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Yogodzinski C, Arab A, Pritchard JR, Goodarzi H, Gilbert LA. A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy. Genome Med 2021; 13:167. [PMID: 34663427 PMCID: PMC8524992 DOI: 10.1186/s13073-021-00987-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/05/2021] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Advances in cancer biology are increasingly dependent on integration of heterogeneous datasets. Large-scale efforts have systematically mapped many aspects of cancer cell biology; however, it remains challenging for individual scientists to effectively integrate and understand this data. RESULTS We have developed a new data retrieval and indexing framework that allows us to integrate publicly available data from different sources and to combine publicly available data with new or bespoke datasets. Our approach, which we have named the cancer data integrator (CanDI), is straightforward to implement, is well documented, and is continuously updated which should enable individual users to take full advantage of efforts to map cancer cell biology. We show that CanDI empowered testable hypotheses of new synthetic lethal gene pairs, genes associated with sex disparity, and immunotherapy targets in cancer. CONCLUSIONS CanDI provides a flexible approach for large-scale data integration in cancer research enabling rapid generation of hypotheses. The CanDI data integrator is available at https://github.com/GilbertLabUCSF/CanDI .
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Affiliation(s)
- Christopher Yogodzinski
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA.
- Present Address: University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Abolfazl Arab
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Justin R Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Hani Goodarzi
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Luke A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA, USA.
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Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA. An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer. Nat Commun 2021; 12:4601. [PMID: 34326322 PMCID: PMC8322386 DOI: 10.1038/s41467-021-24919-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Genomic sequencing of thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for cancer cell proliferation or survival in hundreds of cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, there are likely a number of undiscovered tumor specific driver genes that may represent potential drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data reveals known prostate cancer specific driver genes, such as AR and HOXB13, as well as a number of top hits that are poorly characterized. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two top hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.
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Affiliation(s)
- Rajdeep Das
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Yogodzinski
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Emily A Egusa
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lisa N Chesner
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - William S Chen
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donna K Dang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jason T Swinderman
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Alex Ge
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shaheen Kabir
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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Cao S, Slack SD, Levy CN, Hughes SM, Jiang Y, Yogodzinski C, Roychoudhury P, Jerome KR, Schiffer JT, Hladik F, Woodrow KA. Hybrid nanocarriers incorporating mechanistically distinct drugs for lymphatic CD4 + T cell activation and HIV-1 latency reversal. Sci Adv 2019; 5:eaav6322. [PMID: 30944862 PMCID: PMC6436934 DOI: 10.1126/sciadv.aav6322] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/06/2019] [Indexed: 05/10/2023]
Abstract
A proposed strategy to cure HIV uses latency-reversing agents (LRAs) to reactivate latent proviruses for purging HIV reservoirs. A variety of LRAs have been identified, but none has yet proven effective in reducing the reservoir size in vivo. Nanocarriers could address some major challenges by improving drug solubility and safety, providing sustained drug release, and simultaneously delivering multiple drugs to target tissues and cells. Here, we formulated hybrid nanocarriers that incorporate physicochemically diverse LRAs and target lymphatic CD4+ T cells. We identified one LRA combination that displayed synergistic latency reversal and low cytotoxicity in a cell model of HIV and in CD4+ T cells from virologically suppressed patients. Furthermore, our targeted nanocarriers selectively activated CD4+ T cells in nonhuman primate peripheral blood mononuclear cells as well as in murine lymph nodes, and substantially reduced local toxicity. This nanocarrier platform may enable new solutions for delivering anti-HIV agents for an HIV cure.
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Affiliation(s)
- Shijie Cao
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Sarah D. Slack
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Claire N. Levy
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Sean M. Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Yonghou Jiang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kim A. Woodrow
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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