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Zhang Y, Zhang X, Tang Q, Li L, Jiang T, Fang Y, Zhang H, Zhai J, Ren G, Zheng B. A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants. Sci China Life Sci 2024:10.1007/s11427-023-2466-7. [PMID: 38489006 DOI: 10.1007/s11427-023-2466-7] [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] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 03/17/2024]
Abstract
Lariat RNA is concomitantly produced by excised intron during RNA splicing, which is usually debranched by DBR1, an RNA debranching enzyme. However, increasing evidence showed that some lariat RNA could escape debranching. Little is known about how and why these lariat RNAs could be retained. By comparing the atlas of lariat RNAs between the non-dividing cell (mature pollen) and three actively dividing tissues (young shoot apex, young seeds, and young roots), we identified hundreds to thousands of lariat RNA naturally retained in each tissue, and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen. Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-mRNA could be retained in one tissue while degraded in the other tissues. By deciphering lariat RNA sequences, we identified an AG-rich (RAAAAVAAAR) motif and a UC-rich (UCUCUYUCUC) motif for pollen-specific and the other three tissues-retained lariat RNAs, respectively. Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants. Biologically, hundreds of lariat RNAs harbored miRNA binding sites, and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of miRNA target genes. Collectively, our results uncover that selective retention of lariat RNA is an actively regulatory process, and provide new insights into understanding how lariat RNA metabolism may impact miRNA activity.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaotuo Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yixiao Fang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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Townley BA, Buerer L, Tsao N, Bacolla A, Mansoori F, Rusanov T, Clark N, Goodarzi N, Schmidt N, Srivatsan SN, Sun H, Sample RA, Brickner JR, McDonald D, Tsai MS, Walter MJ, Wozniak DF, Holehouse AS, Pena V, Tainer JA, Fairbrother WG, Mosammaparast N. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Mol Cell 2023; 83:2258-2275.e11. [PMID: 37369199 PMCID: PMC10483886 DOI: 10.1016/j.molcel.2023.06.011] [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: 06/20/2022] [Revised: 03/25/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-binding complex (IBC). TTDN1 loss, or a mutated IDR, causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. A Ttdn1-deficient mouse model recapitulates intron-processing defects and certain neurodevelopmental phenotypes seen in NP-TTD. Fusing DBR1 to the TTDN1 IDR is sufficient to recruit DBR1 to the IBC and circumvents the functional requirement for TTDN1. Collectively, our findings link RNA lariat processing with splicing outcomes by revealing the molecular function of TTDN1.
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Affiliation(s)
- Brittany A Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Luke Buerer
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ning Tsao
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Fadhel Mansoori
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timur Rusanov
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathanial Clark
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Negar Goodarzi
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - Nicolas Schmidt
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Hua Sun
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Reilly A Sample
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Drew McDonald
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David F Wozniak
- Department of Psychiatry, Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alex S Holehouse
- Department of Biochemistry & Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Vladimir Pena
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William G Fairbrother
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA; Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI 02912, USA.
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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, 74648Shanxi 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, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Xue Liu
- Key Laboratory of Cellular Physiology, Ministry of Education, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Yanghui Bi
- Key Laboratory of Cellular Physiology, Ministry of Education, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology, Ministry of Education, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Yanqiang Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, 74648Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology, Ministry of Education, 74648Shanxi 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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4
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Zhang SY, Clark NE, Freije CA, Pauwels E, Taggart A, 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 W, Abel L, Rosenberg B, Hart J, 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: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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 Taggart
- Center for Computational Molecular Biology, 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, Haifa 31096,
Israel,Rappaport Faculty of Medicine, Haifa 31096, Israel
| | - Paula Garcia
- Pediatric Hospital of Coimbra, Coimbra 3000-075, 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
- Center for Computational Molecular Biology, Brown University,
Providence, RI 02912, USA
| | - 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, New York University Langone Medical
Center, New York 10016, NY, USA
| | - Stefano Volpi
- Department of Pediatrics, Giannina Gaslini Institute, 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, Hospital Pediátrico, Centro
Hospitalar e Universitário de 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
| | - 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
H3A0G4, 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,
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 734-8551, 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
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montréal
H3A0G4, 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 Genomics, 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
| | - 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 Fairbrother
- Center for Computational Molecular Biology, 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 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
| | - John Hart
- Department of Biochemistry and Structural Biology, University of
Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA,X-ray Crystallography Core Laboratory, University of Texas Health
Science Center at San Antonio, San Antonio, TX 78229, USA,Department of Veterans Affairs, South Texas Veterans Health Care
System, San Antonio, TX 78229, USA
| | - Amos Etzioni
- Metabolic Unit, Ruth Children’s Hospital, Haifa 31096,
Israel,Rappaport Faculty of Medicine, 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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