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Suarez-Pajes E, Tosco-Herrera E, Ramirez-Falcon M, Gonzalez-Barbuzano S, Hernandez-Beeftink T, Guillen-Guio B, Villar J, Flores C. Genetic Determinants of the Acute Respiratory Distress Syndrome. J Clin Med 2023; 12:3713. [PMID: 37297908 PMCID: PMC10253474 DOI: 10.3390/jcm12113713] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung condition that arises from multiple causes, including sepsis, pneumonia, trauma, and severe coronavirus disease 2019 (COVID-19). Given the heterogeneity of causes and the lack of specific therapeutic options, it is crucial to understand the genetic and molecular mechanisms that underlie this condition. The identification of genetic risks and pharmacogenetic loci, which are involved in determining drug responses, could help enhance early patient diagnosis, assist in risk stratification of patients, and reveal novel targets for pharmacological interventions, including possibilities for drug repositioning. Here, we highlight the basis and importance of the most common genetic approaches to understanding the pathogenesis of ARDS and its critical triggers. We summarize the findings of screening common genetic variation via genome-wide association studies and analyses based on other approaches, such as polygenic risk scores, multi-trait analyses, or Mendelian randomization studies. We also provide an overview of results from rare genetic variation studies using Next-Generation Sequencing techniques and their links with inborn errors of immunity. Lastly, we discuss the genetic overlap between severe COVID-19 and ARDS by other causes.
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Eva Tosco-Herrera
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Melody Ramirez-Falcon
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Silvia Gonzalez-Barbuzano
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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DiBlasi E, Shabalin AA, Monson ET, Keeshin BR, Bakian AV, Kirby AV, Ferris E, Chen D, William N, Gaj E, Klein M, Jerominski L, Callor WB, Christensen E, Smith KR, Fraser A, Yu Z, Gray D, Camp NJ, Stahl EA, Li QS, Docherty AR, Coon H. Rare protein-coding variants implicate genes involved in risk of suicide death. Am J Med Genet B Neuropsychiatr Genet 2021; 186:508-520. [PMID: 34042246 PMCID: PMC9292859 DOI: 10.1002/ajmg.b.32861] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/24/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
Identification of genetic factors leading to increased risk of suicide death is critical to combat rising suicide rates, however, only a fraction of the genetic variation influencing risk has been accounted for. To address this limitation, we conducted the first comprehensive analysis of rare genetic variation in suicide death leveraging the largest suicide death biobank, the Utah Suicide Genetic Risk Study (USGRS). We conducted a single-variant association analysis of rare (minor allele frequency <1%) putatively functional single-nucleotide polymorphisms (SNPs) present on the Illumina PsychArray genotyping array in 2,672 USGRS suicide deaths of non-Finnish European (NFE) ancestry and 51,583 NFE controls from the Genome Aggregation Database. Secondary analyses used an independent control sample of 21,324 NFE controls from the Psychiatric Genomics Consortium. Five novel, high-impact, rare SNPs were identified with significant associations with suicide death (SNAPC1, rs75418419; TNKS1BP1, rs143883793; ADGRF5, rs149197213; PER1, rs145053802; and ESS2, rs62223875). 119 suicide decedents carried these high-impact SNPs. Both PER1 and SNAPC1 have other supporting gene-level evidence of suicide risk, and psychiatric associations exist for PER1 (bipolar disorder, schizophrenia), and for TNKS1BP1 and ESS2 (schizophrenia). Three of the genes (PER1, TNKS1BP1, and ADGRF5), together with additional genes implicated by genome-wide association studies on suicidal behavior, showed significant enrichment in immune system, homeostatic and signal transduction processes. No specific diagnostic phenotypes were associated with the subset of suicide deaths with the identified rare variants. These findings suggest an important role for rare variants in suicide risk and implicate genes and gene pathways for targeted replication.
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Affiliation(s)
- Emily DiBlasi
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Andrey A. Shabalin
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Eric T. Monson
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Brooks R. Keeshin
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA,Department of PediatricsUniversity of UtahSalt Lake CityUtahUSA,Safe and Healthy Families, Primary Children's HospitalIntermountain HealthcareSalt Lake CityUtahUSA
| | - Amanda V. Bakian
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Anne V. Kirby
- Department of Occupational & Recreational TherapiesUniversity of UtahSalt Lake CityUtahUSA
| | - Elliott Ferris
- Department of Neurobiology & AnatomyUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Danli Chen
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Nancy William
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Eoin Gaj
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - Michael Klein
- Health Sciences Center Core Research FacilityUniversity of UtahSalt Lake CityUtahUSA
| | - Leslie Jerominski
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | - W. Brandon Callor
- Utah State Office of the Medical ExaminerUtah Department of HealthSalt Lake CityUtahUSA
| | - Erik Christensen
- Utah State Office of the Medical ExaminerUtah Department of HealthSalt Lake CityUtahUSA
| | - Ken R. Smith
- Pedigree & Population Resource, Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtahUSA
| | - Alison Fraser
- Pedigree & Population Resource, Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtahUSA
| | - Zhe Yu
- Pedigree & Population Resource, Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtahUSA
| | - Douglas Gray
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
| | | | - Nicola J. Camp
- Department of Internal MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Eli A. Stahl
- Pamela Sklar Division of Psychiatric GenomicsIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA,Medical and Population Genetics, Broad InstituteCambridgeMassachusettsUSA
| | - Qingqin S. Li
- Neuroscience Data Science, Janssen Research & Development LLCTitusvilleNew JerseyUSA
| | - Anna R. Docherty
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA,Virginia Institute for Psychiatric & Behavioral GeneticsVirginia Commonwealth School of MedicineRichmondVirginiaUSA
| | - Hilary Coon
- Department of PsychiatryUniversity of Utah School of MedicineSalt Lake CityUtahUSA,University of Utah Health, Huntsman Mental Health InstituteSalt Lake CityUtahUSA
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O’Dushlaine C, Ripke S, Ruderfer DM, Hamilton SP, Fava M, Iosifescu DV, Kohane IS, Churchill SE, Castro VM, Clements CC, Blumenthal SR, Murphy SN, Smoller JW, Perlis RH. Rare copy number variation in treatment-resistant major depressive disorder. Biol Psychiatry 2014; 76:536-41. [PMID: 24529801 PMCID: PMC4104153 DOI: 10.1016/j.biopsych.2013.10.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/03/2013] [Accepted: 10/26/2013] [Indexed: 12/28/2022]
Abstract
BACKGROUND While antidepressant treatment response appears to be partially heritable, no consistent genetic associations have been identified. Large, rare copy number variants (CNVs) play a role in other neuropsychiatric diseases, so we assessed their association with treatment-resistant depression (TRD). METHODS We analyzed data from two genome-wide association studies comprising 1263 Caucasian patients with major depressive disorder. One was drawn from a large health system by applying natural language processing to electronic health records (i2b2 cohort). The second consisted of a multicenter study of sequential antidepressant treatments, Sequenced Treatment Alternatives to Relieve Depression. The Birdsuite package was used to identify rare deletions and duplications. Individuals without symptomatic remission, despite two antidepressant treatment trials, were contrasted with those who remitted with a first treatment trial. RESULTS CNV data were derived for 778 subjects in the i2b2 cohort, including 300 subjects (37%) with TRD, and 485 subjects in Sequenced Treatment Alternatives to Relieve Depression cohort, including 152 (31%) with TRD. CNV burden analyses identified modest enrichment of duplications in cases (empirical p = .04 for duplications of 100-200 kilobase) and a particular deletion region spanning gene PABPC4L (empirical p = .02, 6 cases: 0 controls). Pathway analysis suggested enrichment of CNVs intersecting genes regulating actin cytoskeleton. However, none of these associations survived genome-wide correction. CONCLUSIONS Contribution of rare CNVs to TRD appears to be modest, individually or in aggregate. The electronic health record-based methodology demonstrated here should facilitate collection of larger TRD cohorts necessary to further characterize these effects.
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