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Clark NE, Katolik A, Gallant P, Welch A, Murphy E, Buerer L, Schorl C, Naik N, Naik MT, Holloway SP, Cano K, Weintraub ST, Howard KM, Hart PJ, Jogl G, Damha MJ, Fairbrother WG. Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain. J Biol Chem 2023; 299:105100. [PMID: 37507019 PMCID: PMC10470207 DOI: 10.1016/j.jbc.2023.105100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
In eukaryotic cells, the introns are excised from pre-mRNA by the spliceosome. These introns typically have a lariat configuration due to the 2'-5' phosphodiester bond between an internal branched residue and the 5' terminus of the RNA. The only enzyme known to selectively hydrolyze the 2'-5' linkage of these lariats is the RNA lariat debranching enzyme Dbr1. In humans, Dbr1 is involved in processes such as class-switch recombination of immunoglobulin genes, and its dysfunction is implicated in viral encephalitis, HIV, ALS, and cancer. However, mechanistic details of precisely how Dbr1 affects these processes are missing. Here we show that human Dbr1 contains a disordered C-terminal domain through sequence analysis and nuclear magnetic resonance. This domain stabilizes Dbr1 in vitro by reducing aggregation but is dispensable for debranching activity. We establish that Dbr1 requires Fe2+ for efficient catalysis and demonstrate that the noncatalytic protein Drn1 and the uncharacterized protein trichothiodystrophy nonphotosensitive 1 directly bind to Dbr1. We demonstrate addition of trichothiodystrophy nonphotosensitive 1 to in vitro debranching reactions increases the catalytic efficiency of human Dbr1 19-fold but has no effect on the activity of Dbr1 from the amoeba Entamoeba histolytica, which lacks a disordered C-terminal domain. Finally, we systematically examine how the identity of the branchpoint nucleotide affects debranching rates. These findings describe new aspects of Dbr1 function in humans and further clarify how Dbr1 contributes to human health and disease.
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Affiliation(s)
- Nathaniel E Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA.
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Pascal Gallant
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Eileen Murphy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Christoph Schorl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Nandita Naik
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Mandar T Naik
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Kristin Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Katherine M Howard
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada-Las Vegas, Las Vegas, Nevada, USA
| | - P John Hart
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada.
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA.
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Clark NE, Katolik A, Welch A, Schorl C, Holloway SP, Schuermann JP, Hart PJ, Taylor AB, Damha MJ, Fairbrother WG. Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product. Biochemistry 2022; 61:2933-2939. [PMID: 36484984 DOI: 10.1021/acs.biochem.2c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RNA lariat debranching enzyme is the sole enzyme responsible for hydrolyzing the 2'-5' phosphodiester bond in RNA lariats produced by the spliceosome. Here, we test the ability of Dbr1 to hydrolyze branched RNAs (bRNAs) that contain a 2'-5'-phosphorothioate linkage, a modification commonly used to resist degradation. We attempted to cocrystallize a phosphorothioate-branched RNA (PS-bRNA) with wild-type Entamoeba histolytica Dbr1 (EhDbr1) but observed in-crystal hydrolysis of the phosphorothioate bond. The crystal structure revealed EhDbr1 in a product-bound state, with the hydrolyzed 2'-5' fragment of the PS-bRNA mimicking the binding mode of the native bRNA substrate. These findings suggest that product inhibition may contribute to the kinetic mechanism of Dbr1. We show that Dbr1 enzymes cleave phosphorothioate linkages at rates ∼10,000-fold more slowly than native phosphate linkages. This new product-bound crystal structure offers atomic details, which can aid inhibitor design. Dbr1 inhibitors could be therapeutic or investigative compounds for human diseases such as human immunodeficiency virus (HIV), amyotrophic lateral sclerosis (ALS), cancer, and viral encephalitis.
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Affiliation(s)
- Nathaniel E. Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
| | - Christoph Schorl
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
| | - Stephen P. Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Jonathan P. Schuermann
- Northeastern Collaborative Access Team, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - P. John Hart
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Alexander B. Taylor
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - William G. Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02891, United States
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3
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Clark NE, Katolik A, Taggart AJ, Buerer L, Holloway SP, Miller N, Phillips JD, Farrell CP, Damha MJ, Fairbrother WG. Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1. RNA (NEW YORK, N.Y.) 2022; 28:927-936. [PMID: 35459748 PMCID: PMC9202583 DOI: 10.1261/rna.079159.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
In eukaryotic cells, intron lariats produced by the spliceosome contain a 2'5' phosphodiester linkage. The RNA lariat debranching enzyme, Dbr1, is the only enzyme known to hydrolyze this bond. Dbr1 is a member of the metallophosphoesterase (MPE) family of enzymes, and recent X-ray crystal structures and biochemistry data demonstrate that Dbr1 from Entamoeba histolytica uses combinations of Mn2+, Zn2+, and Fe2+ as enzymatic cofactors. Here, we examine the kinetic properties and metal dependence of the Dbr1 homolog from Saccharomyces cerevisiae (yDbr1). Elemental analysis measured stoichiometric quantities of Fe and Zn in yDbr1 purified following heterologous expression E. coli We analyzed the ability of Fe2+, Zn2+, and Mn2+ to reconstitute activity in metal-free apoenzyme. Purified yDbr1 was highly active, turning over substrate at 5.6 sec-1, and apo-yDbr1 reconstituted with Fe2+ was the most active species, turning over at 9.2 sec-1 We treated human lymphoblastoid cells with the iron-chelator deferoxamine and measured a twofold increase in cellular lariats. These data suggest that Fe is an important biological cofactor for Dbr1 enzymes.
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Affiliation(s)
- Nathaniel E Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, USA
| | - Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Nathaniel Miller
- Department of Geological Sciences, University of Texas Austin, Austin, Texas 78712, USA
| | - John D Phillips
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Colin P Farrell
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
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4
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Xu X, Yang X, Liu X, Bi Y, Kong P, Wang Y, Cheng X, Xi Y. The Role of DBR1 as a Candidate Prognosis Biomarker in Esophageal Squamous Cell Carcinoma. Technol Cancer Res Treat 2022; 21:15330338221083105. [PMID: 35244467 PMCID: PMC8902023 DOI: 10.1177/15330338221083105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/20/2022] [Accepted: 02/02/2022] [Indexed: 11/16/2022] Open
Abstract
Aims: Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies with unfavorable clinical outcomes and limited therapeutic methods. As a key enzyme in RNA metabolism, debranching RNA Lariats 1 (DBR1) is involved in intron turnover and biogenesis of noncoding RNA. Although cancer cells often show disorder of nucleic acid metabolism, it is unclear whether DBR1 has any effect on the carcinogenesis and progression of ESCC. Methods: Here we detected DBR1 expression in 112 ESCC samples by immunohistochemistry and analyzed its correlation with clinical parameters and survival. Results: DBR1 is mainly located in the nucleus of ESCC tissue. And DBR1 was associated with several malignant clinical features in patients, including tumor location (χ2 = 9.687, P = .021), pathologic T stage (χ2 = 5.771, P = .016), lymph node metastasis (χ2 = 8.215, P = .004) and N classification (χ2 = 10.066, P = .018). Moreover, Kaplan-Meier analysis showed that ESCC patients harboring lower DBR1 expression had a worse prognosis in comparison with those with higher DBR1 expression (P = .005). Univariate and multivariate Cox proportional hazards regression analyses indicated that decreased DBR1 might act as an independent predictor of poor prognosis for ESCC patients. Conclusion: Abnormal RNA metabolism might play a critical role in promoting the progression of ESCC, and DBR1 may be a promising potential biomarker for predicting the prognosis of ESCC patients.
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Affiliation(s)
- Xiaoqin Xu
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People’s Republic of China
| | - Xin Yang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Xue Liu
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Yanghui Bi
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Yanqiang Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Yanfeng Xi
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People’s Republic of China
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Zhang SY, Harschnitz O, Studer L, Casanova JL. Neuron-intrinsic immunity to viruses in mice and humans. Curr Opin Immunol 2021; 72:309-317. [PMID: 34425410 PMCID: PMC8578315 DOI: 10.1016/j.coi.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022]
Abstract
Viral encephalitis is a major neglected medical problem. Host defense mechanisms against viral infection of the central nervous system (CNS) have long remained unclear. The few previous studies of CNS-specific immunity to viruses in mice in vivo and humans in vitro have focused on the contributions of circulating leukocytes, resident microglial cells and astrocytes, with neurons long considered passive victims of viral infection requiring protection from extrinsic antiviral mechanisms. The last decade has witnessed the gradual emergence of the notion that neurons also combat viruses through cell-intrinsic mechanisms. Forward genetic approaches in humans have shown that monogenic inborn errors of TLR3, IFN-α/β, or snoRNA31 immunity confer susceptibility to herpes simplex virus 1 (HSV-1) infection of the forebrain, whereas inborn errors of DBR1 underlie brainstem infections due to various viruses, including HSV-1. The study of human pluripotent stem cell (hPSC)-derived CNS-resident cells has unraveled known (i.e. TLR3-dependent IFN-α/β immunity) and new (i.e. snoRNA31-dependent or DBR1-dependent immunity) cell-intrinsic antiviral mechanisms operating in neurons. Reverse genetic approaches in mice have confirmed that some known antiviral mechanisms also operate in mouse neurons (e.g. TLR3 and IFN-α/β immunity). The search for human inborn errors of immunity (IEIs) underlying various forms of viral encephalitis, coupled with mouse models in vivo, and hPSC-based culture models of CNS and peripheral nervous system cells and organoids in vitro, should shed further light on the cell-specific and tissue-specific mechanisms of host defense against viruses in the human brain.
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Affiliation(s)
- Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University of Paris, Imagine Institute, Paris, France.
| | - Oliver Harschnitz
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University of Paris, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY, USA
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6
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Menees TM. Saccharomyces cerevisiae RNA lariat debranching enzyme, Dbr1p, is required for completion of reverse transcription by the retrovirus-like element Ty1 and cleaves branched Ty1 RNAs. Mol Genet Genomics 2021; 296:409-422. [PMID: 33464395 DOI: 10.1007/s00438-020-01753-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022]
Abstract
RNA debranching enzymes are 2'-5' phosphodiesterases found in all eukaryotes. Their main role is cleavage of intron RNA lariat branch points, promoting RNA turnover via exonucleases. Consistent with this role, cells with reduced RNA debranching enzyme activity accumulate intron RNA lariats. The Saccharomyces cerevisiae RNA debranching enzyme Dbr1p is also a host factor for the yeast long terminal repeat (LTR) retrotransposon Ty1, a model for many aspects of retroviral replication. Fittingly, the human RNA debranching enzyme Dbr1 is a host factor for the human immunodeficiency virus, HIV-1. The yeast and human RNA debranching enzymes act at the reverse transcription stages for Ty1 and HIV-1, respectively. Although efficient production of full-length Ty1 cDNA requires Dbr1p, the findings reported here indicate that production of the earliest distinct cDNA product, minus strand strong stop DNA (-sssDNA), is equivalent in wild type and dbr1∆ mutant cells. Several branched Ty1 RNAs are shown to accumulate in dbr1∆ cells during retrotransposition. These data are consistent with creation of Ty1 RNA branches prior to Ty1 reverse transcription and their removal by Dbr1p to allow efficient extension of early cDNA products. The data support the possibility that RNA branch formation and cleavage play broadly shared, but unknown roles in retroviral and LTR retrotransposon reverse transcription.
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Affiliation(s)
- Thomas M Menees
- School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, MO, USA.
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7
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Mohanta A, Chakrabarti K. Dbr1 functions in mRNA processing, intron turnover and human diseases. Biochimie 2020; 180:134-142. [PMID: 33038423 DOI: 10.1016/j.biochi.2020.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/29/2022]
Abstract
Pre-mRNA processing and mRNA stability play direct roles in controlling protein abundance in a cell. Before the mRNA can be translated into a protein, the introns in the pre-mRNA transcripts need to be removed by splicing, such that exons can be ligated together and can code for a protein. In this process, the function of the RNA lariat debranching enzyme or Dbr1 provides a rate-limiting step in the intron turnover process and possibly regulating the production of translation competent mRNAs. Surprising new roles of Dbr1 are emerging in cellular metabolism which extends beyond intron turnover processes, ranging from splicing regulation to translational control. In this review, we highlight the importance of the Dbr1 enzyme, its structure and how anomalies in its function could relate to various human diseases.
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Affiliation(s)
- Arundhati Mohanta
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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8
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Abstract
Host cell factors are integral to viral replication. Human immunodeficiency virus 1 (HIV-1), the retroviral agent of acquired immune deficiency syndrome, requires several host factors for reverse transcription of the viral genomic RNA (gRNA) into DNA shortly after viral entry. One of these host factors is the RNA lariat debranching enzyme (Dbr1), which cleaves the 2'-5' bond of branched and lariat RNAs. A recent study has revealed that Dbr1 cleaves HIV-1 gRNA lariats that form early after viral entry. Without Dbr1 activity, HIV-1 reverse transcription stalls, consistent with blockage of viral reverse transcriptase at gRNA branch points. These findings echo an earlier study with the long-terminal-repeat retrotransposon of Saccharomyces cerevisiae, Ty1, which is a retrovirus model. Currently, branching and debranching of viral gRNA are not widely recognized as features of HIV-1 replication, and the role of a gRNA lariat is not known. Future studies will determine whether these gRNA dynamics represent fundamental features of retroviral biology and whether they occur for other positive-sense RNA viruses.
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Affiliation(s)
- Thomas M Menees
- School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA;
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9
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Herpes simplex virus encephalitis of childhood: inborn errors of central nervous system cell-intrinsic immunity. Hum Genet 2020; 139:911-918. [PMID: 32040615 DOI: 10.1007/s00439-020-02127-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/02/2020] [Indexed: 12/23/2022]
Abstract
Herpes simplex virus 1 (HSV-1) encephalitis (HSE) is the most common sporadic viral encephalitis in Western countries. Over the last 15 years, human genetic and immunological studies have provided proof-of-principle that childhood HSE can result from inborn errors of central nervous system (CNS)-specific, cell-intrinsic immunity to HSV-1. HSE-causing mutations of eight genes disrupt known (TLR3-dependent IFN-α/β immunity) and novel (dependent on DBR1 or snoRNA31) antiviral mechanisms. Monogenic inborn errors confer susceptibility to forebrain (TLR3-IFN or snoRNA31) or brainstem (DBR1) HSE. Most of these disorders display incomplete clinical penetrance, with the possible exception of DBR1 deficiency. They account for a small, but non-negligible proportion of cases (about 7%). These findings pave the way for the gradual definition of the genetic and immunological architecture of childhood HSE, with both biological and clinical implications.
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10
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Zhang SY, Jouanguy E, Zhang Q, Abel L, Puel A, Casanova JL. Human inborn errors of immunity to infection affecting cells other than leukocytes: from the immune system to the whole organism. Curr Opin Immunol 2019; 59:88-100. [PMID: 31121434 PMCID: PMC6774828 DOI: 10.1016/j.coi.2019.03.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/29/2019] [Indexed: 01/19/2023]
Abstract
Studies of vertebrate immunity have traditionally focused on professional cells, including circulating and tissue-resident leukocytes. Evidence that non-professional cells are also intrinsically essential (i.e. not via their effect on leukocytes) for protective immunity in natural conditions of infection has emerged from three lines of research in human genetics. First, studies of Mendelian resistance to infection have revealed an essential role of DARC-expressing erythrocytes in protection against Plasmodium vivax infection, and an essential role of FUT2-expressing intestinal epithelial cells for protection against norovirus and rotavirus infections. Second, studies of inborn errors of non-hematopoietic cell-extrinsic immunity have shown that APOL1 and complement cascade components secreted by hepatocytes are essential for protective immunity to trypanosome and pyogenic bacteria, respectively. Third, studies of inborn errors of non-hematopoietic cell-intrinsic immunity have suggested that keratinocytes, pulmonary epithelial cells, and cortical neurons are essential for tissue-specific protective immunity to human papillomaviruses, influenza virus, and herpes simplex virus, respectively. Various other types of genetic resistance or predisposition to infection in human populations are not readily explained by inborn variants of genes operating in leukocytes and may, therefore, involve defects in other cells. The probing of this unchartered territory by human genetics is reshaping immunology, by scaling immunity to infection up from the immune system to the whole organism.
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Affiliation(s)
- Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065, USA.
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11
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Zhang X, Zhang Y, Wang T, Li Z, Cheng J, Ge H, Tang Q, Chen K, Liu L, Lu C, Guo J, Zheng B, Zheng Y. A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants. THE PLANT CELL 2019; 31:956-973. [PMID: 30894459 PMCID: PMC6533014 DOI: 10.1105/tpc.18.00711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/29/2019] [Accepted: 03/14/2019] [Indexed: 05/20/2023]
Abstract
Lariats are formed by excised introns, when the 5' splice site joins with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by RNA debranching enzyme 1, recent findings in animals detected many lariat RNAs under physiological conditions. By contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing data sets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13,872, 5199, 29,582, and 13,478 BPs in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), and maize (Zea mays), respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ∼20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10,580 lariat RNAs accumulate in wild-type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns. Moreover, the expression of these lariat RNAs is accompanied by the incidence of back-splicing of parent exons. Collectively, our results provide a comprehensive map of intron BPs and lariat RNAs in four plant species and uncover a link between lariat turnover and splicing.
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Affiliation(s)
- Xiaotuo Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yong Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Taiyun Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziwei Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinping Cheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haoran Ge
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kun Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Chenyu Lu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Junqiang Guo
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
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Döring J, Hurek T. Dual coding potential of a 2',5'-branched ribonucleotide in DNA. RNA (NEW YORK, N.Y.) 2019; 25:105-120. [PMID: 30361268 PMCID: PMC6298571 DOI: 10.1261/rna.068486.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
Branchpoints in RNA templates are highly mutagenic, but it is not known yet whether this also applies to branchpoints in DNA templates. Here, we report how nucleic acid polymerases replicate a 2',5'-branched DNA (bDNA) molecule. We constructed long-chained bDNA templates containing a branch guanosine and T7 promoters at both arms by splinted ligation. Quantitative real-time PCR analysis was used to investigate whether a branchpoint blocks DNA synthesis from the two arms in the same manner. We find that the blocking effect of a branchpoint is arm-specific. DNA synthesis from the 2'-arm is more than 20,000-fold decreased, whereas from the 3'-arm only 15-fold. Our sequence analysis of full-length nucleic acid generated by Taq DNA polymerase, Moloney murine leukemia virus reverse transcriptase, and T7 RNA polymerase from the 2'-arm of bDNA shows that the branched guanine has a dual coding potential and can base-pair with cytosine and guanine. We find that branchpoint templating is influenced by the type of the surrounding nucleic acid and is probably modulated by polymerase and RNase H active sites. We show that the branchpoint bypass by the polymerases from the 3'-arm of bDNA is predominantly error-free, indicating that bDNA is not as highly mutagenic as 2',5'-branched RNA.
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Affiliation(s)
- Jessica Döring
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, D-28334 Bremen, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, D-28334 Bremen, Germany
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13
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Zhang SY, Clark NE, Freije CA, Pauwels E, Taggart AJ, Okada S, Mandel H, Garcia P, Ciancanelli MJ, Biran A, Lafaille FG, Tsumura M, Cobat A, Luo J, Volpi S, Zimmer B, Sakata S, Dinis A, Ohara O, Garcia Reino EJ, Dobbs K, Hasek M, Holloway SP, McCammon K, Hussong SA, DeRosa N, Van Skike CE, Katolik A, Lorenzo L, Hyodo M, Faria E, Halwani R, Fukuhara R, Smith GA, Galvan V, Damha MJ, Al-Muhsen S, Itan Y, Boeke JD, Notarangelo LD, Studer L, Kobayashi M, Diogo L, Fairbrother WG, Abel L, Rosenberg BR, Hart PJ, Etzioni A, Casanova JL. Inborn Errors of RNA Lariat Metabolism in Humans with Brainstem Viral Infection. Cell 2018; 172:952-965.e18. [PMID: 29474921 PMCID: PMC5886375 DOI: 10.1016/j.cell.2018.02.019] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/03/2017] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
Viruses that are typically benign sometimes invade the brainstem in otherwise healthy children. We report bi-allelic DBR1 mutations in unrelated patients from different ethnicities, each of whom had brainstem infection due to herpes simplex virus 1 (HSV1), influenza virus, or norovirus. DBR1 encodes the only known RNA lariat debranching enzyme. We show that DBR1 expression is ubiquitous, but strongest in the spinal cord and brainstem. We also show that all DBR1 mutant alleles are severely hypomorphic, in terms of expression and function. The fibroblasts of DBR1-mutated patients contain higher RNA lariat levels than control cells, this difference becoming even more marked during HSV1 infection. Finally, we show that the patients' fibroblasts are highly susceptible to HSV1. RNA lariat accumulation and viral susceptibility are rescued by wild-type DBR1. Autosomal recessive, partial DBR1 deficiency underlies viral infection of the brainstem in humans through the disruption of tissue-specific and cell-intrinsic immunity to viruses.
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Affiliation(s)
- Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France.
| | - Nathaniel E Clark
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Catherine A Freije
- Program in Immunogenomics, The Rockefeller University, New York, NY 10065, USA
| | - Elodie Pauwels
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Hanna Mandel
- Metabolic Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 31096, Israel; Rappaport Faculty of Medicine, Haifa 31096, Israel
| | - Paula Garcia
- Child Developmental Center, Pediatric Hospital, Hospital and University Center of Coimbra, Coimbra 3000-602, Portugal
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Anat Biran
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Fabien G Lafaille
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France
| | - Jingchuan Luo
- Department of Molecular Biology & Genetics, JHU School of Medicine, Baltimore, MD 21205, USA; Institute for Systems Genetics, NYU Langone Health, New York 10016, NY, USA
| | - Stefano Volpi
- Pediatric and Rheumatology Clinic, Center for Autoinflammatory Diseases and Immunodeficiencies, Istituto Giannina Gaslini and University of Genoa, Genoa 16100, Italy
| | - Bastian Zimmer
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Alexandra Dinis
- Pediatric Intensive Care Unit, Pediatric Hospital, Hospital and University Center of Coimbra, Coimbra 3000-075, Portugal
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan; Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Eduardo J Garcia Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892-1456, USA
| | - Mary Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karen McCammon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Stacy A Hussong
- Department of Cellular and Integrative Physiology and The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, TX 78229, USA; South Texas Veterans Health Care System, Department of Veterans Affairs, TX 78229, USA
| | - Nicholas DeRosa
- Department of Cellular and Integrative Physiology and The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Candice E Van Skike
- Department of Cellular and Integrative Physiology and The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montréal, QC H3A0B8, Canada
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France
| | - Maki Hyodo
- Department of Obstetrics and Gynecology, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Emilia Faria
- Immuno-Allergy Department, Hospital and University of Coimbra, Coimbra 3000-075, Portugal
| | - Rabih Halwani
- Immunology Research Laboratory, Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Rie Fukuhara
- Department of Neonatology, Hiroshima Prefectural Hospital, Hiroshima 734-8115, Japan
| | - Gregory A Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Veronica Galvan
- Department of Cellular and Integrative Physiology and The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, TX 78229, USA; South Texas Veterans Health Care System, Department of Veterans Affairs, TX 78229, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montréal, QC H3A0B8, Canada
| | - Saleh Al-Muhsen
- Immunology Research Laboratory, Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jef D Boeke
- Department of Molecular Biology & Genetics, JHU School of Medicine, Baltimore, MD 21205, USA; Institute for Systems Genetics, NYU Langone Health, New York 10016, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892-1456, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Luisa Diogo
- Pediatric Hospital of Coimbra, Coimbra 3000-075, Portugal
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France
| | - Brad R Rosenberg
- Program in Immunogenomics, The Rockefeller University, New York, NY 10065, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - P John Hart
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; South Texas Veterans Health Care System, Department of Veterans Affairs, TX 78229, USA; X-ray Crystallography Core Laboratory, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Amos Etzioni
- Rappaport Faculty of Medicine, Haifa 31096, Israel; Immunology Unit, Ruth Children's Hospital, Haifa 31096, Israel
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris 75015, France; Paris Descartes University, Imagine Institute, Paris 75015, France; Howard Hughes Medical Institute, New York, NY 10065, USA; Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris 75015, France
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