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Gateau K, Schlueter L, Pierce LJ, Thompson B, Gharib A, Durazo-Arvizu RA, Nelson CA, Levitt P. Exploratory study evaluating the relationships between perinatal adversity, oxidative stress, and infant neurodevelopment across the first year of life. PLOS Glob Public Health 2023; 3:e0001984. [PMID: 38153909 PMCID: PMC10754429 DOI: 10.1371/journal.pgph.0001984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/13/2023] [Indexed: 12/30/2023]
Abstract
Early childhood adversity increases risk for negative lifelong impacts on health and wellbeing. Identifying the risk factors and the associated biological adaptations early in life is critical to develop scalable early screening tools and interventions. Currently, there are limited, reliable early childhood adversity measures that can be deployed prospectively, at scale, to assess risk in pediatric settings. The goal of this two-site longitudinal study was to determine if the gold standard measure of oxidative stress, F2-Isoprostanes, is potentially a reliable measure of a physiological response to adversity of the infant and mother. The study evaluated the independent relationships between F2-Isoprostanes, perinatal adversity and infant neurocognitive development. The study included mother-infant dyads born >36 weeks' gestation. Maternal demographic information and mental health assessments were utilized to generate a perinatal cumulative risk score. Infants' development was assessed at 6 and 12 months and both mothers and infants were assayed for F2-isoprostane levels in blood and urine, respectively. Statistical analysis revealed that cumulative risk scores correlated with higher maternal (p = 0.01) and infant (p = 0.05) F2-isoprostane levels at 6 months. Infant F2-isoprostane measures at 2 months were negatively associated with Mullen Scales of Early Learning Composite scores at 12 months (p = 0.04). Lastly, higher cumulative risk scores predicted higher average maternal F2-isoprostane levels across the 1-year study time period (p = 0.04). The relationship between perinatal cumulative risk scores and higher maternal and infant F2-isoprostanes at 6 months may reflect an oxidative stress status that informs a sensitive period in which a biomarker can be utilized prospectively to reveal the physiological impact of early adversity.
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Affiliation(s)
- Kameelah Gateau
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California, United States of America
- Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Lisa Schlueter
- Developmental Neuroscience and Neurogenetics Program, The Saban Research Institute, Los Angeles, California, United States of America
| | - Lara J. Pierce
- York University, Department of Psychology, Toronto, ON, Canada
| | - Barbara Thompson
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, United States of America
| | - Alma Gharib
- Children’s Hospital Los Angeles, Los Angeles, California, United States of America
- Developmental Neuroscience and Neurogenetics Program, The Saban Research Institute, Los Angeles, California, United States of America
| | - Ramon A. Durazo-Arvizu
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California, United States of America
- Children’s Hospital Los Angeles, Los Angeles, California, United States of America
| | - Charles A. Nelson
- Department of Pediatrics, Division of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Graduate School of Education, Boston, Massachusetts, United States of America
| | - Pat Levitt
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California, United States of America
- Children’s Hospital Los Angeles, Los Angeles, California, United States of America
- York University, Department of Psychology, Toronto, ON, Canada
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Zhang P, Chaldebas M, Ogishi M, Al Qureshah F, Ponsin K, Feng Y, Rinchai D, Milisavljevic B, Han JE, Moncada-Vélez M, Keles S, Schröder B, Stenson PD, Cooper DN, Cobat A, Boisson B, Zhang Q, Boisson-Dupuis S, Abel L, Casanova JL. Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites. Proc Natl Acad Sci U S A 2023; 120:e2314225120. [PMID: 37931111 PMCID: PMC10655562 DOI: 10.1073/pnas.2314225120] [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: 08/19/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023] Open
Abstract
Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing. AGAIN is publicly available from https://hgidsoft.rockefeller.edu/AGAIN and https://github.com/casanova-lab/AGAIN.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Fahd Al Qureshah
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Khoren Ponsin
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Yi Feng
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Marcela Moncada-Vélez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Meram Medical Faculty, Konya42080, Turkey
| | - Bernd Schröder
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden01307, Germany
| | - Peter D. Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, CardiffCF14 4XN, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, CardiffCF14 4XN, United Kingdom
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris75015, France
- HHMI, New York, NY10065
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Zhang K, Miorin L, Makio T, Dehghan I, Gao S, Xie Y, Zhong H, Esparza M, Kehrer T, Kumar A, Hobman TC, Ptak C, Gao B, Minna JD, Chen Z, García-Sastre A, Ren Y, Wozniak RW, Fontoura BMA. Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression. Sci Adv 2021; 7:7/6/eabe7386. [PMID: 33547084 PMCID: PMC7864571 DOI: 10.1126/sciadv.abe7386] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/16/2020] [Indexed: 05/04/2023]
Abstract
The ongoing unprecedented severe acute respiratory syndrome caused by the SARS-CoV-2 outbreak worldwide has highlighted the need for understanding viral-host interactions involved in mechanisms of virulence. Here, we show that the virulence factor Nsp1 protein of SARS-CoV-2 interacts with the host messenger RNA (mRNA) export receptor heterodimer NXF1-NXT1, which is responsible for nuclear export of cellular mRNAs. Nsp1 prevents proper binding of NXF1 to mRNA export adaptors and NXF1 docking at the nuclear pore complex. As a result, a significant number of cellular mRNAs are retained in the nucleus during infection. Increased levels of NXF1 rescues the Nsp1-mediated mRNA export block and inhibits SARS-CoV-2 infection. Thus, antagonizing the Nsp1 inhibitory function on mRNA export may represent a strategy to restoring proper antiviral host gene expression in infected cells.
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Affiliation(s)
- Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tadashi Makio
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ishmael Dehghan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Hualin Zhong
- Department of Biological Sciences, Hunter College, New York, NY 10065, USA
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil Kumar
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Tom C Hobman
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Boning Gao
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D Minna
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhijian Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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