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Pizzato HA, Alonso-Guallart P, Woods J, Johannesson B, Connelly JP, Fehniger TA, Atkinson JP, Pruett-Miller SM, Monsma FJ, Bhattacharya D. Engineering human pluripotent stem cell lines to evade xenogeneic transplantation barriers. Stem Cell Reports 2024; 19:596. [PMID: 38518782 DOI: 10.1016/j.stemcr.2024.03.006] [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: 03/24/2024] Open
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2
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Singh S, Fang J, Jin H, Van de Velde LA, Wu Q, Cortes A, Morton CL, Woolard MA, Quarni W, Steele JA, Connelly JP, He L, Thorne R, Turner G, Confer T, Johnson M, Caufield WV, Freeman BB, Lockey T, Pruett-Miller SM, Wang R, Davidoff AM, Thomas PG, Yang J. RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticity. bioRxiv 2024:2024.03.21.586157. [PMID: 38585889 PMCID: PMC10996557 DOI: 10.1101/2024.03.21.586157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown and how to eradicate neuroblastoma regardless of their cell states is a clinical challenge. To better understand the lineage switch of neuroblastoma in chemoresistance, we comprehensively defined the transcriptomic and epigenetic map of ADRN and MES types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We showed that cancer cells not only undergo a bidirectional switch between ADRN and MES states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. The lineage alterations are coupled with epigenetic reprogramming and dependency switch of lineage-specific transcription factors, epigenetic modifiers and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
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3
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Pizzato HA, Alonso-Guallart P, Woods J, Connelly JP, Fehniger TA, Atkinson JP, Pruett-Miller SM, Monsma FJ, Bhattacharya D. Engineering human pluripotent stem cell lines to evade xenogeneic transplantation barriers. Stem Cell Reports 2024; 19:299-313. [PMID: 38215755 PMCID: PMC10874864 DOI: 10.1016/j.stemcr.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/14/2024] Open
Abstract
Successful allogeneic human pluripotent stem cell (hPSC)-derived therapies must overcome immunological rejection by the recipient. To build reagents to define these barriers, we genetically ablated β2M, TAP1, CIITA, CD74, MICA, and MICB to limit expression of HLA-I, HLA-II, and natural killer (NK) cell activating ligands in hPSCs. Transplantation of these cells that also expressed covalent single chain trimers of Qa1 and H2-Kb to inhibit NK cells and CD55, Crry, and CD59 to inhibit complement deposition led to persistent teratomas in wild-type mice. Transplantation of HLA-deficient hPSCs into mice genetically deficient in complement and depleted of NK cells also led to persistent teratomas. Thus, T cell, NK cell, and complement evasion are necessary to prevent immunological rejection of hPSCs and their progeny. These cells and versions expressing human orthologs of immune evasion factors can be used to define cell type-specific immune barriers and conduct preclinical testing in immunocompetent mouse models.
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Affiliation(s)
- Hannah A Pizzato
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | | | - James Woods
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, USA
| | - Jon P Connelly
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Todd A Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John P Atkinson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Frederick J Monsma
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, USA
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA; Department of Surgery, University of Arizona College of Medicine, Tucson, AZ 85724, USA; BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA.
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4
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Zhou P, Shi H, Huang H, Sun X, Yuan S, Chapman NM, Connelly JP, Lim SA, Saravia J, Kc A, Pruett-Miller SM, Chi H. Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer. Nature 2023; 624:154-163. [PMID: 37968405 PMCID: PMC10700132 DOI: 10.1038/s41586-023-06733-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 10/10/2023] [Indexed: 11/17/2023]
Abstract
CD8+ cytotoxic T cells (CTLs) orchestrate antitumour immunity and exhibit inherent heterogeneity1,2, with precursor exhausted T (Tpex) cells but not terminally exhausted T (Tex) cells capable of responding to existing immunotherapies3-7. The gene regulatory network that underlies CTL differentiation and whether Tex cell responses can be functionally reinvigorated are incompletely understood. Here we systematically mapped causal gene regulatory networks using single-cell CRISPR screens in vivo and discovered checkpoints for CTL differentiation. First, the exit from quiescence of Tpex cells initiated successive differentiation into intermediate Tex cells. This process is differentially regulated by IKAROS and ETS1, the deficiencies of which dampened and increased mTORC1-associated metabolic activities, respectively. IKAROS-deficient cells accumulated as a metabolically quiescent Tpex cell population with limited differentiation potential following immune checkpoint blockade (ICB). Conversely, targeting ETS1 improved antitumour immunity and ICB efficacy by boosting differentiation of Tpex to intermediate Tex cells and metabolic rewiring. Mechanistically, TCF-1 and BATF are the targets for IKAROS and ETS1, respectively. Second, the RBPJ-IRF1 axis promoted differentiation of intermediate Tex to terminal Tex cells. Accordingly, targeting RBPJ enhanced functional and epigenetic reprogramming of Tex cells towards the proliferative state and improved therapeutic effects and ICB efficacy. Collectively, our study reveals that promoting the exit from quiescence of Tpex cells and enriching the proliferative Tex cell state act as key modalities for antitumour effects and provides a systemic framework to integrate cell fate regulomes and reprogrammable functional determinants for cancer immunity.
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Affiliation(s)
- Peipei Zhou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongling Huang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Sun
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sujing Yuan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole M Chapman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seon Ah Lim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jordy Saravia
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anil Kc
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Malireddi RKS, Bynigeri RR, Mall R, Connelly JP, Pruett-Miller SM, Kanneganti TD. Inflammatory cell death, PANoptosis, screen identifies host factors in coronavirus innate immune response as therapeutic targets. Commun Biol 2023; 6:1071. [PMID: 37864059 PMCID: PMC10589293 DOI: 10.1038/s42003-023-05414-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
The COVID-19 pandemic, caused by the β-coronavirus (β-CoV) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to cause significant global morbidity and mortality. While vaccines have reduced the overall number of severe infections, there remains an incomplete understanding of viral entry and innate immune activation, which can drive pathology. Innate immune responses characterized by positive feedback between cell death and cytokine release can amplify the inflammatory cytokine storm during β-CoV-mediated infection to drive pathology. Therefore, there remains an unmet need to understand innate immune processes in response to β-CoV infections to identify therapeutic strategies. To address this gap, here we used an MHV model and developed a whole genome CRISPR-Cas9 screening approach to elucidate host molecules required for β-CoV infection and inflammatory cell death, PANoptosis, in macrophages, a sentinel innate immune cell. Our screen was validated through the identification of the known MHV receptor Ceacam1 as the top hit, and its deletion significantly reduced viral replication due to loss of viral entry, resulting in a downstream reduction in MHV-induced cell death. Moreover, this screen identified several other host factors required for MHV infection-induced macrophage cell death. Overall, these findings demonstrate the feasibility and power of using genome-wide PANoptosis screens in macrophage cell lines to accelerate the discovery of key host factors in innate immune processes and suggest new targets for therapeutic development to prevent β-CoV-induced pathology.
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Affiliation(s)
- R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ratnakar R Bynigeri
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, P.O. Box 9639, United Arab Emirates
| | - Jon P Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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6
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Chen YH, Connelly JP, Florian C, Cui X, Pruett-Miller SM. Short tandem repeat profiling via next-generation sequencing for cell line authentication. Dis Model Mech 2023; 16:dmm050150. [PMID: 37712227 PMCID: PMC10618599 DOI: 10.1242/dmm.050150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Cell lines are indispensable models for modern biomedical research. A large part of their usefulness derives from the ability of a cell line to proliferate over multiple passages (often indefinitely), allowing multiple experiments to be performed. However, over time, cell line identity and purity can be compromised by human errors. Cross-contamination from other cell lines and complete misidentification are both possible. Routine cell line authentication is a necessary preventive measure and has become a requirement for many funding applications and publications. Short tandem repeat (STR) profiling is the most common method for cell line authentication and is usually carried out using standard polymerase chain reaction-capillary electrophoresis analysis (STR-CE). Here, we evaluated next-generation sequencing (NGS)-based STR profiling of human and mouse cell lines at 18 and 15 loci, respectively, in a high-throughput format. Using the Python program STRight, we demonstrate that NGS-based analysis (STR-NGS) is superior to standard STR-CE in terms of the ability to report the sequence context of repeat motifs, sensitivity and flexible multiplexing capability. STR-NGS is thus a valuable alternative for cell line authentication.
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Affiliation(s)
- Yi-Hsien Chen
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jon P. Connelly
- Center for Advanced Genome Engineering (CAGE), Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Colin Florian
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Xiaoxia Cui
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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7
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Park CS, Yoshihara H, Gao Q, Qu C, Iacobucci I, Ghate PS, Connelly JP, Pruett-Miller SM, Wagner B, Robinson CG, Mishra A, Peng J, Yang L, Rankovic Z, Finkelstein D, Luger S, Litzow M, Paietta EM, Hebbar N, Velasquez MP, Mullighan CG. Stromal-induced epithelial-mesenchymal transition induces targetable drug resistance in acute lymphoblastic leukemia. Cell Rep 2023; 42:112804. [PMID: 37453060 PMCID: PMC10529385 DOI: 10.1016/j.celrep.2023.112804] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 04/05/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
The bone marrow microenvironment (BME) drives drug resistance in acute lymphoblastic leukemia (ALL) through leukemic cell interactions with bone marrow (BM) niches, but the underlying mechanisms remain unclear. Here, we show that the interaction between ALL and mesenchymal stem cells (MSCs) through integrin β1 induces an epithelial-mesenchymal transition (EMT)-like program in MSC-adherent ALL cells, resulting in drug resistance and enhanced survival. Moreover, single-cell RNA sequencing analysis of ALL-MSC co-culture identifies a hybrid cluster of MSC-adherent ALL cells expressing both B-ALL and MSC signature genes, orchestrated by a WNT/β-catenin-mediated EMT-like program. Blockade of interaction between β-catenin and CREB binding protein impairs the survival and drug resistance of MSC-adherent ALL cells in vitro and results in a reduction in leukemic burden in vivo. Targeting of this WNT/β-catenin-mediated EMT-like program is a potential therapeutic approach to overcome cell extrinsically acquired drug resistance in ALL.
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Affiliation(s)
- Chun Shik Park
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hiroki Yoshihara
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Qingsong Gao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pankaj S Ghate
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ben Wagner
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Camenzind G Robinson
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Selina Luger
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19106, USA
| | - Mark Litzow
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Nikhil Hebbar
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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8
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Fang J, Singh S, Cheng C, Natarajan S, Sheppard H, Abu-Zaid A, Durbin AD, Lee HW, Wu Q, Steele J, Connelly JP, Jin H, Chen W, Fan Y, Pruett-Miller SM, Rehg JE, Koo SC, Santiago T, Emmons J, Cairo S, Wang R, Glazer ES, Murphy AJ, Chen T, Davidoff AM, Armengol C, Easton J, Chen X, Yang J. Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma. Nat Commun 2023; 14:4003. [PMID: 37414763 PMCID: PMC10326052 DOI: 10.1038/s41467-023-39717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
A lack of relevant genetic models and cell lines hampers our understanding of hepatoblastoma pathogenesis and the development of new therapies for this neoplasm. Here, we report an improved MYC-driven hepatoblastoma-like murine model that recapitulates the pathological features of embryonal type of hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of the human disease. Single-cell RNA-sequencing and spatial transcriptomics identify distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we map cancer dependency genes using CRISPR-Cas9 screening and identify druggable targets shared with human hepatoblastoma (e.g., CDK7, CDK9, PRMT1, PRMT5). Our screen also reveals oncogenes and tumor suppressor genes in hepatoblastoma that engage multiple, druggable cancer signaling pathways. Chemotherapy is critical for human hepatoblastoma treatment. A genetic mapping of doxorubicin response by CRISPR-Cas9 screening identifies modifiers whose loss-of-function synergizes with (e.g., PRKDC) or antagonizes (e.g., apoptosis genes) the effect of chemotherapy. The combination of PRKDC inhibition and doxorubicin-based chemotherapy greatly enhances therapeutic efficacy. These studies provide a set of resources including disease models suitable for identifying and validating potential therapeutic targets in human high-risk hepatoblastoma.
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Affiliation(s)
- Jie Fang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shivendra Singh
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Changde Cheng
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraman Natarajan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ha Won Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jacob Steele
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerold E Rehg
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Teresa Santiago
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joseph Emmons
- VPC Diagnostic Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefano Cairo
- Champions Oncology, 1330 Piccard dr, Rockville, MD, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Hematology/Oncology & BMT, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Evan S Glazer
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Carolina Armengol
- Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Translational Program in Cancer Research (CARE), Badalona, Spain
- CIBER, Hepatic and Digestive Diseases, Barcelona, Spain
- CIBERehd, Madrid, Spain
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA.
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9
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Pizzato HA, Alonso-Guallart P, Woods J, Johannesson B, Connelly JP, Fehniger TA, Atkinson JP, Pruett-Miller SM, Monsma FJ, Bhattacharya D. Engineering Human Pluripotent Stem Cell Lines to Evade Xenogeneic Transplantation Barriers. bioRxiv 2023:2023.06.27.546594. [PMID: 37425790 PMCID: PMC10326974 DOI: 10.1101/2023.06.27.546594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Allogeneic human pluripotent stem cell (hPSC)-derived cells and tissues for therapeutic transplantation must necessarily overcome immunological rejection by the recipient. To define these barriers and to create cells capable of evading rejection for preclinical testing in immunocompetent mouse models, we genetically ablated β2m, Tap1, Ciita, Cd74, Mica, and Micb to limit expression of HLA-I, HLA-II, and natural killer cell activating ligands in hPSCs. Though these and even unedited hPSCs readily formed teratomas in cord blood-humanized immunodeficient mice, grafts were rapidly rejected by immunocompetent wild-type mice. Transplantation of these cells that also expressed covalent single chain trimers of Qa1 and H2-Kb to inhibit natural killer cells and CD55, Crry, and CD59 to inhibit complement deposition led to persistent teratomas in wild-type mice. Expression of additional inhibitory factors such as CD24, CD47, and/or PD-L1 had no discernible impact on teratoma growth or persistence. Transplantation of HLA-deficient hPSCs into mice genetically deficient in complement and depleted of natural killer cells also led to persistent teratomas. Thus, T cell, NK cell, and complement evasion are necessary to prevent immunological rejection of hPSCs and their progeny. These cells and versions expressing human orthologs of immune evasion factors can be used to refine tissue- and cell type-specific immune barriers, and to conduct preclinical testing in immunocompetent mouse models.
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Affiliation(s)
- Hannah A. Pizzato
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | | | - James Woods
- The New York Stem Cell Foundation Research Institute, New York, NY, USA
| | | | - Jon P. Connelly
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Todd A. Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - John P. Atkinson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Shondra M. Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
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10
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Malireddi RS, Bynigeri RR, Mall R, Nadendla EK, Connelly JP, Pruett-Miller SM, Kanneganti TD. Whole-genome CRISPR screen identifies RAVER1 as a key regulator of RIPK1-mediated inflammatory cell death, PANoptosis. iScience 2023; 26:106938. [PMID: 37324531 PMCID: PMC10265528 DOI: 10.1016/j.isci.2023.106938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Transforming growth factor-β-activated kinase 1 (TAK1) is a central regulator of innate immunity, cell death, inflammation, and cellular homeostasis. Therefore, many pathogens carry TAK1 inhibitors (TAK1i). As a host strategy to counteract this, inhibition or deletion of TAK1 induces spontaneous inflammatory cell death, PANoptosis, through the RIPK1-PANoptosome complex, containing the NLRP3 inflammasome and caspase-8/FADD/RIPK3 as integral components; however, PANoptosis also promotes pathological inflammation. Therefore, understanding molecular mechanisms that regulate TAK1i-induced cell death is essential. Here, we report a genome-wide CRISPR screen in macrophages that identified TAK1i-induced cell death regulators, including polypyrimidine tract-binding (PTB) protein 1 (PTBP1), a known regulator of RIPK1, and a previously unknown regulator RAVER1. RAVER1 blocked alternative splicing of Ripk1, and its genetic depletion inhibited TAK1i-induced, RIPK1-mediated inflammasome activation and PANoptosis. Overall, our CRISPR screen identified several positive regulators of PANoptosis. Moreover, our study highlights the utility of genome-wide CRISPR-Cas9 screens in myeloid cells for comprehensive characterization of complex cell death pathways to discover therapeutic targets.
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Affiliation(s)
| | - Ratnakar R. Bynigeri
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Eswar Kumar Nadendla
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jon P. Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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11
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Abstract
Genome editing using the CRISPR-Cas9 platform creates precise modifications in cells and whole organisms. Although knockout (KO) mutations can occur at high frequencies, determining the editing rates in a pool of cells or selecting clones that contain only KO alleles can be a challenge. User-defined knock-in (KI) modifications are achieved at much lower rates, making the identification of correctly modified clones even more challenging. The high-throughput format of targeted next-generation sequencing (NGS) provides a platform allowing sequence information to be gathered from a one to thousands of samples. However, it also poses a challenge in terms of analyzing the large amount of data that is generated. In this chapter, we present and discuss CRIS.py, a simple and highly versatile Python-based program for analyzing NGS data for genome-editing outcomes. CRIS.py can be used to analyze sequencing results for any kind of modification or multiplex modifications specified by the user. Moreover, CRIS.py runs on all fastq files found in a directory, thereby concurrently analyzing all uniquely indexed samples. CRIS.py results are consolidated into two summary files, which allows users to sort and filter results and quickly identify the clones (or animals) of greatest interest.
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Affiliation(s)
- Shilpa Narina
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis, TN, USA
- St. Jude Children's Research Hospital, Center for Advanced Genome Engineering, Memphis, TN, USA
| | - Jon P Connelly
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis, TN, USA
- St. Jude Children's Research Hospital, Center for Advanced Genome Engineering, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis, TN, USA.
- St. Jude Children's Research Hospital, Center for Advanced Genome Engineering, Memphis, TN, USA.
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12
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Karki R, Lee S, Mall R, Pandian N, Wang Y, Sharma BR, Malireddi RKS, Yang D, Trifkovic S, Steele JA, Connelly JP, Vishwanath G, Sasikala M, Reddy DN, Vogel P, Pruett-Miller SM, Webby R, Jonsson CB, Kanneganti TD. ZBP1-dependent inflammatory cell death, PANoptosis, and cytokine storm disrupt IFN therapeutic efficacy during coronavirus infection. Sci Immunol 2022; 7:eabo6294. [PMID: 35587515 PMCID: PMC9161373 DOI: 10.1126/sciimmunol.abo6294] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [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: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), continues to cause substantial morbidity and mortality in the ongoing global pandemic. Understanding the fundamental mechanisms that govern innate immune and inflammatory responses during SARS-CoV-2 infection is critical for developing effective therapeutic strategies. Whereas interferon (IFN)-based therapies are generally expected to be beneficial during viral infection, clinical trials in COVID-19 have shown limited efficacy and potential detrimental effects of IFN treatment during SARS-CoV-2 infection. However, the underlying mechanisms responsible for this failure remain unknown. In this study, we found that IFN induced Z-DNA-binding protein 1 (ZBP1)-mediated inflammatory cell death, PANoptosis, in human and murine macrophages and in the lungs of mice infected with β-coronaviruses, including SARS-CoV-2 and mouse hepatitis virus (MHV). In patients with COVID-19, expression of the innate immune sensor ZBP1 was increased in immune cells from those who succumbed to the disease compared with those who recovered, further suggesting a link between ZBP1 and pathology. In mice, IFN-β treatment after β-coronavirus infection increased lethality, and genetic deletion of Zbp1 or its Zα domain suppressed cell death and protected the mice from IFN-mediated lethality during β-coronavirus infection. Overall, our results identify that ZBP1 induced during coronavirus infection limits the efficacy of IFN therapy by driving inflammatory cell death and lethality. Therefore, inhibiting ZBP1 activity may improve the efficacy of IFN therapy, paving the way for the development of new and critically needed therapeutics for COVID-19 as well as other infections and inflammatory conditions where IFN-mediated cell death and pathology occur.
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Affiliation(s)
- Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - SangJoon Lee
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nagakannan Pandian
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yaqiu Wang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - RK Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dong Yang
- UTHSC Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jacob A. Steele
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jon P. Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Gella Vishwanath
- Institute of Pulmonary Medicine and Sleep Disorders, Continental Hospitals, Asian Institute of Gastroenterology, Hyderabad, India
| | - Mitnala Sasikala
- Department of Basic Science, Asian Healthcare Foundation, Asian Institute of Gastroenterology, Hyderabad, India
| | - Duvvur Nageshwar Reddy
- Department of Medical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | - Peter Vogel
- Animal Resources Center and the Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Colleen Beth Jonsson
- Department of Microbiology, Immunology, & Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
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13
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Guo A, Huang H, Zhu Z, Chen MJ, Shi H, Yuan S, Sharma P, Connelly JP, Liedmann S, Dhungana Y, Li Z, Haydar D, Yang M, Beere H, Yustein JT, DeRenzo C, Pruett-Miller SM, Crawford JC, Krenciute G, Roberts CWM, Chi H, Green DR. cBAF complex components and MYC cooperate early in CD8 + T cell fate. Nature 2022; 607:135-141. [PMID: 35732731 PMCID: PMC9623036 DOI: 10.1038/s41586-022-04849-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 05/10/2022] [Indexed: 01/03/2023]
Abstract
The identification of mechanisms to promote memory T (Tmem) cells has important implications for vaccination and anti-cancer immunotherapy1-4. Using a CRISPR-based screen for negative regulators of Tmem cell generation in vivo5, here we identify multiple components of the mammalian canonical BRG1/BRM-associated factor (cBAF)6,7. Several components of the cBAF complex are essential for the differentiation of activated CD8+ T cells into T effector (Teff) cells, and their loss promotes Tmem cell formation in vivo. During the first division of activated CD8+ T cells, cBAF and MYC8 frequently co-assort asymmetrically to the two daughter cells. Daughter cells with high MYC and high cBAF display a cell fate trajectory towards Teff cells, whereas those with low MYC and low cBAF preferentially differentiate towards Tmem cells. The cBAF complex and MYC physically interact to establish the chromatin landscape in activated CD8+ T cells. Treatment of naive CD8+ T cells with a putative cBAF inhibitor during the first 48 h of activation, before the generation of chimeric antigen receptor T (CAR-T) cells, markedly improves efficacy in a mouse solid tumour model. Our results establish cBAF as a negative determinant of Tmem cell fate and suggest that manipulation of cBAF early in T cell differentiation can improve cancer immunotherapy.
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Affiliation(s)
- Ao Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongling Huang
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhexin Zhu
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark J Chen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sujing Yuan
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Piyush Sharma
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Swantje Liedmann
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yogesh Dhungana
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhenrui Li
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mao Yang
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Helen Beere
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason T Yustein
- Baylor Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Long L, Wei J, Lim SA, Raynor JL, Shi H, Connelly JP, Wang H, Guy C, Xie B, Chapman NM, Fu G, Wang Y, Huang H, Su W, Saravia J, Risch I, Wang YD, Li Y, Niu M, Dhungana Y, Kc A, Zhou P, Vogel P, Yu J, Pruett-Miller SM, Peng J, Chi H. CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity. Nature 2021; 600:308-313. [PMID: 34795452 PMCID: PMC8887674 DOI: 10.1038/s41586-021-04109-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [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: 11/12/2020] [Accepted: 10/07/2021] [Indexed: 12/26/2022]
Abstract
Nutrients are emerging regulators of adaptive immunity1. Selective nutrients interplay with immunological signals to activate mechanistic target of rapamycin complex 1 (mTORC1), a key driver of cell metabolism2-4, but how these environmental signals are integrated for immune regulation remains unclear. Here we use genome-wide CRISPR screening combined with protein-protein interaction networks to identify regulatory modules that mediate immune receptor- and nutrient-dependent signalling to mTORC1 in mouse regulatory T (Treg) cells. SEC31A is identified to promote mTORC1 activation by interacting with the GATOR2 component SEC13 to protect it from SKP1-dependent proteasomal degradation. Accordingly, loss of SEC31A impairs T cell priming and Treg suppressive function in mice. In addition, the SWI/SNF complex restricts expression of the amino acid sensor CASTOR1, thereby enhancing mTORC1 activation. Moreover, we reveal that the CCDC101-associated SAGA complex is a potent inhibitor of mTORC1, which limits the expression of glucose and amino acid transporters and maintains T cell quiescence in vivo. Specific deletion of Ccdc101 in mouse Treg cells results in uncontrolled inflammation but improved antitumour immunity. Collectively, our results establish epigenetic and post-translational mechanisms that underpin how nutrient transporters, sensors and transducers interplay with immune signals for three-tiered regulation of mTORC1 activity and identify their pivotal roles in licensing T cell immunity and immune tolerance.
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Affiliation(s)
- Lingyun Long
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun Wei
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Seon Ah Lim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jana L Raynor
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hong Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole M Chapman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guotong Fu
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yanyan Wang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongling Huang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wei Su
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jordy Saravia
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Isabel Risch
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mingming Niu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yogesh Dhungana
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anil Kc
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peipei Zhou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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15
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Zong X, Hao X, Xu B, Crawford JC, Wright S, Li J, Zhang Y, Bai L, He M, Jiang M, Fan Y, Connelly JP, Pruett-Miller SM, Berns H, Janke L, Li C, Feng Y. Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity. J Exp Med 2021; 218:e20202415. [PMID: 34086055 PMCID: PMC8185987 DOI: 10.1084/jem.20202415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/11/2020] [Revised: 04/05/2021] [Accepted: 05/12/2021] [Indexed: 12/22/2022] Open
Abstract
T reg cells bearing a diverse antigen receptor repertoire suppress pathogenic T cells and maintain immune homeostasis during their long lifespan. How their robust function is determined genetically remains elusive. Here, we investigate the regulatory space of the cis-regulatory elements of T reg lineage-specifying factor Foxp3. Foxp3 enhancers are known as distinct readers of environmental cues controlling T reg cell induction or lineage stability. However, their single deficiencies cause mild, if any, immune dysregulation, leaving the key transcriptional mechanisms determining Foxp3 expression and thereby T reg cell suppressive capacity uncertain. We examined the collective activities of Foxp3 enhancers and found that they coordinate to maximize T reg cell induction, Foxp3 expression level, or lineage stability through distinct modes and that ablation of synergistic enhancers leads to lethal autoimmunity in young mice. Thus, the induction and maintenance of a diverse, stable T reg cell repertoire rely on combinatorial Foxp3 enhancers, suggesting broad, stage-specific, synergistic activities of cell-intrinsic factors and cell-extrinsic cues in determining T reg cell suppressive capacity.
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Affiliation(s)
- Xinying Zong
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xiaolei Hao
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jun Li
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Lu Bai
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Minghong He
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Menglin Jiang
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jon P. Connelly
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Hartmut Berns
- Transgenic Gene Knockout Shared Resource, St. Jude Children’s Research Hospital, Memphis, TN
| | - Laura Janke
- Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN
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16
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Smith KH, Budhraja A, Lynch J, Roberts K, Panetta JC, Connelly JP, Turnis ME, Pruett-Miller SM, Schuetz JD, Mullighan CG, Opferman JT. The Heme-Regulated Inhibitor Pathway Modulates Susceptibility of Poor Prognosis B-Lineage Acute Leukemia to BH3-Mimetics. Mol Cancer Res 2020; 19:636-650. [PMID: 33288732 DOI: 10.1158/1541-7786.mcr-20-0586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/28/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022]
Abstract
Antiapoptotic MCL1 is one of the most frequently amplified genes in human cancers and elevated expression confers resistance to many therapeutics including the BH3-mimetic agents ABT-199 and ABT-263. The antimalarial, dihydroartemisinin (DHA) translationally represses MCL-1 and synergizes with BH3-mimetics. To explore how DHA represses MCL-1, a genome-wide CRISPR screen identified that loss of genes in the heme synthesis pathway renders mouse BCR-ABL+ B-ALL cells resistant to DHA-induced death. Mechanistically, DHA disrupts the interaction between heme and the eIF2α kinase heme-regulated inhibitor (HRI) triggering the integrated stress response. Genetic ablation of Eif2ak1, which encodes HRI, blocks MCL-1 repression in response to DHA treatment and represses the synergistic killing of DHA and BH3-mimetics compared with wild-type leukemia. Furthermore, BTdCPU, a small-molecule activator of HRI, similarly triggers MCL-1 repression and synergizes with BH3-mimetics in mouse and human leukemia including both Ph+ and Ph-like B-ALL. Finally, combinatorial treatment of leukemia bearing mice with both BTdCPU and a BH3-mimetic extended survival and repressed MCL-1 in vivo. These findings reveal for the first time that the HRI-dependent cellular heme-sensing pathway can modulate apoptosis in leukemic cells by repressing MCL-1 and increasing their responsiveness to BH3-mimetics. This signaling pathway could represent a generalizable mechanism for repressing MCL-1 expression in malignant cells and sensitizing them to available therapeutics. IMPLICATIONS: The HRI-dependent cellular heme-sensing pathway can modulate apoptotic sensitivity in leukemic cells by repressing antiapoptotic MCL-1 and increasing their responsiveness to BH3-mimetics.
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Affiliation(s)
- Kaitlyn H Smith
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Integrated Program in Biomedical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Amit Budhraja
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John Lynch
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kathryn Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John C Panetta
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jon P Connelly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Meghan E Turnis
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - John D Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Joseph T Opferman
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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17
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Pinto EM, Figueiredo BC, Chen W, Galvao HC, Formiga MN, Fragoso MCB, Ashton-Prolla P, Ribeiro EM, Felix G, Costa TE, Savage SA, Yeager M, Palmero EI, Volc S, Salvador H, Fuster-Soler JL, Lavarino C, Chantada G, Vaur D, Odone-Filho V, Brugières L, Else T, Stoffel EM, Maxwell KN, Achatz MI, Kowalski L, de Andrade KC, Pappo A, Letouze E, Latronico AC, Mendonca BB, Almeida MQ, Brondani VB, Bittar CM, Soares EW, Mathias C, Ramos CR, Machado M, Zhou W, Jones K, Vogt A, Klincha PP, Santiago KM, Komechen H, Paraizo MM, Parise IZ, Hamilton KV, Wang J, Rampersaud E, Clay MR, Murphy AJ, Lalli E, Nichols KE, Ribeiro RC, Rodriguez-Galindo C, Korbonits M, Zhang J, Thomas MG, Connelly JP, Pruett-Miller S, Diekmann Y, Neale G, Wu G, Zambetti GP. XAF1 as a modifier of p53 function and cancer susceptibility. Sci Adv 2020; 6:eaba3231. [PMID: 32637605 PMCID: PMC7314530 DOI: 10.1126/sciadv.aba3231] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/14/2020] [Indexed: 05/15/2023]
Abstract
Cancer risk is highly variable in carriers of the common TP53-R337H founder allele, possibly due to the influence of modifier genes. Whole-genome sequencing identified a variant in the tumor suppressor XAF1 (E134*/Glu134Ter/rs146752602) in a subset of R337H carriers. Haplotype-defining variants were verified in 203 patients with cancer, 582 relatives, and 42,438 newborns. The compound mutant haplotype was enriched in patients with cancer, conferring risk for sarcoma (P = 0.003) and subsequent malignancies (P = 0.006). Functional analyses demonstrated that wild-type XAF1 enhances transactivation of wild-type and hypomorphic TP53 variants, whereas XAF1-E134* is markedly attenuated in this activity. We propose that cosegregation of XAF1-E134* and TP53-R337H mutations leads to a more aggressive cancer phenotype than TP53-R337H alone, with implications for genetic counseling and clinical management of hypomorphic TP53 mutant carriers.
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Affiliation(s)
- Emilia M. Pinto
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Corresponding author. (E.M.P.); (G.P.Z.)
| | | | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | | | | | | | | | | | | | | | | | | | - Sahlua Volc
- Hospital de Cancer de Barretos, Barretos, SP, Brazil
| | - Hector Salvador
- Pediatric Oncology Department, Sant Joan de Deu Hospital, Barcelona, Spain
| | | | - Cinzia Lavarino
- Pediatric Oncology Department, Sant Joan de Deu Hospital, Barcelona, Spain
| | - Guillermo Chantada
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Dominique Vaur
- Comprehensive Cancer Center François Baclesse, Caen, France
| | - Vicente Odone-Filho
- ITACI–Instituto de Tratamento do Câncer Infantil do Departamento de Pediatria da Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | | | | | - Kara N. Maxwell
- Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Alberto Pappo
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Eric Letouze
- Centre de Recherche des Cordeliers, Paris, France
| | | | | | | | | | - Camila M. Bittar
- Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | | | | | - Weiyin Zhou
- National Cancer Institute, Rockville, MD, USA
| | | | | | | | | | - Heloisa Komechen
- Instituto de Pesquisa Pelé Pequeno Principe, Curitiba, PR, Brazil
| | | | - Ivy Z.S. Parise
- Instituto de Pesquisa Pelé Pequeno Principe, Curitiba, PR, Brazil
| | - Kayla V. Hamilton
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinling Wang
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Michael R. Clay
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Andrew J. Murphy
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Enzo Lalli
- Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Raul C. Ribeiro
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Carlos Rodriguez-Galindo
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marta Korbonits
- Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jinghui Zhang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mark G. Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Jon P. Connelly
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Shondra Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Gerard P. Zambetti
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Corresponding author. (E.M.P.); (G.P.Z.)
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Yang SW, Li L, Connelly JP, Porter SN, Kodali K, Gan H, Park JM, Tacer KF, Tillman H, Peng J, Pruett-Miller SM, Li W, Potts PR. A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3' End Processing Complex. Mol Cell 2020; 77:1206-1221.e7. [PMID: 31980388 DOI: 10.1016/j.molcel.2019.12.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022]
Abstract
Alternative polyadenylation (APA) contributes to transcriptome complexity by generating mRNA isoforms with varying 3' UTR lengths. APA leading to 3' UTR shortening (3' US) is a common feature of most cancer cells; however, the molecular mechanisms are not understood. Here, we describe a widespread mechanism promoting 3' US in cancer through ubiquitination of the mRNA 3' end processing complex protein, PCF11, by the cancer-specific MAGE-A11-HUWE1 ubiquitin ligase. MAGE-A11 is normally expressed only in the male germline but is frequently re-activated in cancers. MAGE-A11 is necessary for cancer cell viability and is sufficient to drive tumorigenesis. Screening for targets of MAGE-A11 revealed that it ubiquitinates PCF11, resulting in loss of CFIm25 from the mRNA 3' end processing complex. This leads to APA of many transcripts affecting core oncogenic and tumor suppressors, including cyclin D2 and PTEN. These findings provide insights into the molecular mechanisms driving APA in cancer and suggest therapeutic strategies.
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Affiliation(s)
- Seung Wook Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jon P Connelly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kiran Kodali
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Haiyun Gan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jung Mi Park
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Klementina Fon Tacer
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Tillman
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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19
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Fon Tacer K, Montoya MC, Oatley MJ, Lord T, Oatley JM, Klein J, Ravichandran R, Tillman H, Kim M, Connelly JP, Pruett-Miller SM, Bookout AL, Binshtock E, Kamiński MM, Potts PR. MAGE cancer-testis antigens protect the mammalian germline under environmental stress. Sci Adv 2019; 5:eaav4832. [PMID: 31149633 PMCID: PMC6541465 DOI: 10.1126/sciadv.aav4832] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/17/2019] [Indexed: 05/17/2023]
Abstract
Ensuring robust gamete production even in the face of environmental stress is of utmost importance for species survival, especially in mammals that have low reproductive rates. Here, we describe a family of genes called melanoma antigens (MAGEs) that evolved in eutherian mammals and are normally restricted to expression in the testis (http://MAGE.stjude.org) but are often aberrantly activated in cancer. Depletion of Mage-a genes disrupts spermatogonial stem cell maintenance and impairs repopulation efficiency in vivo. Exposure of Mage-a knockout mice to genotoxic stress or long-term starvation that mimics famine in nature causes defects in spermatogenesis, decreased testis weights, diminished sperm production, and reduced fertility. Last, human MAGE-As are activated in many cancers where they promote fuel switching and growth of cells. These results suggest that mammalian-specific MAGE genes have evolved to protect the male germline against environmental stress, ensure reproductive success under non-optimal conditions, and are hijacked by cancer cells.
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Affiliation(s)
- Klementina Fon Tacer
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marhiah C. Montoya
- Clinical & Translational Science Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Departments of Pediatrics, Microbiology and Immunology, Carver College of Medicine, University of Iowa, IA, USA
| | - Melissa J. Oatley
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Tessa Lord
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Jon M. Oatley
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Jonathon Klein
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ramya Ravichandran
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Heather Tillman
- Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - MinSoo Kim
- Departments of Internal Medicine and Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jon P. Connelly
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Angie L. Bookout
- Department of Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emily Binshtock
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marcin M. Kamiński
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Patrick Ryan Potts
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Corresponding author.
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20
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Connelly JP, Pruett-Miller SM. CRIS.py: A Versatile and High-throughput Analysis Program for CRISPR-based Genome Editing. Sci Rep 2019; 9:4194. [PMID: 30862905 PMCID: PMC6414496 DOI: 10.1038/s41598-019-40896-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/25/2019] [Indexed: 01/16/2023] Open
Abstract
CRISPR-Cas9 technology allows the creation of user-defined genomic modifications in cells and whole organisms. However, quantifying editing rates in pools of cells or identifying correctly edited clones is tedious. Targeted next-generation sequencing provides a high-throughput platform for optimizing editing reagents and identifying correctly modified clones, but the large amount of data produced can be difficult to analyze. Here, we present CRIS.py, a simple and highly versatile python-based program which concurrently analyzes next-generation sequencing data for both knock-out and multiple user-specified knock-in modifications from one or many edited samples. Compared to available NGS analysis programs for CRISPR based-editing, CRIS.py has many advantages: (1) the ability to analyze from one to thousands of samples at once, (2) the capacity to check each sample for multiple sequence modifications, including those induced by base-editors, (3) an output in an easily searchable file format enabling users to quickly sort through and identify correctly targeted clones.
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Affiliation(s)
- Jon P Connelly
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis, 38105, USA. .,St. Jude Children's Research Hospital, Center for Advanced Genome Engineering, Memphis, USA.
| | - Shondra M Pruett-Miller
- St. Jude Children's Research Hospital, Department of Cell & Molecular Biology, Memphis, 38105, USA. .,St. Jude Children's Research Hospital, Center for Advanced Genome Engineering, Memphis, USA.
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Wen Y, Liao G, Pritchard T, Zhao TT, Connelly JP, Pruett-Miller SM, Blanc V, Davidson NO, Madison BB. A stable but reversible integrated surrogate reporter for assaying CRISPR/Cas9-stimulated homology-directed repair. J Biol Chem 2017; 292:6148-6162. [PMID: 28228480 DOI: 10.1074/jbc.m117.777722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The discovery and application of CRISPR/Cas9 technology for genome editing has greatly accelerated targeted mutagenesis in a variety of organisms. CRISPR/Cas9-mediated site-specific cleavage is typically exploited for the generation of insertions or deletions (indels) after aberrant dsDNA repair via the endogenous non-homology end-joining (NHEJ) pathway or, alternatively, for enhancing homology-directed repair to facilitate the generation of a specific mutation (or "knock-in"). However, there is a need for efficient cellular assays that can measure Cas9/guide RNA activity. Reliable methods for enriching and identifying desired mutants are also lacking. Here we describe a method using the Piggybac transposon for stable genomic integration of an H2B-GFP reporter or a hygromycin resistance gene for assaying Cas9 target cleavage and homology-directed repair. The H2B-GFP fusion protein provides increased stability and an obvious pattern of nuclear localization. This method, called SRIRACCHA (i.e. a stable, but reversible, integrated reporter for assaying CRISPR/Cas-stimulated HDR activity), enables the enrichment of mutants via selection of GFP-positive or hygromycin-resistant mammalian cells (immortalized or non-immortalized) as a surrogate for the modification of the endogenous target site. Currently available hyperactive Piggybac transposase mutants allow both delivery and removal of the surrogate reporters, with minimal risk of generating undesirable mutations. This assay permits rapid screening for efficient guide RNAs and the accelerated identification of mutant clones and is applicable to many cell types. We foresee the utility of this approach in contexts in which the maintenance of genomic integrity is essential, for example, when engineering cells for therapeutic purposes.
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Affiliation(s)
- Yahong Wen
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Grace Liao
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Thomas Pritchard
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Ting-Ting Zhao
- First Hospital of China Medical University, Department of Breast Surgery, Shenyang, China 110001
| | - Jon P Connelly
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University, Saint Louis, Missouri 63110, and
| | - Shondra M Pruett-Miller
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University, Saint Louis, Missouri 63110, and
| | - Valerie Blanc
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Nicholas O Davidson
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Blair B Madison
- From the Division of Gastroenterology, Washington University School of Medicine, Saint Louis, Missouri 63110,
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22
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Connelly JP, Neilson AM, Peters ST, Martinez R, Milbrandt JD, Miller SM. 659. Precision Genome Engineering in Human Induced Pluripotent Stem Cells Using CRISPR/CAS9. Mol Ther 2015. [DOI: 10.1016/s1525-0016(16)34268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Ellis BL, Hirsch ML, Barker JC, Connelly JP, Steininger RJ, Porteus MH. A survey of ex vivo/in vitro transduction efficiency of mammalian primary cells and cell lines with Nine natural adeno-associated virus (AAV1-9) and one engineered adeno-associated virus serotype. Virol J 2013; 10:74. [PMID: 23497173 PMCID: PMC3607841 DOI: 10.1186/1743-422x-10-74] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [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: 07/12/2012] [Accepted: 02/14/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The ability to deliver a gene of interest into a specific cell type is an essential aspect of biomedical research. Viruses can be a useful tool for this delivery, particularly in difficult to transfect cell types. Adeno-associated virus (AAV) is a useful gene transfer vector because of its ability to mediate efficient gene transduction in numerous dividing and quiescent cell types, without inducing any known pathogenicity. There are now a number of natural for that designed AAV serotypes that each has a differential ability to infect a variety of cell types. Although transduction studies have been completed, the bulk of the studies have been done in vivo, and there has never been a comprehensive study of transduction ex vivo/in vitro. METHODS Each cell type was infected with each serotype at a multiplicity of infection of 100,000 viral genomes/cell and transduction was analyzed by flow cytometry + . RESULTS We found that AAV1 and AAV6 have the greatest ability to transduce a wide range of cell types, however, for particular cell types, there are specific serotypes that provide optimal transduction. CONCLUSIONS In this work, we describe the transduction efficiency of ten different AAV serotypes in thirty-four different mammalian cell lines and primary cell types. Although these results may not be universal due to numerous factors such as, culture conditions and/ or cell growth rates and cell heterogeneity, these results provide an important and unique resource for investigators who use AAV as an ex vivo gene delivery vector or who work with cells that are difficult to transfect.
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Affiliation(s)
- Brian L Ellis
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
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24
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Abstract
The concept of gene therapy has long appealed to biomedical researchers and clinicians because it promised to treat certain diseases at their origins. In the last several years, there have been several trials in which patients have benefited from gene therapy protocols. This progress, however, has revealed important problems, including the problem of insertional oncogenesis. In this review, which focuses on monogenic diseases, we discuss the problem of insertional oncogenesis and identify areas for future research, such as developing more quantitative assays for risk and efficacy, and ways of minimizing the genotoxic effects of gene therapy protocols, which will be important if gene therapy is to fulfill its conceptual promise.
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25
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Gerscher S, Connelly JP, Beijersbergen Van Henegouwen GM, MacRobert AJ, Watt P, Rhodes LE. A quantitative assessment of protoporphyrin IX metabolism and phototoxicity in human skin following dose-controlled delivery of the prodrugs 5-aminolaevulinic acid and 5-aminolaevulinic acid-n-pentylester. Br J Dermatol 2001; 144:983-90. [PMID: 11359385 DOI: 10.1046/j.1365-2133.2001.04186.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [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: 11/20/2022]
Abstract
BACKGROUND Topical 5-aminolaevulinic acid (ALA) is widely used in photodynamic therapy (PDT) to generate protoporphyrin IX (PpIX) in the skin. However, other prodrugs may be more effective. OBJECTIVES The pharmacokinetics of ALA- and ALA-n-pentylester-induced PpIX, together with the phototoxicity after PDT, were compared in human skin in vivo, using iontophoresis as a quantitative drug delivery system. METHODS A series of six increasing doses of equimolar prodrug solutions was iontophoresed into normal skin of the upper inner arms of 20 healthy subjects. The kinetics of PpIX metabolism in skin (n = 4) and the response to light exposure, performed at 4.5 h (n = 6) and 6 h (n = 10) after application, were assessed by skin surface PpIX fluorescence and postirradiation erythema. RESULTS ALA and ALA-n-pentylester showed a linear correlation between logarithm of dose and PpIX fluorescence (P < 0.005), and logarithm of dose and skin phototoxicity with irradiation at 4.5 h (P < 0.001 and P < 0.005, respectively) and 6 h (P < 0.05 and P < 0.0001, respectively) after iontophoresis. Higher phototoxicity was observed with ALA-n-pentylester than with ALA when sites were irradiated at 6 h, as indicated by the significantly lower theoretical threshold dose for erythema (P < 0.05) and the shift of the PpIX fluorescence/phototoxicity curve towards greater skin erythema at equal PpIX fluorescence levels. Depth of PpIX fluorescence in skin, as determined by fluorescence microscopy, was similar for both prodrugs, but a more homogeneous distribution of PpIX was seen with the more lipophilic ALA-n-pentylester. CONCLUSIONS The observed greater phototoxicity of ALA-n-pentylester relative to ALA may be attributable to a more favourable PpIX localization in tissue and/or greater intrinsic toxicity.
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Affiliation(s)
- S Gerscher
- Dermatology Unit, Department of Medicine, University of Liverpool, Liverpool, U.K
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26
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Gerscher S, Connelly JP, Griffiths J, Brown SB, MacRobert AJ, Wong G, Rhodes LE. Comparison of the pharmacokinetics and phototoxicity of protoporphyrin IX metabolized from 5-aminolevulinic acid and two derivatives in human skin in vivo. Photochem Photobiol 2000; 72:569-74. [PMID: 11045731 DOI: 10.1562/0031-8655(2000)072<0569:cotpap>2.0.co;2] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [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: 11/19/2022]
Abstract
Our novel approach was to compare the pharmacokinetics of 5-aminolevulinic acid (ALA), ALA-n-butyl and ALA-n-hexylester induced protoporphyrin IX (PpIX), together with the phototoxicity after photodynamic therapy (PDT) in human skin in vivo, using iontophoresis as a dose-control system. A series of four increasing doses of each compound was iontophoresed into healthy skin of 10 volunteers. The kinetics of PpIX metabolism (n = 4) and the response to PDT (n = 6) performed 5 h after iontophoresis, were assessed by surface PpIX fluorescence and post-irradiation erythema. Whilst ALA-induced PpIX peaked at 7.5 h, highest PpIX fluorescence induced by ALA-n-hexylester was observed at 3-6 h and no clear peak was seen with ALA-n-butylester. With ALA-n-hexylester, more PpIX was formed after 3 (P < 0.05) and 4.5 h, than with ALA or ALA-n-butylester. All compounds showed a linear correlation between logarithm of dose and PpIX fluorescence/phototoxicity at 5 h, with R-values ranging from 0.87 to 1. In addition, the ALA-n-hexylester showed the tendency to cause greater erythema than ALA and ALA-n-butylester. Fluorescence microscopy (n = 2) showed similar PpIX distributions and penetration depths for the three drugs, although both ALA esters led to a more homogeneous PpIX localization. Hence, ALA-n-hexylester appears to have slightly more favorable characteristics for PDT than ALA or ALA-n-butylester.
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Affiliation(s)
- S Gerscher
- Department of Medicine, University of Liverpool, UK.
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27
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Connelly JP, Meuwly M, Auty AR, Howard BJ. The Dynamics of N(2)-O(3) and N(2)-SO(2) Probed by Microwave Spectroscopy. J Mol Spectrosc 2000; 199:205-216. [PMID: 10637105 DOI: 10.1006/jmsp.1999.8020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The microwave spectra of N(2)-O(3) and N(2)-SO(2) have been recorded in the 6-18 GHz range using a pulsed-nozzle, Fourier transform microwave spectrometer. C-type transitions have been observed for both complexes which are slightly shifted by internal tunneling motions of the O(3) or SO(2) moieties. In addition, unshifted a-type transitions have been observed for N(2)-O(3). The nuclear hyperfine pattern is typical of equivalent nitrogen nuclei. Two sets of rotational and hyperfine constants are required to fit the symmetric and antisymmetric nuclear spin states, indicating that the equivalence arises from tunneling rotation of the nitrogen molecule. Internal tunneling motions along three tunneling pathways have been identified, although no information on the N(2) tunneling frequency is available from the spectra. From the N(2)-O(3) data the tunneling frequencies cannot be decorrelated from the rotational parameters; however, the O(3) tunneling frequency upper limit is estimated to be 2.0 MHz and the frequency of the concerted tunneling motion of both moieties is estimated to be about 8.9 MHz. For N(2)-SO(2), the SO(2) tunneling frequency is 11.5 kHz and the concerted frequency 173.9 kHz. Both complexes are roughly T shaped with the N(2) axis approximately perpendicular to the O(3) or SO(2) plane. In the equilibrium structures of both complexes, the a-c inertial plane is a plane of symmetry. The centers of mass separations are estimated from the rotational parameters to be 3.582 Å for N(2)-O(3) and 3.875 Å for N(2)-SO(2). The angle between the symmetry axes of the O(3) or SO(2) and the line joining their centers of mass have been calculated as 130.84 degrees (or 49.16 degrees ) and 119.71 degrees (or 60.29 degrees ), respectively. From the quadrupole analysis, the average angle between the N(2) axis and the a-inertial axis is 32.12 degrees for N(2)-O(3) and 27.81 degrees for N(2)-SO(2). Model electrostatic and ab initio calculations confirm these structures. Differences between the experimental and calculated structural parameters highlight the role of tunneling dynamics in these complexes. Copyright 2000 Academic Press.
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Affiliation(s)
- JP Connelly
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, England
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28
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Torrent J, Connelly JP, Coll MG, Ribó M, Lange R, Vilanova M. Pressure versus heat-induced unfolding of ribonuclease A: the case of hydrophobic interactions within a chain-folding initiation site. Biochemistry 1999; 38:15952-61. [PMID: 10625462 DOI: 10.1021/bi991460b] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [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: 11/30/2022]
Abstract
To investigate the characteristics of the postulated carboxy terminal chain-folding initiation site in bovine pancreatic ribonuclease A (RNase A) (residues 106-118), important in the early stages of the folding pathway, we have engineered by site-directed mutagenesis a set of 14 predominantly conservative hydrophobic variants of the protein. The stability of each variant has been compared by pressure and temperature-induced unfolding, monitored by fourth derivative UV absorbance spectroscopy. Apparently simple two-state, reversible unfolding transitions are observed, suggesting that the disruption of tertiary structure of each protein at high pressure or temperature is strongly cooperative. Within the limits of the technique, we are unable to detect significant differences between the two processes of denaturation. Both steady-state kinetic parameters for the enzyme reaction and UV CD spectra of each RNase A variant indicate that truncation of hydrophobic side chains in this region has, in general, little or no effect on the native structure and function of the enzyme. Furthermore, the decreases in free energy of unfolding upon pressure and thermal denaturation of all the variants, particularly those modified at residues 106 and 108, suggest that the hydrophobic residues and side chain packing interactions of this region play an important role in maintaining the conformational stability of RNase A. We also demonstrate the potential of Tyr115 replacement by Trp as a non-destabilizing fluorescence probe of conformational changes local to the region.
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Affiliation(s)
- J Torrent
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi. E-17071 Girona, Spain
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29
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Mombelli E, Afshar M, Fusi P, Mariani M, Tortora P, Connelly JP, Lange R. The role of phenylalanine 31 in maintaining the conformational stability of ribonuclease P2 from Sulfolobus solfataricus under extreme conditions of temperature and pressure. Biochemistry 1997; 36:8733-42. [PMID: 9220960 DOI: 10.1021/bi970467v] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [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: 02/04/2023]
Abstract
Ribonuclease P2 from the thermophilic archaebacterium Sulfolobus solfataricus is a small protein (7 kDa) with a known three-dimensional structure. Inspection of the structure and molecular dynamics simulation reveal that three aromatic residues (Phe5, Phe31, and Tyr33) from the hydrophobic core have a strong van der Waals interaction energy. We studied the thermodynamics of the heat, cold, and pressure-induced protein conformational changes of the wild type and of the F31A and F31Y mutants by analyzing the protein UV absorbance in the fourth derivative mode. The wild-type protein was extremely stable under all conditions of temperature and pressure. Heat and cold denaturation of both mutants, as well as denaturation by pressure of the F31A mutant, led to significant blue shifts of the derivative spectrum, indicating increased solvent exposure of Tyr33. For the F31Y mutant, high pressure (400 MPa) protected the protein against thermal denaturation. This study, probing the properties of the hydrophobic aromatic core, complements a thermal unfolding study which probes the overall structural changes [Knapp, S., Karshikoff, A., Berndt, K. D., Christova, P., Atanasov, B., & Ladenstein, R. (1996) J. Mol. Biol. 264,1132-1144]. The differences observed in response to extremes of temperature, pressure, and pH may be rationalized by an unfolding mechanism involving larger parts of the peripheral protein while the integrity of the hydrophobic core is maintained.
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Affiliation(s)
- E Mombelli
- INSERM U128, BP 5051, 34033 Montpellier, France
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30
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Connelly JP, Müller MG, Bassi R, Croce R, Holzwarth AR. Femtosecond transient absorption study of carotenoid to chlorophyll energy transfer in the light-harvesting complex II of photosystem II. Biochemistry 1997; 36:281-7. [PMID: 9003179 DOI: 10.1021/bi962467l] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Singlet energy transfer between the carotenoids (Cars) and chlorophylls (Chls) in the light-harvesting complex II (LHC II) from higher plants has been studied using ultrafast transient absorption spectroscopy by exciting the Cars directly in the 475-515 nm wavelength range. LHC II trimers from Arabidopsis thaliana with well-defined Car compositions have been used. From HPLC, the wild type (WT) monomer contains two luteins (Ls), one neoxanthin (N), and a trace of violaxanthin (V) per 12 Chls. The ABA-3 mutant contains 1.4 Ls and 0.6 zeaxanthin (Z) per monomer. Though exploitation of the difference in Car constitution and exciting the WT at 475 and 490 nm, and the ABA-3 mutant at 490 and 515 nm, the different Car contributions to energy transfer have been probed. Evidence for energy transfer mainly from the Car to Chl b is observed in the WT. In the mutant, additional transfer from Car to Chl a correlates with the presence of Z. The results imply predominant energy transfer from the central Ls to Chl b which requires a modification of the currently accepted arrangement of Chl pigments in LHC II.
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Affiliation(s)
- J P Connelly
- Max-Planck-Institut für Strahlenchemie, Mülheim an der Ruhr, Germany
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31
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Petraitis M, Connelly JP, Crannell H, Fagg LW, O'Brien JT, Sober DI, Deininger JR, Williamson SE, Raman S. Low-multipolarity magnetic transitions in 40Ca excited by 180 degrees electron scattering. Phys Rev C Nucl Phys 1995; 51:1014-1016. [PMID: 9970143 DOI: 10.1103/physrevc.51.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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32
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Petraitis M, Connelly JP, Crannell H, Fagg LW, O'Brien JT, Sober DI, Deininger JR, Williamson SE, Lindgren R, Raman S. Low-multipolarity magnetic transitions in 30Si, 32S, and 34S studied by 180 degrees electron scattering. Phys Rev C Nucl Phys 1994; 49:3000-3013. [PMID: 9969577 DOI: 10.1103/physrevc.49.3000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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33
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Wise JE, Calarco JR, Connelly JP, Fayans SA, Hersman FW, Heisenberg JH, Hicks RS, Kim W, Milliman TE, Miskimen RA, Peterson GA, Platonov AP, Saperstein EE, Singhal RP. Ground-state magnetization density of 89Y. Phys Rev C Nucl Phys 1993; 47:2539-2545. [PMID: 9968727 DOI: 10.1103/physrevc.47.2539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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34
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Kelly JJ, Flanders BS, Hersman FW, Heisenberg JH, Calarco J, Connelly JP, Milliman TE, Scott A, Baker FT, Penumetcha V, Jones WP, Emery GT, Bacher AD, Olmer C, Grimm MA, Whiten ML. Neutron transition densities from 88Sr(p,p') at Ep=200 MeV. Phys Rev C Nucl Phys 1993; 47:2146-2158. [PMID: 9968671 DOI: 10.1103/physrevc.47.2146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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35
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Connelly JP, Welch JV. Monitor lyophilization with mass spectrometer gas analysis. J Parenter Sci Technol 1993; 47:70-5. [PMID: 8515347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This paper presents a brief review of the basic issues of lyophilization and the fundamentals of quadrupole mass spectrometry. The emphasis of the paper is on the application of a quadrupole mass spectrometer as a process monitor. The details of sampling and data collection are discussed. Data taken while monitoring lyophilization is presented in conjunction with cycle optimization, end point detection and contaminant detection.
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Affiliation(s)
- J P Connelly
- NGS Division of MKS Instruments, Inc., Walpole, MA
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36
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Kim W, Connelly JP, Heisenberg JH, Hersman FW, Milliman TE, Wise JE, Papanicolas CN, Fayans SA, Platonov AP. Ground-state charge distribution and transition charge densities of the low-lying states in 86Sr. Phys Rev C Nucl Phys 1992; 46:1656-1666. [PMID: 9968284 DOI: 10.1103/physrevc.46.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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37
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Connelly JP, DeAngelis DJ, Heisenberg JH, Hersman FW, Kim W, Leuschner M, Milliman TE, Wise J, Papanicolas CN. High resolution electron scattering from high spin states in 208Pb. Phys Rev C Nucl Phys 1992; 45:2711-2722. [PMID: 9968036 DOI: 10.1103/physrevc.45.2711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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38
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Wise JE, Connelly JP, Hersman FW, Heisenberg JH, Kim W, Leuschner M, Fayans SA, Platonov AP, Saperstein EE, Ponomarev VY. Transition densities of collective excitations in 118Sn. Phys Rev C Nucl Phys 1992; 45:2701-2710. [PMID: 9968035 DOI: 10.1103/physrevc.45.2701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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39
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Kim W, Miller BL, Calarco JR, Cardman LS, Connelly JP, Fayans SA, Frois B, Goutte D, Heisenberg JH, Hersman FW, Meot V, Milliman TE, Mueller P, Papanicolas CN, Platonov AP, Ponomarev VY, Wise JE. Interplay between single-particle and collective degrees of freedom in the excitation of the low-lying states in 140Ce. Phys Rev C Nucl Phys 1992; 45:2290-2299. [PMID: 9967991 DOI: 10.1103/physrevc.45.2290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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40
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Connelly JP, Crannell H, Fagg LW, O'Brien JT, Petraitis M, Sober DI, Deininger JR, Williamson SE. Low-momentum-transfer 180 degrees electron scattering from the 3.68 MeV 3/2(-) and the 3.85 MeV 5/2(+) states in 13C. Phys Rev C Nucl Phys 1992; 45:2494-2497. [PMID: 9968014 DOI: 10.1103/physrevc.45.2494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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41
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Kim W, Calarco JR, Connelly JP, Heisenberg JH, Hersman FW, Milliman TE, Wise JE, Miller BL, Papanicolas CN, Ponomarev VY, Saperstein EE, Platonov AP. Properties of low-lying states in 142Ce via high resolution electron scattering. Phys Rev C Nucl Phys 1991; 44:2400-2412. [PMID: 9967670 DOI: 10.1103/physrevc.44.2400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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42
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Connelly JP, Milliman TE, Heisenberg JH, Hersman FW, Wise JE, Papanicolas CN. Proton core polarization in low-lying states of 86Sr. Phys Rev C Nucl Phys 1990; 42:1948-1952. [PMID: 9966943 DOI: 10.1103/physrevc.42.1948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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43
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Wise JE, Hersman FW, Heisenberg JH, Milliman TE, Connelly JP, Calarco JR, Papanicolas CN. Single-particle excitations in 89Y. Phys Rev C Nucl Phys 1990; 42:1077-1085. [PMID: 9966823 DOI: 10.1103/physrevc.42.1077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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44
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Milliman TE, Connelly JP, Heisenberg JH, Hersman FW, Wise JE, Papanicolas CN. Electron scattering from 92Mo. Phys Rev C Nucl Phys 1990; 41:2586-2604. [PMID: 9966639 DOI: 10.1103/physrevc.41.2586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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45
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Hansen K, Adler J, Blomqvist KI, Nilsson D, Sandell A, Schroder B, Dodge WR, Lightbody JW, O'Connell JS, Calarco JR, Connelly JP, Hersman FW, Kim W, Leuschner M. Electrofission in the quasifree and delta regions. Phys Rev C Nucl Phys 1990; 41:1619-1624. [PMID: 9966509 DOI: 10.1103/physrevc.41.1619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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46
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Miller BL, Cardman LS, Papanicolas CN, Milliman TE, Connelly JP, Heisenberg JH, Hersman FW, Wise JE, Frois B, Goutte D, Meot V. Electroexcitation of high-multipolarity transitions in 140Ce. Phys Rev C Nucl Phys 1988; 37:895-897. [PMID: 9954519 DOI: 10.1103/physrevc.37.895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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47
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Kletke PR, Davidson SM, Perloff JD, Schiff DW, Connelly JP. The extent of physician participation in Medicaid: a comparison of physician estimates and aggregated patient records. Health Serv Res 1985; 20:503-23. [PMID: 3910615 PMCID: PMC1068899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
This article compares two measures of the extent of physician participation in Medicaid programs. The first, which has been used in most research to date on the subject, is based on physician estimates of the proportion of their patients who are Medicaid patients. The second derives from encounter forms for a sample of visits to the interviewed physicians. The comparison shows that physicians in the sample tended to overestimate by 40 percent the extent of their Medicaid participation. Because the two measures are highly correlated, the analysis of the determinants of Medicaid participation was not affected by the measure used. However, since physicians tended to overstate the proportion of Medicaid patients in their practices, interview data should not be used to measure the amount of physician participation or to calculate elasticities for the effects of policy changes on the extent of participation.
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48
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Milliman TE, Heisenberg JH, Hersman FW, Connelly JP, Papanicolas CN, Wise JE, Blok HP. Determination of the pi 1g9/2 orbit size in 88Sr, 90Zr, and 92Mo from inelastic electron scattering. Phys Rev C Nucl Phys 1985; 32:805-808. [PMID: 9952908 DOI: 10.1103/physrevc.32.805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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49
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Perloff JD, LeBailly SA, Kletke PR, Budetti PP, Connelly JP. Premature death in the United States: years of life lost and health priorities. J Public Health Policy 1984; 5:167-84. [PMID: 6470128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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50
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Davidson SM, Perloff JD, Kletke PR, Schiff DW, Connelly JP. Full and limited medicaid participation among pediatricians. Pediatrics 1983; 72:552-9. [PMID: 6351008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Participation in Medicaid by pediatricians is an important element in the access of low income children to health care. Factors that influence whether participating pediatricians choose to participate fully in the program or to limit their acceptance of Medicaid patients are identified and analyzed. Data were derived from interviews conducted with 814 pediatricians in 13 states. A multivariate analysis examining physician, practice, service area, and Medicaid policy characteristics indicates that policy factors are most influential in the physician's decision whether to participate fully in medicaid programs. Factors found to foster the willingness of pediatricians to participate fully in state Medicaid programs included more competitive levels of reimbursement, minimal delays in reimbursement, and eligibility and benefit policies that minimize interference with the exercise of medical judgment.
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