1
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Wang H, Wang Y, Li J, He Z, Boswell SA, Chung M, You F, Han S. Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes. BMC Med 2023; 21:147. [PMID: 37069550 PMCID: PMC10108821 DOI: 10.1186/s12916-023-02838-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Tyrosine kinase inhibitors (TKIs) are anti-cancer therapeutics often prescribed for long-term treatment. Many of these treatments cause cardiotoxicity with limited cure. We aim to clarify molecular mechanisms of TKI-induced cardiotoxicity so as to find potential targets for treating the adverse cardiac complications. METHODS Eight TKIs with different levels of cardiotoxicity reported are selected. Phenotypic and transcriptomic responses of human cardiomyocytes to TKIs at varying doses and times are profiled and analyzed. Stress responses and signaling pathways that modulate cardiotoxicity induced by three TKIs are validated in cardiomyocytes and rat hearts. RESULTS Toxicity rank of the eight TKIs determined by measuring their effects on cell viability, contractility, and respiration is largely consistent with that derived from database or literature, indicating that human cardiomyocytes are a good cellular model for studying cardiotoxicity. When transcriptomes are measured for selected TKI treatments with different levels of toxicity in human cardiomyocytes, the data are classified into 7 clusters with mainly single-drug clusters. Drug-specific effects on the transcriptome dominate over dose-, time- or toxicity-dependent effects. Two clusters with three TKIs (afatinib, ponatinib, and sorafenib) have the top enriched pathway as the endoplasmic reticulum stress (ERS). All three TKIs induce ERS in rat primary cardiomyocytes and ponatinib activates the IRE1α-XBP1s axis downstream of ERS in the hearts of rats underwent a 7-day course of drug treatment. To look for potential triggers of ERS, we find that the three TKIs induce transient reactive oxygen species followed by lipid peroxidation. Inhibiting either PERK or IRE1α downstream of ERS blocks TKI-induced cardiac damages, represented by the induction of cardiac fetal and pro-inflammatory genes without causing more cell death. CONCLUSIONS Our data contain rich information about phenotypic and transcriptional responses of human cardiomyocytes to eight TKIs, uncovering potential molecular mechanisms in modulating cardiotoxicity. ER stress is activated by multiple TKIs and leads to cardiotoxicity through promoting expression of pro-inflammatory factors and cardiac fetal genes. ER stress-induced inflammation is a promising therapeutic target to mitigate ponatinib- and sorafenib-induced cardiotoxicity.
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Affiliation(s)
- Huan Wang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Yiming Wang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jiongyuan Li
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ziyi He
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Fuping You
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Sen Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, 100142, China
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2
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Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori B, Buhrlage SJ, Sorger PK. Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. eLife 2022; 11:72879. [PMID: 35737447 PMCID: PMC9225015 DOI: 10.7554/elife.72879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/26/2022] [Indexed: 12/11/2022] Open
Abstract
Deubiquitinating enzymes (DUBs), ~100 of which are found in human cells, are proteases that remove ubiquitin conjugates from proteins, thereby regulating protein turnover. They are involved in a wide range of cellular activities and are emerging therapeutic targets for cancer and other diseases. Drugs targeting USP1 and USP30 are in clinical development for cancer and kidney disease respectively. However, the majority of substrates and pathways regulated by DUBs remain unknown, impeding efforts to prioritize specific enzymes for research and drug development. To assemble a knowledgebase of DUB activities, co-dependent genes, and substrates, we combined targeted experiments using CRISPR libraries and inhibitors with systematic mining of functional genomic databases. Analysis of the Dependency Map, Connectivity Map, Cancer Cell Line Encyclopedia, and multiple protein-protein interaction databases yielded specific hypotheses about DUB function, a subset of which were confirmed in follow-on experiments. The data in this paper are browsable online in a newly developed DUB Portal and promise to improve understanding of DUBs as a family as well as the activities of incompletely characterized DUBs (e.g. USPL1 and USP32) and those already targeted with investigational cancer therapeutics (e.g. USP14, UCHL5, and USP7).
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Affiliation(s)
- Laura M Doherty
- Harvard Medical School (HMS) Library of Integrated Network-based Cellular Signatures (LINCS) Center, Cambridge, United States.,Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Charles Tapley Hoyt
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Benjamin Gyori
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
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3
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Abstract
Quantitative diagnostics that are rapid, inexpensive, sensitive, robust, and field-deployable are needed to contain the spread of infectious diseases and inform treatment strategies. While current gold-standard techniques are highly sensitive and quantitative, they are slow and require expensive equipment. Conversely, current rapid field-deployable assays available provide essentially binary information about the presence of the target analyte, not a quantitative measure of concentration. Here, we report the development of a molecular diagnostic test [quantitative recombinase polymerase amplification (qRPA)] that utilizes competitive amplification during a recombinase polymerase amplification (RPA) assay to provide semi-quantitative information on a target nucleic acid. We demonstrate that qRPA can quantify DNA, RNA, and viral titers in HIV and COVID-19 patient samples and that it is more robust to environmental perturbations than traditional RPA. These features make qRPA potentially useful for at-home testing to monitor the progress of viral infections or other diseases.
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Affiliation(s)
| | | | | | - Sarah A. Boswell
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States,Massachusetts Consortium on Pathogen Readiness, Boston, Massachusetts 20115, United States
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4
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Pettit ME, Boswell SA, Qian J, Novak R, Springer M. Accessioning and automation compatible anterior nares swab design. J Virol Methods 2021; 294:114153. [PMID: 33984398 PMCID: PMC8108477 DOI: 10.1016/j.jviromet.2021.114153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022]
Abstract
The COVID-19 pandemic has resulted in an unparalleled need for viral testing capacity across the world and is a critical requirement for successful re-opening of economies. The logistical barriers to near-universal testing are considerable. We have designed an injection molded polypropylene anterior nares swab, the Rhinostic, with a screw cap integrated into the swab handle that is compatible with fully automated sample accessioning and processing. The ability to collect and release both human and viral material is comparable to that of several commonly used swabs on the market. SARS-CoV-2 is stable on dry Rhinostic swabs for at least 3 days, even at 42 °C, and elution can be achieved with small volumes. To test the performance of the Rhinostic in patients, 119 samples were collected with Rhinostic and the positive and negative determinations were 100 % concordant with samples collected using Clinical Laboratory Improvement Amendments (CLIA) use approved nasal swabs at a clinical lab. The Rhinostic swab and barcoded tube set can be produced, sterilized, and packaged cost effectively and is designed to be adopted by clinical laboratories using automation to increase throughput and dramatically reduce the cost of a standard SARS-CoV-2 detection pipeline.
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Affiliation(s)
- Mary E Pettit
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Boswell
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jason Qian
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, 20115, USA.
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5
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Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A. Machine learning identifies candidates for drug repurposing in Alzheimer's disease. Nat Commun 2021; 12:1033. [PMID: 33589615 PMCID: PMC7884393 DOI: 10.1038/s41467-021-21330-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/21/2021] [Indexed: 01/31/2023] Open
Abstract
Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a large amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA) for another indication is a more rapid and less expensive option. We present DRIAD (Drug Repurposing In AD), a machine learning framework that quantifies potential associations between the pathology of AD severity (the Braak stage) and molecular mechanisms as encoded in lists of gene names. DRIAD is applied to lists of genes arising from perturbations in differentiated human neural cell cultures by 80 FDA-approved and clinically tested drugs, producing a ranked list of possible repurposing candidates. Top-scoring drugs are inspected for common trends among their targets. We propose that the DRIAD method can be used to nominate drugs that, after additional validation and identification of relevant pharmacodynamic biomarker(s), could be readily evaluated in a clinical trial.
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Affiliation(s)
- Steve Rodriguez
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Clemens Hug
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Petar Todorov
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Nienke Moret
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Kyle Evans
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - George Zhou
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nathan T Johnson
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Mark W Albers
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA.
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
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6
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Mehta AK, Cheney EM, Hartl CA, Pantelidou C, Oliwa M, Castrillon JA, Lin JR, Hurst KE, de Oliveira Taveira M, Johnson NT, Oldham WM, Kalocsay M, Berberich MJ, Boswell SA, Kothari A, Johnson S, Dillon DA, Lipschitz M, Rodig S, Santagata S, Garber JE, Tung N, Yélamos J, Thaxton JE, Mittendorf EA, Sorger PK, Shapiro GI, Guerriero JL. Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Nat Cancer 2021; 2:66-82. [PMID: 33738458 PMCID: PMC7963404 DOI: 10.1038/s43018-020-00148-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/27/2020] [Indexed: 12/26/2022]
Abstract
Despite objective responses to PARP inhibition and improvements in progression-free survival compared to standard chemotherapy in patients with BRCA-associated triple-negative breast cancer (TNBC), benefits are transitory. Using high dimensional single-cell profiling of human TNBC, here we demonstrate that macrophages are the predominant infiltrating immune cell type in BRCA-associated TNBC. Through multi-omics profiling we show that PARP inhibitors enhance both anti- and pro-tumor features of macrophages through glucose and lipid metabolic reprogramming driven by the sterol regulatory element-binding protein 1 (SREBP-1) pathway. Combined PARP inhibitor therapy with CSF-1R blocking antibodies significantly enhanced innate and adaptive anti-tumor immunity and extends survival in BRCA-deficient tumors in vivo and is mediated by CD8+ T-cells. Collectively, our results uncover macrophage-mediated immune suppression as a liability of PARP inhibitor treatment and demonstrate combined PARP inhibition and macrophage targeting therapy induces a durable reprogramming of the tumor microenvironment, thus constituting a promising therapeutic strategy for TNBC.
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Affiliation(s)
- Anita K Mehta
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Emily M Cheney
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina A Hartl
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Constantia Pantelidou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Madisson Oliwa
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessica A Castrillon
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Katie E Hurst
- Department of Orthopedics and Physical Medicine, Medical University of South Carolina, Charleston, SC, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Mateus de Oliveira Taveira
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
- Department of Imaging, AC Camargo Cancer Center, São Paulo, Brazil
| | - Nathan T Johnson
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - William M Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew J Berberich
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Aditi Kothari
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shawn Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mikel Lipschitz
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadine Tung
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jessica E Thaxton
- Department of Orthopedics and Physical Medicine, Medical University of South Carolina, Charleston, SC, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Charleston, SC, USA
| | - Elizabeth A Mittendorf
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jennifer L Guerriero
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA.
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7
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Qian J, Boswell SA, Chidley C, Lu ZX, Pettit ME, Gaudio BL, Fajnzylber JM, Ingram RT, Ward RH, Li JZ, Springer M. An enhanced isothermal amplification assay for viral detection. Nat Commun 2020; 11:5920. [PMID: 33219228 PMCID: PMC7679446 DOI: 10.1038/s41467-020-19258-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. Here we report the development of a molecular diagnostic test for SARS-CoV-2 based on an enhanced recombinase polymerase amplification (eRPA) reaction. eRPA has a detection limit on patient samples down to 5 viral copies, requires minimal instrumentation, and is highly scalable and inexpensive. eRPA does not cross-react with other common coronaviruses, does not require RNA purification, and takes ~45 min from sample collection to results. eRPA represents a first step toward at-home SARS-CoV-2 detection and can be adapted to future viruses within days of genomic sequence availability.
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Affiliation(s)
- Jason Qian
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Boswell
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhi-Xiang Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Mary E Pettit
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin L Gaudio
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jesse M Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ryan T Ingram
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca H Ward
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA.
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8
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Qian J, Lu ZX, Mancuso CP, Jhuang HY, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. Barcoded microbial system for high-resolution object provenance. Science 2020; 368:1135-1140. [PMID: 32499444 DOI: 10.1126/science.aba5584] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 02/22/2024]
Abstract
Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.
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Affiliation(s)
- Jason Qian
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Zhi-Xiang Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher P Mancuso
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Han-Ying Jhuang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sarah A Boswell
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Victoria Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Akhila Sonti
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Kole Sedlack
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Lior Artzi
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Giyoung Jung
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mohammad Arammash
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E Pettit
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Melfi
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lorena Lyon
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Baym
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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9
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Qian J, Boswell SA, Chidley C, Lu ZX, Pettit ME, Gaudio BL, Fajnzylber JM, Ingram RT, Ward RH, Li JZ, Springer M. An enhanced isothermal amplification assay for viral detection. bioRxiv 2020:2020.05.28.118059. [PMID: 32577657 PMCID: PMC7302212 DOI: 10.1101/2020.05.28.118059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
UNLABELLED Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. We developed a molecular diagnostic test for SARS-CoV-2, FIND (Fast Isothermal Nucleic acid Detection), based on an enhanced isothermal recombinase polymerase amplification reaction. FIND has a detection limit on patient samples close to that of RT-qPCR, requires minimal instrumentation, and is highly scalable and cheap. It can be performed in high throughput, does not cross-react with other common coronaviruses, avoids bottlenecks caused by the current worldwide shortage of RNA isolation kits, and takes ~45 minutes from sample collection to results. FIND can be adapted to future novel viruses in days once sequence is available. ONE SENTENCE SUMMARY Sensitive, specific, rapid, scalable, enhanced isothermal amplification method for detecting SARS-CoV-2 from patient samples.
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10
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Schauer NJ, Liu X, Magin RS, Doherty LM, Chan WC, Ficarro SB, Hu W, Roberts RM, Iacob RE, Stolte B, Giacomelli AO, Perera S, McKay K, Boswell SA, Weisberg EL, Ray A, Chauhan D, Dhe-Paganon S, Anderson KC, Griffin JD, Li J, Hahn WC, Sorger PK, Engen JR, Stegmaier K, Marto JA, Buhrlage SJ. Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism. Sci Rep 2020; 10:5324. [PMID: 32210275 PMCID: PMC7093416 DOI: 10.1038/s41598-020-62076-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Ubiquitin specific peptidase 7 (USP7) is a deubiquitinating enzyme (DUB) that removes ubiquitin tags from specific protein substrates in order to alter their degradation rate and sub-cellular localization. USP7 has been proposed as a therapeutic target in several cancers because it has many reported substrates with a role in cancer progression, including FOXO4, MDM2, N-Myc, and PTEN. The multi-substrate nature of USP7, combined with the modest potency and selectivity of early generation USP7 inhibitors, has presented a challenge in defining predictors of response to USP7 and potential patient populations that would benefit most from USP7-targeted drugs. Here, we describe the structure-guided development of XL177A, which irreversibly inhibits USP7 with sub-nM potency and selectivity across the human proteome. Evaluation of the cellular effects of XL177A reveals that selective USP7 inhibition suppresses cancer cell growth predominantly through a p53-dependent mechanism: XL177A specifically upregulates p53 transcriptional targets transcriptome-wide, hotspot mutations in TP53 but not any other genes predict response to XL177A across a panel of ~500 cancer cell lines, and TP53 knockout rescues XL177A-mediated growth suppression of TP53 wild-type (WT) cells. Together, these findings suggest TP53 mutational status as a biomarker for response to USP7 inhibition. We find that Ewing sarcoma and malignant rhabdoid tumor (MRT), two pediatric cancers that are sensitive to other p53-dependent cytotoxic drugs, also display increased sensitivity to XL177A.
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Affiliation(s)
- Nathan J Schauer
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura M Doherty
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wanyi Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Andrew O Giacomelli
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Kyle McKay
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - Sarah A Boswell
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arghya Ray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ken C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - William C Hahn
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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Mehta AK, Cheney EM, Castrillon JA, Lin JR, Taveira MDO, Hartl CA, Johnson NT, Oldham WM, Kalocsay M, Boswell SA, Sonzogni O, Pantelidou C, Gross BP, Johnson S, Dillon DA, Santagata S, Garber JE, Tung N, Mittendorf EA, Wulf GM, Shapiro GI, Sorger PK, Guerriero JL. Abstract A105: PARP inhibition modulates the infiltration, phenotype, and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the antitumor potential of TAMs. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-a105] [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
Patients with BRCA-associated triple-negative breast cancer (TNBC) have few effective treatment options. PARP inhibitors are promising, and we recently showed they induce an influx of white blood cells, including CD8+ T cells and macrophages into the tumor. The influx of CD8+ cells, mediated by activation of the STING pathway in tumor cells, contributes substantially to efficacy of PARP inhibition in mice. Strikingly, in these studies the greatest infiltration of immune cells into the tumor was macrophages. Given that objective responses to PARP inhibition have been observed in clinical trials but the benefits are transitory, we hypothesized that this was due to a suppressive tumor microenvironment, driven by tumor macrophages. To better understand the molecular basis of resistance to PARP inhibitors, we used high-dimensional single-cell immune profiling on human TNBC. We observed a ≥10-fold increase in TAMs in BRCA-associated TNBC compared to BRCA-wild-type TNBC. Using a preclinical model of BRCA1-deficient triple-negative breast cancer, we found that PARP inhibitors not only further increased TAM abundance but also induced functional and phenotypic changes associated with STING pathway activation, antigen presentation, and chemokine and cytokine signaling. PARP inhibitors increased the frequency of TAMs expressing costimulatory molecules CD80 and CD86 as well as the activation and maturation marker CD40, which are indicative of an antitumor phenotype. We also identified a novel negative feedback mechanism that limits the functionality of the anti-tumor TAMs and is consistent with induction of an immune-suppressive macrophage population. Utilizing transcriptomic, proteomic, and metabolic profiling of ex vivo cultured human myeloid cells, we identified multiple biologic processes associated with PARP inhibition, showing that these drugs directly affect macrophage states and phenotypes. Remarkably, in the preclinical BRCA1-deficient TNBC model, the novel combination of PARP inhibition with macrophage modulation significantly extended remissions obtained with PARP inhibitor therapy only, and this advantage persisted when treatment was discontinued, suggestive of a durable reprogramming of the tumor microenvironment. Moreover, CD8+ cells were required for the extension of PARP inhibitor-induced remissions, suggesting that targeting macrophages lifted the constraints imposed by protumor macrophages on CD8+ T cell-mediated tumor cell killing. We identify mechanisms related to macrophage and T-cell activation that increase PFS and provide evidence that TAMs may serve as targets for new therapeutic interventions designed to overcome PARP inhibitor resistance in BRCA-associated TNBC.
Citation Format: Anita K. Mehta, Emily M. Cheney, Jessica A. Castrillon, Jia-Ren Lin, Mateus de Oliveira Taveira, Christina A. Hartl, Nathan T. Johnson, William M. Oldham, Marian Kalocsay, Sarah A. Boswell, Olmo Sonzogni, Constantia Pantelidou, Brett P. Gross, Shawn Johnson, Deborah A. Dillon, Sandro Santagata, Judy E. Garber, Nadine Tung, Elizabeth A. Mittendorf, Gerburg M. Wulf, Geoffrey I. Shapiro, Peter K. Sorger, Jennifer L. Guerriero. PARP inhibition modulates the infiltration, phenotype, and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the antitumor potential of TAMs [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A105.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nadine Tung
- 3Beth Israel Deaconess Medical Center, Boston, MA,
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12
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Guerriero JL, Mehta AK, Cheney EM, Castrillon JA, Lin JR, Taveira MDO, Sonzogni O, Pantelidou C, Hartl CA, Oldham WM, Johnson NT, Boswell SA, Kalocsay M, Berberich MJ, Mei S, Wang D, Johnson S, Gross B, Dillon DA, Lipschitz M, Gjini E, Rodig S, Santagata S, Garber JE, Tung N, Sorger P, Shapiro GI, Wulf GM, Mittendorf EA. Abstract P5-04-01: PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p5-04-01] [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
Patients with BRCA-associated triple negative breast cancer (TNBC) have few effective treatment options. PARP inhibitors are promising, and we recently showed they induce an influx of white blood cells, including CD8+ T-cells and macrophages into the tumor. The influx of CD8+ cells, mediated by activation of the STING pathway in tumor cells, contributes substantially to efficacy of PARP inhibition in mice. Strikingly, in these studies, the greatest infiltration of immune cells into the tumor was macrophages. Given objective responses to PARP inhibition have been observed in clinical trials but the benefits are transitory, we hypothesized that this was presumably due to a suppressive tumor microenvironment, driven by tumor macrophages. To better understand the molecular basis of resistance to PARP inhibitors, we used high dimensional single-cell immune profiling on human TNBC. We observed a ≥10-fold increase in TAMs in BRCA-associated TNBC compared to BRCA-wildtype TNBC. Using a pre-clinical model of BRCA1-deficient triple-negative breast cancer, we found that PARP inhibitors not only further increased TAM abundance but also induced functional and phenotypic changes associated with STING pathway activation, antigen presentation, and chemokine and cytokine signaling. PARP inhibitors increased the frequency of TAMs expressing co-stimulatory molecules CD80 and CD86 as well as the activation and maturation marker CD40, which are indicative of an anti-tumor phenotype. We also identified a novel negative feedback mechanism which limits the functionality of the anti-tumor TAMs, and is consistent with induction of an immune suppressive macrophage population. Utilizing transcriptomic, proteomic and metabolic profiling of ex vivo cultured human myeloid cells, we identified multiple biological processes associate with PARP inhibition, showing that these drugs directly affect macrophage states and phenotypes. Remarkably, in the pre-clinical BRCA1-deficient TNBC model, the novel combination of PARP inhibition with macrophage modulation significantly extended remissions obtained with PARP inhibitor therapy only, and this advantage persisted when treatment was discontinued, suggestive of a durable reprogramming of the tumor microenvironment. Moreover, CD8+ cells were required for the extension of PARP inhibitor-induced remissions, suggesting that targeting macrophages lifted the constraints imposed by pro-tumor macrophages on CD8+ T cell-mediated tumor cell killing. We identify mechanisms related to macrophage and T-cell activation that increase PFS and provide evidence that TAMs may serve as targets for new therapeutic interventions designed to overcome PARP inhibitor resistance in BRCA-associated TNBC.
Citation Format: Jennifer L Guerriero, Anita K Mehta, Emily M Cheney, Jessica A. Castrillon, Jia-Ren Lin, Mateus de Oliveira Taveira, Olmo Sonzogni, Constantia Pantelidou, Christina A Hartl, William M Oldham, Nathan T Johnson, Sarah A Boswell, Marian Kalocsay, Matthew J Berberich, Sholin Mei, Dan Wang, Shawn Johnson, Brett Gross, Deborah A Dillon, Mikel Lipschitz, Evisa Gjini, Scott Rodig, Sandro Santagata, Judy E Garber, Nadine Tung, Peter Sorger, Geoffrey I Shapiro, Gerburg M Wulf, Elizabeth A Mittendorf. PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-04-01.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Wang
- 3Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | | | | | | | | | | | - Nadine Tung
- 3Beth Israel Deaconess Medical Center, Boston, MA
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13
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Mills CE, Hafner MA, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Abstract 4432: Multi-omics profiling establishes the polypharmacology of FDA Approved CDK4/6 inhibitors and its impact on drug response. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4432] [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
FDA approval of multiple drugs with different chemical structures against the same protein target raises the question whether such drugs have sufficiently similar mechanisms of action to be considered functionally equivalent. We compare three recently approved inhibitors of the cyclin-dependent kinases CDK4/6 - palbociclib, ribociclib, and abemaciclib - that have become highly promising therapies for the treatment of breast cancer and potentially other solid tumors. All three drugs have the same nominal targets but differ in selectivity. In humans, abemaciclib uniquely appears to exhibit single-agent activity and has a distinct toxicity profile. We systematically profile targets and activities of these CDK4/6 inhibitors using biochemical assays, mRNA profiling, mass spectrometry-based phospho-proteomics, GR-based dose-response assays, and mouse xenografts. We find that the three drugs differ at a cellular level and that abemaciclib has targets and activities not shared by palbociclib or ribociclib including: induction of cell death (even in pRb-deficient cells), arrest in the G2 phase of the cell cycle, reduced drug adaptation, and unique transcriptional effects in vitro and in vivo. These activities appear to arise from inhibition of CDKs other than CDK4/6 including CDK2/Cyclin A/E and CDK1/Cyclin B. We propose that inhibition of these kinases by abemaciclib target known mechanisms of resistance to CDK4/6 inhibition and thus elicit a response in cell lines that are resistant to palbociclib or ribociclib.
Citation Format: Caitlin E. Mills, Marc A. Hafner, Kartik Subramanian, Chen Chen, Mirra Chung, Sarah A. Boswell, Robert A. Everley, Changchang Liu, Charlotte S. Walmsley, Dejan Juric, Peter K. Sorger. Multi-omics profiling establishes the polypharmacology of FDA Approved CDK4/6 inhibitors and its impact on drug response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4432.
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14
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Pavkovic M, Pantano L, Gerlach CV, Brutus S, Boswell SA, Everley RA, Shah JV, Sui SH, Vaidya VS. Multi omics analysis of fibrotic kidneys in two mouse models. Sci Data 2019; 6:92. [PMID: 31201317 PMCID: PMC6570759 DOI: 10.1038/s41597-019-0095-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Kidney fibrosis represents an urgent unmet clinical need due to the lack of effective therapies and an inadequate understanding of the molecular pathogenesis. We have generated a comprehensive and combined multi-omics dataset (proteomics, mRNA and small RNA transcriptomics) of fibrotic kidneys that is searchable through a user-friendly web application: http://hbcreports.med.harvard.edu/fmm/. Two commonly used mouse models were utilized: a reversible chemical-induced injury model (folic acid (FA) induced nephropathy) and an irreversible surgically-induced fibrosis model (unilateral ureteral obstruction (UUO)). mRNA and small RNA sequencing, as well as 10-plex tandem mass tag (TMT) proteomics were performed with kidney samples from different time points over the course of fibrosis development. The bioinformatics workflow used to process, technically validate, and combine the single omics data will be described. In summary, we present temporal multi-omics data from fibrotic mouse kidneys that are accessible through an interrogation tool (Mouse Kidney Fibromics browser) to provide a searchable transcriptome and proteome for kidney fibrosis researchers. Design Type(s) | transcription profiling design • proteomic profiling design • stimulus or stress design | Measurement Type(s) | transcription profiling assay • protein expression profiling assay | Technology Type(s) | RNA sequencing • mass spectrometry | Factor Type(s) | experimental condition • temporal_instant • biological replicate | Sample Characteristic(s) | Mus musculus • kidney |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Mira Pavkovic
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Lorena Pantano
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cory V Gerlach
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sergine Brutus
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jagesh V Shah
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Shannan H Sui
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Vishal S Vaidya
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA. .,Department of Medicine - Renal Division, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. Cell Chem Biol 2019; 26:1067-1080.e8. [PMID: 31178407 DOI: 10.1016/j.chembiol.2019.05.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [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: 11/12/2018] [Revised: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
The target profiles of many drugs are established early in their development and are not systematically revisited at the time of FDA approval. Thus, it is often unclear whether therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five different phenotypic and biochemical assays to compare approved inhibitors of cyclin-dependent kinases 4/6-collectively regarded as breakthroughs in the treatment of hormone receptor-positive breast cancer. We find that transcriptional, proteomic, and phenotypic changes induced by palbociclib, ribociclib, and abemaciclib differ significantly; abemaciclib in particular has advantageous activities partially overlapping those of alvocidib, an older polyselective CDK inhibitor. In cells and mice, abemaciclib inhibits kinases other than CDK4/6 including CDK2/cyclin A/E-implicated in resistance to CDK4/6 inhibition-and CDK1/cyclin B. The multifaceted experimental and computational approaches described here therefore uncover underappreciated differences in CDK4/6 inhibitor activities with potential importance in treating human patients.
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Affiliation(s)
- Marc Hafner
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Changchang Liu
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte S Walmsley
- Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Dejan Juric
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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Ongusaha PP, Kim HG, Boswell SA, Ridley AJ, Der CJ, Dotto GP, Kim YB, Aaronson SA, Lee SW. Retraction Notice to: RhoE Is a Pro-Survival p53 Target Gene that Inhibits ROCK I-Mediated Apoptosis in Response to Genotoxic Stress. Curr Biol 2019; 29:2107. [DOI: 10.1016/j.cub.2019.05.065] [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: 10/26/2022]
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Gasic I, Boswell SA, Mitchison TJ. Tubulin mRNA stability is sensitive to change in microtubule dynamics caused by multiple physiological and toxic cues. PLoS Biol 2019; 17:e3000225. [PMID: 30964857 PMCID: PMC6474637 DOI: 10.1371/journal.pbio.3000225] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/19/2019] [Accepted: 03/26/2019] [Indexed: 12/19/2022] Open
Abstract
The localization, mass, and dynamics of microtubules are important in many processes. Cells may actively monitor the state of their microtubules and respond to perturbation, but how this occurs outside mitosis is poorly understood. We used gene-expression analysis in quiescent cells to analyze responses to subtle and strong perturbation of microtubules. Genes encoding α-, β, and γ-tubulins (TUBAs, TUBBs, and TUBGs), but not δ- or ε-tubulins (TUBDs or TUBEs), exhibited the strongest differential expression response to microtubule-stabilizing versus destabilizing drugs. Quantitative PCR of exon versus intron sequences confirmed that these changes were caused by regulation of tubulin mRNA stability and not transcription. Using tubulin mRNA stability as a signature to query the Gene Expression Omnibus (GEO) database, we find that tubulin genes respond to toxins known to damage microtubules. Importantly, we find many other experimental perturbations, including multiple signaling and metabolic inputs that trigger tubulin differential expression, suggesting their novel, to our knowledge, role in the regulation of the microtubule cytoskeleton. Mechanistic follow-up confirms that one important physiological signal, phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) activity, indeed regulates tubulin mRNA stability via changes in microtubule dynamics. We propose that tubulin gene expression is regulated as part of many coordinated biological responses, with wide implications in physiology and toxicology. Furthermore, we present a new way to discover microtubule regulation using transcriptomics.
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Affiliation(s)
- Ivana Gasic
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sarah A. Boswell
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy J. Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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Mills CE, Hafner M, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Walmsley CS, Juric D, Sorger PK. Abstract PD1-12: Omics profiling of CDK4/6 inhibitors reveals functionally important secondary targets of abemaciclib. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-pd1-12] [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 recent introduction of small molecule inhibitors of cyclin-dependent kinases (CDK) 4/6 to the clinic has improved the treatment of hormone receptor positive breast cancer, and shown promise in other malignancies. The three clinically used CDK4/6 inhibitors, palbociclib, ribociclib, and abemaciclib, are reported to be broadly similar although recent data suggest that abemaciclib has distinct single-agent activity in patients and a unique adverse effects profile. Key questions are: How do these drugs differ at the molecular level? Should such differences inform their use in the clinic? Can these three agents be used interchangeably or should patient stratification differ between them? We use molecular and functional profiling by mRNA sequencing, mass spectrometry-based proteomics, and GR-based dose-response assays to obtain complementary views of the mechanisms of action of CDK4/6 inhibitors. We show that abemaciclib, but not ribociclib or palbociclib, is a potent inhibitor of kinases other than CDK4/6, including CDK1/Cyclin B, which appears to cause arrest in the G2 phase of the cell cycle, and CDK2/Cyclin E/A, which is implicated in resistance to palbociclib. We show that inhibition of these additional targets is accessible in a xenograft model. Whereas ribociclib and palbociclib induce cytostasis, and cells adapt to these drugs within 2-3 days of exposure, abemaciclib induces cell death and durably blocks cell proliferation. Abemaciclib is active even in retinoblastoma protein (pRb)-deficient cells in which CDK4/6 inhibition by palbociclib or ribociclib is completely ineffective. The degree of polypharmacology of small molecule drugs is increasingly viewed as an important consideration in their design, with implications for efficacy, toxicity, and acquired resistance. In the case of CDK4/6 inhibitors, we propose that abemaciclib polypharmacology elicits unique molecular responses. More generally, we propose that multi-omic approaches are required to fully elucidate the spectrum of targets relevant to drug action in tumor cells. We expect such understanding to assist in stratifying patient populations and ordering sequential therapies when resistance arises.
Citation Format: Mills CE, Hafner M, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Walmsley CS, Juric D, Sorger PK. Omics profiling of CDK4/6 inhibitors reveals functionally important secondary targets of abemaciclib [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 PD1-12.
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Affiliation(s)
- CE Mills
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - M Hafner
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - K Subramanian
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - C Chen
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - M Chung
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - SA Boswell
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - RA Everley
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - CS Walmsley
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - D Juric
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - PK Sorger
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
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Monteiro MB, Ramm S, Chandrasekaran V, Boswell SA, Weber EJ, Lidberg KA, Kelly EJ, Vaidya VS. A High-Throughput Screen Identifies DYRK1A Inhibitor ID-8 that Stimulates Human Kidney Tubular Epithelial Cell Proliferation. J Am Soc Nephrol 2018; 29:2820-2833. [PMID: 30361326 PMCID: PMC6287872 DOI: 10.1681/asn.2018040392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/16/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The death of epithelial cells in the proximal tubules is thought to be the primary cause of AKI, but epithelial cells that survive kidney injury have a remarkable ability to proliferate. Because proximal tubular epithelial cells play a predominant role in kidney regeneration after damage, a potential approach to treat AKI is to discover regenerative therapeutics capable of stimulating proliferation of these cells. METHODS We conducted a high-throughput phenotypic screen using 1902 biologically active compounds to identify new molecules that promote proliferation of primary human proximal tubular epithelial cells in vitro. RESULTS The primary screen identified 129 compounds that stimulated tubular epithelial cell proliferation. A secondary screen against these compounds over a range of four doses confirmed that eight resulted in a significant increase in cell number and incorporation of the modified thymidine analog EdU (indicating actively proliferating cells), compared with control conditions. These eight compounds also stimulated tubular cell proliferation in vitro after damage induced by hypoxia, cadmium chloride, cyclosporin A, or polymyxin B. ID-8, an inhibitor of dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), was the top candidate identified as having a robust proproliferative effect in two-dimensional culture models as well as a microphysiologic, three-dimensional cell culture system. Target engagement and genetic knockdown studies and RNA sequencing confirmed binding of ID-8 to DYRK1A and upregulation of cyclins and other cell cycle regulators, leading to epithelial cell proliferation. CONCLUSIONS We have identified a potential first-in-class compound that stimulates human kidney tubular epithelial cell proliferation after acute damage in vitro.
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Affiliation(s)
- Maria B Monteiro
- Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts
| | - Susanne Ramm
- Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Vidya Chandrasekaran
- Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts
| | - Sarah A Boswell
- Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts
| | - Elijah J Weber
- Department of Pharmaceutics, University of Washington, Seattle, Washington; and
| | - Kevin A Lidberg
- Department of Pharmaceutics, University of Washington, Seattle, Washington; and
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, Washington; and
| | - Vishal S Vaidya
- Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts;
- Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Mills CE, Hafner M, Subramanian K, Chen C, Boswell SA, Everley RA, Juric D, Sorger PK. Abstract B60: Omics profiling of CDK4/6 inhibitors reveals functionally important secondary targets of abemaciclib. Mol Cancer Res 2018. [DOI: 10.1158/1557-3125.advbc17-b60] [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 recent introduction of small-molecule inhibitors of cyclin-dependent kinases (CDK) 4/6 to the clinic has improved the treatment of hormone receptor-positive breast cancer, and shown promise in other malignancies. The three clinically used CDK4/6 inhibitors, palbociclib, ribociclib, and abemaciclib, are reported to be broadly similar, although recent data suggest that abemaciclib has distinct single-agent activity in patients and a unique toxicity profile. In vitro profiling of the CDK4/6 inhibitors has shown abemaciclib to be more potent on target, but less selective than either palbociclib or ribociclib. We sought to systematically investigate the functional consequences of abemaciclib’s polypharmacology. We used molecular and phenotypic profiling by mRNA sequencing, mass spectrometry-based proteomics, and GR-based dose-response assays to characterize the mechanisms of action of the three CDK4/6 inhibitors. Inhibition of CDKs other than CDK4/6 by abemaciclib resulted in an arrest in the G2 phase of the cell cycle, a prolonged inhibition of growth, and cytotoxicity, even in retinoblastoma protein (pRb)-deficient cells. Abemaciclib elicited unique molecular responses at clinically achievable concentrations that are likely to be therapeutically advantageous and prevented cross-resistance with ribociclib and palbociclib. More generally, we propose that multi-omic approaches are required to fully elucidate the spectrum of targets relevant to drug mechanisms of action in cells, and we expect such understanding to assist in stratifying patient populations and in ordering sequential therapies when resistance arises.
Citation Format: Caitlin E. Mills, Marc Hafner, Kartik Subramanian, Chen Chen, Sarah A. Boswell, Robert A. Everley, Dejan Juric, Peter K. Sorger. Omics profiling of CDK4/6 inhibitors reveals functionally important secondary targets of abemaciclib [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr B60.
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Affiliation(s)
| | | | | | - Chen Chen
- 1Harvard Medical School, Boston, MA,
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Mills CE, Subramanian K, Hafner M, Chung M, Boswell SA, Everley RA, Juric D, Sorger PK. Abstract P2-07-03: Systematic characterization of kinase inhibitors reveals heterogeneity in responses by class and cell line. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-07-03] [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
Several publications have addressed concerns surrounding drug response screens by pointing out sources of variability and by presenting recommendations for better experimental methods and more robust analytical approaches. In the presented profiling effort, we integrated the latest advances in drug response measurement and focused on data diversity and quality rather than on breadth. We selected 32 breast cancer cell lines with a strong bias towards triple negative lines as well as 4 cell lines established from relevant patient-derived xenografts. We evaluated a panel of clinically relevant kinase inhibitors using a microscopy-based dose response assay to measure drug potency, and to quantify drug efficacy in terms of growth inhibition (GR metrics) and cell death. The use of the GR metrics to quantify drug sensitivity enabled us to identify and study differences between cytostatic and cytotoxic responses. This systematic dose response dataset is complemented by measurements of baseline transcript expression levels by mRNAseq, quantification of absolute abundance of ˜12,000 proteins, and relative phosphoprotein levels by shotgun mass spectrometry across all cell lines. Additionally, the baseline activity of transcription factors and kinases were inferred from the mRNA (using VIPER) and phosphoprotein (using kinase enrichment analysis) data, respectively. The complementarity of these multi-omics data has allowed us to address questions about the landscape of breast cancer cell lines such as: Where do the patient-derived lines lay relative to the conventional cell lines? How consistent are the landscapes defined by each dataset? How does integration across datasets provide mechanistic insight into signaling pathways that are active in each cancer subtypes? The measured and inferred baseline data were used to build predictors of the observed drug responses with the goal of identifying the biological processes responsible for the differences in sensitivity across drugs and cell lines. Overall the dataset that has been collected is a valuable resource for understanding drug response in triple negative breast cancer, and the molecular mechanisms that influence it.
Citation Format: Mills CE, Subramanian K, Hafner M, Chung M, Boswell SA, Everley RA, Juric D, Sorger PK. Systematic characterization of kinase inhibitors reveals heterogeneity in responses by class and cell line [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-07-03.
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Affiliation(s)
- CE Mills
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - K Subramanian
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - M Hafner
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - M Chung
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - SA Boswell
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - RA Everley
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - D Juric
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
| | - PK Sorger
- Harvard Medical School, Boston, MA; Massachusetts General Hospital, Boston, MA
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22
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Garraway LA, Sorger PK. Abstract PR17: Single-cell analysis reveals an adaptive, slowly-dividing, de-differentiated, drug-resistant cell state selectively inhibitable by drug combinations. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-pr17] [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
Partial responsiveness of tumor cells due to drug adaptation (or tolerance) during the early phase of treatment with targeted therapeutics seems to be essential for creating a population of viable tumor cells from which resistant clones eventually arise. Thus, understanding transient drug adaptation is likely to be important for both improving the initial effectiveness of treatment and delaying or controlling acquired resistance. Despite the wealth of information available about the molecular events and feedback mechanisms leading to drug tolerance or adaptation, most of our knowledge in this area comes from studying drug response in bulk tumor cell populations. Furthermore, the phenotypic consequences of drug adaptation have been studied most frequently at a few fixed time-points, when drug-adapted cells exhibit a high population-average activity in multiple pro-growth or pro-survival signaling cascades. Therefore, it remains unclear how uniform or heterogeneous the early drug adaptation is across individual cells within a tumor cell population, and how the fate of drug-adapted cells is determined by a diversity of early drug-induced adaptive signaling responses. Uncovering the evolution of biochemical and phenotypic heterogeneity in drug-adapted cell populations is key to designing optimal combinations of drugs to overcome resistance and to achieve durable therapy.
In this study, we monitor the responses of BRAFV600E melanoma cells to RAF/MEK inhibitors at the single-cell level in real time using time-lapse live-cell imaging, and then analyze the resulting cell states using transcriptional, biochemical and phenotypic profiling. We found that exposure of tumor cells to RAF/MEK inhibitors elicits heterogeneous and time-variable responses in which some cells die, some arrest and a fraction of slowly-cycling cells adapts to drug, adopting a reversible drug-resistance phenotype characterized by up-regulation of markers of neural crest, a melanocyte precursor, including NGFR (the low affinity nerve growth factor receptor, also known as p75NTR or CD271). The slowly-cycling NFGRHigh state induced by RAF/MEK inhibitors is only transiently stable: after 1-2 weeks of outgrowth in drug-free medium, such cells reset to their initial state as measured by the restoration of RAF/MEK inhibitor sensitivity, accelerated rate of cell division and reduced expression of NGFR. Transcriptional and biochemical profiling of cell lines and human tumors implicates a role for the c-Jun/ECM/FAK/Src cascade in driving the de-differentiated (NGFRHigh) resistance program. We identify multiple drugs targeting this cascade as well as BET bromodomain inhibitors that block the slowly-cycling NGFRHigh state in cell lines and in a BRAFV600E melanoma xenograft model and increase sensitivity to RAF/MEK inhibitors. Our study reveals directly how drug adaptation happens in individual tumor cells leading to emergence of heterogeneous cell sub-populations with reduced drug-sensitivity that may be selectively targeted by drug combinations.
Citation Format: Mohammad Fallahi-Sichani, Verena Becker, Benjamin Izar, Gregory J. Baker, Jia-Ren Lin, Sarah A. Boswell, Levi A. Garraway, Peter K. Sorger. Single-cell analysis reveals an adaptive, slowly-dividing, de-differentiated, drug-resistant cell state selectively inhibitable by drug combinations [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR17.
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Garraway LA, Sorger PK. Abstract 5561: Single-cell analysis reveals an adaptive, transiently heritable, slowly-dividing, drug-resistant state inhibitable by drug combinations. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5561] [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
Adaptation and fractional response of tumor cells to targeted inhibitors of oncogenic pathways creates a population of viable tumor cells from which fully resistant clones can ultimately arise. Thus, understanding transient drug adaptation is key for both improving the effectiveness of treatment and delaying/controlling acquired resistance. Despite the wealth of information available about feedback mechanisms associated with adaptive resistance, most of our knowledge in this area comes from studying drug response in bulk tumor cell populations. Furthermore, the phenotypic consequences of drug adaptation have been often studied at a few fixed time-points, when drug-adapted cells exhibit a high population-average activity in multiple pro-growth signaling cascades. It therefore remains unclear how the initial responses to drug relate to subsequent phenotypes such as cell death or adaptation. This is likely a key point for designing novel approaches to overcome fractional drug response in tumor cells and to achieve durable therapy.
We use real-time live-cell imaging, single-cell analysis and molecular profiling to show that exposure of BRAFV600E melanoma cells to RAF/MEK inhibitors elicits a time-variable and heterogeneous response in which some cells die, some arrest and the remainder adapt to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g. NGFR), a melanocyte precursor, and grow slowly. The drug-induced slowly-cycling NFGRHigh state is only transiently stable, reverting to the drug-naïve state within two weeks of drug withdrawal as measured by the restoration of RAF/MEK inhibitor sensitivity, accelerated rate of cell division and reduced expression of NGFR. Transcriptional and biochemical profiling of cell lines and human tumors implicates a role for the c-Jun/ECM/FAK/Src cascade in driving the de-differentiated resistance program. We identify multiple drugs targeting this cascade as well as BET bromodomain inhibitors that block this resistance program in cell lines and in a BRAFV600E melanoma xenograft model and increase sensitivity and maximal effect (Emax) of RAF/MEK inhibitors. Our study reveals directly how drug adaptation happens in individual tumor cells leading to emergence of heterogeneous cell sub-populations with reduced drug-sensitivity that may be targeted by drug combinations.
Citation Format: Mohammad Fallahi-Sichani, Verena Becker, Benjamin Izar, Gregory J. Baker, Jia-Ren Lin, Sarah A. Boswell, Levi A. Garraway, Peter K. Sorger. Single-cell analysis reveals an adaptive, transiently heritable, slowly-dividing, drug-resistant state inhibitable by drug combinations [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 5561. doi:10.1158/1538-7445.AM2017-5561
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Boswell SA, Snavely A, Landry HM, Churchman LS, Gray JM, Springer M. Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis. Nat Chem Biol 2017; 13:501-507. [PMID: 28263964 DOI: 10.1038/nchembio.2317] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 12/06/2016] [Indexed: 12/27/2022]
Abstract
Pharmacological perturbation is a powerful tool for understanding mRNA synthesis, but identification of the specific steps of this multi-step process that are targeted by small molecules remains challenging. Here we applied strand-specific total RNA sequencing (RNA-seq) to identify and distinguish specific pharmacological effects on transcription and pre-mRNA processing in human cells. We found unexpectedly that the natural product isoginkgetin, previously described as a splicing inhibitor, inhibits transcription elongation. Compared to well-characterized elongation inhibitors that target CDK9, isoginkgetin caused RNA polymerase accumulation within a broader promoter-proximal band, indicating that elongation inhibition by isoginkgetin occurs after release from promoter-proximal pause. RNA-seq distinguished isoginkgetin and CDK9 inhibitors from topoisomerase I inhibition, which alters elongation across gene bodies. We were able to detect these and other specific defects in mRNA synthesis at low sequencing depth using simple metagene-based metrics. These metrics now enable total-RNA-seq-based screening for high-throughput identification of pharmacological effects on individual stages of mRNA synthesis.
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Affiliation(s)
- Sarah A Boswell
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew Snavely
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Heather M Landry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Jesse M Gray
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. Mol Syst Biol 2017; 13:905. [PMID: 28069687 PMCID: PMC5248573 DOI: 10.15252/msb.20166796] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Treatment of BRAF-mutant melanomas with MAP kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use live-cell imaging, single-cell analysis, and molecular profiling to show that exposure of tumor cells to RAF/MEK inhibitors elicits a heterogeneous response in which some cells die, some arrest, and the remainder adapt to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g., NGFR), a melanocyte precursor, and grow slowly. This phenotype is transiently stable, reverting to the drug-naïve state within 9 days of drug withdrawal. Transcriptional profiling of cell lines and human tumors implicates a c-Jun/ECM/FAK/Src cascade in de-differentiation in about one-third of cell lines studied; drug-induced changes in c-Jun and NGFR levels are also observed in xenograft and human tumors. Drugs targeting the c-Jun/ECM/FAK/Src cascade as well as BET bromodomain inhibitors increase the maximum effect (Emax) of RAF/MEK kinase inhibitors by promoting cell killing. Thus, analysis of reversible drug resistance at a single-cell level identifies signaling pathways and inhibitory drugs missed by assays that focus on cell populations.
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Affiliation(s)
- Mohammad Fallahi-Sichani
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Verena Becker
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gregory J Baker
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA .,HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
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Ongusaha PP, Kim HG, Boswell SA, Ridley AJ, Der CJ, Dotto GP, Kim YB, Aaronson SA, Lee SW. RhoE Is a Pro-Survival p53 Target Gene that Inhibits ROCK I-Mediated Apoptosis in Response to Genotoxic Stress. Curr Biol 2016; 26:2221-2222. [PMID: 27554646 DOI: 10.1016/j.cub.2016.07.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M. Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). Mol Cell Proteomics 2014; 14:430-40. [PMID: 25473088 DOI: 10.1074/mcp.m114.044321] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The function of a large percentage of proteins is modulated by post-translational modifications (PTMs). Currently, mass spectrometry (MS) is the only proteome-wide technology that can identify PTMs. Unfortunately, the inability to detect a PTM by MS is not proof that the modification is not present. The detectability of peptides varies significantly making MS potentially blind to a large fraction of peptides. Learning from published algorithms that generally focus on predicting the most detectable peptides we developed a tool that incorporates protein abundance into the peptide prediction algorithm with the aim to determine the detectability of every peptide within a protein. We tested our tool, "Peptide Prediction with Abundance" (PPA), on in-house acquired as well as published data sets from other groups acquired on different instrument platforms. Incorporation of protein abundance into the prediction allows us to assess not only the detectability of all peptides but also whether a peptide of interest is likely to become detectable upon enrichment. We validated the ability of our tool to predict changes in protein detectability with a dilution series of 31 purified proteins at several different concentrations. PPA predicted the concentration dependent peptide detectability in 78% of the cases correctly, demonstrating its utility for predicting the protein enrichment needed to observe a peptide of interest in targeted experiments. This is especially important in the analysis of PTMs. PPA is available as a web-based or executable package that can work with generally applicable defaults or retrained from a pilot MS data set.
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Affiliation(s)
- Jan Muntel
- From the ‡Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Sarah A Boswell
- §Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Shaojun Tang
- From the ‡Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Saima Ahmed
- From the ‡Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Ilan Wapinski
- §Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Greg Foley
- §Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Hanno Steen
- From the ‡Departments of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA;
| | - Michael Springer
- §Department of Systems Biology, Harvard Medical School, Boston, MA
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Muñiz VA, Srinivasan S, Boswell SA, Meinhold DW, Childs T, Osuna R, Colón W. The role of the local environment of engineered Tyr to Trp substitutions for probing the denaturation mechanism of FIS. Protein Sci 2011; 20:302-12. [PMID: 21280122 DOI: 10.1002/pro.561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Factor for inversion stimulation (FIS), a 98-residue homodimeric protein, does not contain tryptophan (Trp) residues but has four tyrosine (Tyr) residues located at positions 38, 51, 69, and 95. The equilibrium denaturation of a P61A mutant of FIS appears to occur via a three-state (N(2) ⇆ I(2) ⇆ 2U) process involving a dimeric intermediate (I(2)). Although it was suggested that this intermediate had a denatured C-terminus, direct evidence was lacking. Therefore, three FIS double mutants, P61A/Y38W, P61A/Y69W, and P61A/Y95W were made, and their denaturation was monitored by circular dichroism and Trp fluorescence. Surprisingly, the P61A/Y38W mutant best monitored the N(2) ⇆ I(2) transition, even though Trp38 is buried within the dimer removed from the C-terminus. In addition, although Trp69 is located on the protein surface, the P61A/Y69W FIS mutant exhibited clearly biphasic denaturation curves. In contrast, P61A/Y95W FIS was the least effective in decoupling the two transitions, exhibiting a monophasic fluorescence transition with modest concentration-dependence. When considering the local environment of the Trp residues and the effect of each mutation on protein stability, these results not only confirm that P61A FIS denatures via a dimeric intermediate involving a disrupted C-terminus but also suggest the occurrence of conformational changes near Tyr38. Thus, the P61A mutation appears to compromise the denaturation cooperativity of FIS by failing to propagate stability to those regions involved mostly in intramolecular interactions. Furthermore, our results highlight the challenge of anticipating the optimal location to engineer a Trp residue for investigating the denaturation mechanism of even small proteins.
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Affiliation(s)
- Virginia A Muñiz
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Hwang SO, Boswell SA, Seo JS, Lee SW. Novel oxidative stress-responsive gene ERS25 functions as a regulator of the heat-shock and cell death response. J Biol Chem 2008; 283:13063-9. [PMID: 18326488 DOI: 10.1074/jbc.m709656200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the yeast p24 family, including Emp24p and Erv25p, exist as heteromeric complexes that have been proposed to cycle between the endoplasmic reticulum (ER) and Golgi compartments. The specific functions and sites of action of p24 proteins are still unknown. Here we identified a human homolog of the yeast p24 family of proteins, named ERS25 (endoplasmic reticulum stress-response protein 25), and investigated its role in stress response. ERS25 is predicted to have an ER localization signal peptide, a GOLD (Golgi dynamics) domain, which is found in several eukaryotic Golgi and lipid-trafficking proteins, a coiled-coil region, and a transmembrane domain. We demonstrate that ERS25 is localized to the ER and is induced by ER-specific stress, heat shock, and oxidative stress. The selective induction of ERS25 by brefeldin A, but not tunicamycin, implicates the involvement of ERS25 in protein trafficking between the ER and the Golgi. Small interfering RNA-mediated inhibition of ERS25 results in a significant decrease in apoptosis as well as a reduction of reactive oxygen species induced by oxidative stress. Moreover, ERS25 depletion results in a significant increase in the levels of the ER chaperone HSP70 in response to heat-shock stress through increased levels of HSF-1. We also found that inhibition of ERS25 induction in response to heat shock enhanced the binding of HSP70 to Apaf-1, which is likely to interfere in stress-mediated apoptosis. Together, the data presented here demonstrate that ERS25 may play a critical role in regulation of heat-shock response and apoptosis.
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Affiliation(s)
- Sun Ok Hwang
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
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Abstract
A crucial unresolved issue about the genotoxic stress response is how the activation of the p53 tumor suppressor can lead either to cell cycle arrest and DNA repair or to apoptosis. p53 is one of the most important tumor suppressor proteins in the cell to prevent to heritable transfer of damaged DNA. In response to different stress conditions p53 rapidly accumulates and functions as a sequence specific DNA-binding transcription factor to regulate a large number of target genes. Activation of p53 has two major outcomes: cell cycle arrest or apoptosis. In this review we attempt to enumerate the different modifications and co-factors that influence p53 promoter selection and demonstrate how p53 chooses life or death for the cell.
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Affiliation(s)
- Sanjeev Das
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, USA
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Ongusaha PP, Kim HG, Boswell SA, Ridley AJ, Der CJ, Dotto GP, Kim YB, Aaronson SA, Lee SW. RhoE is a pro-survival p53 target gene that inhibits ROCK I-mediated apoptosis in response to genotoxic stress. Curr Biol 2006; 16:2466-72. [PMID: 17174923 PMCID: PMC2779528 DOI: 10.1016/j.cub.2006.10.056] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [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: 05/10/2006] [Revised: 10/25/2006] [Accepted: 10/27/2006] [Indexed: 01/14/2023]
Abstract
The Rho family of GTPases regulates many aspects of cellular behavior through alterations to the actin cytoskeleton . The majority of the Rho family proteins function as molecular switches cycling between the active, GTP-bound and the inactive, GDP-bound conformations . Unlike typical Rho-family proteins, the Rnd subfamily members, including Rnd1, Rnd2, RhoE (also known as Rnd3), and RhoH, are GTPase deficient and are thus expected to be constitutively active . Here, we identify an unexpected role for RhoE/Rnd3 in the regulation of the p53-mediated stress response. We show that RhoE is a transcriptional p53 target gene and that genotoxic stress triggers actin depolymerization, resulting in actin-stress-fiber disassembly through p53-dependent RhoE induction. Silencing of RhoE induction in response to genotoxic stress maintains stress fiber formation and strikingly increases apoptosis, implying an antagonistic role for RhoE in p53-dependent apoptosis. We found that RhoE inhibits ROCK I (Rho-associated kinase I) activity during genotoxic stress and thereby suppresses apoptosis. We demonstrate that the p53-mediated induction of RhoE in response to DNA damage favors cell survival partly through inhibition of ROCK I-mediated apoptosis. Thus, RhoE is anticipated to function by regulating ROCK I signaling to control the balance between cell survival and cell death in response to genotoxic stress.
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Affiliation(s)
- Pat P. Ongusaha
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129
| | - Hyung-Gu Kim
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129
| | - Sarah A. Boswell
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129
| | - Anne J. Ridley
- Ludwig Institute for Cancer Research, Royal Free and University College School of Medicine, London, UK
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - G. Paolo Dotto
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129
| | - Young-Bum Kim
- Department of Medicine, Beth Israel Deaconess Medical Center, and, Harvard Medical School, Boston, MA 02215
| | - Stuart A. Aaronson
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029
| | - Sam W. Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129
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Abstract
RhoE, a p53 target gene, was identified as a critical factor for the survival of human keratinocytes in response to UVB. The Rho family of GTPases regulates many aspects of cellular behavior through alterations to the actin cytoskeleton, acting as molecular switches cycling between the active, GTP-bound and the inactive, GDP-bound conformations. Unlike typical Rho family proteins, RhoE (also known as Rnd3) is GTPase-deficient and thus expected to be constitutively active. In this study, we investigated the response of cultured human keratinocyte cells to UVB irradiation. RhoE protein levels increase upon exposure to UVB, and ablation of RhoE induction through small interfering RNA resulted in a significant increase in apoptosis and a reduction in the levels of the pro-survival targets p21, Cox-2, and cyclin D1, as well as an increase of reactive oxygen species levels when compared with control cells. These data indicate that RhoE is a pro-survival factor acting upstream of p38, JNK, p21, and cyclin D1. HaCat cells expressing small interfering RNA to p53 indicate that RhoE functions independently of its known associates, p53 and Rho-associated kinase I (ROCK I). Targeted expression of RhoE in epidermis using skin-specific transgenic mouse model resulted in a significant reduction in the number of apoptotic cells following UVB irradiation. Thus, RhoE induction counteracts UVB-induced apoptosis and may serve as a novel target for the prevention of UVB-induced photodamage regardless of p53 status.
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Affiliation(s)
- Sarah A Boswell
- Dermatology Division, University of Washington, Seattle, Washington 98109
| | - Pat P Ongusaha
- Cutaneous Biology Research Center (CBRC), Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129 and the
| | - Paul Nghiem
- Dermatology Division, University of Washington, Seattle, Washington 98109
| | - Sam W Lee
- Cutaneous Biology Research Center (CBRC), Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129 and the.
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Kissick MW, Boswell SA, Jeraj R, Mackie TR. Confirmation, refinement, and extension of a study in intrafraction motion interplay with sliding jaw motion. Med Phys 2005; 32:2346-2350. [PMID: 16121591 DOI: 10.1118/1.1935774] [Citation(s) in RCA: 52] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 04/21/2005] [Indexed: 11/07/2022] Open
Abstract
The interplay between a constant scan speed and intrafraction oscillatory motion produces interesting fluence intensity modulations along the axis of motion that are sensitive to the motion function, as originally shown in a classic paper by Yu et al. [Phys. Med. Biol. 43, 91-104 (1998)]. The fluence intensity profiles are explored in this note for an intuitive understanding, then compared with Yu et al., and finally further explored for the effects of low scan speed and random components of both intrafraction and interfraction motion. At slow scan speeds typical of helical tomotherapy, these fluence intensity modulations are only a few percent. With the addition of only a small amount of cycle-to-cycle randomness in frequency and amplitude, the fluence intensity profiles change dramatically. It is further shown that after a typical 30-fraction treatment, the sensitivities displayed in the single fraction fluence intensity profiles greatly diminish.
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Affiliation(s)
- Michael W Kissick
- Department of Medical Physics, University of Wisconsin Medical School, Madison, Wisconsin 53706-1532, USA.
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Boswell SA, Jeraj R, Ruchala KJ, Olivera GH, Jaradat HA, James JA, Gutierrez A, Pearson D, Frank G, Mackie TR. A novel method to correct for pitch and yaw patient setup errors in helical tomotherapy. Med Phys 2005; 32:1630-9. [PMID: 16013722 DOI: 10.1118/1.1914543] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
An accurate means of determining and correcting for daily patient setup errors is important to the cancer outcome in radiotherapy. While many tools have been developed to detect setup errors, difficulty may arise in accurately adjusting the patient to account for the rotational error components. A novel, automated method to correct for rotational patient setup errors in helical tomotherapy is proposed for a treatment couch that is restricted to motion along translational axes. In tomotherapy, only a narrow superior/inferior section of the target receives a dose at any instant, thus rotations in the sagittal and coronal planes may be approximately corrected for by very slow continuous couch motion in a direction perpendicular to the scanning direction. Results from proof-of-principle tests indicate that the method improves the accuracy of treatment delivery, especially for long and narrow targets. Rotational corrections about an axis perpendicular to the transverse plane continue to be implemented easily in tomotherapy by adjustment of the initial gantry angle.
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Affiliation(s)
- Sarah A Boswell
- Department of Medical Physics, University of Wisconsin, Madison, Wisconsin 53706, USA.
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Abstract
Over 100 mutants of the enzyme Cu/Zn superoxide dismutase (SOD) have been implicated in the neurodegenerative disease familial amyotrophic lateral sclerosis (FALS). Growing evidence suggests that the aggregation of SOD mutants may play a causative role in FALS and that aberrant copper chemistry, decreased thermodynamic stability, and decreased affinity for metals may contribute independently or synergistically to this process. Since the loss of the copper and zinc ions significantly decreases the thermodynamic stability of SOD, it is expected that this would also decrease its kinetic stability, thereby facilitating partial or global unfolding transitions that may lead to misfolding and aggregation. Here we used wild-type (WT) SOD and five FALS-related mutants (G37R, H46R, G85R, D90A, and L144F) to show that the metals contribute significantly to the kinetic stability of the protein, with demetalated (apo) SOD showing acid-induced unfolding rates about 60-fold greater than the metalated (holo) protein. However, the unfolding rates of SOD WT and mutants were similar to each other in both the holo and apo states, indicating that regardless of the effect of mutation on thermodynamic stability, the kinetic barrier toward SOD unfolding is dependent on the presence of metals. Thus, these results suggest that pathogenic SOD mutations that do not significantly alter the stability of the protein may still lead to SOD aggregation by compromising its ability to bind or retain its metals and thereby decrease its kinetic stability. Furthermore, the mutant-like decrease in the kinetic stability of apo WT SOD raises the possibility that the loss of metals in WT SOD may be involved in nonfamilial forms of ALS.
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Affiliation(s)
- Sandra M Lynch
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, USA
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Scalea TM, Boswell SA, Scott JD, Mitchell KA, Kramer ME, Pollak AN. External fixation as a bridge to intramedullary nailing for patients with multiple injuries and with femur fractures: damage control orthopedics. J Trauma 2000; 48:613-21; discussion 621-3. [PMID: 10780592 DOI: 10.1097/00005373-200004000-00006] [Citation(s) in RCA: 286] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The advantages of early fracture fixation in patients with multiple injuries have been challenged recently, particularly in patients with head injury. External fixation (EF) has been used to stabilize pelvic fractures after multiple injury. It potentially offers similar benefits to intramedullary nail (IMN) in long-bone fractures and may obviate some of the risks. We report on the use of EF as a temporary fracture fixation in a group of patients with multiple injuries and with femoral shaft fractures. METHODS Retrospective review of charts and registry data of patients admitted to our Level 1 trauma center July of 1995 to June of 1998. Forty-three patients initially treated with EF of the femur were compared to 284 patients treated with primary IMN of the femur. RESULTS Patients treated with EF had more severe injuries with significantly higher Injury Severity Scores (26.8 vs. 16.8) and required significantly more fluid (11.9 vs. 6.2 liters) and blood (1.5 vs. 1.0 liters) in the initial 24 hours. Glasgow Coma Scale score was lower (p < 0.01) in those treated with EF (11 vs. 14.2). Twelve patients (28%) had head injuries severe enough to require intracranial pressure monitoring. All 12 required therapy for intracranial pressure control with mannitol (100%), barbiturates (75%), and/or hyperventilation (75%). Most patients had more than one contraindication to IMN, including head injury in 46% of cases, hemodynamic instability in 65%, thoracoabdominal injuries in 51%, and/or other serious injuries in 46%, most often multiple orthopedic injuries. Median operating room time for EF was 35 minutes with estimated blood loss of 90 mL. IMN was performed in 35 of 43 patients at a mean of 4.8 days after EF. Median operating room time for IMN was 135 minutes with an estimated blood loss of 400 mL. One patient died before IMN. One other patient with a mangled extremity was treated with amputation after EF. There was one complication of EF, i.e., bleeding around a pin site, which was self-limited. Four patients in the EF group died, three from head injuries and one from acute organ failure. No death was secondary to the fracture treatment selected. One patient who had EF followed by IMN had bone infection and another had acute hardware failure. CONCLUSION EF is a viable alternative to attain temporary rigid stabilization in patients with multiple injuries. It is rapid, causes negligible blood loss, and can be followed by IMN when the patient is stabilized. There were minimal orthopedic complications.
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Affiliation(s)
- T M Scalea
- R. Adams Cowley Shock Trauma Center, University of Maryland Medical System, Program in Trauma, University of Maryland School of Medicine, Baltimore 21201-1595, USA
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