated by quantitative PCR (Q-PCR) in additional samples. Nuclear stabilization of β-catenin achieved through LiCl treatment in three colorectal cancer (CRC) cell lines followed by Q-PCR and promoter-luciferase assays confirmed up-regulation of XPNPEP3. XPNPEP3 encodes X-prolyl aminopeptidase 3 which functions to remove the penultimate N-terminal Proline residue from nascent proteins and appears to play a role in ciliary function. Immunohistochemistry based expression analysis using a CRC tissue microarray revealed significant correlation between XPNPEP3 levels and β-catenin nuclear localization as well as increased XPNPEP3 expression in tumor compared to matched normal samples. Survival analysis of The Cancer Genome Atlas (TCGA) breast invasive carcinoma, skin cutaneous melanoma and lung adenocarcinoma data sets revealed poor survival among patients having perturbed XPNPEP3 expression. Characterization of possible oncogenic function of XPNPEP3 in CRC cells and in mice tumor xenografts is currently underway. Altogether, our results suggest XPNPEP3 to be a novel transcriptional target of Wnt/β-catenin signalling having a possible significance in CRC tumorigenesis.
Citation Format: Raju Kumar, Ashmala Naz, Viswakalyan Kotapalli, Swarnalata Gowrishankar, Satish Rao, Jonathan R. Pollack, Murali Dharan Bashyam. XPNPEP3: A novel transcriptional target of canonical Wnt/β-catenin signalling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5438.
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Affiliation(s)
- Raju Kumar
- 1Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashmala Naz
- 1Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | | | - Satish Rao
- 3Krishna Institute of Medical Sciences, Hyderabad, India
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Kumar R, Kotapalli V, Naz A, Gowrishankar S, Rao S, Pollack JR, Bashyam MD. XPNPEP3 is a novel transcriptional target of canonical Wnt/β-catenin signaling. Genes Chromosomes Cancer 2018; 57:304-310. [PMID: 29383790 DOI: 10.1002/gcc.22531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022] Open
Abstract
Canonical Wnt/β-catenin signaling plays important roles in embryonic development and adult tissue regeneration while aberrant Wnt activation is the major driver of sporadic colorectal cancer (CRC). Thus, it is important to characterize the complete β-catenin target transcriptome. We previously performed microarray-based mRNA profiling of rectal cancer samples stratified for Wnt status. In addition to AXIN2 and EPHB2, XPNPEP3 transcripts were significantly elevated in tumors exhibiting activated Wnt/β-catenin signaling, validated by Q-PCR. Three different cell lines supported elevated XPNPEP3 transcript levels upon activation of Wnt signaling, confirmed using promoter-luciferase assays. Ectopic expression of XPNPEP3 promoted tumorigenic properties in CRC cells. Immunohistochemistry on a CRC tissue microarray revealed significant correlation between β-catenin nuclear localization and XPNPEP3 levels. More importantly, XPNPEP3 expression was upregulated compared to normal samples in published expression data sets from several cancers including CRC. Finally, XPNPEP3 expression correlated with poor survival in many cancers. Our results therefore suggest XPNPEP3 to be a transcriptional target of Wnt/β-catenin pathway with particular significance for CRC.
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Affiliation(s)
- Raju Kumar
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Viswakalyan Kotapalli
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashmala Naz
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | | | - Satish Rao
- Krishna Institute of Medical Sciences, Hyderabad, India
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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11
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Gong X, Siprashvili Z, Eminaga O, Shen Z, Sato Y, Kume H, Homma Y, Ogawa S, Khavari PA, Pollack JR, Brooks JD. Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer. Oncotarget 2017; 8:18657-18669. [PMID: 28423633 PMCID: PMC5386637 DOI: 10.18632/oncotarget.15703] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/24/2017] [Indexed: 01/01/2023] Open
Abstract
Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. We sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized into discovery and validation sets) annotated for ~21,000 lncRNAs. A previously uncharacterized lincRNA, SLINKY (Survival-predictive LINcRNA in KidneY cancer), was the top-ranked prognostic lincRNA, and validated in an independent University of Tokyo cohort (P=0.004). In multivariable analysis, SLINKY expression predicted overall survival independent of tumor stage and grade [TCGA HR=3.5 (CI, 2.2-5.7), P < 0.001; Tokyo HR=8.4 (CI, 1.8-40.2), P = 0.007], and by decision tree, ROC and decision curve analysis, added independent prognostic value. In ccRCC cell lines, SLINKY knockdown reduced cancer cell proliferation (with cell-cycle G1 arrest) and induced transcriptome changes enriched for cell proliferation and survival processes. Notably, the genes affected by SLINKY knockdown in cell lines were themselves prognostic and correlated with SLINKY expression in the ccRCC patient samples. From a screen for binding partners, we identified direct binding of SLINKY to Heterogeneous Nuclear Ribonucleoprotein K (HNRNPK), whose knockdown recapitulated SLINKY knockdown phenotypes. Thus, SLINKY is a robust prognostic biomarker in ccRCC, where it functions possibly together with HNRNPK in cancer cell proliferation.
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Affiliation(s)
- Xue Gong
- Department of Urology, School of Medicine, Stanford University, Stanford, California, USA.,Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Okyaz Eminaga
- Department of Urology, School of Medicine, Stanford University, Stanford, California, USA.,Department of Urology, University Hospital Cologne, Cologne, Germany
| | - Zhewei Shen
- Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Paul A Khavari
- Program in Epithelial Biology, School of Medicine, Stanford University, Stanford, California, USA
| | - Jonathan R Pollack
- Department of Pathology, School of Medicine, Stanford University, Stanford, California, USA
| | - James D Brooks
- Department of Urology, School of Medicine, Stanford University, Stanford, California, USA
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12
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Kwon MJ, Kim RN, Song K, Jeon S, Jeong HM, Kim JS, Han J, Hong S, Oh E, Choi JS, An J, Pollack JR, Choi YL, Park CK, Shin YK. Genes co-amplified with ERBB2 or MET as novel potential cancer-promoting genes in gastric cancer. Oncotarget 2017; 8:92209-92226. [PMID: 29190909 PMCID: PMC5696175 DOI: 10.18632/oncotarget.21150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/27/2017] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer (GC), one of the most common cancers worldwide, has a high mortality rate due to limited treatment options. Identifying novel and promising molecular targets is a major challenge that must be overcome if treatment of advanced GC is to be successful. Here, we used comparative genomic hybridization and gene expression microarrays to examine genome-wide DNA copy number alterations (CNAs) and global gene expression in 38 GC samples from old and young patients. We identified frequent CNAs, which included copy number gains on chromosomes 3q, 7p, 8q, 20p, and 20q and copy number losses on chromosomes 19p and 21p. The most frequently gained region was 7p21.1 (55%), whereas the most frequently deleted region was 21p11.1 (50%). Recurrent highly amplified regions 17q12 and 7q31.1-7q31.31 harbored two well-known oncogenes: ERBB2 and MET. Correlation analysis of CNAs and gene expression levels identified CAPZA2 (co-amplified with MET) and genes GRB7, MIEN1, PGAP3, and STARD3 (co-amplified with ERBB2) as potential candidate cancer-promoting genes (CPGs). Public dataset analysis confirmed co-amplification of these genes with MET or ERBB2 in GC tissue samples, and revealed that high expression (except for PGAP3) was significantly associated with shorter overall survival. Knockdown of these genes using small interfering RNA led to significant suppression of GC cell proliferation and migration. Reduced GC cell proliferation mediated by CAPZA2 knockdown was attributable to attenuated cell cycle progression and increased apoptosis. This study identified novel candidate CPGs co-amplified with MET or ERBB2, and suggests that they play a functional role in GC.
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Affiliation(s)
- Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Korea
| | - Ryong Nam Kim
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Korea
| | - Kyoung Song
- R&D center, ABION Inc., Guro-gu, Seoul, Korea
| | - Sinyoung Jeon
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hae Min Jeong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Joo Seok Kim
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Jinil Han
- Gencurix, Inc., Guro-gu, Seoul, Korea
| | - Sungyoul Hong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Ensel Oh
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Sun Choi
- The Center for Anti-cancer Companion Diagnostics, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea
| | - Jungsuk An
- Department of Pathology, Gachon University Gil Medical Center, Incheon, Korea
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yoon-La Choi
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Cheol-Keun Park
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Korea.,The Center for Anti-cancer Companion Diagnostics, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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13
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Abstract
While gemcitabine has been the mainstay therapy for advanced pancreatic cancer, newer combination regimens (e.g. FOLFIRINOX) have extended patient survival, though carry greater toxicity. Biomarkers are needed to better stratify patients for appropriate therapy. Previously, we reported that one-third of pancreatic cancers harbor deletions or deleterious mutations in key subunits of the SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling complex. The SWI/SNF complex mobilizes nucleosomes on DNA, and plays a key role in modulating DNA transcription and repair. Thus, we hypothesized that pancreatic cancers with SWI/SNF aberrations might exhibit compromised DNA repair, and show increased sensitivity to DNA damaging agents. Here, we studied human pancreatic cancer cell lines with deficient (or else exogenously reconstituted) SWI/SNF subunits, as well as normal pancreatic epithelial cells following SWI/SNF subunit knockdown. Cells were challenged with DNA damaging agents, including those used in current combination regimens, and then cell viability assayed. We found that pancreatic cells with SWI/SNF dysfunction showed markedly increased sensitivity to DNA damaging agents, and in particular DNA crosslinking agents (cisplatin and oxaliplatin). Assaying clearance of γH2AX confirmed that SWI/SNF dysfunction impaired DNA damage response/repair. Finally, by analyzing pancreatic cancer patient data from The Cancer Genome Atlas, we found that pancreatic cancers with SWI/SNF deficiency (subunit mutation and/or decreased expression) were associated with extended patient survival specifically when treated with platinum containing regimens. Thus, SWI/SNF dysfunction sensitizes pancreatic cancer cells to DNA crosslinking agents, and SWI/SNF mutation status may provide a useful biomarker to predict which patients are likely to benefit from platinum-containing chemotherapy regimens.
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Affiliation(s)
- Jean Davidson
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Current address: Department of Cardiovascular Research, Stanford University School of Medicine, Stanford, California, USA
| | - Zhewei Shen
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Xue Gong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Urology, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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14
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Cornish-Bowden A, Cornish-Bowden A, Rasnick D, Heng HH, Horne S, Abdallah B, Liu G, Ye CJ, Bloomfield M, Vincent MD, Aldaz CM, Karlsson J, Valind A, Jansson C, Gisselsson D, Graves JAM, Stepanenko AA, Andreieva SV, Korets KV, Mykytenko DO, Huleyuk NL, Baklaushev VP, Kovaleva OA, Chekhonin VP, Vassetzky YS, Avdieiev SS, Bakker B, Taudt AS, Belderbos ME, Porubsky D, Spierings DCJ, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ESJM, van den Berg A, Guryev V, Lansdorp PM, Tatché MC, Foijer F, Liehr T, Baudoin NC, Nicholson JM, Soto K, Quintanilla I, Camps J, Cimini D, Dürrbaum M, Donnelly N, Passerini V, Kruse C, Habermann B, Storchová Z, Mandrioli D, Belpoggi F, Silbergeld EK, Perry MJ, Skotheim RI, Løvf M, Johannessen B, Hoff AM, Zhao S, SveeStrømme JM, Sveen A, Lothe RA, Hehlmann R, Voskanyan A, Fabarius A, Böcking A, Biesterfeld S, Berynskyy L, Börgermann C, Engers R, Dietz J, Fritz A, Sehgal N, Vecerova J, Stojkovicz B, Ding H, Page N, Tye C, Bhattacharya S, Xu J, Stein G, Stein J, Berezney R, Gong X, Grasedieck S, Swoboda J, Rücker FG, Bullinger L, Pollack JR, Roumelioti FM, Chiourea M, Raftopoulou C, Gagos S, Duesberg P, Bloomfield M, Hwang S, Gustafsson HT, O’Sullivan C, Acevedo-Colina A, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM, Stampfer MR, Vrba L, LaBarge MA, Futscher B, Garbe JC, Zhou YH, Trinh AL, Zhou YH, Digman M. Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects. Mol Cytogenet 2017. [PMCID: PMC5499067 DOI: 10.1186/s13039-017-0320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Barasch N, Gong X, Kwei KA, Varma S, Biscocho J, Qu K, Xiao N, Lipsick JS, Pelham RJ, West RB, Pollack JR. Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma. PLoS One 2017; 12:e0171265. [PMID: 28212443 PMCID: PMC5315303 DOI: 10.1371/journal.pone.0171265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 01/17/2017] [Indexed: 12/22/2022] Open
Abstract
Pathogenic gene fusions have been identified in several histologic types of salivary gland neoplasia, but not previously in acinic cell carcinoma (AcCC). To discover novel gene fusions, we performed whole-transcriptome sequencing surveys of three AcCC archival cases. In one specimen we identified a novel HTN3-MSANTD3 gene fusion, and in another a novel PRB3-ZNF217 gene fusion. The structure of both fusions was consistent with the promoter of the 5’ partner (HTN3 or PRB3), both highly expressed salivary gland genes, driving overexpression of full-length MSANTD3 or ZNF217. By fluorescence in situ hybridization of an expanded AcCC case series, we observed MSANTD3 rearrangements altogether in 3 of 20 evaluable cases (15%), but found no additional ZNF217 rearrangements. MSANTD3 encodes a previously uncharacterized Myb/SANT domain-containing protein. Immunohistochemical staining demonstrated diffuse nuclear MSANTD3 expression in 8 of 27 AcCC cases (30%), including the three cases with MSANTD3 rearrangement. MSANTD3 displayed heterogeneous expression in normal salivary ductal epithelium, as well as among other histologic types of salivary gland cancer though without evidence of translocation. In a broader survey, MSANTD3 showed variable expression across a wide range of normal and neoplastic human tissue specimens. In preliminary functional studies, engineered MSANTD3 overexpression in rodent salivary gland epithelial cells did not enhance cell proliferation, but led to significant upregulation of gene sets involved in protein synthesis. Our findings newly identify MSANTD3 rearrangement as a recurrent event in salivary gland AcCC, providing new insight into disease pathogenesis, and identifying a putative novel human oncogene.
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Affiliation(s)
- Nicholas Barasch
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Xue Gong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kevin A. Kwei
- Genomic Health, Redwood City, California, United States of America
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jewison Biscocho
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kunbin Qu
- Genomic Health, Redwood City, California, United States of America
| | - Nan Xiao
- Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, California, United States of America
| | - Joseph S. Lipsick
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert J. Pelham
- Genomic Health, Redwood City, California, United States of America
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (RBW); (JRP)
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (RBW); (JRP)
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16
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Brooks JD, Wei W, Pollack JR, West RB, Shin JH, Sunwoo JB, Hawley SJ, Auman H, Newcomb LF, Simko J, Hurtado-Coll A, Troyer DA, Carroll PR, Gleave ME, Lin DW, Nelson PS, Thompson IM, True LD, McKenney JK, Feng Z, Fazli L. Loss of Expression of AZGP1 Is Associated With Worse Clinical Outcomes in a Multi-Institutional Radical Prostatectomy Cohort. Prostate 2016; 76:1409-19. [PMID: 27325561 PMCID: PMC5557496 DOI: 10.1002/pros.23225] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Given the uncertainties inherent in clinical measures of prostate cancer aggressiveness, clinically validated tissue biomarkers are needed. We tested whether Alpha-2-Glycoprotein 1, Zinc-Binding (AZGP1) protein levels, measured by immunohistochemistry, and RNA expression, by RNA in situ hybridization (RISH), predict recurrence after radical prostatectomy independent of clinical and pathological parameters. METHODS AZGP1 IHC and RISH were performed on a large multi-institutional tissue microarray resource including 1,275 men with 5 year median follow-up. The relationship between IHC and RISH expression levels was assessed using the Kappa analysis. Associations with clinical and pathological parameters were tested by the Chi-square test and the Wilcoxon rank sum test. Relationships with outcome were assessed with univariable and multivariable Cox proportional hazards models and the Log-rank test. RESULTS Absent or weak expression of AZGP1 protein was associated with worse recurrence free survival (RFS), disease specific survival, and overall survival after radical prostatectomy in univariable analysis. AZGP1 protein expression, along with pre-operative serum PSA levels, surgical margin status, seminal vesicle invasion, extracapsular extension, and Gleason score predicted RFS on multivariable analysis. Similarly, absent or low AZGP1 RNA expression by RISH predicted worse RFS after prostatectomy in univariable and multivariable analysis. CONCLUSIONS In our large, rigorously designed validation cohort, loss of AZGP1 expression predicts RFS after radical prostatectomy independent of clinical and pathological variables. Prostate 76:1409-1419, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- James D Brooks
- Department of Urology, Stanford University, Stanford, California.
| | - Wei Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Robert B West
- Department of Pathology, Stanford University, Stanford, California
| | - Jun Ho Shin
- Department of Otolaryngology-Head and Neck Surgery, Stanford University, Stanford, California
| | - John B Sunwoo
- Department of Otolaryngology-Head and Neck Surgery, Stanford University, Stanford, California
| | - Sarah J Hawley
- Canary Foundation, Canary Center at Stanford, Palo Alto, California
| | - Heidi Auman
- Canary Foundation, Canary Center at Stanford, Palo Alto, California
| | - Lisa F Newcomb
- Department of Urology, University of Washington Medical Center, Seattle, Washington
| | - Jeff Simko
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Antonio Hurtado-Coll
- Department of Urologic Sciences and Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Dean A Troyer
- Department of Pathology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
- Eastern Virginia Medical School, Pathology and Microbiology and Molecular Biology, Norfolk, Virginia
| | - Peter R Carroll
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Martin E Gleave
- Department of Urologic Sciences and Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Daniel W Lin
- Department of Urology, University of Washington Medical Center, Seattle, Washington
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ian M Thompson
- Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Lawrence D True
- Department of Pathology, University of Washington Medical Center, Seattle, Washington
| | | | - Ziding Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ladan Fazli
- Department of Urologic Sciences and Vancouver Prostate Centre, Vancouver, British Columbia, Canada
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17
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Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB. BRAF inhibitor treatment of primary BRAF-mutant ameloblastoma with pathologic assessment of response. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 122:e5-7. [PMID: 27209484 DOI: 10.1016/j.oooo.2015.12.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/15/2015] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Molecular characterization of ameloblastoma has indicated a high frequency of driver mutations in BRAF and SMO. Preclinical data suggest that Food and Drug Administration-approved BRAF-targeted therapies may be immediately relevant for patients with ameloblastoma positive for the BRAF V600E mutation. METHODS A neoadjuvant treatment regime of dabrafenib was given to a patient with recurrent BRAF-mutant mandibular ameloblastoma. The patient subsequently underwent left mandible composite resection of the tumor and pathologic evaluation of treatment response. RESULTS The ameloblastoma had a slow but dramatic response with >90% tumor volume reduction. The inner areas of the tumor underwent degeneration and squamous differentiation, and intact ameloblastoma was present in the outer areas associated with bone. CONCLUSIONS Targeted neoadjuvant therapy for ameloblastoma may be useful in certain clinical settings of primary ameloblastoma. These might include tumors of advanced local stage when a neoadjuvant reduction could alter the extent of surgery and instances of local recurrence when surgical options are limited.
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Affiliation(s)
- Serena Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Kaplan
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - A Dimitri Colevas
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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18
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Clarke N, Biscocho J, Kwei KA, Davidson JM, Sridhar S, Gong X, Pollack JR. Integrative Genomics Implicates EGFR as a Downstream Mediator in NKX2-1 Amplified Non-Small Cell Lung Cancer. PLoS One 2015; 10:e0142061. [PMID: 26556242 PMCID: PMC4640868 DOI: 10.1371/journal.pone.0142061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 10/16/2015] [Indexed: 02/07/2023] Open
Abstract
NKX2-1, encoding a homeobox transcription factor, is amplified in approximately 15% of non-small cell lung cancers (NSCLC), where it is thought to drive cancer cell proliferation and survival. However, its mechanism of action remains largely unknown. To identify relevant downstream transcriptional targets, here we carried out a combined NKX2-1 transcriptome (NKX2-1 knockdown followed by RNAseq) and cistrome (NKX2-1 binding sites by ChIPseq) analysis in four NKX2-1-amplified human NSCLC cell lines. While NKX2-1 regulated genes differed among the four cell lines assayed, cell proliferation emerged as a common theme. Moreover, in 3 of the 4 cell lines, epidermal growth factor receptor (EGFR) was among the top NKX2-1 upregulated targets, which we confirmed at the protein level by western blot. Interestingly, EGFR knockdown led to upregulation of NKX2-1, suggesting a negative feedback loop. Consistent with this finding, combined knockdown of NKX2-1 and EGFR in NCI-H1819 lung cancer cells reduced cell proliferation (as well as MAP-kinase and PI3-kinase signaling) more than knockdown of either alone. Likewise, NKX2-1 knockdown enhanced the growth-inhibitory effect of the EGFR-inhibitor erlotinib. Taken together, our findings implicate EGFR as a downstream effector of NKX2-1 in NKX2-1 amplified NSCLC, with possible clinical implications, and provide a rich dataset for investigating additional mediators of NKX2-1 driven oncogenesis.
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Affiliation(s)
- Nicole Clarke
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jewison Biscocho
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kevin A. Kwei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jean M. Davidson
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sushmita Sridhar
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Xue Gong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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19
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McClary AC, Sweeney RT, Biscocho J, Myers BR, Neahring L, Kwei KA, Qu K, Gong X, Ng T, Jones CD, Varma S, Odegaard JI, Rubin B, Troxell ML, Pelham RJ, Zehnder JL, Beachy PA, Pollack JR, West RB. Abstract 3436: Ameloblastoma driver mutations revealed by next-generation sequencing of formalin-fixed paraffin-embedded specimens. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Rare cancer types are not only understudied, but are typically represented by formalin-fixed paraffin-embedded (FFPE) (rather than freshly-frozen) specimens that are suboptimal for genomic analysis. Ameloblastoma is one such rare tumor type, thought to arise from ameloblasts, the cells that deposit enamel during tooth development. Though typically benign, ameloblastomas are locally destructive to the jaw and face, and new non-surgical interventions are needed. To discover novel driver mutations and therapeutic targets, we optimized methods and performed whole-transcriptome sequencing and/or targeted exon sequencing (TruSeq Cancer Panel) of 8 FFPE cases. Identified mutations were verified, and then evaluated on a larger, independent set of 21 FFPE cases by PCR and Sanger sequencing. From the analysis, we identified recurrent somatic mutations in three key developmental or signaling pathways, including Hedgehog, fibroblast growth factor, and MAP kinase pathways. Functional interrogation of a novel Hedgehog pathway mutation confirmed increased basal pathway activity, and defined the response profile to various pharmacologic Hedgehog inhibitors. Together, our results define new ameloblastoma drivers and nominate new molecularly-directed therapies for this rare but disfiguring disease. More generally, our findings validate a robust approach for discovering driver mutations in rare cancers.
Citation Format: Andrew C. McClary, Robert T. Sweeney, Jewison Biscocho, Benjamin R. Myers, Lila Neahring, Kevin A. Kwei, Kunbin Qu, Xue Gong, Tony Ng, Carol D. Jones, Sushama Varma, Justin I. Odegaard, Brian Rubin, Megan L. Troxell, Robert J. Pelham, James L. Zehnder, Philip A. Beachy, Jonathan R. Pollack, Robert B. West. Ameloblastoma driver mutations revealed by next-generation sequencing of formalin-fixed paraffin-embedded specimens. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3436. doi:10.1158/1538-7445.AM2014-3436
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Affiliation(s)
| | | | | | | | | | | | | | - Xue Gong
- 1Stanford University, Stanford, CA
| | - Tony Ng
- 3University of British Columbia, Vancouver, British Columbia, Canada
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Sweeney RT, McClary AC, Myers BR, Biscocho J, Neahring L, Kwei KA, Qu K, Gong X, Ng T, Jones CD, Varma S, Odegaard JI, Sugiyama T, Koyota S, Rubin BP, Troxell ML, Pelham RJ, Zehnder JL, Beachy PA, Pollack JR, West RB. Identification of recurrent SMO and BRAF mutations in ameloblastomas. Nat Genet 2014; 46:722-5. [PMID: 24859340 DOI: 10.1038/ng.2986] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/21/2014] [Indexed: 12/18/2022]
Abstract
Here we report the discovery of oncogenic mutations in the Hedgehog and mitogen-activated protein kinase (MAPK) pathways in over 80% of ameloblastomas, locally destructive odontogenic tumors of the jaw, by genomic analysis of archival material. Mutations in SMO (encoding Smoothened, SMO) are common in ameloblastomas of the maxilla, whereas BRAF mutations are predominant in tumors of the mandible. We show that a frequently occurring SMO alteration encoding p.Leu412Phe is an activating mutation and that its effect on Hedgehog-pathway activity can be inhibited by arsenic trioxide (ATO), an anti-leukemia drug approved by the US Food and Drug Administration (FDA) that is currently in clinical trials for its Hedgehog-inhibitory activity. In a similar manner, ameloblastoma cells harboring an activating BRAF mutation encoding p.Val600Glu are sensitive to the BRAF inhibitor vemurafenib. Our findings establish a new paradigm for the diagnostic classification and treatment of ameloblastomas.
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Affiliation(s)
- Robert T Sweeney
- 1] Department of Pathology, Stanford University, Stanford, California, USA. [2]
| | - Andrew C McClary
- 1] Department of Pathology, Stanford University, Stanford, California, USA. [2]
| | - Benjamin R Myers
- 1] Department of Biochemistry, Stanford University, Stanford, California, USA. [2] Department of Developmental Biology, Stanford University, Stanford, California, USA. [3] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA. [4] Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA. [5]
| | - Jewison Biscocho
- 1] Department of Pathology, Stanford University, Stanford, California, USA. [2]
| | - Lila Neahring
- 1] Department of Biochemistry, Stanford University, Stanford, California, USA. [2] Department of Developmental Biology, Stanford University, Stanford, California, USA. [3] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA. [4] Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Kevin A Kwei
- 1] Genomic Health, Redwood City, California, USA. [2]
| | - Kunbin Qu
- Genomic Health, Redwood City, California, USA
| | - Xue Gong
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carol D Jones
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Justin I Odegaard
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Toshihiro Sugiyama
- Department of Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Souichi Koyota
- Department of Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Brian P Rubin
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Megan L Troxell
- Department of Pathology, Oregon Health and Sciences University, Portland, Oregon, USA
| | | | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Philip A Beachy
- 1] Department of Biochemistry, Stanford University, Stanford, California, USA. [2] Department of Developmental Biology, Stanford University, Stanford, California, USA. [3] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA. [4] Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | | | - Robert B West
- Department of Pathology, Stanford University, Stanford, California, USA
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Shain AH, Salari K, Giacomini CP, Pollack JR. Integrative genomic and functional profiling of the pancreatic cancer genome. BMC Genomics 2013; 14:624. [PMID: 24041470 PMCID: PMC3848637 DOI: 10.1186/1471-2164-14-624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 09/12/2013] [Indexed: 11/20/2022] Open
Abstract
Background Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candidate cancer genes has lagged behind. To address this challenge, here we have devised a highly-parallel RNA interference-based functional screen to evaluate many genomically-nominated candidate pancreatic cancer genes simultaneously. Results For 185 candidate pancreatic cancer genes, selected from recurrently altered genomic loci, we performed a pooled shRNA library screen of cell growth/viability across 10 different cell lines. Knockdown-associated effects on cell growth were assessed by enrichment or depletion of shRNA hairpins, by hybridization to barcode microarrays. A novel analytical approach (COrrelated Phenotypes for On-Target Effects; COPOTE) was used to discern probable on-target knockdown, based on identifying different shRNAs targeting the same gene and displaying concordant phenotypes across cell lines. Knockdown data were integrated with genomic architecture and gene-expression profiles, and selected findings validated using individual shRNAs and/or independent siRNAs. The pooled shRNA library design delivered reproducible data. In all, COPOTE analysis identified 52 probable on-target gene-knockdowns. Knockdown of known oncogenes (KRAS, MYC, SMURF1 and CCNE1) and a tumor suppressor (CDKN2A) showed the expected contrasting effects on cell growth. In addition, the screen corroborated purported roles of PLEKHG2 and MED29 as 19q13 amplicon drivers. Most notably, the analysis also revealed novel possible oncogenic functions of nucleoporin NUP153 (ostensibly by modulating TGFβ signaling) and Kruppel-like transcription factor KLF5 in pancreatic cancer. Conclusions By integrating physical and functional genomic data, we were able to simultaneously evaluate many candidate pancreatic cancer genes. Our findings uncover new facets of pancreatic cancer biology, with possible therapeutic implications. More broadly, our study provides a general strategy for the efficient characterization of candidate genes emerging from cancer genome studies.
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Affiliation(s)
- A Hunter Shain
- Departments of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR-3245A, Stanford, CA 94305-5176, USA.
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Khursheed M, Kolla JN, Kotapalli V, Gupta N, Gowrishankar S, Uppin SG, Sastry RA, Koganti S, Sundaram C, Pollack JR, Bashyam MD. ARID1B, a member of the human SWI/SNF chromatin remodeling complex, exhibits tumour-suppressor activities in pancreatic cancer cell lines. Br J Cancer 2013; 108:2056-62. [PMID: 23660946 PMCID: PMC3670478 DOI: 10.1038/bjc.2013.200] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: The human ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) complex functions as a primary chromatin remodeler during ontogeny, as well as in adult life. Several components of the complex have been suggested to function as important regulators of tumorigenesis in various cancers. In the current study, we have characterised a possible tumour suppressor role for the largest subunit of the complex, namely the AT-rich interaction domain 1B (ARID1B). Methods: We performed Azacytidine and Trichostatin A treatments, followed by bisulphite sequencing to determine the possible DNA methylation-induced transcription repression of the gene in pancreatic cancer (PaCa) cell lines. Functional characterisation of effect of ARID1B ectopic expression in MiaPaCa2 PaCa cell line, which harboured ARID1B homozygous deletion, was carried out. Finally, we evaluated ARID1B protein expression in pancreatic tumour samples using immunohistochemistry on a tissue microarray. Results: ARID1B was transcriptionally repressed due to promoter hypermethylation, and ectopic expression severely compromised the ability of MiaPaCa2 cells to form colonies in liquid culture and soft agar. In addition, ARID1B exhibited significantly reduced/loss of expression in PaCa tissue, especially in samples from advanced-stage tumours, when compared with normal pancreas. Conclusion: The results therefore suggest a possible tumour-suppressor function for ARID1B in PaCa, thus adding to the growing list of SWI/SNF components with a similar function. Given the urgent need to design efficient targeted therapies for PaCa, our study assumes significance.
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Affiliation(s)
- M Khursheed
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, Clarke N, Montgomery KD, Zhu S, Wong AJ, van de Rijn M, West RB, Pollack JR. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet 2013; 9:e1003464. [PMID: 23637631 PMCID: PMC3636093 DOI: 10.1371/journal.pgen.1003464] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a “breakpoint analysis” pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis. Gene fusions represent an important class of cancer genes, created by rearrangements of the genome that bring together two different genes. Because they are unique to cancer cells, gene fusions are ideal diagnostic markers and therapeutic targets. While gene fusions were once thought restricted mainly to blood cancers, recent discoveries suggest they are more widespread. Here, we have developed an approach for mining DNA microarray data to detect the tell-tale signatures of gene fusions, as “breakpoints” occurring within the encoding DNA or expressed transcripts. We apply this approach to a large collection of nearly 1,000 human cancer specimens. From this analysis, we discover and verify twelve new gene fusions occurring in diverse cancer types. We verify that some of these rearrangements recur in other samples of the same cancer type (supporting a causal role) and that the cancers show dependency on the fusion for cancer cell growth. Notably, some of these fusions (e.g. CEP85L/ROS1 in angiosarcoma) represent the first for that cancer type and thus provide important new biological insight. Some are also good drug targets (including rearrangements of ROS1, RAF1, and CDK6 kinases), with clear implications for therapy.
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Affiliation(s)
- Craig P. Giacomini
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Steven Sun
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - A. Hunter Shain
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marilyn M. Giacomini
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jay Balagtas
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert T. Sweeney
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Everett Lai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Catherine A. Del Vecchio
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrew D. Forster
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicole Clarke
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kelli D. Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shirley Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Albert J. Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, Tibshirani R, Chang HY, van de Rijn M, West RB. Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol 2012; 13:R75. [PMID: 22929540 PMCID: PMC4053743 DOI: 10.1186/gb-2012-13-8-r75] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 08/28/2012] [Indexed: 02/06/2023] Open
Abstract
Background Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. Results We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. Conclusions This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research.
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Del Vecchio CA, Giacomini CP, Vogel H, Jensen KC, Florio T, Merlo A, Pollack JR, Wong AJ. Abstract 10: Oncogenic variant EGFRvIII defines a hierarchy in glioblastoma and expression is restricted by epigenetic mechanisms despite the presence of gene amplification. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Glioblastoma multiforme (GBM) is the most common and deadly primary brain tumor. Amplification and rearrangements of the epidermal growth factor receptor (EGFR) gene are frequently found in GBM. The most common variant is EGFRvIII, an exon 2-7 deletion mutant resulting from amplification and rearrangement of the EGFR locus. We have hypothesized that EGFRvIII could mark a cancer stem cell or tumor initiating cell population. If amplification and rearrangement are early events in tumorigenesis, this implies that they should be preserved throughout the tumor. However, in primary GBM EGFRvIII expression was focal and sporadic. To understand the relationship between EGFRvIII expression and the underlying genomic alterations, we utilized manual dissection to separate EGFRvIII positive and negative cells and a quantitative PCR assay that detects independently both EGFR amplification and rearrangement. Unexpectedly, we found EGFR amplification and rearrangement throughout the tumor, including regions with no EGFRvIII expression. This supports our hypothesis and further suggests that mechanisms exist to modulate EGFRvIII expression even in the presence of high gene amplification. To study this phenomenon, we characterized three GBM cell lines with endogenous EGFRvIII expression and corresponding EGFR amplification and rearrangement, confirmed by Western blot, RT-PCR and FISH. By flow cytometry analysis EGFRvIII expression was heterogeneous, with 9-50% EGFRvIII positive cells in each cell line. Both positive and negative populations maintained the genetic alterations, recapitulating what we observed in primary GBM. Importantly, EGFRvIII defined a hierarchy where EGFRvIII-positive cells gave rise to additional positive and negative cells. However, only cells that had recently lost EGFRvIII expression could re-express EGFRvIII. Epigenetic mechanisms played a role in modulating EGFRvIII expression to maintain a heterogeneous population. Demethylation induced a 20-60% increase in the percentage of EGFRvIII-positive cells, indicating that some cells could re-express EGFRvIII. Surprisingly, inhibition of histone deacetylation resulted in a 50-80% reduction in EGFRvIII expression. Collectively, this data demonstrates that EGFRvIII does follow a stem cell model for hierarchical expression and sheds light on the existence of a transient population that is able to re-express EGFRvIII, an important buffer for maintaining EGFRvIII-positive cell numbers. Furthermore, we provide the first evidence that EGFRvIII expression can be silenced by epigenetic mechanisms, suggesting that drugs which modulate the epigenome might be used successfully in glioblastoma tumors.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 10. doi:1538-7445.AM2012-10
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Huang S, Gulzar ZG, Salari K, Lapointe J, Brooks JD, Pollack JR. Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness. Oncogene 2011; 31:4164-70. [PMID: 22179824 DOI: 10.1038/onc.2011.590] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Though prostate cancer is often indolent, it is nonetheless a leading cause of cancer death. Defining the underlying molecular genetic alterations may lead to new strategies for prevention or treatment. Towards this goal, we performed array-based comparative genomic hybridization (CGH) on 86 primary prostate tumors. Among the most frequent alterations not associated with a known cancer gene, we identified focal deletions within 5q21 in 15 out of 86 (17%) cases. By high-resolution tiling array CGH, the smallest common deletion targeted just one gene, the chromatin remodeler chromodomain helicase DNA-binding protein 1 (CHD1). Expression of CHD1 was significantly reduced in tumors with deletion (P=0.03), and compared with normal prostate (P=0.04). Exon sequencing analysis also uncovered nonsynonymous mutations in 1 out of 7 (14%) cell lines (LAPC4) and in 1 out of 24 (4%) prostate tumors surveyed. RNA interference-mediated knockdown of CHD1 in two nontumorigenic prostate epithelial cell lines, OPCN2 and RWPE-1, did not alter cell growth, but promoted cell invasiveness, and in OPCN2-enhanced cell clonogenicity. Taken together, our findings suggest that CHD1 deletion may underlie cell invasiveness in a subset of prostate cancers, and indicate a possible novel role of altered chromatin remodeling in prostate tumorigenesis.
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Affiliation(s)
- S Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305-5176, USA
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Kwei KA, Shain AH, Bair R, Montgomery K, Karikari CA, van de Rijn M, Hidalgo M, Maitra A, Bashyam MD, Pollack JR. SMURF1 amplification promotes invasiveness in pancreatic cancer. PLoS One 2011; 6:e23924. [PMID: 21887346 PMCID: PMC3161761 DOI: 10.1371/journal.pone.0023924] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 08/01/2011] [Indexed: 01/19/2023] Open
Abstract
Pancreatic cancer is a deadly disease, and new therapeutic targets are urgently needed. We previously identified DNA amplification at 7q21-q22 in pancreatic cancer cell lines. Now, by high-resolution genomic profiling of human pancreatic cancer cell lines and human tumors (engrafted in immunodeficient mice to enrich the cancer epithelial fraction), we define a 325 Kb minimal amplicon spanning SMURF1, an E3 ubiquitin ligase and known negative regulator of transforming growth factor β (TGFβ) growth inhibitory signaling. SMURF1 amplification was confirmed in primary human pancreatic cancers by fluorescence in situ hybridization (FISH), where 4 of 95 cases (4.2%) exhibited amplification. By RNA interference (RNAi), knockdown of SMURF1 in a human pancreatic cancer line with focal amplification (AsPC-1) did not alter cell growth, but led to reduced cell invasion and anchorage-independent growth. Interestingly, this effect was not mediated through altered TGFβ signaling, assayed by transcriptional reporter. Finally, overexpression of SMURF1 (but not a catalytic mutant) led to loss of contact inhibition in NIH-3T3 mouse embryo fibroblast cells. Together, these findings identify SMURF1 as an amplified oncogene driving multiple tumorigenic phenotypes in pancreatic cancer, and provide a new druggable target for molecularly directed therapy.
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Affiliation(s)
- Kevin A. Kwei
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - A. Hunter Shain
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Ryan Bair
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Kelli Montgomery
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Collins A. Karikari
- Department of Pathology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Manuel Hidalgo
- Department of Oncology, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Clinical Research Program, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Anirban Maitra
- Department of Pathology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Murali D. Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, India
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University, Stanford, California, United States of America
- * E-mail:
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Abstract
Array-based comparative genomic hybridization (aCGH) enables the measurement of DNA copy number across thousands of locations in a genome. The main goals of analyzing aCGH data are to identify the regions of copy number variation (CNV) and to quantify the amount of CNV. Although there are many methods for analyzing single-sample aCGH data, the analysis of multi-sample aCGH data is a relatively new area of research. Further, many of the current approaches for analyzing multi-sample aCGH data do not appropriately utilize the additional information present in the multiple samples. We propose a procedure called the Fused Lasso Latent Feature Model (FLLat) that provides a statistical framework for modeling multi-sample aCGH data and identifying regions of CNV. The procedure involves modeling each sample of aCGH data as a weighted sum of a fixed number of features. Regions of CNV are then identified through an application of the fused lasso penalty to each feature. Some simulation analyses show that FLLat outperforms single-sample methods when the simulated samples share common information. We also propose a method for estimating the false discovery rate. An analysis of an aCGH data set obtained from human breast tumors, focusing on chromosomes 8 and 17, shows that FLLat and Significance Testing of Aberrant Copy number (an alternative, existing approach) identify similar regions of CNV that are consistent with previous findings. However, through the estimated features and their corresponding weights, FLLat is further able to discern specific relationships between the samples, for example, identifying 3 distinct groups of samples based on their patterns of CNV for chromosome 17.
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Affiliation(s)
- Gen Nowak
- Department of Biostatistics, Harvard University, Boston, MA 02115, USA.
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Malhotra S, Lapointe J, Salari K, Higgins JP, Ferrari M, Montgomery K, van de Rijn M, Brooks JD, Pollack JR. A tri-marker proliferation index predicts biochemical recurrence after surgery for prostate cancer. PLoS One 2011; 6:e20293. [PMID: 21629784 PMCID: PMC3100337 DOI: 10.1371/journal.pone.0020293] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/28/2011] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer exhibits tremendous variability in clinical behavior, ranging
from indolent to lethal disease. Better prognostic markers are needed to
stratify patients for appropriately aggressive therapy. By expression profiling,
we can identify a proliferation signature variably expressed in prostate
cancers. Here, we asked whether one or more tissue biomarkers might capture that
information, and provide prognostic utility. We assayed three proliferation
signature genes: MKI67 (Ki-67; also a classic proliferation
biomarker), TOP2A (DNA topoisomerase II, alpha), and
E2F1 (E2F transcription factor 1). Immunohistochemical
staining was evaluable on 139 radical prostatectomy cases (in tissue microarray
format), with a median clinical follow-up of eight years. Each of the three
proliferation markers was by itself prognostic. Notably, combining the three
markers together as a “proliferation index” (0 or 1,
vs. 2 or 3 positive markers) provided superior prognostic
performance (hazard ratio = 2.6 (95% CI:
1.4–4.9); P = 0.001). In a
multivariate analysis that included preoperative serum prostate specific antigen
(PSA) levels, Gleason grade and pathologic tumor stage, the composite
proliferation index remained a significant predictor
(P = 0.005). Analysis of
receiver-operating characteristic (ROC) curves confirmed the improved
prognostication afforded by incorporating the proliferation index (compared to
the clinicopathologic data alone). Our findings highlight the potential value of
a multi-gene signature-based diagnostic, and define a tri-marker proliferation
index with possible utility for improved prognostication and treatment
stratification in prostate cancer.
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Affiliation(s)
- Sameer Malhotra
- Department of Urology, Stanford University, Stanford, California, United
States of America
| | - Jacques Lapointe
- Department of Surgery, Urology Division, McGill University, Montreal,
Quebec, Canada
| | - Keyan Salari
- Department of Pathology, Stanford University, Stanford, California,
United States of America
- Department of Genetics, Stanford University, Stanford, California, United
States of America
| | - John P. Higgins
- Department of Pathology, Stanford University, Stanford, California,
United States of America
| | - Michelle Ferrari
- Department of Urology, Stanford University, Stanford, California, United
States of America
| | - Kelli Montgomery
- Department of Pathology, Stanford University, Stanford, California,
United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, California,
United States of America
| | - James D. Brooks
- Department of Urology, Stanford University, Stanford, California, United
States of America
- * E-mail: (JDB); (JRP)
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University, Stanford, California,
United States of America
- * E-mail: (JDB); (JRP)
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Shain AH, Matsukuma K, Giacomini C, Karikari CA, Hidalgo M, Maitra A, Pollack JR. Abstract 3930: Integrative genomic analysis reveals SWI/SNF chromatin remodeling complex to be a TGFβ-mediating tumor suppressor pathway in pancreatic cancer. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains a leading cause of cancer deaths in the developed world. A more complete characterization of molecular alterations may suggest new avenues for targeted therapy. Here we report the high-resolution genomic and transcriptional profiling of seventy PDAC early-passage tumor xenografts and cell lines – the largest PDAC dataset currently available of this sample size and resolution. Notable among novel loci, genomic deletion/mutation frequently targeted components of the SWI/SNF chromatin remodeling complex, including ARID1A, ARID1B, PBRM1, SMARCA2 and SMARCA4. Overall, focal deletion/mutation of a SWI/SNF component occurred in at least one-third of all PDAC specimens. In cell culture, RNAi-mediated knockdown of SWI/SNF subunits enhanced cell growth, growth-factor independence, and resistance to TGFβ growth-inhibition. Previously, SWI/SNF was reported to mediate TGFβ signaling. Remarkably, we found that five of the top ten SWI/SNF-mediated TGFβ-downregulated genes were focally amplified (MYC, BIRC3, PARD6B, KLF5, and CEBPD), while two of the top ten upregulated genes were focally deleted (PPAP2B, TNC), implying that its role in TGFβ growth-inhibitory signaling drives SWI/SNF loss in PDAC. In summary, we report the SWI/SNF chromatin remodeling complex, likely through mediating TGFβ signaling, to be a major tumour suppressor pathway in PDAC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3930. doi:10.1158/1538-7445.AM2011-3930
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Affiliation(s)
- Alan H. Shain
- 1Stanford Univ. Department of Pathology, Stanford, CA
| | | | | | - Collins A. Karikari
- 3The John Hopkins University School of Medicine Department of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center, Baltimore, MD
| | - Manuel Hidalgo
- 4Clinical Research Program, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Anirban Maitra
- 3The John Hopkins University School of Medicine Department of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center, Baltimore, MD
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31
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Lin AY, Chua MS, Choi YL, Yeh W, Kim YH, Azzi R, Adams GA, Sainani K, van de Rijn M, So SK, Pollack JR. Comparative profiling of primary colorectal carcinomas and liver metastases identifies LEF1 as a prognostic biomarker. PLoS One 2011; 6:e16636. [PMID: 21383983 PMCID: PMC3044708 DOI: 10.1371/journal.pone.0016636] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 01/03/2011] [Indexed: 12/19/2022] Open
Abstract
Purpose We sought to identify genes of clinical significance to predict survival and the risk for colorectal liver metastasis (CLM), the most common site of metastasis from colorectal cancer (CRC). Patients and Methods We profiled gene expression in 31 specimens from primary CRC and 32 unmatched specimens of CLM, and performed Significance Analysis of Microarrays (SAM) to identify genes differentially expressed between these two groups. To characterize the clinical relevance of two highly-ranked differentially-expressed genes, we analyzed the expression of secreted phosphoprotein 1 (SPP1 or osteopontin) and lymphoid enhancer factor-1 (LEF1) by immunohistochemistry using a tissue microarray (TMA) representing an independent set of 154 patients with primary CRC. Results Supervised analysis using SAM identified 963 genes with significantly higher expression in CLM compared to primary CRC, with a false discovery rate of <0.5%. TMA analysis showed SPP1 and LEF1 protein overexpression in 60% and 44% of CRC cases, respectively. Subsequent occurrence of CLM was significantly correlated with the overexpression of LEF1 (chi-square p = 0.042), but not SPP1 (p = 0.14). Kaplan Meier analysis revealed significantly worse survival in patients with overexpression of LEF1 (p<0.01), but not SPP1 (p = 0.11). Both univariate and multivariate analyses identified stage (p<0.0001) and LEF1 overexpression (p<0.05) as important prognostic markers, but not tumor grade or SPP1. Conclusion Among genes differentially expressed between CLM and primary CRC, we demonstrate overexpression of LEF1 in primary CRC to be a prognostic factor for poor survival and increased risk for liver metastasis.
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Affiliation(s)
- Albert Y Lin
- Department of Medicine, Santa Clara Valley Medical Center, San Jose, California, United States of America.
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32
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Cai D, Shames DS, Raso MG, Xie Y, Kim YH, Pollack JR, Girard L, Sullivan JP, Gao B, Peyton M, Nanjundan M, Heymach J, Mills G, Gazdar AF, Wistuba I, Kodadek TJ, Minna JD, Minna JD. Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation. Cancer Res 2010; 70:6477-85. [PMID: 20663904 PMCID: PMC2922434 DOI: 10.1158/0008-5472.can-10-0005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Steroid receptor coactivator-3 (SRC-3) is a histone acetyltransferase and nuclear hormone receptor coactivator, located on 20q12, which is amplified in several epithelial cancers and well studied in breast cancer. However, its possible role in lung cancer pathogenesis is unknown. We found SRC-3 to be overexpressed in 27% of non-small cell lung cancer (NSCLC) patients (n = 311) by immunohistochemistry, which correlated with poor disease-free (P = 0.0015) and overall (P = 0.0008) survival. Twenty-seven percent of NSCLCs exhibited SRC-3 gene amplification, and we found that lung cancer cell lines expressed higher levels of SRC-3 than did immortalized human bronchial epithelial cells (HBEC), which in turn expressed higher levels of SRC-3 than did cultured primary human HBECs. Small interfering RNA-mediated downregulation of SRC-3 in high-expressing, but not in low-expressing, lung cancer cells significantly inhibited tumor cell growth and induced apoptosis. Finally, we found that SRC-3 expression is inversely correlated with gefitinib sensitivity and that SRC-3 knockdown results in epidermal growth factor receptor tyrosine kinase inhibitor-resistant lung cancers becoming more sensitive to gefitinib. Taken together, these data suggest that SRC-3 may be an important oncogene and therapeutic target for lung cancer.
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Affiliation(s)
- Di Cai
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX,Division of Translational Research, UT Southwestern Medical Center, Dallas, TX
| | - David S. Shames
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX
| | | | - Yang Xie
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Young H Kim
- Department of Pathology, Stanford University Medical Center, Stanford, CA
| | | | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX
| | - James P. Sullivan
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX
| | - Boning Gao
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX
| | - Michael Peyton
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX
| | - Meera Nanjundan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - John Heymach
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX
| | - Gordon Mills
- Department of Molecular Therapeutics, MD Anderson Cancer Center, Houston, TX
| | - Adi F. Gazdar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX
| | - Ignacio Wistuba
- Department of Pathology, MD Anderson Cancer Center, Houston, TX
| | - Thomas J. Kodadek
- Division of Translational Research, UT Southwestern Medical Center, Dallas, TX,To whom correspondence may be addressed. J.D.M.: . T.K.:
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX,The Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX,To whom correspondence may be addressed. J.D.M.: . T.K.:
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33
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Tseng WW, Winer D, Kenkel JA, Choi O, Shain AH, Pollack JR, French R, Lowy AM, Engleman EG. Development of an orthotopic model of invasive pancreatic cancer in an immunocompetent murine host. Clin Cancer Res 2010; 16:3684-95. [PMID: 20534740 DOI: 10.1158/1078-0432.ccr-09-2384] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE The most common preclinical models of pancreatic adenocarcinoma utilize human cells or tissues that are xenografted into immunodeficient hosts. Several immunocompetent, genetically engineered mouse models of pancreatic cancer exist; however, tumor latency and disease progression in these models are highly variable. We sought to develop an immunocompetent, orthotopic mouse model of pancreatic cancer with rapid and predictable growth kinetics. EXPERIMENTAL DESIGN Cell lines with epithelial morphology were derived from liver metastases obtained from Kras(G12D/+);LSL-Trp53(R172H/+);Pdx-1-Cre mice. Tumor cells were implanted in the pancreas of immunocompetent, histocompatible B6/129 mice, and the mice were monitored for disease progression. Relevant tissues were harvested for histologic, genomic, and immunophenotypic analysis. RESULTS All mice developed pancreatic tumors by two weeks. Invasive disease and liver metastases were noted by six to eight weeks. Histologic examination of tumors showed cytokeratin-19-positive adenocarcinoma with regions of desmoplasia. Genomic analysis revealed broad chromosomal changes along with focal gains and losses. Pancreatic tumors were infiltrated with dendritic cells, myeloid-derived suppressor cells, macrophages, and T lymphocytes. Survival was decreased in RAG(-/-) mice, which are deficient in T cells, suggesting that an adaptive immune response alters the course of disease in wild-type mice. CONCLUSIONS We have developed a rapid, predictable orthotopic model of pancreatic adenocarcinoma in immunocompetent mice that mimics human pancreatic cancer with regard to genetic mutations, histologic appearance, and pattern of disease progression. This model highlights both the complexity and relevance of the immune response to invasive pancreatic cancer and may be useful for the preclinical evaluation of new therapeutic agents.
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Affiliation(s)
- William W Tseng
- Department of Pathology, Stanford University, Palo Alto, California, USA
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Salari K, Cuff J, Giacomini CP, Lin A, van de Rijn M, Pollack JR. Abstract 2130: Genomic profiling identifies CDX2 as a lineage-dependent oncogene amplified in colorectal cancer. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-2130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Somatic DNA alteration underlies tumor development and progression, and gives rise to tumors with diverse genetic contexts. Characterizing these contexts helps identify driving genetic lesions and potential therapeutic vulnerabilities. Here, we surveyed a collection of 29 colorectal cancer cell lines for DNA copy number alterations and identified in a subset of samples gain/amplification on chromosome 13, which was well represented among the genomic profiles of 344 primary colorectal tumors examined, but not in other tumor types. A minimal region of high-level amplification on 13q12.2, containing the caudal type homeobox transcription factor CDX2, was identified in one cell line and 7 of 123 (6%) primary colorectal tumors. A tissue microarray consisting of an independent set of 83 colorectal tumors confirmed the presence of a subset of tumors harboring copy number gain/amplification of 13q with increased CDX2 protein expression. In the context of genomic amplification, RNA interference experiments showed CDX2 is required for proliferation of colorectal cancer cells and promotes cell cycle progression without an effect on apoptosis. CDX2 is a known transcriptional regulator of normal gut development and intestinal epithelial cell differentiation and maintenance. Here we have shown that for a subset of lineage-derived colorectal tumors, cell proliferation is dependent on the abnormal amplification and overexpression of CDX2. Thus, we nominate CDX2 as a novel lineage-dependent oncogene deregulated in colorectal cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2130.
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Affiliation(s)
- Keyan Salari
- 1Stanford Univ. School of Medicine, Stanford, CA
| | - Justin Cuff
- 1Stanford Univ. School of Medicine, Stanford, CA
| | | | - Albert Lin
- 1Stanford Univ. School of Medicine, Stanford, CA
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Kwei KA, Kung Y, Salari K, Holcomb IN, Pollack JR. Genomic instability in breast cancer: pathogenesis and clinical implications. Mol Oncol 2010; 4:255-66. [PMID: 20434415 DOI: 10.1016/j.molonc.2010.04.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/27/2010] [Accepted: 04/02/2010] [Indexed: 10/19/2022] Open
Abstract
Breast cancer is a heterogeneous disease, appreciable by molecular markers, gene-expression profiles, and most recently, patterns of genomic alteration. In particular, genomic profiling has revealed three distinct patterns of DNA copy-number alteration: a "simple" type with few gains or losses of whole chromosome arms, an "amplifier" type with focal high-level DNA amplifications, and a "complex" type marked by numerous low-amplitude changes and copy-number transitions. The three patterns are associated with distinct gene-expression subtypes, and preferentially target different loci in the genome (implicating distinct cancer genes). Moreover, the different patterns of alteration imply distinct underlying mechanisms of genomic instability. The amplifier pattern may arise from transient telomere dysfunction, although new data suggest ongoing "amplifier" instability. The complex pattern shows similarity to breast cancers with germline BRCA1 mutation, which also exhibit "basal-like" expression profiles and complex-pattern genomes, implicating a possible defect in BRCA1-associated repair of DNA double-strand breaks. As such, targeting presumptive DNA repair defects represents a promising area of clinical investigation. Future studies should clarify the pathogenesis of breast cancers with amplifier and complex-pattern genomes, and will likely identify new therapeutic opportunities.
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Affiliation(s)
- Kevin A Kwei
- Department of Pathology, Stanford University School of Medicine, CCSR-3245A, 269 Campus Drive, Stanford, CA 94305-5176, USA
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36
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Choi YL, Bocanegra M, Kwon MJ, Shin YK, Nam SJ, Yang JH, Kao J, Godwin AK, Pollack JR. LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer. Cancer Res 2010; 70:2296-306. [PMID: 20215510 DOI: 10.1158/0008-5472.can-09-3141] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epithelial-mesenchymal transition (EMT), a switch of polarized epithelial cells to a migratory, fibroblastoid phenotype, is considered a key process driving tumor cell invasiveness and metastasis. Using breast cancer cell lines as a model system, we sought to discover gene expression signatures of EMT with clinical and mechanistic relevance. A supervised comparison of epithelial and mesenchymal breast cancer lines defined a 200-gene EMT signature that was prognostic across multiple breast cancer cohorts. The immunostaining of LYN, a top-ranked EMT signature gene and Src-family tyrosine kinase, was associated with significantly shorter overall survival (P = 0.02) and correlated with the basal-like ("triple-negative") phenotype. In mesenchymal breast cancer lines, RNAi-mediated knockdown of LYN inhibited cell migration and invasion, but not proliferation. Dasatinib, a dual-specificity tyrosine kinase inhibitor, also blocked invasion (but not proliferation) at nanomolar concentrations that inhibit LYN kinase activity, suggesting that LYN is a likely target and that invasion is a relevant end point for dasatinib therapy. Our findings define a prognostically relevant EMT signature in breast cancer and identify LYN as a mediator of invasion and a possible new therapeutic target (and theranostic marker for dasatinib response), with particular relevance to clinically aggressive basal-like breast cancer.
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Affiliation(s)
- Yoon-La Choi
- Department of Pathology and Division of Breast and Endocrine Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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37
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Peng J, Zhu J, Bergamaschi A, Han W, Noh DY, Pollack JR, Wang P. Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer. Ann Appl Stat 2010. [DOI: 10.1214/09-aoas271] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Peng J, Zhu J, Bergamaschi A, Han W, Noh DY, Pollack JR, Wang P. Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of Breast Cancer. Ann Appl Stat 2010; 4:53-77. [PMID: 24489618 PMCID: PMC3905690 DOI: 10.1214/09-aoas271supp] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this paper, we propose a new method remMap - REgularized Multivariate regression for identifying MAster Predictors - for fitting multivariate response regression models under the high-dimension-low-sample-size setting. remMap is motivated by investigating the regulatory relationships among different biological molecules based on multiple types of high dimensional genomic data. Particularly, we are interested in studying the influence of DNA copy number alterations on RNA transcript levels. For this purpose, we model the dependence of the RNA expression levels on DNA copy numbers through multivariate linear regressions and utilize proper regularization to deal with the high dimensionality as well as to incorporate desired network structures. Criteria for selecting the tuning parameters are also discussed. The performance of the proposed method is illustrated through extensive simulation studies. Finally, remMap is applied to a breast cancer study, in which genome wide RNA transcript levels and DNA copy numbers were measured for 172 tumor samples. We identify a trans-hub region in cytoband 17q12-q21, whose amplification influences the RNA expression levels of more than 30 unlinked genes. These findings may lead to a better understanding of breast cancer pathology.
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Affiliation(s)
- Jie Peng
- Department of Statistics, University of California, Davis, CA, USA
| | - Ji Zhu
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA
| | - Anna Bergamaschi
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway
| | - Wonshik Han
- Cancer Research Institute and Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong-Young Noh
- Cancer Research Institute and Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Pei Wang
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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39
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Lück SC, Russ AC, Du J, Gaidzik V, Schlenk RF, Pollack JR, Döhner K, Döhner H, Bullinger L. KITmutations confer a distinct gene expression signature in core binding factor leukaemia. Br J Haematol 2010; 148:925-37. [DOI: 10.1111/j.1365-2141.2009.08035.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage. However, only a subset of genes with altered dosage exhibit concordant changes in gene expression. This subset is likely to be enriched for oncogenes and tumor suppressor genes, and can be identified by integrating these two layers of genome-scale data. We introduce DNA/RNA-Integrator (DR-Integrator), a statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between DNA copy number and gene expression, and implements a supervised analysis that captures genes with significant alterations in both DNA copy number and gene expression between two sample classes. Availability: DR-Integrator is freely available for non-commercial use from the Pollack Lab at http://pollacklab.stanford.edu/ and can be downloaded as a plug-in application to Microsoft Excel and as a package for the R statistical computing environment. The R package is available under the name ‘DRI’ at http://cran.r-project.org/. An example analysis using DR-Integrator is included as supplemental material. Contact:ksalari@stanford.edu; pollack1@stanford.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Keyan Salari
- Department of Pathology, Stanford University, Stanford, CA, USA.
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41
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Kim YH, Kwei KA, Girard L, Salari K, Kao J, Pacyna-Gengelbach M, Wang P, Hernandez-Boussard T, Gazdar AF, Petersen I, Minna JD, Pollack JR. Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer. Oncogene 2009; 29:1421-30. [PMID: 19966867 PMCID: PMC3320568 DOI: 10.1038/onc.2009.437] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA amplifications, leading to the overexpression of oncogenes, are a cardinal feature of lung cancer and directly contribute to its pathogenesis. To uncover novel such alterations, we performed an array-based comparative genomic hybridization survey of 128 non-small cell lung cancer cell lines and tumors. Prominent among our findings, we identified recurrent high-level amplification at cytoband 22q11.21 in 3% of lung cancer specimens, with another 11% of specimens exhibiting low-level gain spanning that locus. The 22q11.21 amplicon core contained eight named genes, only four of which were overexpressed (by transcript profiling) when amplified. Among these, CRKL encodes an adaptor protein functioning in signal transduction, best known as a substrate of the BCR-ABL kinase in chronic myelogenous leukemia. RNA interference-mediated knockdown of CRKL in lung cancer cell lines with (but not without) amplification led to significantly decreased cell proliferation, cell-cycle progression, cell survival, and cell motility and invasion. In addition, overexpression of CRKL in immortalized human bronchial epithelial cells led to EGF-independent cell growth. Our findings indicate that amplification and resultant overexpression of CRKL contributes to diverse oncogenic phenotypes in lung cancer, with implications for targeted therapy, and highlighting a role of adapter proteins as primary genetic drivers of tumorigenesis.
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Affiliation(s)
- Y H Kim
- Department of Pathology, Stanford University, Stanford, CA 94305-5176, USA
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Bocanegra M, Bergamaschi A, Kim YH, Miller MA, Rajput AB, Kao J, Langerød A, Han W, Noh DY, Jeffrey SS, Huntsman DG, Børresen-Dale AL, Pollack JR. Focal amplification and oncogene dependency of GAB2 in breast cancer. Oncogene 2009; 29:774-9. [PMID: 19881546 DOI: 10.1038/onc.2009.364] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
DNA amplifications in breast cancer are frequent on chromosome 11q, in which multiple driver oncogenes likely reside in addition to cyclin D1 (CCND1). One such candidate, the scaffolding adapter protein, GRB2-associated binding protein 2 (GAB2), functions in ErbB signaling and was recently shown to enhance mammary epithelial cell proliferation, and metastasis of ERBB2 (HER2/neu)-driven murine breast cancer. However, the amplification status and function of GAB2 in the context of amplification remain undefined. In this study, by genomic profiling of 172 breast tumors, and fluorescence in situ hybridization validation in an independent set of 210 scorable cases, we observed focal amplification spanning GAB2 (11q14.1) independent of CCND1 (11q13.2) amplification, consistent with a driver role. Further, small interfering RNA (siRNA)-mediated knockdown of GAB2 in breast cancer lines (SUM52, SUM44PE and MDA468) with GAB2 amplification revealed a dependency on GAB2 for cell proliferation, cell-cycle progression, survival and invasion, likely mediated through altered phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) signaling. GAB2 knockdown also reduced proliferation and survival in a cell line (BT474) with ERBB2 amplification, consistent with the possibility that GAB2 can function downstream of ERBB2. Our studies implicate focal amplification of GAB2 in breast carcinogenesis, and underscore an oncogenic role of scaffolding adapter proteins, and a potential new point of therapeutic intervention.
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Affiliation(s)
- M Bocanegra
- Department of Pathology, Stanford University, Stanford, CA 94305-5176, USA
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Abstract
DNA microarray technology has revolutionized biological research by enabling genome-scale explorations. This chapter provides an overview of DNA microarray technology and its application to characterizing the physical genome, with a focus on cancer genomes. Specific areas discussed include investigations of DNA copy number alteration (and loss of heterozygosity), DNA methylation, DNA-protein (i.e., chromatin and transcription factor) interactions, DNA replication, and the integration of diverse genome-scale data types. Also provided is a perspective on recent advances and future directions in characterizing the physical genome.
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Abstract
Over the past decade, DNA microarrays have proven to be a powerful tool in biological research for the molecular surveillance of cells and tissues. The expansive utility of DNA microarrays owes its nascence to the development of a multitude of microarray platforms that enable the systematic and comprehensive exploration of diverse genomic properties and processes. Concomitant with the explosive generation of microarray data over the last several years has been an increasing interest in the integration of such diverse data types, thus spurring the development of novel statistical techniques and integrative bioinformatics tools. This chapter will outline general approaches to microarray data integration and provide an introduction to DR-Integrator, a broadly useful analysis tool for the integration of DNA copy number and gene-expression microarray data.
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Affiliation(s)
- Keyan Salari
- Departments of Pathology and Genetics, Stanford University, Stanford, CA, USA
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Bergamaschi A, Kim YH, Kwei KA, La Choi Y, Bocanegra M, Langerød A, Han W, Noh DY, Huntsman DG, Jeffrey SS, Børresen-Dale AL, Pollack JR. CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer. Mol Oncol 2008; 2:327-39. [PMID: 19383354 DOI: 10.1016/j.molonc.2008.09.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/17/2008] [Accepted: 09/17/2008] [Indexed: 01/27/2023] Open
Abstract
Breast cancer exhibits clinical and molecular heterogeneity, where expression profiling studies have identified five major molecular subtypes. The basal-like subtype, expressing basal epithelial markers and negative for estrogen receptor (ER), progesterone receptor (PR) and HER2, is associated with higher overall levels of DNA copy number alteration (CNA), specific CNAs (like gain on chromosome 10p), and poor prognosis. Discovering the molecular genetic basis of tumor subtypes may provide new opportunities for therapy. To identify the driver oncogene on 10p associated with basal-like tumors, we analyzed genomic profiles of 172 breast carcinomas. The smallest shared region of gain spanned just seven genes at 10p13, including calcium/calmodulin-dependent protein kinase ID (CAMK1D), functioning in intracellular signaling but not previously linked to cancer. By microarray, CAMK1D was overexpressed when amplified, and by immunohistochemistry exhibited elevated expression in invasive carcinomas compared to carcinoma in situ. Engineered overexpression of CAMK1D in non-tumorigenic breast epithelial cells led to increased cell proliferation, and molecular and phenotypic alterations indicative of epithelial-mesenchymal transition (EMT), including loss of cell-cell adhesions and increased cell migration and invasion. Our findings identify CAMK1D as a novel amplified oncogene linked to EMT in breast cancer, and as a potential therapeutic target with particular relevance to clinically unfavorable basal-like tumors.
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Affiliation(s)
- Anna Bergamaschi
- Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway
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Thompson M, Lapointe J, Choi YL, Ong DE, Higgins JP, Brooks JD, Pollack JR. Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle. Prostate 2008; 68:1248-56. [PMID: 18500686 PMCID: PMC2516917 DOI: 10.1002/pros.20792] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Prostate cancer is the most frequently diagnosed cancer among men in the United States. In contrast, cancer of the seminal vesicle is exceedingly rare, despite that the prostate and seminal vesicle share similar histology, secretory function, androgen dependency, blood supply, and (in part) embryonic origin. We hypothesized that gene-expression differences between prostate and seminal vesicle might inform mechanisms underlying the higher incidence of prostate cancer. METHODS Whole-genome DNA microarrays were used to profile gene expression of 11 normal prostate and 7 seminal vesicle specimens (including six matched pairs) obtained from radical prostatectomy. Supervised analysis was used to identify genes differentially expressed between normal prostate and seminal vesicle, and this list was then cross-referenced to genes differentially expressed between normal and cancerous prostate. Expression patterns of selected genes were confirmed by immunohistochemistry using a tissue microarray. RESULTS We identified 32 genes that displayed a highly statistically significant expression pattern with highest levels in seminal vesicle, lower levels in normal prostate, and lowest levels in prostate cancer. Among these genes was the known candidate prostate tumor suppressor GSTP1 (involved in xenobiotic detoxification). The expression pattern of GSTP1 and four other genes, ABCG2 (xenobiotic transport), CRABP2 (retinoic acid signaling), GATA3 (lineage-specific transcription), and SLPI (immune response), was confirmed by immunohistochemistry. CONCLUSIONS Our findings identify candidate prostate cancer genes whose reduced expression in prostate (compared to seminal vesicle) may be permissive to prostate cancer initiation. Such genes and their pathways may inform mechanisms of prostate carcinogenesis, and suggest new opportunities for prostate cancer prevention.
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Affiliation(s)
- Maxwell Thompson
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
| | - Jacques Lapointe
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
- Department of Urology, Stanford University, Stanford, California, 94305, USA
| | - Yoon-La Choi
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
- Department of Pathology, Samsung Medical Center, Seoul, 135-710, Korea
| | - David E. Ong
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John P. Higgins
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
| | - James D. Brooks
- Department of Urology, Stanford University, Stanford, California, 94305, USA
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University, Stanford, California, 94305, USA
- To whom correspondence and reprint requests should be addressed at: Department of Pathology, Stanford University School of Medicine, CCSR-3245A, 269 Campus Drive, Stanford, CA 94305-5176, Telephone: 650-736-1987; Fax: 650-736-0073, E-mail:
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47
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Miller MA, Huntsman DG, Lapointe J, Pollack JR. Reply to Perner and Rubin. Mod Pathol 2008. [DOI: 10.1038/modpathol.2008.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Kwei KA, Kim YH, Girard L, Kao J, Pacyna-Gengelbach M, Salari K, Lee J, Choi YL, Sato M, Wang P, Hernandez-Boussard T, Gazdar AF, Petersen I, Minna JD, Pollack JR. Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer. Oncogene 2008; 27:3635-40. [PMID: 18212743 DOI: 10.1038/sj.onc.1211012] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer is a leading cause of cancer death, where the amplification of oncogenes contributes to tumorigenesis. Genomic profiling of 128 lung cancer cell lines and tumors revealed frequent focal DNA amplification at cytoband 14q13.3, a locus not amplified in other tumor types. The smallest region of recurrent amplification spanned the homeobox transcription factor TITF1 (thyroid transcription factor 1; also called NKX2-1), previously linked to normal lung development and function. When amplified, TITF1 exhibited increased expression at both the RNA and protein levels. Small interfering RNA (siRNA)-mediated knockdown of TITF1 in lung cancer cell lines with amplification led to reduced cell proliferation, manifested by both decreased cell-cycle progression and increased apoptosis. Our findings indicate that TITF1 amplification and overexpression contribute to lung cancer cell proliferation rates and survival and implicate TITF1 as a lineage-specific oncogene in lung cancer.
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Affiliation(s)
- K A Kwei
- Department of Pathology, Stanford University, Stanford, CA 94305-5176, USA
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49
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Dumur CI, Lyons-Weiler M, Sciulli C, Garrett CT, Schrijver I, Holley TK, Rodriguez-Paris J, Pollack JR, Zehnder JL, Price M, Hagenkord JM, Rigl CT, Buturovic LJ, Anderson GG, Monzon FA. Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers. J Mol Diagn 2008; 10:67-77. [PMID: 18083688 PMCID: PMC2175545 DOI: 10.2353/jmoldx.2008.070099] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2007] [Indexed: 02/02/2023] Open
Abstract
Clinical workup of metastatic malignancies of unknown origin is often arduous and expensive and is reported to be unsuccessful in 30 to 60% of cases. Accurate classification of uncertain primary cancers may improve with microarray-based gene expression testing. We evaluated the analytical performance characteristics of the Pathwork tissue of origin test, which uses expression signals from 1668 probe sets in a gene expression microarray, to quantify the similarity of tumor specimens to 15 known tissues of origin. Sixty archived tissue specimens from poorly and undifferentiated tumors (metastatic and primary) were analyzed at four laboratories representing a wide range of preanalytical conditions (eg, personnel, reagents, instrumentation, and protocols). Cross-laboratory comparisons showed highly reproducible results between laboratories, with correlation coefficients between 0.95 to 0.97 for measurements of similarity scores, and an average 93.8% overall concordance between laboratories in terms of final tissue calls. Bland-Altman plots (mean coefficients of reproducibility of 32.48+/-3.97) and kappa statistics (kappa >0.86) also indicated a high level of agreement between laboratories. We conclude that the Pathwork tissue of origin test is a robust assay that produces consistent results in diverse laboratory conditions reflecting the preanalytical variations found in the everyday clinical practice of molecular diagnostics laboratories.
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Affiliation(s)
- Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Maureen Lyons-Weiler
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christin Sciulli
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Carleton T. Garrett
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Iris Schrijver
- Department of Pathology, Stanford University, Stanford, California
| | - Tara K. Holley
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | | | | | - James L. Zehnder
- Department of Pathology, Stanford University, Stanford, California
| | - Melissa Price
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jill M. Hagenkord
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | | | - Federico A. Monzon
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
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50
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Lapointe J, Li C, Giacomini CP, Salari K, Huang S, Wang P, Ferrari M, Hernandez-Boussard T, Brooks JD, Pollack JR. Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis. Cancer Res 2007; 67:8504-10. [PMID: 17875689 DOI: 10.1158/0008-5472.can-07-0673] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Prostate cancer is clinically heterogeneous, ranging from indolent to lethal disease. Expression profiling previously defined three subtypes of prostate cancer, one (subtype-1) linked to clinically favorable behavior, and the others (subtypes-2 and -3) linked with a more aggressive form of the disease. To explore disease heterogeneity at the genomic level, we carried out array-based comparative genomic hybridization (array CGH) on 64 prostate tumor specimens, including 55 primary tumors and 9 pelvic lymph node metastases. Unsupervised cluster analysis of DNA copy number alterations (CNA) identified recurrent aberrations, including a 6q15-deletion group associated with subtype-1 gene expression patterns and decreased tumor recurrence. Supervised analysis further disclosed distinct patterns of CNA among gene-expression subtypes, where subtype-1 tumors exhibited characteristic deletions at 5q21 and 6q15, and subtype-2 cases harbored deletions at 8p21 (NKX3-1) and 21q22 (resulting in TMPRSS2-ERG fusion). Lymph node metastases, predominantly subtype-3, displayed overall higher frequencies of CNA, and in particular gains at 8q24 (MYC) and 16p13, and loss at 10q23 (PTEN) and 16q23. Our findings reveal that prostate cancers develop via a limited number of alternative preferred genetic pathways. The resultant molecular genetic subtypes provide a new framework for investigating prostate cancer biology and explain in part the clinical heterogeneity of the disease.
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Affiliation(s)
- Jacques Lapointe
- Department of Pathology, Stanford University, Stanford, California, USA
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