1
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Tong AJ, Leylek R, Herzner AM, Rigas D, Wichner S, Blanchette C, Tahtinen S, Kemball CC, Mellman I, Haley B, Freund EC, Delamarre L. Nucleotide modifications enable rational design of TLR7-selective ligands by blocking RNase cleavage. J Exp Med 2024; 221:e20230341. [PMID: 38095631 PMCID: PMC10720541 DOI: 10.1084/jem.20230341] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 02/24/2023] [Revised: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Toll-like receptors 7 (TLR7) and 8 (TLR8) each sense single-stranded RNA (ssRNA), but their activation results in different immune activation profiles. Attempts to selectively target either TLR7 or TLR8 have been hindered by their high degree of homology. However, recent studies revealed that TLR7 and TLR8 bind different ligands resulting from the processing of ssRNA by endolysosomal RNases. We demonstrate that by introducing precise 2' sugar-modified bases into oligoribonucleotides (ORNs) containing known TLR7 and TLR8 binding motifs, we could prevent RNase-mediated degradation into the monomeric uridine required for TLR8 activation while preserving TLR7 activation. Furthermore, a novel, optimized protocol for CRISPR-Cas9 knockout in primary human plasmacytoid dendritic cells showed that TLR7 activation is dependent on RNase processing of ORNs and revealed a previously undescribed role for RNase 6 in degrading ORNs into TLR ligands. Finally, 2' sugar-modified ORNs demonstrated robust innate immune activation in mice. Altogether, we identified a strategy for creating tunable TLR7-selective agonists.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ira Mellman
- Genentech, Inc., South San Francisco, CA, USA
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2
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Guidi R, Wedeles C, Xu D, Kolmus K, Headland SE, Teng G, Guillory J, Zeng YJ, Cheung TK, Chaudhuri S, Modrusan Z, Liang Y, Horswell S, Haley B, Rutz S, Rose C, Franke Y, Kirkpatrick DS, Hackney JA, Wilson MS. Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain type 2 immunity. Cell Rep 2023; 42:113515. [PMID: 38096048 DOI: 10.1016/j.celrep.2023.113515] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/28/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Argonaute (AGO) proteins execute microRNA (miRNA)-mediated gene silencing. However, it is unclear whether all 4 mammalian AGO proteins (AGO1, AGO2, AGO3, and AGO4) are required for miRNA activity. We generate Ago1, Ago3, and Ago4-deficient mice (Ago134Δ) and find AGO1/3/4 to be redundant for miRNA biogenesis, homeostasis, or function, a role that is carried out by AGO2. Instead, AGO1/3/4 regulate the expansion of type 2 immunity via precursor mRNA splicing in CD4+ T helper (Th) lymphocytes. Gain- and loss-of-function experiments demonstrate that nuclear AGO3 interacts directly with SF3B3, a component of the U2 spliceosome complex, to aid global mRNA splicing, and in particular the isoforms of the gene Nisch, resulting in a dysregulated Nisch isoform ratio. This work uncouples AGO1, AGO3, and AGO4 from miRNA-mediated RNA interference, identifies an AGO3:SF3B3 complex in the nucleus, and reveals a mechanism by which AGO proteins regulate inflammatory diseases.
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Affiliation(s)
- Riccardo Guidi
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | | | - Daqi Xu
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Krzysztof Kolmus
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Sarah E Headland
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Grace Teng
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Joseph Guillory
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yi Jimmy Zeng
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Tommy K Cheung
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Stuart Horswell
- Bioinformatic and Biostatistics, The Francis Crick Institute, London, UK
| | - Benjamin Haley
- Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Sascha Rutz
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Christopher Rose
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Yvonne Franke
- Protein Sciences, Genentech, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Mark S Wilson
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA.
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3
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Gurung HR, Heidersbach AJ, Darwish M, Chan PPF, Li J, Beresini M, Zill OA, Wallace A, Tong AJ, Hascall D, Torres E, Chang A, Lou K'HW, Abdolazimi Y, Hammer C, Xavier-Magalhães A, Marcu A, Vaidya S, Le DD, Akhmetzyanova I, Oh SA, Moore AJ, Uche UN, Laur MB, Notturno RJ, Ebert PJR, Blanchette C, Haley B, Rose CM. Systematic discovery of neoepitope-HLA pairs for neoantigens shared among patients and tumor types. Nat Biotechnol 2023:10.1038/s41587-023-01945-y. [PMID: 37857725 DOI: 10.1038/s41587-023-01945-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/14/2023] [Indexed: 10/21/2023]
Abstract
The broad application of precision cancer immunotherapies is limited by the number of validated neoepitopes that are common among patients or tumor types. To expand the known repertoire of shared neoantigen-human leukocyte antigen (HLA) complexes, we developed a high-throughput platform that coupled an in vitro peptide-HLA binding assay with engineered cellular models expressing individual HLA alleles in combination with a concatenated transgene harboring 47 common cancer neoantigens. From more than 24,000 possible neoepitope-HLA combinations, biochemical and computational assessment yielded 844 unique candidates, of which 86 were verified after immunoprecipitation mass spectrometry analyses of engineered, monoallelic cell lines. To evaluate the potential for immunogenicity, we identified T cell receptors that recognized select neoepitope-HLA pairs and elicited a response after introduction into human T cells. These cellular systems and our data on therapeutically relevant neoepitopes in their HLA contexts will aid researchers studying antigen processing as well as neoepitope targeting therapies.
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Affiliation(s)
| | | | | | | | - Jenny Li
- Genentech, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ana Marcu
- Genentech, South San Francisco, CA, USA
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4
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Ortiz-Muñoz G, Brown M, Carbone CB, Pechuan-Jorge X, Rouilly V, Lindberg H, Ritter AT, Raghupathi G, Sun Q, Nicotra T, Mantri SR, Yang A, Doerr J, Nagarkar D, Darmanis S, Haley B, Mariathasan S, Wang Y, Gomez-Roca C, de Andrea CE, Spigel D, Wu T, Delamarre L, Schöneberg J, Modrusan Z, Price R, Turley SJ, Mellman I, Moussion C. In situ tumour arrays reveal early environmental control of cancer immunity. Nature 2023:10.1038/s41586-023-06132-2. [PMID: 37258670 DOI: 10.1038/s41586-023-06132-2] [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: 05/03/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The immune phenotype of a tumour is a key predictor of its response to immunotherapy1-4. Patients who respond to checkpoint blockade generally present with immune-inflamed5-7 tumours that are highly infiltrated by T cells. However, not all inflamed tumours respond to therapy, and even lower response rates occur among tumours that lack T cells (immune desert) or that spatially exclude T cells to the periphery of the tumour lesion (immune excluded)8. Despite the importance of these tumour immune phenotypes in patients, little is known about their development, heterogeneity or dynamics owing to the technical difficulty of tracking these features in situ. Here we introduce skin tumour array by microporation (STAMP)-a preclinical approach that combines high-throughput time-lapse imaging with next-generation sequencing of tumour arrays. Using STAMP, we followed the development of thousands of arrayed tumours in vivo to show that tumour immune phenotypes and outcomes vary between adjacent tumours and are controlled by local factors within the tumour microenvironment. Particularly, the recruitment of T cells by fibroblasts and monocytes into the tumour core was supportive of T cell cytotoxic activity and tumour rejection. Tumour immune phenotypes were dynamic over time and an early conversion to an immune-inflamed phenotype was predictive of spontaneous or therapy-induced tumour rejection. Thus, STAMP captures the dynamic relationships of the spatial, cellular and molecular components of tumour rejection and has the potential to translate therapeutic concepts into successful clinical strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Carlos Gomez-Roca
- IUCT, Institut Universitaire du Cancer de Toulouse, Toulouse, France
| | | | - David Spigel
- Sarah Cannon Research Institute, Nashville, TN, USA
| | - Thomas Wu
- Genentech, South San Francisco, CA, USA
| | | | - Johannes Schöneberg
- Department of Pharmacology, UCSD, San Diego, CA, USA
- Department of Chemistry & Biochemistry, UCSD, San Diego, CA, USA
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5
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Heidersbach AJ, Dorighi KM, Gomez JA, Jacobi AM, Haley B. A versatile, high-efficiency platform for CRISPR-based gene activation. Nat Commun 2023; 14:902. [PMID: 36804928 PMCID: PMC9938141 DOI: 10.1038/s41467-023-36452-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
CRISPR-mediated transcriptional activation (CRISPRa) is a powerful technology for inducing gene expression from endogenous loci with exciting applications in high throughput gain-of-function genomic screens and the engineering of cell-based models. However, current strategies for generating potent, stable, CRISPRa-competent cell lines present limitations for the broad utility of this approach. Here, we provide a high-efficiency, self-selecting CRISPRa enrichment strategy, which combined with piggyBac transposon technology enables rapid production of CRISPRa-ready cell populations compatible with a variety of downstream assays. We complement this with an optimized guide RNA scaffold that significantly enhances CRISPRa functionality. Finally, we describe a synthetic guide RNA tool set that enables transient, population-wide gene activation when used with the self-selecting CRISPRa system. Taken together, this versatile platform greatly enhances the potential for CRISPRa across a wide variety of cellular contexts.
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Affiliation(s)
- Amy J Heidersbach
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA.
| | - Kristel M Dorighi
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | | | | | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA.
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6
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Calses PC, Pham VC, Guarnaccia AD, Choi M, Verschueren E, Bakker ST, Pham TH, Hinkle T, Liu C, Chang MT, Kljavin N, Bakalarski C, Haley B, Zou J, Yan C, Song X, Lin X, Rowntree R, Ashworth A, Dey A, Lill JR. TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage. Mol Cell Proteomics 2023; 22:100496. [PMID: 36640924 PMCID: PMC9947421 DOI: 10.1016/j.mcpro.2023.100496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Transcriptional enhanced associate domain family members 1 to 4 (TEADs) are a family of four transcription factors and the major transcriptional effectors of the Hippo pathway. In order to activate transcription, TEADs rely on interactions with other proteins, such as the transcriptional effectors Yes-associated protein and transcriptional co-activator with PDZ-binding motif. Nuclear protein interactions involving TEADs influence the transcriptional regulation of genes involved in cell growth, tissue homeostasis, and tumorigenesis. Clearly, protein interactions for TEADs are functionally important, but the full repertoire of TEAD interaction partners remains unknown. Here, we employed an affinity purification mass spectrometry approach to identify nuclear interacting partners of TEADs. We performed affinity purification mass spectrometry experiment in parallel in two different cell types and compared a wildtype TEAD bait protein to a nuclear localization sequence mutant that does not localize to the nucleus. We quantified the results using SAINT analysis and found a significant enrichment of proteins linked to DNA damage including X-ray repair cross-complementing protein 5 (XRCC5), X-ray repair cross-complementing protein 6 (XRCC6), poly(ADP-ribose) polymerase 1 (PARP1), and Rap1-interacting factor 1 (RIF1). In cellular assays, we found that TEADs co-localize with DNA damage-induced nuclear foci marked by histone H2AX phosphorylated on S139 (γH2AX) and Rap1-interacting factor 1. We also found that depletion of TEAD proteins makes cells more susceptible to DNA damage by various agents and that depletion of TEADs promotes genomic instability. Additionally, depleting TEADs dampens the efficiency of DNA double-stranded break repair in reporter assays. Our results connect TEADs to DNA damage response processes, positioning DNA damage as an important avenue for further research of TEAD proteins.
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Affiliation(s)
- Philamer C Calses
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA; Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Victoria C Pham
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Alissa D Guarnaccia
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA; Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Meena Choi
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Erik Verschueren
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Sietske T Bakker
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Trang H Pham
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA
| | - Trent Hinkle
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Chad Liu
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA
| | - Matthew T Chang
- Department of Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Noelyn Kljavin
- Department of Molecular Oncology, Genentech Inc, South San Francisco, California, USA
| | - Corey Bakalarski
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Benjamin Haley
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA
| | - Jianing Zou
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Cuicui Yan
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Xia Song
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Xiaoyan Lin
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Rebecca Rowntree
- Department of Molecular Oncology, Genentech Inc, South San Francisco, California, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Anwesha Dey
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA.
| | - Jennie R Lill
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA.
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7
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Freund EC, Haag SM, Haley B, Murthy A. Optimized Nonviral Gene Disruption in Primary Murine and Human Myeloid Cells. Methods Mol Biol 2023; 2618:201-217. [PMID: 36905519 DOI: 10.1007/978-1-0716-2938-3_15] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Genetically engineered myeloid cells such as monocytes, macrophages, and dendritic cells have broad applications in basic and translational research. Their central roles in innate and adaptive immunity make them attractive as putative therapeutic cell products. However, efficient gene editing of primary myeloid cells presents unique challenges owing to their sensitivity to foreign nucleic acids and poor editing efficiencies using current methodologies (Hornung et al., Science 314:994-997, 2006; Coch et al., PLoS One 8:e71057, 2013; Bartok and Hartmann, Immunity 53:54-77, 2020; Hartmann, Adv Immunol 133:121-169, 2017; Bobadilla et al., Gene Ther 20:514-520, 2013; Schlee and Hartmann, Nat Rev Immunol 16:566-580, 2016; Leyva et al., BMC Biotechnol 11:13, 2011). This chapter describes nonviral CRISPR-mediated gene knockout in primary human and murine monocytes as well as monocyte-derived or bone marrow-derived macrophages and dendritic cells. Electroporation-mediated delivery of recombinant Cas9 complexed with synthetic guide RNAs can be applied for population-level disruption of single or multiple gene targets.
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Affiliation(s)
- Emily C Freund
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA.
| | - Simone M Haag
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Aditya Murthy
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA. .,Gilead Sciences, Foster City, CA, USA.
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8
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Chen H, Durinck S, Patel H, Foreman O, Mesh K, Eastham J, Caothien R, Newman RJ, Roose-Girma M, Darmanis S, Warming S, Lattanzi A, Liang Y, Haley B. Population-wide gene disruption in the murine lung epithelium via AAV-mediated delivery of CRISPR-Cas9 components. Molecular Therapy - Methods & Clinical Development 2022; 27:431-449. [DOI: 10.1016/j.omtm.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
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9
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Haley B, Zander A, Popović J, Paunesku T, Woloschak GE. Findings from international archived data: Fractionation reduces mortality risk of ionizing radiation for total doses below 4 Gray in rodents. Mutat Res Genet Toxicol Environ Mutagen 2022; 882:503537. [PMID: 36155139 DOI: 10.1016/j.mrgentox.2022.503537] [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] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Ionizing radiation is omnipresent and unavoidable on Earth; nevertheless, the range of doses and modes of radiation delivery that represent health risks remain controversial. Radiation protection policy for civilians in US is set at 1 mSv per year. Average persons from contemporary populations are exposed to several hundred milliSieverts (mSv) over their lifetimes from both natural and human made sources such as radon, cosmic rays, CT-scans (20-50 mSv partial body exposure per scan), etc. Health risks associated with these and larger exposures are focus of many epidemiological studies, but uncertainties of these estimates coupled with individual and environmental variation make it is prudent to attempt to use animal models and tightly controlled experimental conditions to supplement our evaluation of radiation risk question. Data on 11,528 of rodents of both genders exposed to x-ray or gamma-ray radiation in facilities in US and Europe were used for this analysis; animal mortality data argue that fractionated radiation exposures have about 2 fold less risk per Gray than acute radiation exposures in the range of doses between 0.25 and 4 Gy.
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Affiliation(s)
- Benjamin Haley
- Feinberg School of Medicine, Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA; ClassDojo, 735 Tehama Street, San Francisco CA 94103, USA
| | - Alia Zander
- Feinberg School of Medicine, Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA; Chicago-Tempus Headquarters and Lab, 600 West Chicago Avenue, Suite 510, Chicago, IL 60654, USA
| | - Jelena Popović
- Feinberg School of Medicine, Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA
| | - Tatjana Paunesku
- Feinberg School of Medicine, Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA
| | - Gayle E Woloschak
- Feinberg School of Medicine, Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA.
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10
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Senger K, Akhmetzyanova I, Haley B, Rutz S, Oh SA. Plasmid-Based Donor Templates for Nonviral CRISPR/Cas9-Mediated Gene Knock-In in Human T Cells. Curr Protoc 2022; 2:e538. [PMID: 36130036 DOI: 10.1002/cpz1.538] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Effective and precise gene editing of T lymphocytes is critical for advancing the understanding of T cell biology and the development of next-generation cellular therapies. Although methods for effective CRISPR/Cas9-mediated gene knock-out in primary human T cells have been developed, complementary techniques for nonviral gene knock-in can be cumbersome and inefficient. Here, we report a simple and efficient method for nonviral CRISPR/Cas9-based gene knock-in utilizing plasmid-based donor DNA templates. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Purification of human CD4+ or CD8+ T cells from blood Basic Protocol 2: Activation of purified CD4+ or CD8+ T cells using TransAct CD3/CD28 agonist-conjugated nanomatrix Basic Protocol 3: Preparation of Cas9/sgRNA RNPs Basic Protocol 4: Transfection of CAS9-RNP and knock-in template into human T cells Support Protocol 1: Purity check following magnetic T cell isolation Support Protocol 2: Dextramer staining of TCR-edited T cells Support Protocol 3: Functional characterization of TCR knock-in T cells Support Protocol 4: Detection of knock-in reporter activity in CRISPR/CAS9-edited T cells.
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Affiliation(s)
- Kate Senger
- Molecular Biology, Genentech, South San Francisco, California
| | | | - Benjamin Haley
- Molecular Biology, Genentech, South San Francisco, California
| | - Sascha Rutz
- Cancer Immunology, Genentech, South San Francisco, California
| | - Soyoung A Oh
- Cancer Immunology, Genentech, South San Francisco, California
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11
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Deng Y, Diepstraten ST, Potts MA, Giner G, Trezise S, Ng AP, Healey G, Kane SR, Cooray A, Behrens K, Heidersbach A, Kueh AJ, Pal M, Wilcox S, Tai L, Alexander WS, Visvader JE, Nutt SL, Strasser A, Haley B, Zhao Q, Kelly GL, Herold MJ. Author Correction: Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance. Nat Commun 2022; 13:5007. [PMID: 36008403 PMCID: PMC9411186 DOI: 10.1038/s41467-022-32817-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yexuan Deng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Margaret A Potts
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Göknur Giner
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephanie Trezise
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ashley P Ng
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Gerry Healey
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Serena R Kane
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Amali Cooray
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kira Behrens
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Amy Heidersbach
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Martin Pal
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jane E Visvader
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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12
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Pribluda A, Daemen A, Lima AN, Wang X, Hafner M, Poon C, Modrusan Z, Katakam AK, Foreman O, Eastham J, Hung J, Haley B, Garcia JT, Jackson EL, Junttila MR. EHMT2 methyltransferase governs cell identity in the lung and is required for KRAS G12D tumor development and propagation. eLife 2022; 11:57648. [PMID: 35983994 PMCID: PMC9439681 DOI: 10.7554/elife.57648] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Lung development, integrity and repair rely on precise Wnt signaling, which is corrupted in diverse diseases, including cancer. Here, we discover that EHMT2 methyltransferase regulates Wnt signaling in the lung by controlling the transcriptional activity of chromatin-bound β-catenin, through a non-histone substrate in mouse lung. Inhibition of EHMT2 induces transcriptional, morphologic, and molecular changes consistent with alveolar type 2 (AT2) lineage commitment. Mechanistically, EHMT2 activity functions to support regenerative properties of KrasG12D tumors and normal AT2 cells—the predominant cell of origin of this cancer. Consequently, EHMT2 inhibition prevents KrasG12D lung adenocarcinoma (LUAD) tumor formation and propagation and disrupts normal AT2 cell differentiation. Consistent with these findings, low gene EHMT2 expression in human LUAD correlates with enhanced AT2 gene expression and improved prognosis. These data reveal EHMT2 as a critical regulator of Wnt signaling, implicating Ehmt2 as a potential target in lung cancer and other AT2-mediated lung pathologies.
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Affiliation(s)
- Ariel Pribluda
- Discovery Biology, Surrozen, South San Francisco, United States
| | - Anneleen Daemen
- Computational biology, Oric Pharma, South San Francisco, United States
| | - Anthony Nelson Lima
- Department of Translational Oncology, Genentech, Inc, South San Francisco, United States
| | - Xi Wang
- Department of Translational Oncology, Genentech, Inc, South San Francisco, United States
| | - Marc Hafner
- Department of Bioinformatics and Computational Biology, Genentech, Inc, South San Francisco, United States
| | - Chungkee Poon
- Department of Immunology, Genentech, Inc, South San Francisco, United States
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, Inc, South San Francisco, United States
| | | | - Oded Foreman
- Department of Pathology, Genentech, Inc, South San Francisco, United States
| | - Jefferey Eastham
- Department of Pathology, Genentech, Inc, South San Francisco, United States
| | - Jefferey Hung
- Department of Pathology, Genentech, Inc, South San Francisco, United States
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc, South San Francisco, United States
| | - Julia T Garcia
- Department of Genetics, Stanford University, Stanford, United States
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13
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Deng Y, Diepstraten ST, Potts MA, Giner G, Trezise S, Ng AP, Healey G, Kane SR, Cooray A, Behrens K, Heidersbach A, Kueh AJ, Pal M, Wilcox S, Tai L, Alexander WS, Visvader JE, Nutt SL, Strasser A, Haley B, Zhao Q, Kelly GL, Herold MJ. Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance. Nat Commun 2022; 13:4739. [PMID: 35961968 PMCID: PMC9374748 DOI: 10.1038/s41467-022-32485-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Received: 08/29/2021] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
CRISPR technologies have advanced cancer modelling in mice, but CRISPR activation (CRISPRa) methods have not been exploited in this context. We establish a CRISPRa mouse (dCas9a-SAMKI) for inducing gene expression in vivo and in vitro. Using dCas9a-SAMKI primary lymphocytes, we induce B cell restricted genes in T cells and vice versa, demonstrating the power of this system. There are limited models of aggressive double hit lymphoma. Therefore, we transactivate pro-survival BCL-2 in Eµ-MycT/+;dCas9a-SAMKI/+ haematopoietic stem and progenitor cells. Mice transplanted with these cells rapidly develop lymphomas expressing high BCL-2 and MYC. Unlike standard Eµ-Myc lymphomas, BCL-2 expressing lymphomas are highly sensitive to the BCL-2 inhibitor venetoclax. We perform genome-wide activation screens in these lymphoma cells and find a dominant role for the BCL-2 protein A1 in venetoclax resistance. Here we show the potential of our CRISPRa model for mimicking disease and providing insights into resistance mechanisms towards targeted therapies. Modelling of aggressive lymphomas, such as double hit lymphoma, has been challenging. Here the authors engineer a CRISPR activation mouse to enable the generation of these aggressive lymphomas and identify the pro-survival BCL-2 protein A1 as a venetoclax resistance factor.
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Affiliation(s)
- Yexuan Deng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Margaret A Potts
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Göknur Giner
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephanie Trezise
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ashley P Ng
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Gerry Healey
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Serena R Kane
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Amali Cooray
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kira Behrens
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Amy Heidersbach
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Martin Pal
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jane E Visvader
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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14
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Oh SA, Senger K, Madireddi S, Akhmetzyanova I, Ishizuka IE, Tarighat S, Lo JH, Shaw D, Haley B, Rutz S. High-efficiency nonviral CRISPR/Cas9-mediated gene editing of human T cells using plasmid donor DNA. J Exp Med 2022; 219:213176. [PMID: 35452075 PMCID: PMC9040063 DOI: 10.1084/jem.20211530] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Received: 07/18/2021] [Revised: 02/10/2022] [Accepted: 03/23/2022] [Indexed: 12/26/2022] Open
Abstract
Genome engineering of T lymphocytes, the main effectors of antitumor adaptive immune responses, has the potential to uncover unique insights into their functions and enable the development of next-generation adoptive T cell therapies. Viral gene delivery into T cells, which is currently used to generate CAR T cells, has limitations in regard to targeting precision, cargo flexibility, and reagent production. Nonviral methods for effective CRISPR/Cas9-mediated gene knock-out in primary human T cells have been developed, but complementary techniques for nonviral gene knock-in can be cumbersome and inefficient. Here, we report a convenient and scalable nonviral method that allows precise gene edits and transgene integration in primary human T cells, using plasmid donor DNA template and Cas9-RNP. This method is highly efficient for single and multiplex gene manipulation, without compromising T cell function, and is thus valuable for use in basic and translational research.
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Affiliation(s)
- Soyoung A Oh
- Cancer Immunology, Genentech, South San Francisco, CA
| | - Kate Senger
- Molecular Biology, Genentech, South San Francisco, CA
| | | | | | | | - Somayeh Tarighat
- Cell Therapy Engineering and Development, Genentech, South San Francisco, CA
| | - Jerry H Lo
- Oncology Bioinformatics, Genentech, South San Francisco, CA
| | - David Shaw
- Cell Therapy Engineering and Development, Genentech, South San Francisco, CA
| | | | - Sascha Rutz
- Cancer Immunology, Genentech, South San Francisco, CA
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15
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Tahtinen S, Tong AJ, Himmels P, Oh J, Paler-Martinez A, Kim L, Wichner S, Oei Y, McCarron MJ, Freund EC, Amir ZA, de la Cruz CC, Haley B, Blanchette C, Schartner JM, Ye W, Yadav M, Sahin U, Delamarre L, Mellman I. IL-1 and IL-1ra are key regulators of the inflammatory response to RNA vaccines. Nat Immunol 2022; 23:532-542. [PMID: 35332327 DOI: 10.1038/s41590-022-01160-y] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/15/2022] [Indexed: 02/07/2023]
Abstract
The use of lipid-formulated RNA vaccines for cancer or COVID-19 is associated with dose-limiting systemic inflammatory responses in humans that were not predicted from preclinical studies. Here, we show that the 'interleukin 1 (IL-1)-interleukin 1 receptor antagonist (IL-1ra)' axis regulates vaccine-mediated systemic inflammation in a host-specific manner. In human immune cells, RNA vaccines induce production of IL-1 cytokines, predominantly IL-1β, which is dependent on both the RNA and lipid formulation. IL-1 in turn triggers the induction of the broad spectrum of pro-inflammatory cytokines (including IL-6). Unlike humans, murine leukocytes respond to RNA vaccines by upregulating anti-inflammatory IL-1ra relative to IL-1 (predominantly IL-1α), protecting mice from cytokine-mediated toxicities at >1,000-fold higher vaccine doses. Thus, the IL-1 pathway plays a key role in triggering RNA vaccine-associated innate signaling, an effect that was unexpectedly amplified by certain lipids used in vaccine formulations incorporating N1-methyl-pseudouridine-modified RNA to reduce activation of Toll-like receptor signaling.
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Affiliation(s)
| | | | | | - Jaehak Oh
- Genentech, South San Francisco, CA, USA
| | | | | | | | - Yoko Oei
- Genentech, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Weilan Ye
- Genentech, South San Francisco, CA, USA
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16
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Venkatanarayan A, Liang J, Yen I, Shanahan F, Haley B, Phu L, Verschueren E, Hinkle TB, Kan D, Segal E, Long JE, Lima T, Liau NPD, Sudhamsu J, Li J, Klijn C, Piskol R, Junttila MR, Shaw AS, Merchant M, Chang MT, Kirkpatrick DS, Malek S. CRAF dimerization with ARAF regulates KRAS-driven tumor growth. Cell Rep 2022; 38:110351. [PMID: 35139374 DOI: 10.1016/j.celrep.2022.110351] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 12/08/2020] [Revised: 09/21/2021] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
KRAS, which is mutated in ∼30% of all cancers, activates the RAF-MEK-ERK signaling cascade. CRAF is required for growth of KRAS mutant lung tumors, but the requirement for CRAF kinase activity is unknown. Here, we show that subsets of KRAS mutant tumors are dependent on CRAF for growth. Kinase-dead but not dimer-defective CRAF rescues growth inhibition, suggesting that dimerization but not kinase activity is required. Quantitative proteomics demonstrates increased levels of CRAF:ARAF dimers in KRAS mutant cells, and depletion of both CRAF and ARAF rescues the CRAF-loss phenotype. Mechanistically, CRAF depletion causes sustained ERK activation and induction of cell-cycle arrest, while treatment with low-dose MEK or ERK inhibitor rescues the CRAF-loss phenotype. Our studies highlight the role of CRAF in regulating MAPK signal intensity to promote tumorigenesis downstream of mutant KRAS and suggest that disrupting CRAF dimerization or degrading CRAF may have therapeutic benefit.
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Affiliation(s)
| | - Jason Liang
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA; Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivana Yen
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lilian Phu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erik Verschueren
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Trent B Hinkle
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - David Kan
- Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ehud Segal
- Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason E Long
- Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tony Lima
- Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nicholas P D Liau
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason Li
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christiaan Klijn
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert Piskol
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Melissa R Junttila
- Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Andrey S Shaw
- Department of Research Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mark Merchant
- Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Matthew T Chang
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Shiva Malek
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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17
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Chang MT, Shanahan F, Nguyen TTT, Staben ST, Gazzard L, Yamazoe S, Wertz IE, Piskol R, Yang YA, Modrusan Z, Haley B, Evangelista M, Malek S, Foster SA, Ye X. Identifying transcriptional programs underlying cancer drug response with TraCe-seq. Nat Biotechnol 2022; 40:86-93. [PMID: 34531539 DOI: 10.1038/s41587-021-01005-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Genetic and non-genetic heterogeneity within cancer cell populations represent major challenges to anticancer therapies. We currently lack robust methods to determine how preexisting and adaptive features affect cellular responses to therapies. Here, by conducting clonal fitness mapping and transcriptional characterization using expressed barcodes and single-cell RNA sequencing (scRNA-seq), we have developed tracking differential clonal response by scRNA-seq (TraCe-seq). TraCe-seq is a method that captures at clonal resolution the origin, fate and differential early adaptive transcriptional programs of cells in a complex population in response to distinct treatments. We used TraCe-seq to benchmark how next-generation dual epidermal growth factor receptor (EGFR) inhibitor-degraders compare to standard EGFR kinase inhibitors in EGFR-mutant lung cancer cells. We identified a loss of antigrowth activity associated with targeted degradation of EGFR protein and an essential role of the endoplasmic reticulum (ER) protein processing pathway in anti-EGFR therapeutic efficacy. Our results suggest that targeted degradation is not always superior to enzymatic inhibition and establish TraCe-seq as an approach to study how preexisting transcriptional programs affect treatment responses.
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Affiliation(s)
- Matthew T Chang
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Thi Thu Thao Nguyen
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Staben
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Lewis Gazzard
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Sayumi Yamazoe
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Discovery Biotherapeutics, Bristol-Myers Squibb, Redwood City, CA, USA
| | - Ingrid E Wertz
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Robert Piskol
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Yeqing Angela Yang
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Marie Evangelista
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Shiva Malek
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Scott A Foster
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.
| | - Xin Ye
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.
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18
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Luchetti G, Roncaioli JL, Chavez RA, Schubert AF, Kofoed EM, Reja R, Cheung TK, Liang Y, Webster JD, Lehoux I, Skippington E, Reeder J, Haley B, Tan MW, Rose CM, Newton K, Kayagaki N, Vance RE, Dixit VM. Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection. Cell Host Microbe 2021; 29:1521-1530.e10. [PMID: 34492225 DOI: 10.1016/j.chom.2021.08.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [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: 03/22/2021] [Revised: 06/08/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
The pore-forming protein gasdermin D (GSDMD) executes lytic cell death called pyroptosis to eliminate the replicative niche of intracellular pathogens. Evolution favors pathogens that circumvent this host defense mechanism. Here, we show that the Shigella ubiquitin ligase IpaH7.8 functions as an inhibitor of GSDMD. Shigella is an enteroinvasive bacterium that causes hemorrhagic gastroenteritis in primates, but not rodents. IpaH7.8 contributes to species specificity by ubiquitinating human, but not mouse, GSDMD and targeting it for proteasomal degradation. Accordingly, infection of human epithelial cells with IpaH7.8-deficient Shigella flexneri results in increased GSDMD-dependent cell death compared with wild type. Consistent with pyroptosis contributing to murine disease resistance, eliminating GSDMD from NLRC4-deficient mice, which are already sensitized to oral infection with Shigella flexneri, leads to further enhanced bacterial replication and increased disease severity. This work highlights a species-specific pathogen arms race focused on maintenance of host cell viability.
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Affiliation(s)
- Giovanni Luchetti
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Justin L Roncaioli
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA
| | - Roberto A Chavez
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA
| | - Alexander F Schubert
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eric M Kofoed
- Department of Immunology and Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Oncology Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tommy K Cheung
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isabelle Lehoux
- Department of Biomolecular Resources, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Elizabeth Skippington
- Department of OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janina Reeder
- Department of OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Man Wah Tan
- Department of Immunology and Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nobuhiko Kayagaki
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Russell E Vance
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley CA 94720, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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19
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Herzner AM, Khan Z, Van Nostrand EL, Chan S, Cuellar T, Chen R, Pechuan-Jorge X, Komuves L, Solon M, Modrusan Z, Haley B, Yeo GW, Behrens TW, Albert ML. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses. J Exp Med 2021; 218:212507. [PMID: 34297039 PMCID: PMC8313407 DOI: 10.1084/jem.20201833] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Received: 08/24/2020] [Revised: 09/11/2020] [Accepted: 06/24/2021] [Indexed: 01/26/2023] Open
Abstract
Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA checkpoints, we conducted a candidate screen in THP-1 monocytes and found that hnRNPC and ADAR deficiency resulted in synergistic induction of MDA5-dependent IFN responses. RNA-seq analysis demonstrated dysregulation of Alu-containing introns in hnRNPC-deficient cells via utilization of unmasked cryptic splice sites, including introns containing ADAR-dependent A-to-I editing clusters. These putative MDA5 ligands showed reduced editing in the absence of ADAR, providing a plausible mechanism for the combined effects of hnRNPC and ADAR. This study contributes to our understanding of the control of repetitive element-induced autoinflammation and suggests that patients with hnRNPC-mutated tumors might maximally benefit from ADAR inhibition-based immunotherapy.
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Affiliation(s)
| | - Zia Khan
- Department of Human Genetics, Genentech, South San Francisco, CA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Stem Cell Program and the Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | - Sara Chan
- Department of Pathology, Genentech, South San Francisco, CA
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Ronald Chen
- Department of Human Genetics, Genentech, South San Francisco, CA
| | | | - Laszlo Komuves
- Department of Pathology, Genentech, South San Francisco, CA
| | - Margaret Solon
- Department of Pathology, Genentech, South San Francisco, CA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics & Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and the Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | | | - Matthew L Albert
- Department of Cancer Immunology, Genentech, South San Francisco, CA
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20
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Boni V, Dooms C, Haley B, Viteri S, Mahipal A, Suga J, Eli L, Lalani A, Bryce R, Xu F, Shah N, Kabbinavar F, Goldman J. OA04.06 Neratinib in Pretreated EGFR Exon 18-Mutant Non-Small Cell Lung Cancer (NSCLC): Initial Findings From the SUMMIT Basket Trial. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Capietto AH, Jhunjhunwala S, Pollock SB, Lupardus P, Wong J, Hänsch L, Cevallos J, Chestnut Y, Fernandez A, Lounsbury N, Nozawa T, Singh M, Fan Z, de la Cruz CC, Phung QT, Taraborrelli L, Haley B, Lill JR, Mellman I, Bourgon R, Delamarre L. Mutation position is an important determinant for predicting cancer neoantigens. J Exp Med 2020; 217:133605. [PMID: 31940002 PMCID: PMC7144530 DOI: 10.1084/jem.20190179] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [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] [Received: 01/28/2019] [Revised: 09/28/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Tumor-specific mutations can generate neoantigens that drive CD8 T cell responses against cancer. Next-generation sequencing and computational methods have been successfully applied to identify mutations and predict neoantigens. However, only a small fraction of predicted neoantigens are immunogenic. Currently, predicted peptide binding affinity for MHC-I is often the major criterion for prioritizing neoantigens, although little progress has been made toward understanding the precise functional relationship between affinity and immunogenicity. We therefore systematically assessed the immunogenicity of peptides containing single amino acid mutations in mouse tumor models and divided them into two classes of immunogenic mutations. The first comprises mutations at a nonanchor residue, for which we find that the predicted absolute binding affinity is predictive of immunogenicity. The second involves mutations at an anchor residue; here, predicted relative affinity (compared with the WT counterpart) is a better predictor. Incorporating these features into an immunogenicity model significantly improves neoantigen ranking. Importantly, these properties of neoantigens are also predictive in human datasets, suggesting that they can be used to prioritize neoantigens for individualized neoantigen-specific immunotherapies.
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Affiliation(s)
| | | | | | | | - Jim Wong
- Genentech, South San Francisco, CA
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22
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Gupta N, Wang X, Wen X, Moran P, Paluch M, Hass PE, Heidersbach A, Haley B, Kirchhofer D, Brezski RJ, Peterson AS, Scales SJ. Domain-Specific Antibodies Reveal Differences in the Membrane Topologies of Apolipoprotein L1 in Serum and Podocytes. J Am Soc Nephrol 2020; 31:2065-2082. [PMID: 32764138 DOI: 10.1681/asn.2019080830] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/22/2019] [Accepted: 05/10/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Circulating APOL1 lyses trypanosomes, protecting against human sleeping sickness. Two common African gene variants of APOL1, G1 and G2, protect against infection by species of trypanosomes that resist wild-type APOL1. At the same time, the protection predisposes humans to CKD, an elegant example of balanced polymorphism. However, the exact mechanism of APOL1-mediated podocyte damage is not clear, including APOL1's subcellular localization, topology, and whether the damage is related to trypanolysis. METHODS APOL1 topology in serum (HDL particles) and in kidney podocytes was mapped with flow cytometry, immunoprecipitation, and trypanolysis assays that tracked 170 APOL1 domain-specific monoclonal antibodies. APOL1 knockout podocytes confirmed antibody specificity. RESULTS APOL1 localizes to the surface of podocytes, with most of the pore-forming domain (PFD) and C terminus of the Serum Resistance Associated-interacting domain (SRA-ID), but not the membrane-addressing domain (MAD), being exposed. In contrast, differential trypanolytic blocking activity reveals that the MAD is exposed in serum APOL1, with less of the PFD accessible. Low pH did not detectably alter the gross topology of APOL1, as determined by antibody accessibility, in serum or on podocytes. CONCLUSIONS Our antibodies highlighted different conformations of native APOL1 topology in serum (HDL particles) and at the podocyte surface. Our findings support the surface ion channel model for APOL1 risk variant-mediated podocyte injury, as well as providing domain accessibility information for designing APOL1-targeted therapeutics.
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Affiliation(s)
- Nidhi Gupta
- Department of Molecular Biology, Genentech, South San Francisco, California.,Department of Immunology, Genentech, South San Francisco, California
| | - Xinhua Wang
- Department of Antibody Engineering, Genentech, South San Francisco, California
| | - Xiaohui Wen
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Paul Moran
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Maciej Paluch
- Department of Protein Chemistry, Genentech, South San Francisco, California
| | - Philip E Hass
- Department of Protein Chemistry, Genentech, South San Francisco, California
| | - Amy Heidersbach
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Randall J Brezski
- Department of Antibody Engineering, Genentech, South San Francisco, California
| | - Andrew S Peterson
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Suzie J Scales
- Department of Molecular Biology, Genentech, South San Francisco, California .,Department of Immunology, Genentech, South San Francisco, California
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23
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Calses PC, Pham V, Verschueren E, Kljavin N, Chang M, Seidel K, Haley B, Pham T, Noland C, Hinkle T, Hagenbeek T, Lill J, Dey A. Abstract A18: Location, location, location: Avenues to regulating Hippo. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.hippo19-a18] [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
The TEAD family of the transcription factors (TEAD1-4) are the major transcription factors for YAP/TAZ transcription activators in the Hippo pathway. TEADs regulate many biologic processes, including development, tissue homeostasis, and tumorigenesis by regulating target genes involved in cellular proliferation and survival. Amplification or upregulation of YAP/TAZ/TEAD correlates with poor prognosis in cancer patients. The mechanisms of TEADs regulation and localization remain largely unknown. TEADs contain a highly conserved nuclear localization signal (NLS) embedded in the DNA binding domain (DBD). Overexpression of an NLS mutant TEAD in a Hippo-dependent cancer cell line is dominant negative and suppresses cellular proliferation and tumor growth. These results suggest that TEAD nuclear expression is regulated by a highly conserved NLS that may be important in the development of cancer. In light of these results, we have identified physiologic conditions where TEADs are expressed in the cytoplasm and the nucleus. By performing comparative immunoprecipitation-mass spectrometry between WT and NLS mutant TEAD, we found novel interacting partners for cytoplasmic and nuclear TEAD, thus uncovering novel roles for TEADs in cancer.
Citation Format: Philamer C. Calses, Victoria Pham, Erik Verschueren, Noelyn Kljavin, Matt Chang, Kerstin Seidel, Benjamin Haley, Trang Pham, Cameron Noland, Trent Hinkle, Thijs Hagenbeek, Jennie Lill, Anwesha Dey. Location, location, location: Avenues to regulating Hippo [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr A18.
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24
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Abstract
Functional genomics describes a field of biology that uses a range of approaches for assessing gene function with high-throughput molecular, genetic, and cellular technologies. The near limitless potential for applying these concepts to study the activities of all genetic loci has completely upended how today's cancer biologists tackle drug target discovery. We provide an overview of contemporary functional genomics platforms, highlighting areas of distinction and complementarity across technologies, so as to aid in the development or interpretation of cancer-focused screening efforts.
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Affiliation(s)
- Benjamin Haley
- Molecular Biology Department, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Filip Roudnicky
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland.
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25
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Freund EC, Lock JY, Oh J, Maculins T, Delamarre L, Bohlen CJ, Haley B, Murthy A. Efficient gene knockout in primary human and murine myeloid cells by non-viral delivery of CRISPR-Cas9. J Exp Med 2020; 217:e20191692. [PMID: 32357367 PMCID: PMC7336301 DOI: 10.1084/jem.20191692] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 09/17/2019] [Revised: 02/17/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Myeloid cells play critical and diverse roles in mammalian physiology, including tissue development and repair, innate defense against pathogens, and generation of adaptive immunity. As cells that show prolonged recruitment to sites of injury or pathology, myeloid cells represent therapeutic targets for a broad range of diseases. However, few approaches have been developed for gene editing of these cell types, likely owing to their sensitivity to foreign genetic material or virus-based manipulation. Here we describe optimized strategies for gene disruption in primary myeloid cells of human and murine origin. Using nucleofection-based delivery of Cas9-ribonuclear proteins (RNPs), we achieved near population-level genetic knockout of single and multiple targets in a range of cell types without selection or enrichment. Importantly, we show that cellular fitness and response to immunological stimuli is not significantly impacted by the gene editing process. This provides a significant advance in the study of myeloid cell biology, thus enabling pathway discovery and drug target validation across species in the field of innate immunity.
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Affiliation(s)
- Emily C. Freund
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Jaclyn Y. Lock
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Jaehak Oh
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Timurs Maculins
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Lelia Delamarre
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | | | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Aditya Murthy
- Department of Cancer Immunology, Genentech, South San Francisco, CA
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26
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Tang D, Sandoval W, Lam C, Haley B, Liu P, Xue D, Roy D, Patapoff T, Louie S, Snedecor B, Misaghi S. UBR E3 ligases and the PDIA3 protease control degradation of unfolded antibody heavy chain by ERAD. J Cell Biol 2020; 219:151862. [PMID: 32558906 PMCID: PMC7337499 DOI: 10.1083/jcb.201908087] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/01/2022] Open
Abstract
Accumulation of unfolded antibody chains in the ER triggers ER stress that may lead to reduced productivity in therapeutic antibody manufacturing processes. We identified UBR4 and UBR5 as ubiquitin E3 ligases involved in HC ER-associated degradation. Knockdown of UBR4 and UBR5 resulted in intracellular accumulation, enhanced secretion, and reduced ubiquitination of HC. In concert with these E3 ligases, PDIA3 was shown to cleave ubiquitinated HC molecules to accelerate HC dislocation. Interestingly, UBR5, and to a lesser degree UBR4, were down-regulated as cellular demand for antibody expression increased in CHO cells during the production phase, or in plasma B cells. Reducing UBR4/UBR5 expression before the production phase increased antibody productivity in CHO cells, possibly by redirecting antibody molecules from degradation to secretion. Altogether we have characterized a novel proteolysis/proteasome-dependent pathway involved in degradation of unfolded antibody HC. Proteins characterized in this pathway may be novel targets for CHO cell engineering.
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Affiliation(s)
- Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA
| | - Peter Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Di Xue
- Department of Research Biology, Genentech Inc., South San Francisco, CA
| | - Deepankar Roy
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Tom Patapoff
- Department of Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA
| | - Salina Louie
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
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27
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Louie S, Lakkyreddy J, Castellano BM, Haley B, Nguyen Dang A, Lam C, Tang D, Lang S, Snedecor B, Misaghi S. Insulin degrading enzyme (IDE) expressed by Chinese hamster ovary (CHO) cells is responsible for degradation of insulin in culture media. J Biotechnol 2020; 320:44-49. [PMID: 32526262 DOI: 10.1016/j.jbiotec.2020.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/10/2019] [Revised: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 12/01/2022]
Abstract
Chinese hamster ovary (CHO) cells cultured in serum-free chemically-defined media (CDM) are used for manufacturing of therapeutic proteins. Growth factors, such as insulin are commonly utilized in manufacturing platforms to enhance CHO cell viability and growth. Here we report that insulin is degraded in the culture media over time mainly due to the activity of the insulin degrading enzyme (IDE). Insulin degradation was faster in cell lines that released more IDE, which negatively impacted cell growth and in turn, production titers. Deletion of the IDE gene in a representative CHO cell line nearly abolished insulin degradation in seed train and end-of-production media. In summary, our data suggests that selecting cell lines that have lower IDE expression or targeted-deletion of the IDE gene can improve culture viability and growth for insulin-dependent CHO production platforms.
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Affiliation(s)
- Salina Louie
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Jayanthi Lakkyreddy
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Brian M Castellano
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Benjamin Haley
- Molecular Biology Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Anh Nguyen Dang
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Danming Tang
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Steven Lang
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations (CCBO) Department, Genentech, Inc. 1 DNA Way, South San Francisco, CA, 94080, United States.
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28
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Louie S, Heidersbach A, Blanco N, Haley B, Rose CM, Liu PS, Yim M, Tang D, Lam C, Sandoval WN, Shaw D, Snedecor B, Misaghi S. Endothelial intercellular cell adhesion molecule 1 contributes to cell aggregate formation in CHO cells cultured in serum‐free media. Biotechnol Prog 2020; 36:e2951. [DOI: 10.1002/btpr.2951] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/14/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Salina Louie
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Amy Heidersbach
- Molecular Biology DepartmentGenentech, Inc. South San Francisco California
| | - Noelia Blanco
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Benjamin Haley
- Molecular Biology DepartmentGenentech, Inc. South San Francisco California
| | - Christopher M. Rose
- Microchemistry Proteomic and Lipidomic (MPL) DepartmentGenentech, Inc. South San Francisco California
| | - Peter S. Liu
- Microchemistry Proteomic and Lipidomic (MPL) DepartmentGenentech, Inc. South San Francisco California
| | - Mandy Yim
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Danming Tang
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Cynthia Lam
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Wendy N. Sandoval
- Microchemistry Proteomic and Lipidomic (MPL) DepartmentGenentech, Inc. South San Francisco California
| | - David Shaw
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Brad Snedecor
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Shahram Misaghi
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
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29
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Yuan W, Goldstein LD, Durinck S, Chen YJ, Nguyen TT, Kljavin NM, Sokol ES, Stawiski EW, Haley B, Ziai J, Modrusan Z, Seshagiri S. S100a4 upregulation in Pik3caH1047R;Trp53R270H;MMTV-Cre-driven mammary tumors promotes metastasis. Breast Cancer Res 2019; 21:152. [PMID: 31881983 PMCID: PMC6935129 DOI: 10.1186/s13058-019-1238-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 02/14/2019] [Accepted: 12/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background PIK3CA mutations are frequent in human breast cancer. Pik3caH1047R mutant expression in mouse mammary gland promotes tumorigenesis. TP53 mutations co-occur with PIK3CA mutations in human breast cancers. We previously generated a conditionally activatable Pik3caH1047R;MMTV-Cre mouse model and found a few malignant sarcomatoid (spindle cell) carcinomas that had acquired spontaneous dominant-negative Trp53 mutations. Methods A Pik3caH1047R;Trp53R270H;MMTV-Cre double mutant mouse breast cancer model was generated. Tumors were characterized by histology, marker analysis, transcriptional profiling, single-cell RNA-seq, and bioinformatics. Cell lines were developed from mutant tumors and used to identify and confirm genes involved in metastasis. Results We found Pik3caH1047R and Trp53R270H cooperate in driving oncogenesis in mammary glands leading to a shorter latency than either alone. Double mutant mice develop multiple histologically distinct mammary tumors, including adenocarcinoma and sarcomatoid (spindle cell) carcinoma. We found some tumors to be invasive and a few metastasized to the lung and/or the lymph node. Single-cell RNA-seq analysis of the tumors identified epithelial, stromal, myeloid, and T cell groups. Expression analysis of the metastatic tumors identified S100a4 as a top candidate gene associated with metastasis. Metastatic tumors contained a much higher percentage of epithelial–mesenchymal transition (EMT)-signature positive and S100a4-expressing cells. CRISPR/CAS9-mediated knockout of S100a4 in a metastatic tumor-derived cell line disrupted its metastatic potential indicating a role for S100a4 in metastasis. Conclusions Pik3caH1047R;Trp53R270H;MMTV-Cre mouse provides a preclinical model to mimic a subtype of human breast cancers that carry both PIK3CA and TP53 mutations. It also allows for understanding the cooperation between the two mutant genes in tumorigenesis. Our model also provides a system to study metastasis and develop therapeutic strategies for PIK3CA/TP53 double-positive cancers. S100a4 found involved in metastasis in this model can be a potential diagnostic and therapeutic target.
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Affiliation(s)
- Wenlin Yuan
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Leonard D Goldstein
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Steffen Durinck
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Thong T Nguyen
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Noelyn M Kljavin
- Department of Cancer Signaling, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ethan S Sokol
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Eric W Stawiski
- Research and Development Department, MedGenome Inc., Foster City, CA, 94404, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - James Ziai
- Department of Pathology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA. .,SciGenom Research Foundation, Bangalore, 560099, India.
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30
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Hartmaier RJ, Trabucco SE, Priedigkeit N, Chung JH, Parachoniak CA, Vanden Borre P, Morley S, Rosenzweig M, Gay LM, Goldberg ME, Suh J, Ali SM, Ross J, Leyland-Jones B, Young B, Williams C, Park B, Tsai M, Haley B, Peguero J, Callahan RD, Sachelarie I, Cho J, Atkinson JM, Bahreini A, Nagle AM, Puhalla SL, Watters RJ, Erdogan-Yildirim Z, Cao L, Oesterreich S, Mathew A, Lucas PC, Davidson NE, Brufsky AM, Frampton GM, Stephens PJ, Chmielecki J, Lee AV. Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer. Ann Oncol 2019; 29:872-880. [PMID: 29360925 PMCID: PMC5913625 DOI: 10.1093/annonc/mdy025] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 12/31/2022] Open
Abstract
Background Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer. Patients and methods To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots. Results We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations. Conclusions Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.
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Affiliation(s)
- R J Hartmaier
- Foundation Medicine Inc., Cambridge; Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA.
| | | | - N Priedigkeit
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | | | | | | | - S Morley
- Foundation Medicine Inc., Cambridge
| | | | - L M Gay
- Foundation Medicine Inc., Cambridge
| | | | - J Suh
- Foundation Medicine Inc., Cambridge
| | - S M Ali
- Foundation Medicine Inc., Cambridge
| | - J Ross
- Foundation Medicine Inc., Cambridge
| | - B Leyland-Jones
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - B Young
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - C Williams
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - B Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore, USA
| | - M Tsai
- Minnesota Oncology, Minneapolis, USA
| | - B Haley
- UT Southwestern Medical Center, Dallas, USA
| | - J Peguero
- Oncology Consultants Research Department, Houston, USA
| | | | | | - J Cho
- New Bern Cancer Care, New Bern, USA
| | - J M Atkinson
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - A Bahreini
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA; Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A M Nagle
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - S L Puhalla
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - R J Watters
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, USA
| | - Z Erdogan-Yildirim
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, USA
| | - L Cao
- Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA; Central South University Xiangya School of Medicine, China
| | - S Oesterreich
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
| | - A Mathew
- Department of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - P C Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, USA
| | - N E Davidson
- Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - A M Brufsky
- Foundation Medicine Inc., Cambridge; Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | | | | | | | - A V Lee
- Department of Pharmacology and Chemical Biolog, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA; Women's Cancer Research Center, Magee-Women's Research Institute, Pittsburgh, USA
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31
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Vartanian S, Lee J, Klijn C, Gnad F, Bagniewska M, Schaefer G, Zhang D, Tan J, Watson SA, Liu L, Chen H, Liang Y, Watanabe C, Cuellar T, Kan D, Hartmaier RJ, Lau T, Costa MR, Martin SE, Merchant M, Haley B, Stokoe D. ERBB3 and IGF1R Signaling Are Required for Nrf2-Dependent Growth in KEAP1-Mutant Lung Cancer. Cancer Res 2019; 79:4828-4839. [PMID: 31416841 DOI: 10.1158/0008-5472.can-18-2086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 11/07/2018] [Accepted: 08/06/2019] [Indexed: 11/16/2022]
Abstract
Mutations in KEAP1 and NFE2L2 (encoding the protein Nrf2) are prevalent in both adeno and squamous subtypes of non-small cell lung cancer, as well as additional tumor indications. The consequence of these mutations is stabilized Nrf2 and chronic induction of a battery of Nrf2 target genes. We show that knockdown of Nrf2 caused modest growth inhibition of cells growing in two-dimension, which was more pronounced in cell lines expressing mutant KEAP1. In contrast, Nrf2 knockdown caused almost complete regression of established KEAP1-mutant tumors in mice, with little effect on wild-type (WT) KEAP1 tumors. The strong dependency on Nrf2 could be recapitulated in certain anchorage-independent growth environments and was not prevented by excess extracellular glutathione. A CRISPR screen was used to investigate the mechanism(s) underlying this dependence. We identified alternative pathways critical for Nrf2-dependent growth in KEAP1-mutant cell lines, including the redox proteins thioredoxin and peroxiredoxin, as well as the growth factor receptors IGF1R and ERBB3. IGF1R inhibition was effective in KEAP1-mutant cells compared with WT, especially under conditions of anchorage-independent growth. These results point to addiction of KEAP1-mutant tumor cells to Nrf2 and suggest that inhibition of Nrf2 or discrete druggable Nrf2 target genes such as IGF1R could be an effective therapeutic strategy for disabling these tumors. SIGNIFICANCE: This study identifies pathways activated by Nrf2 that are important for the proliferation and tumorigenicity of KEAP1-mutant non-small cell lung cancer.
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Affiliation(s)
| | | | | | - Florian Gnad
- Department of Bioinformatics and Computational Biology
| | | | | | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics
| | | | | | - Liling Liu
- Department of Drug Metabolism and Pharmacokinetics
| | - Honglin Chen
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
| | - Yuxin Liang
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
| | | | - Trinna Cuellar
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
| | | | | | - Ted Lau
- Department of Discovery Oncology
| | | | | | | | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, California
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32
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Fleck D, Phu L, Verschueren E, Hinkle T, Reichelt M, Bhangale T, Haley B, Wang Y, Graham R, Kirkpatrick DS, Sheng M, Bingol B. PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease. J Neurosci 2019; 39:4636-4656. [PMID: 30948477 PMCID: PMC6561697 DOI: 10.1523/jneurosci.0116-19.2019] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
In addition to amyloid-β plaques and tau tangles, mitochondrial dysfunction is implicated in the pathology of Alzheimer's disease (AD). Neurons heavily rely on mitochondrial function, and deficits in brain energy metabolism are detected early in AD; however, direct human genetic evidence for mitochondrial involvement in AD pathogenesis is limited. We analyzed whole-exome sequencing data of 4549 AD cases and 3332 age-matched controls and discovered that rare protein altering variants in the gene pentatricopeptide repeat-containing protein 1 (PTCD1) show a trend for enrichment in cases compared with controls. We show here that PTCD1 is required for normal mitochondrial rRNA levels, proper assembly of the mitochondrial ribosome and hence for mitochondrial translation and assembly of the electron transport chain. Loss of PTCD1 function impairs oxidative phosphorylation and forces cells to rely on glycolysis for energy production. Cells expressing the AD-linked variant of PTCD1 fail to sustain energy production under increased metabolic stress. In neurons, reduced PTCD1 expression leads to lower ATP levels and impacts spontaneous synaptic activity. Thus, our study uncovers a possible link between a protein required for mitochondrial function and energy metabolism and AD risk.SIGNIFICANCE STATEMENT Mitochondria are the main source of cellular energy and mitochondrial dysfunction is implicated in the pathology of Alzheimer's disease (AD) and other neurodegenerative disorders. Here, we identify a variant in the gene PTCD1 that is enriched in AD patients and demonstrate that PTCD1 is required for ATP generation through oxidative phosphorylation. PTCD1 regulates the level of 16S rRNA, the backbone of the mitoribosome, and is essential for mitochondrial translation and assembly of the electron transport chain. Cells expressing the AD-associated variant fail to maintain adequate ATP production during metabolic stress, and reduced PTCD1 activity disrupts neuronal energy homeostasis and dampens spontaneous transmission. Our work provides a mechanistic link between a protein required for mitochondrial function and genetic AD risk.
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Affiliation(s)
| | - Lilian Phu
- Microchemistry, Proteomics, and Lipidomics
| | | | | | | | | | - Benjamin Haley
- Molecular Biology, Genentech Inc., South San Francisco, California 94080
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33
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Kayagaki N, Lee BL, Stowe IB, Kornfeld OS, O'Rourke K, Mirrashidi KM, Haley B, Watanabe C, Roose-Girma M, Modrusan Z, Kummerfeld S, Reja R, Zhang Y, Cho V, Andrews TD, Morris LX, Goodnow CC, Bertram EM, Dixit VM. IRF2 transcriptionally induces GSDMD expression for pyroptosis. Sci Signal 2019; 12:12/582/eaax4917. [DOI: 10.1126/scisignal.aax4917] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gasdermin-D (GSDMD) is cleaved by caspase-1, caspase-4, and caspase-11 in response to canonical and noncanonical inflammasome activation. Upon cleavage, GSDMD oligomerizes and forms plasma membrane pores, resulting in interleukin-1β (IL-1β) secretion, pyroptotic cell death, and inflammatory pathologies, including periodic fever syndromes and septic shock—a plague on modern medicine. Here, we showed that IRF2, a member of the interferon regulatory factor (IRF) family of transcription factors, was essential for the transcriptional activation of GSDMD. A forward genetic screen with N-ethyl-N-nitrosourea (ENU)–mutagenized mice linked IRF2 to inflammasome signaling. GSDMD expression was substantially attenuated in IRF2-deficient macrophages, endothelial cells, and multiple tissues, which corresponded with reduced IL-1β secretion and inhibited pyroptosis. Mechanistically, IRF2 bound to a previously uncharacterized but unique site within the GSDMD promoter to directly drive GSDMD transcription for the execution of pyroptosis. Disruption of this single IRF2-binding site abolished signaling by both the canonical and noncanonical inflammasomes. Together, our data illuminate a key transcriptional mechanism for expression of the gene encoding GSDMD, a critical mediator of inflammatory pathologies.
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34
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He M, Chaurushiya MS, Webster JD, Kummerfeld S, Reja R, Chaudhuri S, Chen YJ, Modrusan Z, Haley B, Dugger DL, Eastham-Anderson J, Lau S, Dey A, Caothien R, Roose-Girma M, Newton K, Dixit VM. Intrinsic apoptosis shapes the tumor spectrum linked to inactivation of the deubiquitinase BAP1. Science 2019; 364:283-285. [PMID: 31000662 DOI: 10.1126/science.aav4902] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/15/2019] [Indexed: 11/02/2022]
Abstract
Malignancies arising from mutation of tumor suppressors have unexplained tissue proclivity. For example, BAP1 encodes a widely expressed deubiquitinase for histone H2A, but germline mutations are predominantly associated with uveal melanomas and mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells, fibroblasts, liver, and pancreatic tissue but not in melanocytes and mesothelial cells. Ubiquitin ligase RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient cells by suppressing expression of the prosurvival genes Bcl2 and Mcl1. In contrast, BAP1 loss in melanocytes had little impact on expression of prosurvival genes, instead inducing Mitf Thus, BAP1 appears to modulate gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in cells that do not engage an RNF2-dependent apoptotic program.
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Affiliation(s)
- Meng He
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mira S Chaurushiya
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah Kummerfeld
- Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Shari Lau
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Roger Caothien
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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35
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Schwab R, Clark A, Yau C, Wolf D, Chien AJ, Majure M, Ewing C, Wallace A, Roesch E, Helsten T, Forero A, Stringer-Reasor E, Vaklavas C, Nanda R, Jaskowiak N, Boughey J, Haddad T, Han H, Lee C, Albain K, Isaacs C, Elias A, Ellis E, Shah P, Lang J, Lu J, Tripathy D, Kemmer K, Yee D, Haley B, Korde L, Edmiston K, Northfelt D, Viscusi R, Khan Q, Symmans WF, Perlmutter J, Hylton N, Rugo H, Melisko M, Wilson A, Singhrao R, Asare S, van't Veer L, DeMichele A, Berry D, Esserman L. Abstract P1-15-02: Withdrawn. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p1-15-02] [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
This abstract was withdrawn by the authors.
Citation Format: Schwab R, Clark A, Yau C, Wolf D, Chien AJ, Majure M, Ewing C, Wallace A, Roesch E, Helsten T, Forero A, Stringer-Reasor E, Vaklavas C, Nanda R, Jaskowiak N, Boughey J, Haddad T, Han H, Lee C, Albain K, Isaacs C, Elias A, Ellis E, Shah P, Lang J, Lu J, Tripathy D, Kemmer K, Yee D, Haley B, Korde L, Edmiston K, Northfelt D, Viscusi R, Khan Q, I-SPY 2 Consortium, Symmans WF, Perlmutter J, Hylton N, Rugo H, Melisko M, Wilson A, Singhrao R, Asare S, van't Veer L, DeMichele A, Berry D, Esserman L. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-02.
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Affiliation(s)
- R Schwab
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - A Clark
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - C Yau
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - D Wolf
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - AJ Chien
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - M Majure
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - C Ewing
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - A Wallace
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - E Roesch
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - T Helsten
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - A Forero
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - E Stringer-Reasor
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - C Vaklavas
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - R Nanda
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - N Jaskowiak
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - J Boughey
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - T Haddad
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - H Han
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - C Lee
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - K Albain
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - C Isaacs
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - A Elias
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - E Ellis
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - P Shah
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - J Lang
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - J Lu
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - D Tripathy
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - K Kemmer
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - D Yee
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - B Haley
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - L Korde
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - K Edmiston
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - D Northfelt
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - R Viscusi
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - Q Khan
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - WF Symmans
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - J Perlmutter
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - N Hylton
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - H Rugo
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - M Melisko
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - A Wilson
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - R Singhrao
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - S Asare
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - L van't Veer
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - A DeMichele
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - D Berry
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
| | - L Esserman
- University of California San Diego, La Jolla, CA; University of Pennsylvania, Philadelphia, PA; University of California San Francisco, San Francisco, CA; Quantum Leap Health Care Collaborative, San Francisco, CA; University of Alabama Birmingham, Birmingham, AL; University of Chicago, Chicago, IL; Mayo Rochester, Rochester, MN; Moffitt Cancer Center, Tampa, FL; Loyola University, Chicago, IL; Georgetown University, Washington, DC; University of Colorado Denver, Denver, CO; Swedish Cancer Institute, Seattle, WA; University of Southern California, Los Angeles, CA; MD Anderson Cancer Center, Houston, TX; Oregon Health and Sciences University, Portland, OR; University of Minnesota, Minneapolis, MN; University of Texas Southwestern, Dallas, TX; CTEP, National Cancer Institute, Bethesda, Washington DC; Mayo Scottsdale, Scottsdale, AZ; University of Arizona, Tuscon, AZ; University of Kansas, Lawrence, KS; Berry Consultants, LLC, Houston, TX; Gemini Group, Ann Arbor; Inova Health System, Fairfax, VA
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Joseph JD, Darimont B, Zhou W, Arrazate A, Young A, Ingalla E, Walter K, Blake RA, Nonomiya J, Guan Z, Kategaya L, Govek SP, Lai AG, Kahraman M, Brigham D, Sensintaffar J, Lu N, Shao G, Qian J, Grillot K, Moon M, Prudente R, Bischoff E, Lee KJ, Bonnefous C, Douglas KL, Julien JD, Nagasawa JY, Aparicio A, Kaufman J, Haley B, Giltnane JM, Wertz IE, Lackner MR, Nannini MA, Sampath D, Schwarz L, Manning HC, Tantawy MN, Arteaga CL, Heyman RA, Rix PJ, Friedman L, Smith ND, Metcalfe C, Hager JH. Correction: The selective estrogen receptor downregulator GDC-0810 is efficacious in diverse models of ER+ breast cancer. eLife 2019; 8:44851. [PMID: 30614786 PMCID: PMC6322858 DOI: 10.7554/elife.44851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Mohamad O, Spangler A, Kim D, Thomas K, Albuquerque K, Wooldridge R, Rivers A, Leitch M, Rao R, Haley B, Ahn C, Rahimi A. Novel Hyaluronan Formulation for Preventing Acute Skin Reactions in Breast During Radiation Therapy: A Randomized Clinical Trial. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1677] [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: 10/28/2022]
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38
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Shen T, Li C, Haley B, Desai S, Strachan A. Crystalline and pseudo-crystalline phases of polyacrylonitrile from molecular dynamics: Implications for carbon fiber precursors. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.09.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Tang D, Subramanian J, Haley B, Baker J, Luo L, Hsu W, Liu P, Sandoval W, Laird MW, Snedecor B, Shiratori M, Misaghi S. Pyruvate Kinase Muscle‐1 Expression Appears to Drive Lactogenic Behavior in CHO Cell Lines, Triggering Lower Viability and Productivity: A Case Study. Biotechnol J 2018; 14:e1800332. [DOI: 10.1002/biot.201800332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/29/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Danming Tang
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | | | - Benjamin Haley
- Department of Molecular BiologyGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Jordan Baker
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Lucas Luo
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Wendy Hsu
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Peter Liu
- Department of Microchemistry, Proteomics & LipidomicsGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics & LipidomicsGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Michael W. Laird
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Brad Snedecor
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Masaru Shiratori
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Shahram Misaghi
- Cell Culture DepartmentGenentech, Inc.1 DNA WaySouth San FranciscoCA94080USA
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40
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Dompe N, Klijn C, Watson SA, Leng K, Port J, Cuellar T, Watanabe C, Haley B, Neve R, Evangelista M, Stokoe D. A CRISPR screen identifies MAPK7 as a target for combination with MEK inhibition in KRAS mutant NSCLC. PLoS One 2018; 13:e0199264. [PMID: 29912950 PMCID: PMC6005515 DOI: 10.1371/journal.pone.0199264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 04/25/2018] [Accepted: 06/04/2018] [Indexed: 11/22/2022] Open
Abstract
Mutant KRAS represents one of the most frequently observed oncogenes in NSCLC, yet no therapies are approved for tumors that express activated KRAS variants. While there is strong rationale for the use of MEK inhibitors to treat tumors with activated RAS/MAPK signaling, these have proven ineffective clinically. We therefore implemented a CRISPR screening approach to identify novel agents to sensitize KRAS mutant NSCLC cells to MEK inhibitor treatment. This approach identified multiple components of the canonical RAS/MAPK pathway consistent with previous studies. In addition, we identified MAPK7 as a novel, strong hit and validated this finding using multiple orthogonal approaches including knockdown and pharmacological inhibition. We show that MAPK7 inhibition attenuates the re-activation of MAPK signaling occurring following long-term MEK inhibition, thereby illustrating that MAPK7 mediates pathway reactivation in the face of MEK inhibition. Finally, genetic knockdown of MAPK7 combined with the MEK inhibitor cobimetinib in a mutant KRAS NSCLC xenograft model to mediate improved tumor growth inhibition. These data highlight that MAPK7 represents a promising target for combination treatment with MEK inhibition in KRAS mutant NSCLC.
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Affiliation(s)
- Nicholas Dompe
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
| | - Christiaan Klijn
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, United States of America
| | - Sara A. Watson
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
| | - Katherine Leng
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
| | - Jenna Port
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Colin Watanabe
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, United States of America
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, United States of America
| | - Richard Neve
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
| | - Marie Evangelista
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
| | - David Stokoe
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, United States of America
- * E-mail:
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41
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Manzanillo P, Mouchess M, Ota N, Dai B, Ichikawa R, Wuster A, Haley B, Alvarado G, Kwon Y, Caothien R, Roose-Girma M, Warming S, McKenzie BS, Keir ME, Scherl A, Ouyang W, Yi T. Inflammatory Bowel Disease Susceptibility Gene C1ORF106 Regulates Intestinal Epithelial Permeability. Immunohorizons 2018; 2:164-171. [PMID: 31022698 DOI: 10.4049/immunohorizons.1800027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/07/2018] [Indexed: 11/19/2022] Open
Abstract
Intestinal epithelial cells form a physical barrier that is tightly regulated to control intestinal permeability. Proinflammatory cytokines, such as TNF-α, increase epithelial permeability through disruption of epithelial junctions. The regulation of the epithelial barrier in inflammatory gastrointestinal disease remains to be fully characterized. In this article, we show that the human inflammatory bowel disease genetic susceptibility gene C1ORF106 plays a key role in regulating gut epithelial permeability. C1ORF106 directly interacts with cytohesins to maintain functional epithelial cell junctions. C1orf106-deficient mice are hypersensitive to TNF-α-induced increase in epithelial permeability, and this is associated with increased diarrhea. This study identifies C1ORF106 as an epithelial cell junction protein, and the loss of C1ORF106 augments TNF-α-induced intestinal epithelial leakage and diarrhea that may play a critical role in the development of inflammatory bowel disease.
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Affiliation(s)
- Paolo Manzanillo
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080;
| | - Maria Mouchess
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Naruhisa Ota
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Bingbing Dai
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Ryan Ichikawa
- Department of Biomarker Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Arthur Wuster
- Department of Human Genetics, Genentech Inc., South San Francisco, CA 94080
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Gabriela Alvarado
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Youngsu Kwon
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA 94080; and
| | - Roger Caothien
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Meron Roose-Girma
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Soren Warming
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080
| | - Brent S McKenzie
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA 94080; and
| | - Mary E Keir
- Department of Biomarker Discovery, Genentech Inc., South San Francisco, CA 94080
| | - Alexis Scherl
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080
| | - Wenjun Ouyang
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080;
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA 94080;
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42
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Lee BL, Mirrashidi KM, Stowe IB, Kummerfeld SK, Watanabe C, Haley B, Cuellar TL, Reichelt M, Kayagaki N. ASC- and caspase-8-dependent apoptotic pathway diverges from the NLRC4 inflammasome in macrophages. Sci Rep 2018; 8:3788. [PMID: 29491424 PMCID: PMC5830643 DOI: 10.1038/s41598-018-21998-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [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] [Received: 09/27/2017] [Accepted: 02/14/2018] [Indexed: 11/09/2022] Open
Abstract
The NLRC4 inflammasome recognizes bacterial flagellin and components of the type III secretion apparatus. NLRC4 stimulation leads to caspase-1 activation followed by a rapid lytic cell death known as pyroptosis. NLRC4 is linked to pathogen-free auto-inflammatory diseases, suggesting a role for NLRC4 in sterile inflammation. Here, we show that NLRC4 activates an alternative cell death program morphologically similar to apoptosis in caspase-1-deficient BMDMs. By performing an unbiased genome-wide CRISPR/Cas9 screen with subsequent validation studies in gene-targeted mice, we highlight a critical role for caspase-8 and ASC adaptor in an alternative apoptotic pathway downstream of NLRC4. Furthermore, caspase-1 catalytically dead knock-in (Casp1 C284A KI) BMDMs genetically segregate pyroptosis and apoptosis, and confirm that caspase-1 does not functionally compete with ASC for NLRC4 interactions. We show that NLRC4/caspase-8-mediated apoptotic cells eventually undergo plasma cell membrane damage in vitro, suggesting that this pathway can lead to secondary necrosis. Unexpectedly, we found that DFNA5/GSDME, a member of the pore-forming gasdermin family, is dispensable for the secondary necrosis that follows NLRC4-mediated apoptosis in macrophages. Together, our data confirm the existence of an alternative caspase-8 activation pathway diverging from the NLRC4 inflammasome in primary macrophages.
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Affiliation(s)
- Bettina L Lee
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Kathleen M Mirrashidi
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Irma B Stowe
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, California, USA
| | - Sarah K Kummerfeld
- Department of Bioinformatics, Genentech Inc., South San Francisco, California, USA
| | - Colin Watanabe
- Department of Bioinformatics, Genentech Inc., South San Francisco, California, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA
| | - Trinna L Cuellar
- Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA
| | - Michael Reichelt
- Department of Pathology, Genentech Inc., South San Francisco, California, USA
| | - Nobuhiko Kayagaki
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, California, USA.
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43
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Callow MG, Watanabe C, Wickliffe KE, Bainer R, Kummerfield S, Weng J, Cuellar T, Janakiraman V, Chen H, Chih B, Liang Y, Haley B, Newton K, Costa MR. CRISPR whole-genome screening identifies new necroptosis regulators and RIPK1 alternative splicing. Cell Death Dis 2018; 9:261. [PMID: 29449584 PMCID: PMC5833675 DOI: 10.1038/s41419-018-0301-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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] [Received: 12/14/2017] [Accepted: 01/04/2018] [Indexed: 12/04/2022]
Abstract
The necroptotic cell death pathway is a key component of human pathogen defense that can become aberrantly derepressed during tissue homeostasis to contribute to multiple types of tissue damage and disease. While formation of the necrosome kinase signaling complex containing RIPK1, RIPK3, and MLKL has been extensively characterized, additional mechanisms of its regulation and effector functions likely remain to be discovered. We screened 19,883 mouse protein-coding genes by CRISPR/Cas9-mediated gene knockout for resistance to cytokine-induced necroptosis and identified 112 regulators and mediators of necroptosis, including 59 new candidate pathway components with minimal or no effect on cell growth in the absence of necroptosis induction. Among these, we further characterized the function of PTBP1, an RNA binding protein whose activity is required to maintain RIPK1 protein abundance by regulating alternative splice-site selection.
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Affiliation(s)
- Marinella G Callow
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Colin Watanabe
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Katherine E Wickliffe
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Russell Bainer
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sarah Kummerfield
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Julie Weng
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | | | - Honglin Chen
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ben Chih
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuxin Liang
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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44
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Viotti M, Wilson C, McCleland M, Koeppen H, Haley B, Jhunjhunwala S, Klijn C, Modrusan Z, Arnott D, Classon M, Stephan JP, Mellman I. SUV420H2 is an epigenetic regulator of epithelial/mesenchymal states in pancreatic cancer. J Cell Biol 2017; 217:763-777. [PMID: 29229751 PMCID: PMC5800801 DOI: 10.1083/jcb.201705031] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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] [Received: 05/04/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 12/23/2022] Open
Abstract
Epithelial-to-mesenchymal transition is implicated in metastasis. Viotti et al. show that the histone methyltransferase SUV420H2 favors the mesenchymal identity in pancreatic tumor cells by silencing key drivers of the epithelial state. High levels of SUV420H2 also correlate with a loss of epithelial characteristics in invasive cancer. Epithelial-to-mesenchymal transition is implicated in metastasis, where carcinoma cells lose sessile epithelial traits and acquire mesenchymal migratory potential. The mesenchymal state is also associated with cancer stem cells and resistance to chemotherapy. It might therefore be therapeutically beneficial to promote epithelial identity in cancer. Because large-scale cell identity shifts are often orchestrated on an epigenetic level, we screened for candidate epigenetic factors and identified the histone methyltransferase SUV420H2 (KMT5C) as favoring the mesenchymal identity in pancreatic cancer cell lines. Through its repressive mark H4K20me3, SUV420H2 silences several key drivers of the epithelial state. Its knockdown elicited mesenchymal-to-epithelial transition on a molecular and functional level, and cells displayed decreased stemness and increased drug sensitivity. An analysis of human pancreatic cancer biopsies was concordant with these findings, because high levels of SUV420H2 correlated with a loss of epithelial characteristics in progressively invasive cancer. Together, these data indicate that SUV420H2 is an upstream epigenetic regulator of epithelial/mesenchymal state control.
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45
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Caculitan NG, dela Cruz Chuh J, Ma Y, Zhang D, Kozak KR, Liu Y, Pillow TH, Sadowsky J, Cheung TK, Phung Q, Haley B, Lee BC, Akita RW, Sliwkowski MX, Polson AG. Cathepsin B Is Dispensable for Cellular Processing of Cathepsin B-Cleavable Antibody–Drug Conjugates. Cancer Res 2017; 77:7027-7037. [DOI: 10.1158/0008-5472.can-17-2391] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/18/2017] [Accepted: 10/13/2017] [Indexed: 11/16/2022]
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46
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Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ. Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins. eLife 2017; 6. [PMID: 28933694 PMCID: PMC5608509 DOI: 10.7554/elife.26435] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 03/01/2017] [Accepted: 08/22/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquilins (Ubqlns) are a family of ubiquitin receptors that promote the delivery of hydrophobic and aggregated ubiquitinated proteins to the proteasome for degradation. We carried out a proteomic analysis of a B cell lymphoma-derived cell line, BJAB, that requires UBQLN1 for survival to identify UBQLN1 client proteins. When UBQLN1 expression was acutely inhibited, 120 mitochondrial proteins were enriched in the cytoplasm, suggesting that the accumulation of mitochondrial client proteins in the absence of UBQLN1 is cytostatic. Using a Ubqln1−/− mouse strain, we found that B cell receptor (BCR) ligation of Ubqln1−/− B cells led to a defect in cell cycle entry. As in BJAB cells, mitochondrial proteins accumulated in BCR-stimulated cells, leading to protein synthesis inhibition and cell cycle block. Thus, UBQLN1 plays an important role in clearing mislocalized mitochondrial proteins upon cell stimulation, and its absence leads to suppression of protein synthesis and cell cycle arrest.
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Affiliation(s)
- Alexandra M Whiteley
- Department of Infectious Disease, Genentech, South San Francisco, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Ivan Peng
- Department of Translational Immunology, Genentech, South San Francisco, United States
| | - Alexander R Abbas
- Department of Bioinformatics, Genentech, South San Francisco, United States
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Mike Reichelt
- Department of Pathology, Genentech, South San Francisco, United States
| | - Anand Katakam
- Department of Pathology, Genentech, South San Francisco, United States
| | - Meredith Sagolla
- Department of Pathology, Genentech, South San Francisco, United States
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, United States
| | - Dong Yun Lee
- Department of Infectious Disease, Genentech, South San Francisco, United States
| | - Merone Roose-Girma
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, United States
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, United States
| | - Brent S McKenzie
- Department of Translational Immunology, Genentech, South San Francisco, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Eric J Brown
- Department of Infectious Disease, Genentech, South San Francisco, United States
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47
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Cuellar TL, Herzner AM, Zhang X, Goyal Y, Watanabe C, Friedman BA, Janakiraman V, Durinck S, Stinson J, Arnott D, Cheung TK, Chaudhuri S, Modrusan Z, Doerr JM, Classon M, Haley B. Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia. J Cell Biol 2017; 216:3535-3549. [PMID: 28887438 PMCID: PMC5674883 DOI: 10.1083/jcb.201612160] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [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] [Received: 12/21/2016] [Revised: 05/15/2017] [Accepted: 08/03/2017] [Indexed: 01/23/2023] Open
Abstract
Cancer cells can rewire genetic and epigenetic regulatory networks to promote cell proliferation and evade the immune system. Using a focused CRISPR/Cas9 genetic screen, Cuellar et al. identify a novel role for the SETDB1 histone methyltransferase in regulating the antiviral response in AML cells via the suppression of transposable elements. A propensity for rewiring genetic and epigenetic regulatory networks, thus enabling sustained cell proliferation, suppression of apoptosis, and the ability to evade the immune system, is vital to cancer cell propagation. An increased understanding of how this is achieved is critical for identifying or improving therapeutic interventions. In this study, using acute myeloid leukemia (AML) human cell lines and a custom CRISPR/Cas9 screening platform, we identify the H3K9 methyltransferase SETDB1 as a novel, negative regulator of innate immunity. SETDB1 is overexpressed in many cancers, and loss of this gene in AML cells triggers desilencing of retrotransposable elements that leads to the production of double-stranded RNAs (dsRNAs). This is coincident with induction of a type I interferon response and apoptosis through the dsRNA-sensing pathway. Collectively, our findings establish a unique gene regulatory axis that cancer cells can exploit to circumvent the immune system.
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Affiliation(s)
- Trinna L Cuellar
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | | | - Xiaotian Zhang
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Yogesh Goyal
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Colin Watanabe
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA
| | - Brad A Friedman
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA
| | | | - Steffen Durinck
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA.,Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - David Arnott
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA
| | - Tommy K Cheung
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Jonas Martin Doerr
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Marie Classon
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
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48
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Guler GD, Tindell CA, Pitti R, Wilson C, Nichols K, KaiWai Cheung T, Kim HJ, Wongchenko M, Yan Y, Haley B, Cuellar T, Webster J, Alag N, Hegde G, Jackson E, Nance TL, Giresi PG, Chen KB, Liu J, Jhunjhunwala S, Settleman J, Stephan JP, Arnott D, Classon M. Repression of Stress-Induced LINE-1 Expression Protects Cancer Cell Subpopulations from Lethal Drug Exposure. Cancer Cell 2017; 32:221-237.e13. [PMID: 28781121 DOI: 10.1016/j.ccell.2017.07.002] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 05/02/2017] [Accepted: 07/05/2017] [Indexed: 12/30/2022]
Abstract
Maintenance of phenotypic heterogeneity within cell populations is an evolutionarily conserved mechanism that underlies population survival upon stressful exposures. We show that the genomes of a cancer cell subpopulation that survives treatment with otherwise lethal drugs, the drug-tolerant persisters (DTPs), exhibit a repressed chromatin state characterized by increased methylation of histone H3 lysines 9 and 27 (H3K9 and H3K27). We also show that survival of DTPs is, in part, maintained by regulators of H3K9me3-mediated heterochromatin formation and that the observed increase in H3K9me3 in DTPs is most prominent over long interspersed repeat element 1 (LINE-1). Disruption of the repressive chromatin over LINE-1 elements in DTPs results in DTP ablation, which is partially rescued by reducing LINE-1 expression or function.
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Affiliation(s)
- Gulfem Dilek Guler
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Robert Pitti
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Catherine Wilson
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Katrina Nichols
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | | | - Hyo-Jin Kim
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Yibing Yan
- LS Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Trinna Cuellar
- Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | | | - Navneet Alag
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ganapati Hegde
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erica Jackson
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | | | - Jinfeng Liu
- Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | | | - Jeff Settleman
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David Arnott
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Marie Classon
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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49
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Oppikofer M, Bai T, Gan Y, Haley B, Liu P, Sandoval W, Ciferri C, Cochran AG. Expansion of the ISWI chromatin remodeler family with new active complexes. EMBO Rep 2017; 18:1697-1706. [PMID: 28801535 DOI: 10.15252/embr.201744011] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
ISWI chromatin remodelers mobilize nucleosomes to control DNA accessibility. Complexes isolated to date pair one of six regulatory subunits with one of two highly similar ATPases. However, we find that each endogenously expressed ATPase co-purifies with every regulatory subunit, substantially increasing the diversity of ISWI complexes, and we additionally identify BAZ2B as a novel, seventh regulatory subunit. Through reconstitution of catalytically active human ISWI complexes, we demonstrate that the new interactions described here are stable and direct. Finally, we profile the nucleosome remodeling functions of the now expanded family of ISWI chromatin remodelers. By revealing the combinatorial nature of ISWI complexes, we provide a basis for better understanding ISWI function in normal settings and disease.
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Affiliation(s)
- Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Tianyi Bai
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yutian Gan
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Liu
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
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50
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Januario T, Ye X, Bainer R, Alicke B, Solon M, Haley B, Modrusan Z, Gould S, Koeppen H, Yauch RL. Abstract 2790: PRC2 mediated repression of SMARCA2 predicts for EZH2 inhibitor activity in tumors with SWI/SNF mutations. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2790] [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
A synthetic lethality caused by EZH2 inhibition in the context of SNF5 mutations is supported by both preclinical and recent clinical data, however the extent of the synthetic lethal relationship in the context of other SWI/SNF subunit mutations is not well understood. We determined that a subset of SMARCA4 mutant cancer models are sensitive to EZH2 inhibition. EZH2 inhibition resulted in a heterogenous phenotypic response characterized by senescence and/or apoptosis amongst models, and further lead to tumor growth inhibition in vivo. The differential sensitivity to EZH2 inhibition was not caused by a differential pharmacodynamic effect of the drug, nor differences in basal histone methylation or PRC2 subunit levels. However, expression of the SWI/SNF subunit, SMARCA2, delineated sensitivity amongst SMARCA4 mutant models tested. Expression of SMARCA2 further delineated sensitivity amongst other SWI/SNF mutant models tested, including SNF5 and ARID1A mutants. We determined that SMARCA2 is under PRC2 mediated suppression and the derepression of SMARCA2 was necessary for apoptosis, but not senescence, in response to EZH2 inhibition. SMARCA2 has been shown to be concurrently lost in a high percentage of SNF5 mutant malignant rhabdoid tumors and SMARCA4 mutant SCCOHT tumors, however we determined that ≈15% of SMARCA4 mutant NSCLCs concurrently lose SMARCA2. Our data supports monitoring SMARCA2 expression as a predictive biomarker for EZH2-targeted therapies that are currently being developed in the context of SWI/SNF mutant cancers.
Citation Format: Thomas Januario, Xiaofen Ye, Russell Bainer, Bruno Alicke, Margaret Solon, Benjamin Haley, Zora Modrusan, Stephen Gould, Hartmut Koeppen, Robert L. Yauch. PRC2 mediated repression of SMARCA2 predicts for EZH2 inhibitor activity in tumors with SWI/SNF mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2790. doi:10.1158/1538-7445.AM2017-2790
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Affiliation(s)
| | - Xiaofen Ye
- Genentech, Inc., South San Francisco, CA
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