1
|
Mishra-Gorur K, Barak T, Kaulen LD, Henegariu O, Jin SC, Aguilera SM, Yalbir E, Goles G, Nishimura S, Miyagishima D, Djenoune L, Altinok S, Rai DK, Viviano S, Prendergast A, Zerillo C, Ozcan K, Baran B, Sencar L, Goc N, Yarman Y, Ercan-Encicek AG, Bilguvar K, Lifton RP, Moliterno J, Louvi A, Yuan S, Deniz E, Brueckner M, Gunel M. Reply to Pisan et al.: Pathogenicity of inherited TRAF7 mutations in congenital heart disease. Proc Natl Acad Sci U S A 2024; 121:e2319578121. [PMID: 38466853 DOI: 10.1073/pnas.2319578121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Affiliation(s)
- Ketu Mishra-Gorur
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Tanyeri Barak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Leon D Kaulen
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Octavian Henegariu
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510
| | | | - Ezgi Yalbir
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Gizem Goles
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Sayoko Nishimura
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | | | - Lydia Djenoune
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | - Selin Altinok
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Devendra K Rai
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Stephen Viviano
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510
| | - Andrew Prendergast
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT 06510
| | - Cynthia Zerillo
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Kent Ozcan
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Burcin Baran
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Leman Sencar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Nukte Goc
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | - Yanki Yarman
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
| | | | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065
| | - Jennifer Moliterno
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT 06510
| | - Angeliki Louvi
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
| | - Shiaulou Yuan
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129
| | - Engin Deniz
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510
| | - Martina Brueckner
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT 06510
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
| |
Collapse
|
2
|
Mishra-Gorur K, Barak T, Kaulen LD, Henegariu O, Jin SC, Aguilera SM, Yalbir E, Goles G, Nishimura S, Miyagishima D, Djenoune L, Altinok S, Rai DK, Viviano S, Prendergast A, Zerillo C, Ozcan K, Baran B, Sencar L, Goc N, Yarman Y, Ercan-Sencicek AG, Bilguvar K, Lifton RP, Moliterno J, Louvi A, Yuan S, Deniz E, Brueckner M, Gunel M. Pleiotropic role of TRAF7 in skull-base meningiomas and congenital heart disease. Proc Natl Acad Sci U S A 2023; 120:e2214997120. [PMID: 37043537 PMCID: PMC10120005 DOI: 10.1073/pnas.2214997120] [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: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 04/13/2023] Open
Abstract
While somatic variants of TRAF7 (Tumor necrosis factor receptor-associated factor 7) underlie anterior skull-base meningiomas, here we report the inherited mutations of TRAF7 that cause congenital heart defects. We show that TRAF7 mutants operate in a dominant manner, inhibiting protein function via heterodimerization with wild-type protein. Further, the shared genetics of the two disparate pathologies can be traced to the common origin of forebrain meninges and cardiac outflow tract from the TRAF7-expressing neural crest. Somatic and inherited mutations disrupt TRAF7-IFT57 interactions leading to cilia degradation. TRAF7-mutant meningioma primary cultures lack cilia, and TRAF7 knockdown causes cardiac, craniofacial, and ciliary defects in Xenopus and zebrafish, suggesting a mechanistic convergence for TRAF7-driven meningiomas and developmental heart defects.
Collapse
Affiliation(s)
- Ketu Mishra-Gorur
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Tanyeri Barak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Leon D. Kaulen
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | | | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
| | | | - Ezgi Yalbir
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Gizem Goles
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Sayoko Nishimura
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | | | - Lydia Djenoune
- Cardiology Division, Department of Medicine, Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA02129
| | - Selin Altinok
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Devendra K. Rai
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Stephen Viviano
- Department of Pediatrics, Yale School of Medicine, New Haven, CT06510
| | - Andrew Prendergast
- Department of Internal Medicine, Section of Cardiology, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT06510
| | - Cynthia Zerillo
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Kent Ozcan
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Burcin Baran
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Leman Sencar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Nukte Goc
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Yanki Yarman
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | | | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
| | - Richard P. Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY10065
| | - Jennifer Moliterno
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT06510
| | - Angeliki Louvi
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
- Department of Neuroscience, Yale School of Medicine, New Haven, CT06510
| | - Shiaulou Yuan
- Cardiology Division, Department of Medicine, Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA02129
| | - Engin Deniz
- Department of Pediatrics, Yale School of Medicine, New Haven, CT06510
| | - Martina Brueckner
- Department of Pediatrics, Yale School of Medicine, New Haven, CT06510
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT06510
- Department of Neuroscience, Yale School of Medicine, New Haven, CT06510
| |
Collapse
|
3
|
Umano A, Fang K, Qu Z, Scaglione JB, Altinok S, Treadway CJ, Wick ET, Paulakonis E, Karunanayake C, Chou S, Bardakjian TM, Gonzalez-Alegre P, Page RC, Schisler JC, Brown NG, Yan D, Scaglione KM. The molecular basis of spinocerebellar ataxia type 48 caused by a de novo mutation in the ubiquitin ligase CHIP. J Biol Chem 2022; 298:101899. [PMID: 35398354 PMCID: PMC9097460 DOI: 10.1016/j.jbc.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
The spinocerebellar ataxias (SCAs) are a class of incurable diseases characterized by degeneration of the cerebellum that results in movement disorder. Recently, a new heritable form of SCA, spinocerebellar ataxia type 48 (SCA48), was attributed to dominant mutations in STIP1 homology and U box-containing 1 (STUB1); however, little is known about how these mutations cause SCA48. STUB1 encodes for the protein C terminus of Hsc70 interacting protein (CHIP), an E3 ubiquitin ligase. CHIP is known to regulate proteostasis by recruiting chaperones via a N-terminal tetratricopeptide repeat domain and recruiting E2 ubiquitin-conjugating enzymes via a C-terminal U-box domain. These interactions allow CHIP to mediate the ubiquitination of chaperone-bound, misfolded proteins to promote their degradation via the proteasome. Here we have identified a novel, de novo mutation in STUB1 in a patient with SCA48 encoding for an A52G point mutation in the tetratricopeptide repeat domain of CHIP. Utilizing an array of biophysical, biochemical, and cellular assays, we demonstrate that the CHIPA52G point mutant retains E3-ligase activity but has decreased affinity for chaperones. We further show that this mutant decreases cellular fitness in response to certain cellular stressors and induces neurodegeneration in a transgenic Caenorhabditis elegans model of SCA48. Together, our data identify the A52G mutant as a cause of SCA48 and provide molecular insight into how mutations in STUB1 cause SCA48.
Collapse
Affiliation(s)
- A Umano
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - K Fang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Z Qu
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - J B Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - S Altinok
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - C J Treadway
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - E T Wick
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - E Paulakonis
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - C Karunanayake
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - S Chou
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - T M Bardakjian
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - P Gonzalez-Alegre
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - R C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - J C Schisler
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - N G Brown
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - D Yan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - K M Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA; Department of Neurology, Duke University, Durham, North Carolina, USA; Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, North Carolina, USA.
| |
Collapse
|
4
|
Apriamashvili G, Vredevoogd DW, Krijgsman O, Bleijerveld OB, Ligtenberg MA, de Bruijn B, Boshuizen J, Traets JJH, D'Empaire Altimari D, van Vliet A, Lin CP, Visser NL, Londino JD, Sanchez-Hodge R, Oswalt LE, Altinok S, Schisler JC, Altelaar M, Peeper DS. Ubiquitin ligase STUB1 destabilizes IFNγ-receptor complex to suppress tumor IFNγ signaling. Nat Commun 2022; 13:1923. [PMID: 35395848 PMCID: PMC8993893 DOI: 10.1038/s41467-022-29442-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/11/2022] [Indexed: 12/30/2022] Open
Abstract
The cytokine IFNγ differentially impacts on tumors upon immune checkpoint blockade (ICB). Despite our understanding of downstream signaling events, less is known about regulation of its receptor (IFNγ-R1). With an unbiased genome-wide CRISPR/Cas9 screen for critical regulators of IFNγ-R1 cell surface abundance, we identify STUB1 as an E3 ubiquitin ligase for IFNγ-R1 in complex with its signal-relaying kinase JAK1. STUB1 mediates ubiquitination-dependent proteasomal degradation of IFNγ-R1/JAK1 complex through IFNγ-R1K285 and JAK1K249. Conversely, STUB1 inactivation amplifies IFNγ signaling, sensitizing tumor cells to cytotoxic T cells in vitro. This is corroborated by an anticorrelation between STUB1 expression and IFNγ response in ICB-treated patients. Consistent with the context-dependent effects of IFNγ in vivo, anti-PD-1 response is increased in heterogenous tumors comprising both wildtype and STUB1-deficient cells, but not full STUB1 knockout tumors. These results uncover STUB1 as a critical regulator of IFNγ-R1, and highlight the context-dependency of STUB1-regulated IFNγ signaling for ICB outcome.
Collapse
Affiliation(s)
- Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Onno B Bleijerveld
- Proteomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Daniela D'Empaire Altimari
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - James D Londino
- Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, 410 W 10th Avenue, Columbus, OH, USA
| | - Rebekah Sanchez-Hodge
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Leah E Oswalt
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Selin Altinok
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, 111 Mason Farm Rd., 3340 C MBRB CB #7126, Chapel Hill, NC, USA
| | - Maarten Altelaar
- Proteomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, and Netherlands Proteomics Center, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
| |
Collapse
|
5
|
Barak T, Ristori E, Ercan-Sencicek AG, Miyagishima DF, Nelson-Williams C, Dong W, Jin SC, Prendergast A, Armero W, Henegariu O, Erson-Omay EZ, Harmancı AS, Guy M, Gültekin B, Kilic D, Rai DK, Goc N, Aguilera SM, Gülez B, Altinok S, Ozcan K, Yarman Y, Coskun S, Sempou E, Deniz E, Hintzen J, Cox A, Fomchenko E, Jung SW, Ozturk AK, Louvi A, Bilgüvar K, Connolly ES, Khokha MK, Kahle KT, Yasuno K, Lifton RP, Mishra-Gorur K, Nicoli S, Günel M. PPIL4 is essential for brain angiogenesis and implicated in intracranial aneurysms in humans. Nat Med 2021; 27:2165-2175. [PMID: 34887573 PMCID: PMC8768030 DOI: 10.1038/s41591-021-01572-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 01/24/2021] [Accepted: 10/05/2021] [Indexed: 12/16/2022]
Abstract
Intracranial aneurysm (IA) rupture leads to subarachnoid hemorrhage, a sudden-onset disease that often causes death or severe disability. Although genome-wide association studies have identified common genetic variants that increase IA risk moderately, the contribution of variants with large effect remains poorly defined. Using whole-exome sequencing, we identified significant enrichment of rare, deleterious mutations in PPIL4, encoding peptidyl-prolyl cis-trans isomerase-like 4, in both familial and index IA cases. Ppil4 depletion in vertebrate models causes intracerebral hemorrhage, defects in cerebrovascular morphology and impaired Wnt signaling. Wild-type, but not IA-mutant, PPIL4 potentiates Wnt signaling by binding JMJD6, a known angiogenesis regulator and Wnt activator. These findings identify a novel PPIL4-dependent Wnt signaling mechanism involved in brain-specific angiogenesis and maintenance of cerebrovascular integrity and implicate PPIL4 gene mutations in the pathogenesis of IA.
Collapse
Affiliation(s)
- Tanyeri Barak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Emma Ristori
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT, USA
| | - A Gulhan Ercan-Sencicek
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Danielle F Miyagishima
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Prendergast
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT, USA
| | - William Armero
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT, USA
| | - Octavian Henegariu
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Akdes Serin Harmancı
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Mikhael Guy
- Yale Center for Research Computing, Yale University, New Haven, CT, USA
| | - Batur Gültekin
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Deniz Kilic
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Devendra K Rai
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Nükte Goc
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Burcu Gülez
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Selin Altinok
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Kent Ozcan
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Yanki Yarman
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Süleyman Coskun
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Emily Sempou
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Engin Deniz
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Jared Hintzen
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew Cox
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Elena Fomchenko
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Su Woong Jung
- Division of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Korea
| | - Ali Kemal Ozturk
- Department of Neurosurgery, Pennsylvania Hospital, University of Pennsylvania Health System, Philadelphia, Pennsylvania, USA
| | - Angeliki Louvi
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Kaya Bilgüvar
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - E Sander Connolly
- Department of Neurosurgery, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Mustafa K Khokha
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katsuhito Yasuno
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Ketu Mishra-Gorur
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA.
| | - Stefania Nicoli
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Yale Program on Neurogenetics, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
6
|
McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler JC, Mason CE, Chatterjee A, Meller R, Beheshti A. Role of miR-2392 in driving SARS-CoV-2 infection. Cell Rep 2021; 37:109839. [PMID: 34624208 PMCID: PMC8481092 DOI: 10.1016/j.celrep.2021.109839] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/13/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans.
Collapse
Affiliation(s)
- J Tyson McDonald
- COVID-19 International Research Team; Georgetown University School of Medicine, Washington, DC 20007, USA
| | - Francisco J Enguita
- COVID-19 International Research Team; Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Deanne Taylor
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Griffin
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Waldemar Priebe
- COVID-19 International Research Team; University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team; University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Anthony D Harris
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jean Clement
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph M Dybas
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Joseph W Guarnieri
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter Grabham
- COVID-19 International Research Team; Columbia University, New York, NY 10032, USA
| | - Stephen B Baylin
- COVID-19 International Research Team; Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Aliza Yousey
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | - Peter M Corry
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team; Logyx LLC, Mountain View, CA 94043, USA; NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Sadhana Sharma
- University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA
| | - Prashant Nagpal
- Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA; Quantum Biology Inc., Boulder, CO 80301, USA
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Bianca Cerqueira
- COVID-19 International Research Team; KBR Space & Science, San Antonio, TX 78235, USA; United States Air Force School of Aerospace Medicine, Lackland AFB, San Antonio, TX 78236, USA
| | - Viktorija Zaksas
- COVID-19 International Research Team; University of Chicago, Chicago, IL 60615, USA
| | - Urminder Singh
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | | | | | - Diego Galeano
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Alberto Paccanaro
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; University of London, Egham Hill, Egham, UK
| | - Suzanne L Meinig
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert S Hagan
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie M Bowman
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Selin Altinok
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | | - Douglas C Wallace
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- COVID-19 International Research Team; Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY, USA
| | - Anushree Chatterjee
- COVID-19 International Research Team; University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA
| | - Robert Meller
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Afshin Beheshti
- COVID-19 International Research Team; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| |
Collapse
|
7
|
McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler J, Mason CE, Chatterjee A, Meller R, Beheshti A. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. bioRxiv 2021. [PMID: 33948587 DOI: 10.1101/2021.04.23.441024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.
Collapse
|
8
|
|