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Martin-Lagos J, Bernal-Robledano A, Perez-Carpena P, Lamolda M, Escalera-Balsera A, Frejo L, Lopez-Escamez JA. Phenotypic spectrum of tinnitus patients bearing rare ANK2 gene variants. Eur Arch Otorhinolaryngol 2024; 281:4071-4080. [PMID: 38507076 PMCID: PMC11266272 DOI: 10.1007/s00405-024-08561-9] [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: 12/23/2023] [Accepted: 02/14/2024] [Indexed: 03/22/2024]
Abstract
PURPOSE To describe the clinical, audiological, and psychometric features observed in patients with chronic tinnitus and rare variants in the ANK2 gene. METHODS We report a case series of 12 patients with chronic tinnitus and heterozygous variants in the ANK2 gene. Tinnitus phenotyping included audiological (standard and high-frequency audiometry, Auditory Brainstem Responses (ABR) and Auditory Middle Latency Responses (AMLR)), psychoacoustic and psychometric assessment by a Visual Analog Scale (VAS) for tinnitus annoyance, the Tinnitus Handicap Inventory (THI), the test on Hypersensitivity to Sound (THS-GÜF), the Patient Health Questionnaire (PHQ-9), the Hospital Anxiety and Depression Scale (HADS) and the Montreal Cognitive Assessment (MoCA). RESULTS All patients reported a persistent, unilateral noise-type tinnitus, mainly described as white noise or narrowband noise. Seven patients (58%) were considered to have extreme phenotype (THI score > 76), and all patients reported some degree of hyperacusis (THS-GÜF score > 18 in 75% of patients). Seven patients scored MoCA < 26, regardless of the age reported, suggesting a mild cognitive disorder. ABR showed no significant differences in latencies and amplitudes between ears with or without tinnitus. Similarly, the latencies of Pa, Pb waves, and NaPa complex in the AMLR did not differ based on the presence of tinnitus. However, there were statistical differences in the amplitudes of Pa waves in AMLR, with significantly greater amplitudes observed in ears with tinnitus. CONCLUSION Patients with ANK2 variants and severe tinnitus exhibit an endophenotype featuring hyperacusis, persistent noise-like tinnitus, high-frequency hearing loss, and decreased amplitudes in AMLR. However, anxiety, depression, and cognitive symptoms vary among individuals.
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Affiliation(s)
- Juan Martin-Lagos
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Department of Otorhinolaryngology, Hospital Clínico Universitario San Cecilio, Instituto de Investigación Biosanitaria, ibs.Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Alberto Bernal-Robledano
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Patricia Perez-Carpena
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otolaryngology, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria, ibs.Granada, Granada, Spain
| | - Mar Lamolda
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Alba Escalera-Balsera
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Lidia Frejo
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Rm 611024, Level 11 Kolling Institute | 10 Westbourne St, St Leonards, Sydney, NSW, 2064, Australia
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071, Granada, Spain.
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Rm 611024, Level 11 Kolling Institute | 10 Westbourne St, St Leonards, Sydney, NSW, 2064, Australia.
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Yélamos Lorente MÁ, Perez-Carpena P, Lopez-Escamez JA. A Systematic Review on Heritability of Sudden Sensorineural Hearing Loss. Laryngoscope 2024; 134:3447-3457. [PMID: 38270208 DOI: 10.1002/lary.31308] [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: 10/25/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
OBJECTIVE To assess the evidence supporting the heritability and genetic basis of sudden sensorineural hearing loss (SSNHL). DATA SOURCE Records were extracted from PubMed, Scopus, and Cochrane databases. REVIEW METHODS The protocol was registered on PROSPERO (CRD42022357389) and includes a systematic review on the genetic contribution to SSNHL. The search strategy yielded 1.483 articles from electronic databases. After quality assessment, 34 records were selected, including 369.650 patients with SSNHL from nine prevalence studies, two familial aggregation studies, one twin study, and 22 genetic studies. The prevalence of SSNHL was calculated from data on its incidence from population-based studies (period prevalence). To evaluate the heritability of SSNHL, the sibling recurrence risk ratio (λs) was calculated, by comparing the prevalence of SSNHL among siblings within the same generation to the estimated prevalence in the overall population. Genetic variants were grouped, based on the pathological mechanism related to SSNHL. RESULTS The prevalence of SSNHL ranged from 0.1% to 0.0003% in America to 0.12%-0.0093% in Asia. The estimated sibling recurrence risk ratio for SSNHL (λs = 20.8-83.3) supports a significant familial aggregation. Although several genetic variants were reported to be associated with SSHL in controlled studies, neither was replicated in an independent cohort. CONCLUSIONS Evidence supporting heritability of SSNHL is limited to epidemiological studies showing prevalence differences across different populations and familial aggregation. Genetic studies are of low quality and they lack replication cohort to confirm their findings. According to its low prevalence, exome or genome sequencing familial-based studies are needed to identify rare genetic variants in SSNHL. LEVEL OF EVIDENCE NA Laryngoscope, 134:3447-3457, 2024.
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Affiliation(s)
- Mª Á Yélamos Lorente
- Division of Otolaryngology, Department of Surgery, University of Granada, Granada, Spain
- Family and Community Medicine, Zaidin Sur Health Center (Granada), San Cecilio University Hospital, Granada, Spain
| | - Patricia Perez-Carpena
- Division of Otolaryngology, Department of Surgery, University of Granada, Granada, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Jose A Lopez-Escamez
- Division of Otolaryngology, Department of Surgery, University of Granada, Granada, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
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Xu IRL, Danzi MC, Ruiz A, Raposo J, De Jesus YA, Reilly MM, Cortese A, Shy ME, Scherer SS, Hermann D, Fridman V, Baets J, Saporta M, Seyedsadjadi R, Stojkovic T, Claeys KG, Patel P, Feely S, Rebelo A, Dohrn MF, Züchner S. A study concept of expeditious clinical enrollment for genetic modifier studies in Charcot-Marie-Tooth neuropathy 1A. J Peripher Nerv Syst 2024; 29:202-212. [PMID: 38581130 PMCID: PMC11209807 DOI: 10.1111/jns.12621] [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: 01/24/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Caused by duplications of the gene encoding peripheral myelin protein 22 (PMP22), Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common hereditary neuropathy. Despite this shared genetic origin, there is considerable variability in clinical severity. It is hypothesized that genetic modifiers contribute to this heterogeneity, the identification of which may reveal novel therapeutic targets. In this study, we present a comprehensive analysis of clinical examination results from 1564 CMT1A patients sourced from a prospective natural history study conducted by the RDCRN-INC (Inherited Neuropathy Consortium). Our primary objective is to delineate extreme phenotype profiles (mild and severe) within this patient cohort, thereby enhancing our ability to detect genetic modifiers with large effects. METHODS We have conducted large-scale statistical analyses of the RDCRN-INC database to characterize CMT1A severity across multiple metrics. RESULTS We defined patients below the 10th (mild) and above the 90th (severe) percentiles of age-normalized disease severity based on the CMT Examination Score V2 and foot dorsiflexion strength (MRC scale). Based on extreme phenotype categories, we defined a statistically justified recruitment strategy, which we propose to use in future modifier studies. INTERPRETATION Leveraging whole genome sequencing with base pair resolution, a future genetic modifier evaluation will include single nucleotide association, gene burden tests, and structural variant analysis. The present work not only provides insight into the severity and course of CMT1A, but also elucidates the statistical foundation and practical considerations for a cost-efficient and straightforward patient enrollment strategy that we intend to conduct on additional patients recruited globally.
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Affiliation(s)
- Isaac R. L. Xu
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Matt C. Danzi
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Ariel Ruiz
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jacquelyn Raposo
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Yeisha Arcia De Jesus
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square
| | - Andrea Cortese
- Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square
| | - Michael E Shy
- Department of Neurology, University of Iowa, Iowa City, Iowa, USA
| | - Steven S. Scherer
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, United States
| | - David Hermann
- Department of Neurology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 673, Rochester, New York, 14642, USA
| | - Vera Fridman
- Department of Neurology, University of Colorado Anschutz Medical Campus, 12631 E 17th Avenue, Mailstop B185, Room 5113C, Aurora, CO, 80045, USA
| | - Jonathan Baets
- Department of Neurology, Neuromuscular Reference Centre, Antwerp University Hospital, Antwerp, Belgium
- Faculty of Medicine and Health Sciences, Translational Neurosciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Mario Saporta
- Department of Neurology, University of Miami Miller School of Medicine, United States
| | - Reza Seyedsadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tanya Stojkovic
- AP-HP, Centre de référence des maladies neuromusculaires Nord/Est/Ile de France, Hôpital Pitié-Salpêtrière, 47-83, boulevard de l’Hôpital, 75013 Paris, France
| | - Kristl G. Claeys
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
- Department of Neurosciences, Laboratory for Muscle Diseases and Neuropathies, KU Leuven, Leuven, Belgium
| | - Pooja Patel
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Shawna Feely
- Department of Neurology, University of Iowa, Iowa City, Iowa, USA
| | - Adriana Rebelo
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | | | - Maike F. Dohrn
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Neurology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
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Curtis D. Weighted burden analysis of rare coding variants in 470,000 exome-sequenced UK Biobank participants characterises effects on hyperlipidaemia risk. J Hum Genet 2024; 69:255-262. [PMID: 38454133 PMCID: PMC11126377 DOI: 10.1038/s10038-024-01235-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
A previous study of 200,000 exome-sequenced UK Biobank participants investigating the association between rare coding variants and hyperlipidaemia had implicated four genes, LDLR, PCSK9, APOC3 and IFITM5, at exome-wide significance. In addition, a further 43 protein-coding genes were significant with an uncorrected p value of <0.001. Exome sequence data has become available for a further 270,000 participants and weighted burden analysis to test for association with hyperlipidaemia was carried out in this sample for the 47 genes highlighted by the previous study. There was no evidence to implicate IFITM5 but LDLR, PCSK9, APOC3, ANGPTL3, ABCG5 and NPC1L1 were all statistically significant after correction for multiple testing. These six genes were also all exome-wide significant in the combined sample of 470,000 participants. Variants impairing function of LDLR and ABCG5 were associated with increased risk whereas variants in the other genes were protective. Variant categories associated with large effect sizes are cumulatively very rare and the main benefit of this kind of study seems to be to throw light on the molecular mechanisms impacting hyperlipidaemia risk, hopefully supporting attempts to develop improved therapies.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, UK.
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Bossini L, Sessa A. Need of orthogonal approaches in neurological disease modeling in mouse. Front Mol Neurosci 2024; 17:1399953. [PMID: 38756706 PMCID: PMC11096479 DOI: 10.3389/fnmol.2024.1399953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Over the years, advancements in modeling neurological diseases have revealed innovative strategies aimed at gaining deeper insights and developing more effective treatments for these complex conditions. However, these progresses have recently been overshadowed by an increasing number of failures in clinical trials, raising doubts about the reliability and translatability of this type of disease modeling. This mini-review does not aim to provide a comprehensive overview of the current state-of-the-art in disease mouse modeling. Instead, it offers a brief excursus over some recent approaches in modeling neurological diseases to pinpoint a few intriguing strategies applied in the field that may serve as sources of inspiration for improving currently available animal models. In particular, we aim to guide the reader toward the potential success of adopting a more orthogonal approach in the study of human diseases.
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Affiliation(s)
- Linda Bossini
- Neuroepigenetics Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- “Vita e Salute” San Raffaele University, Milan, Italy
| | - Alessandro Sessa
- Neuroepigenetics Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Lecca M, Scribante A, Errichiello E. Commentary on "Craniofacial Syndromes and class III phenotype: common genotype fingerprints? A scoping review and meta-analysis". Pediatr Res 2024; 95:1412-1414. [PMID: 38245629 DOI: 10.1038/s41390-024-03036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024]
Affiliation(s)
- Mauro Lecca
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy
| | - Andrea Scribante
- Unit of Dental Hygiene, Section of Dentistry, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100, Pavia, Italy
- Unit of Orthodontics and Pediatric Dentistry, Section of Dentistry, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100, Pavia, Italy
| | - Edoardo Errichiello
- Unit of Medical Genetics, Department of Molecular Medicine, University of Pavia, 27100, Pavia, Italy.
- Neurogenetics Research Center, IRCCS Mondino Foundation, 27100, Pavia, Italy.
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Mušálková D, Přistoupilová A, Jedličková I, Hartmannová H, Trešlová H, Nosková L, Hodaňová K, Bittmanová P, Stránecký V, Jiřička V, Langmajerová M, Woodbury‐Smith M, Zarrei M, Trost B, Scherer SW, Bleyer AJ, Vevera J, Kmoch S. Increased burden of rare protein-truncating variants in constrained, brain-specific and synaptic genes in extremely impulsively violent males with antisocial personality disorder. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12882. [PMID: 38359179 PMCID: PMC10869132 DOI: 10.1111/gbb.12882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
The genetic correlates of extreme impulsive violence are poorly understood, and there have been few studies that have characterized a large group of affected individuals both clinically and genetically. We performed whole exome sequencing (WES) in 290 males with the life-course-persistent, extremely impulsively violent form of antisocial personality disorder (APD) and analyzed the spectrum of rare protein-truncating variants (rPTVs). Comparisons were made with 314 male controls and publicly available genotype data. Functional annotation tools were used for biological interpretation. Participants were significantly more likely to harbor rPTVs in genes that are intolerant to loss-of-function variants (odds ratio [OR] 2.06; p < 0.001), specifically expressed in brain (OR 2.80; p = 0.036) and enriched for those involved in neurotransmitter transport and synaptic processes. In 60 individuals (20%), we identified rPTVs that we classified as clinically relevant based on their clinical associations, biological function and gene expression patterns. Of these, 37 individuals harbored rPTVs in 23 genes that are associated with a monogenic neurological disorder, and 23 individuals harbored rPTVs in 20 genes reportedly intolerant to loss-of-function variants. The analysis presents evidence in support of a model where presence of either one or several private, functionally relevant mutations contribute significantly to individual risk of life-course-persistent APD and reveals multiple individuals who could be affected by clinically unrecognized neuropsychiatric Mendelian disease. Thus, Mendelian diseases and increased rPTV burden may represent important factors for the development of extremely impulsive violent life-course-persistent forms of APD irrespective of their clinical presentation.
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Affiliation(s)
- Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Petra Bittmanová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Václav Jiřička
- Department of PsychologyPrison Service of the Czech RepublicPragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Michaela Langmajerová
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Marc Woodbury‐Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Faculty of Medical Sciences, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Molecular Genetics and McLaughlin CentreUniversity of TorontoTorontoOntarioCanada
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Section on Nephrology, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Jan Vevera
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
- Department of PsychiatryUniversity Hospital PilsenPilsenCzech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
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Perez-Carpena P, Lopez-Escamez JA, Gallego-Martinez Á. A Systematic Review on the Genetic Contribution to Tinnitus. J Assoc Res Otolaryngol 2024; 25:13-33. [PMID: 38334885 PMCID: PMC10907330 DOI: 10.1007/s10162-024-00925-6] [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: 08/13/2023] [Accepted: 12/31/2023] [Indexed: 02/10/2024] Open
Abstract
PURPOSE To assess the available evidence to support a genetic contribution and define the role of common and rare variants in tinnitus. METHODS After a systematic search and quality assessment, 31 records including 383,063 patients were selected (14 epidemiological studies and 17 genetic association studies). General information on the sample size, age, sex, tinnitus prevalence, severe tinnitus distribution, and sensorineural hearing loss was retrieved. Studies that did not include data on hearing assessment were excluded. Relative frequencies were used for qualitative variables to compare different studies and to obtain average values. Genetic variants and genes were listed and clustered according to their potential role in tinnitus development. RESULTS The average prevalence of tinnitus estimated from population-based studies was 26.3% for any tinnitus, and 20% of patients with tinnitus reported it as an annoying symptom. One study has reported population-specific differences in the prevalence of tinnitus, the white ancestry being the population with a higher prevalence. Genome-wide association studies have identified and replicated two common variants in the Chinese population (rs2846071; rs4149577) in the intron of TNFRSF1A, associated with noise-induced tinnitus. Moreover, gene burden analyses in sequencing data from Spanish and Swede patients with severe tinnitus have identified and replicated ANK2, AKAP9, and TSC2 genes. CONCLUSIONS The genetic contribution to tinnitus is starting to be revealed and it shows population-specific effects in European and Asian populations. The common allelic variants associated with tinnitus that showed replication are associated with noise-induced tinnitus. Although severe tinnitus has been associated with rare variants with large effect, their role on hearing or hyperacusis has not been established.
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Affiliation(s)
- Patricia Perez-Carpena
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.GRANADA, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- Department of Otolaryngology, Instituto de Investigación Biosanitaria Ibs.GRANADA, Hospital Universitario Virgen de Las Nieves, Granada, Spain.
| | - Jose A Lopez-Escamez
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.GRANADA, Universidad de Granada, Granada, Spain.
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW, Australia.
| | - Álvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
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9
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Zenteno JC, Chacón-Camacho OF, Ordoñez-Labastida V, Miranda-Duarte A, Del Castillo C, Nava J, Mendoza F, Montes-Almanza L, Mora-Roldán G, Gazarian K. Identification of Genetic Variants for Diabetic Retinopathy Risk Applying Exome Sequencing in Extreme Phenotypes. BIOMED RESEARCH INTERNATIONAL 2024; 2024:2052766. [PMID: 38249632 PMCID: PMC10799704 DOI: 10.1155/2024/2052766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/16/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024]
Abstract
Background Diabetic retinopathy (DR) risk has been shown to vary depending on ethnic backgrounds, and thus, it is worthy that underrepresented populations are analyzed for the potential identification of DR-associated genetic variants. We conducted a case-control study for the identification of DR-risk variants in Mexican population. Methods We ascertained 60 type 2 diabetes mellitus (T2DM) patients. Cases (n = 30) were patients with advanced proliferative DR (PDR) with less than 15 years after a T2DM diagnosis while controls (n = 30) were patients with no DR 15 years after the diagnosis of T2DM. Exome sequencing was performed in all patients, and the frequency of rare variants was compared. In addition, the frequency of variants occurring in a set of 169 DR-associated genes were compared. Results Statistically significant differences were identified for rare missense and splice variants and for rare splice variants occurring more than once in either group. A strong statistical difference was observed when the number of rare missense variants with an aggregated prediction of pathogenicity and occurring more than once in either group was compared (p = 0.0035). Moreover, 8 variants identified more than once in either group, occurring in previously identified DR-associated genes were recognized. The p.Pro234Ser KIR2DS4 variant showed a strong protective effect (OR = 0.04 [0.001-0.36]; p = 0.04). Conclusions Our study showed an enrichment of rare splice acceptor/donor variants in patients with PDR and identified a potential protective variant in KIR2DS4. Although statistical significance was not reached, our results support the replication of 8 previously identified DR-associated genes.
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Affiliation(s)
- Juan C. Zenteno
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Faculty of Medicine, Department of Biochemistry, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, UNAM, Mexico City, Mexico
| | - Oscar F. Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Laboratorio 5 Edificio A-4, Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico
| | - Vianey Ordoñez-Labastida
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, UNAM, Mexico City, Mexico
- Faculty of Medicine, Autonomous University of the State of Morelos (UAEM), Morelos, Mexico
| | - Antonio Miranda-Duarte
- Department of Genomic Medicine, Instituto Nacional de Rehabilitación “Luis Guillermo Ibarra Ibarra”, Mexico City, Mexico
| | - Camila Del Castillo
- Retina Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Jessica Nava
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Fatima Mendoza
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Luis Montes-Almanza
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Germán Mora-Roldán
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Karlen Gazarian
- Biomedical Research Institute, Department of Genomic Medicine, National Autonomous University of Mexico, Mexico City, Mexico
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10
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O'Neil-Pirozzi TM, Sevigny M, Pinto SM, Hammond FM, Juengst SB. Early Factors Predictive of Extreme High and Low Life Satisfaction 10 Years Post-Moderate to Severe Traumatic Brain Injury. J Head Trauma Rehabil 2023; 38:448-457. [PMID: 36854110 PMCID: PMC10460820 DOI: 10.1097/htr.0000000000000860] [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] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To identify demographic, injury-related, and 1-year postinjury clinical and functional predictors of high and low life satisfaction at 10 years after moderate to severe traumatic brain injury (TBI) using an extreme phenotyping approach. SETTING Multicenter longitudinal database study. PARTICIPANTS A total of 3040 people from the National Institute on Disability, Independent Living, and Rehabilitation Research TBI Model Systems database with life satisfaction data at 10 years post-TBI. DESIGN Multicenter, cross-sectional, observational design. MAIN MEASURES Satisfaction With Life Scale (outcome), Glasgow Coma Scale, Disability Rating Scale, Functional Independence Measure, Participation Assessment with Recombined Tools-Objective, Patient Health Questionnaire-9, and General Anxiety Disorder-7 (standardized predictors). RESULTS Greater cognitive and motor independence, more frequent community participation, and less depressive symptoms 1 year post-moderate to severe TBI predicted extreme high life satisfaction 10 years later. Non-Hispanic White and Hispanic individuals were significantly more likely than Black individuals to have extreme high life satisfaction 10 years post-TBI. CONCLUSIONS Extreme phenotyping analysis complements existing knowledge regarding life satisfaction post-moderate to severe TBI. From a chronic disease management perspective, future studies are needed to examine the feasibility and impact of early postinjury medical and rehabilitative interventions targeting cognitive and motor function, community participation, and mood on the maintenance/enhancement of long-term life satisfaction post-TBI.
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Affiliation(s)
- Therese M O'Neil-Pirozzi
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Boston, Massachusetts (Dr O'Neil-Pirozzi); Department of Communication Sciences and Disorders, Northeastern University, Boston, Massachusetts (Dr O'Neil-Pirozzi); Research Department, Craig Hospital, Denver, Colorado (Mr Sevigny); Department of Physical Medicine and Rehabilitation, University of Texas Southwestern Medical Center, Dallas (Dr Pinto); Department of Physical Medicine and Rehabilitation, Indiana University School of Medicine, Rehabilitation Hospital of Indiana, Indianapolis (Dr Hammond); Brain Injury Research Center, TIRR Memorial Hermann, Houston, Texas (Dr Juengst); and Department of Physical Medicine and Rehabilitation, UT Houston Health Sciences Center, Houston, Texas (Dr Juengst)
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11
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Lopez-Escamez JA, Vela J, Frejo L. Immune-Related Disorders Associated With Ménière's Disease: A Systematic Review and Meta-analysis. Otolaryngol Head Neck Surg 2023; 169:1122-1131. [PMID: 37272729 DOI: 10.1002/ohn.386] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To analyze evidence supporting an association between immune-related diseases and Ménière's disease (MD) since it has long been thought to be related to autoimmune disorders and allergies. DATA SOURCES We retrieved records from Pubmed, Web of Science, Scopus, and Cochrane Library to identify studies published between January 2002 and October 2022. REVIEW METHODS Articles were independently assessed by 2 reviewers and verified by a third reviewer. Published cross-sectional studies, cohort/longitudinal studies, case series, and noncomparative cohort studies were considered eligible for inclusion. We conducted a systematic review and meta-analysis according to a registered protocol on the International Prospective Register of Systematic Reviews and Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Selected studies were classified into 2 groups: epidemiological and genetic association studies. Relative frequencies and odds ratios (ORs) for each autoinflammatory/autoimmune disease or genetic marker reported to be associated with MD. RESULTS Fifteen studies from 6 countries met our inclusion criteria. Nine are epidemiological studies and 6 are genetic association studies. The epidemiological studies were used to perform 3 different meta-analyses. Airway allergic disease and autoimmune thyroid disease showed a significant association with MD (OR = 2.27 [2.08-2.48] and OR = 1.35 [1.25-1.46]); while rheumatoid arthritis did not (OR = 0.63 [0.28-1.41]). Other comorbidities also showed a significant association with MD like chronic obstructive pulmonary disease, vitiligo, fibromyalgia, arthritis, and psoriasis. CONCLUSION Epidemiological evidence supports an association between MD and immune-related disorders in European and Asian populations, with population-specific effects. The evaluation of thyroid diseases, airway allergic diseases, and other inflammatory diseases should be implemented in the clinical management of MD patients.
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Affiliation(s)
- Jose A Lopez-Escamez
- Department of Surgery, Division of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Jesus Vela
- Department of Surgery, Division of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
| | - Lidia Frejo
- Department of Surgery, Division of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
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12
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Rohlfing ML, Hillel AT, Wohler E, Sobreira N, Phillips EJ, Mallal SA, Gelbard A. Human Leukocyte Antigen Genotyping of Idiopathic Subglottic Stenosis. Laryngoscope 2023; 133:2533-2539. [PMID: 36728247 PMCID: PMC10394115 DOI: 10.1002/lary.30580] [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: 09/15/2022] [Revised: 12/13/2022] [Accepted: 01/02/2023] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Despite recent scientific inquiry, idiopathic subglottic stenosis (iSGS) remains an enigmatic disease. The consistent demographics of the affected population suggest genetic factors may contribute to disease susceptibility. Given the inflammation observed in the affected proximal airway mucosa, we interrogated disease association with human leukocyte antigen (HLA) polymorphisms. Polymorphisms in the HLA locus have previously been shown to influence individuals' susceptibility to distinct inflammatory diseases. METHODS High-resolution HLA typing of 37 iSGS patients was compared with 1,242,890 healthy Caucasian controls of European ancestry from the USA National Marrow Donor Program and 281 patients with granulomatosis with polyangiitis (GPA). RESULTS Complete HLA genotyping of an iSGS population showed no significant associations when compared to a North American Caucasian control population. Unlike GPA patients, iSGS was not associated with allele DPB1*04:01 nor did allele homozygosity correlate with disease severity. CONCLUSIONS There was not a detectable HLA association observed in iSGS. These results support the concept that iSGS possesses a distinct genetic architecture from GPA. If genetic susceptibility exists in iSGS, it likely lies outside the HLA locus. LEVEL OF EVIDENCE NA, basic science Laryngoscope, 133:2533-2539, 2023.
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Affiliation(s)
- Matthew L Rohlfing
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexander T Hillel
- Department of Otolaryngology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Elizabeth J Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Simon A Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexander Gelbard
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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13
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Sekulic M, Puche R, Bodmer D, Petkovic V. Human blood-labyrinth barrier model to study the effects of cytokines and inflammation. Front Mol Neurosci 2023; 16:1243370. [PMID: 37808472 PMCID: PMC10551159 DOI: 10.3389/fnmol.2023.1243370] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Hearing loss is one of the 10 leading causes of disability worldwide. No drug therapies are currently available to protect or restore hearing. Inner ear auditory hair cells and the blood-labyrinth barrier (BLB) are critical for normal hearing, and the BLB between the systemic circulation and stria vascularis is crucial for maintaining cochlear and vestibular homeostasis. BLB defects are associated with inner ear diseases that lead to hearing loss, including vascular malformations, inflammation, and Meniere's disease (MD). Antibodies against proteins in the inner ear and cytokines in the cochlea, including IL-1α, TNF-α, and NF-kβ, are detected in the blood of more than half of MD patients. There is also emerging evidence of inner ear inflammation in some diseases, including MD, progressive sensorineural hearing loss, otosclerosis, and sudden deafness. Here, we examined the effects of TNF-α, IL6, and LPS on human stria vascularis-derived primary endothelial cells cultured together with pericytes in a Transwell system. By measuring trans-endothelial electrical resistance, we found that TNF-α causes the most significant disruption of the endothelial barrier. IL6 had a moderate influence on the barrier, whereas LPS had a minimal impact on barrier integrity. The prominent effect of TNF-α on the barrier was confirmed in the expression of the major junctional genes responsible for forming the tight endothelial monolayer, the decreased expression of ZO1 and OCL. We further tested permeability using 2 μg of daptomycin (1,619 Da), which does not pass the BLB under normal conditions, by measuring its passage through the barrier by HPLC. Treatment with TNF-α resulted in higher permeability in treated samples compared to controls. LPS-treated cells behaved similarly to the untreated cells and did not show differences in permeability compared to control. The endothelial damage caused by TNF-α was confirmed by decreased expression of an essential endothelial proteoglycan, syndecan1. These results allowed us to create an inflammatory environment model that increased BLB permeability in culture and mimicked an inflammatory state within the stria vascularis.
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Affiliation(s)
- Marijana Sekulic
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Raoul Puche
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Daniel Bodmer
- University Hospital Basel, Clinic for Otorhinolaryngology, Basel, Switzerland
| | - Vesna Petkovic
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
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14
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Shah SB, Peddada TN, Song C, Mensah M, Sung H, Yavi M, Yuan P, Zarate CA, Mickey BJ, Burmeister M, Akula N, McMahon FJ. Exome-wide association study of treatment-resistant depression suggests novel treatment targets. Sci Rep 2023; 13:12467. [PMID: 37528149 PMCID: PMC10394052 DOI: 10.1038/s41598-023-38984-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Treatment-resistant depression (TRD) is a severe form of major depressive disorder (MDD) with substantial public health impact and poor treatment outcome. Treatment outcome in MDD is significantly heritable, but genome-wide association studies have failed to identify replicable common marker alleles, suggesting a potential role for uncommon variants. Here we investigated the hypothesis that uncommon, putatively functional genetic variants are associated with TRD. Whole-exome sequencing data was obtained from 182 TRD cases and 2021 psychiatrically healthy controls. After quality control, the remaining 149 TRD cases and 1976 controls were analyzed with tests designed to detect excess burdens of uncommon variants. At the gene level, 5 genes, ZNF248, PRKRA, PYHIN1, SLC7A8, and STK19 each carried exome-wide significant excess burdens of variants in TRD cases (q < 0.05). Analysis of 41 pre-selected gene sets suggested an excess of uncommon, functional variants among genes involved in lithium response. Among the genes identified in previous TRD studies, ZDHHC3 was also significant in this sample after multiple test correction. ZNF248 and STK19 are involved in transcriptional regulation, PHYIN1 and PRKRA are involved in immune response, SLC7A8 is associated with thyroid hormone transporter activity, and ZDHHC3 regulates synaptic clustering of GABA and glutamate receptors. These results implicate uncommon, functional alleles in TRD and suggest promising novel targets for future research.
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Affiliation(s)
- Shrey B Shah
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
- Rutgers New Jersey Medical School, Newark, NJ, USA.
| | - Teja N Peddada
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher Song
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Maame Mensah
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Heejong Sung
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Mani Yavi
- Experimental Therapeutics and Pathophysiology Branch and Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Peixiong Yuan
- Experimental Therapeutics and Pathophysiology Branch and Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Carlos A Zarate
- Experimental Therapeutics and Pathophysiology Branch and Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Brian J Mickey
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Margit Burmeister
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
- Michigan Neuroscience Institute and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Nirmala Akula
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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15
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Mortlock S, Lord A, Montgomery G, Zakrzewski M, Simms LA, Krishnaprasad K, Hanigan K, Doecke JD, Walsh A, Lawrance IC, Bampton PA, Andrews JM, Mahy G, Connor SJ, Sparrow MP, Bell S, Florin TH, Begun J, Gearry RB, Radford-Smith GL. An Extremes of Phenotype Approach Confirms Significant Genetic Heterogeneity in Patients with Ulcerative Colitis. J Crohns Colitis 2023; 17:277-288. [PMID: 36111848 PMCID: PMC10024548 DOI: 10.1093/ecco-jcc/jjac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Ulcerative colitis [UC] is a major form of inflammatory bowel disease globally. Phenotypic heterogeneity is defined by several variables including age of onset and disease extent. The genetics of disease severity remains poorly understood. To further investigate this, we performed a genome wide association [GWA] study using an extremes of phenotype strategy. METHODS We conducted GWA analyses in 311 patients with medically refractory UC [MRUC], 287 with non-medically refractory UC [non-MRUC] and 583 controls. Odds ratios [ORs] were calculated for known risk variants comparing MRUC and non-MRUC, and controls. RESULTS MRUC-control analysis had the greatest yield of genome-wide significant single nucleotide polymorphisms [SNPs] [2018], including lead SNP = rs111838972 [OR = 1.82, p = 6.28 × 10-9] near MMEL1 and a locus in the human leukocyte antigen [HLA] region [lead SNP = rs144717024, OR = 12.23, p = 1.7 × 10-19]. ORs for the lead SNPs were significantly higher in MRUC compared to non-MRUC [p < 9.0 × 10-6]. No SNPs reached significance in the non-MRUC-control analysis (top SNP, rs7680780 [OR 2.70, p = 5.56 × 10-8). We replicate findings for rs4151651 in the Complement Factor B [CFB] gene and demonstrate significant changes in CFB gene expression in active UC. Detailed HLA analyses support the strong associations with MHC II genes, particularly HLA-DQA1, HLA-DQB1 and HLA-DRB1 in MRUC. CONCLUSIONS Our MRUC subgroup replicates multiple known UC risk variants in contrast to non-MRUC and demonstrates significant differences in effect sizes compared to those published. Non-MRUC cases demonstrate lower ORs similar to those published. Additional risk and prognostic loci may be identified by targeted recruitment of individuals with severe disease.
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Affiliation(s)
- Sally Mortlock
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Anton Lord
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Centre for Health Services Research, University of Queensland, Brisbane, QLD, Australia
| | - Grant Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Lisa A Simms
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | - James D Doecke
- Australian eHealth Research Centre, CSIRO, Brisbane, QLD, Australia
| | - Alissa Walsh
- Department of Gastroenterology, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ian C Lawrance
- Centre of Inflammatory Bowel Diseases, Saint John of God Hospital Subiaco, University of Western Australia, WA, Australia
| | | | - Jane M Andrews
- Department of Gastroenterology and Hepatology, Royal Adelaide Hospital & University of Adelaide, Adelaide, SA, Australia
| | - Gillian Mahy
- Department of Gastroenterology and Hepatology, Townsville University Hospital, Townsville, QLD, Australia
| | - Susan J Connor
- Department of Gastroenterology and Hepatology, Liverpool Hospital, Sydney, NSW, Australia
- South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Miles P Sparrow
- Department of Gastroenterology, Alfred Health, Melbourne, VIC, Australia
| | - Sally Bell
- Department of Gastroenterology and Hepatology, Monash Health, Melbourne, VIC, Australia
| | - Timothy H Florin
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Jakob Begun
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Inflammatory Disease Biology and Therapeutics Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Graham L Radford-Smith
- Corresponding author: Graham Radford-Smith, Gut Health Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. Tel: +617 3362 0499; Fax: +617 3009 0053;
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16
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Aziz K, Patel T, Canner JK, Swenor BK, Singh MS. Risk of Tertiary, Quaternary, and Quinary Proliferative Vitreoretinopathy: Analysis of a Nationwide Database (2010-2017). Ophthalmol Retina 2023:S2468-6530(23)00030-1. [PMID: 36717076 DOI: 10.1016/j.oret.2023.01.015] [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: 11/28/2021] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/29/2023]
Abstract
OBJECTIVE Primary proliferative vitreoretinopathy (PVR) is established as an important cause of the failed repair of a fresh retinal detachment (RD) and the consequent need for secondary repair. However, the burden of multiple repairs beyond the initial failure has not been studied in detail. We aimed to determine the association between primary PVR and the occurrence of tertiary, quaternary, and quinary RD repairs, using a nationwide database. DESIGN Retrospective cohort study of insurance claims. SUBJECTS Cases of rhegmatogenous RD that underwent primary surgical repair. METHODS Cases of primary RD repair from 2010 to 2017 were categorized based on the absence (P0 group) or presence (P1 group) of primary PVR. In each group, we analyzed the frequency of subsequent RD repair procedures with concurrent PVR. MAIN OUTCOME MEASURE The risk of secondary and higher multiples of PVR-associated RD repair. RESULTS A total of 27 137 cases were included, with 24 500 (90.3%) in the P0 group and 2637 (9.7%) in the P1 group. The frequency (%) of cases ultimately requiring secondary, tertiary, quaternary, and quinary repair in P0 versus P1 was 1.88 versus 10.24 (P < 0.001), 0.26 versus 2.50 (P < 0.001), 0.07 versus 0.64 (P < 0.001), and 0.03 versus 0.08 (P = 0.272), respectively. The risk of undergoing secondary repair was higher in the P1 than in the P0 group (hazard ratio [HR], 6.02; 95% confidence interval [CI], 5.24-6.92; P < 0.001). The risk of undergoing tertiary repair was also higher in the P1 than in the P0 group (HR, 1.67; CI, 1.23-2.28; P = 0.001). There was no difference in the risk of undergoing quaternary repair between the groups (HR, 0.76; CI, 0.41-1.40; P = 0.37). Senary repairs were not detected in this dataset. CONCLUSIONS Primary PVR may increase the risk of requiring multiple sequential retinal reattachment surgeries beyond the initial repair failure. Retinal detachment cases with primary PVR at the initial presentation of RD were more likely to undergo secondary and tertiary repairs than cases without primary PVR. Health care claims analysis may be a useful tool to study population-based estimates for multiple recurrences of RD in cases with PVR. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Kanza Aziz
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tapan Patel
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph K Canner
- Johns Hopkins Surgery Center for Outcomes Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bonnielin K Swenor
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Mandeep S Singh
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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17
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Gurung RL, Burdon KP, McComish BJ. A Guide to Genome-Wide Association Study Design for Diabetic Retinopathy. Methods Mol Biol 2023; 2678:49-89. [PMID: 37326705 DOI: 10.1007/978-1-0716-3255-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Diabetic retinopathy (DR) is the most common microvascular complication related to diabetes. There is evidence that genetics play an important role in DR pathogenesis, but the complexity of the disease makes genetic studies a challenge. This chapter is a practical overview of the basic steps for genome-wide association studies with respect to DR and its associated traits. Also described are approaches that can be adopted in future DR studies. This is intended to serve as a guide for beginners and to provide a framework for further in-depth analysis.
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Affiliation(s)
- Rajya L Gurung
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Bennet J McComish
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
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18
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Gallego-Martinez A, Escalera-Balsera A, Trpchevska N, Robles-Bolivar P, Roman-Naranjo P, Frejo L, Perez-Carpena P, Bulla J, Gallus S, Canlon B, Cederroth CR, Lopez-Escamez JA. Using coding and non-coding rare variants to target candidate genes in patients with severe tinnitus. NPJ Genom Med 2022; 7:70. [PMID: 36450758 PMCID: PMC9712652 DOI: 10.1038/s41525-022-00341-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Tinnitus is the phantom percept of an internal non-verbal set of noises and tones. It is reported by 15% of the population and it is usually associated with hearing and/or brain disorders. The role of structural variants (SVs) in coding and non-coding regions has not been investigated in patients with severe tinnitus. In this study, we performed whole-genome sequencing in 97 unrelated Swedish individuals with chronic tinnitus (TIGER cohort). Rare single nucleotide variants (SNV), large structural variants (LSV), and copy number variations (CNV) were retrieved to perform a gene enrichment analysis in TIGER and in a subgroup of patients with severe tinnitus (SEVTIN, n = 34), according to the tinnitus handicap inventory (THI) scores. An independent exome sequencing dataset of 147 Swedish tinnitus patients was used as a replication cohort (JAGUAR cohort) and population-specific datasets from Sweden (SweGen) and Non-Finish Europeans (NFE) from gnomAD were used as control groups. SEVTIN patients showed a higher prevalence of hyperacusis, hearing loss, and anxiety when they were compared to individuals in the TIGER cohort. We found an enrichment of rare missense variants in 6 and 8 high-constraint genes in SEVTIN and TIGER cohorts, respectively. Of note, an enrichment of missense variants was found in the CACNA1E gene in both SEVTIN and TIGER. We replicated the burden of missense variants in 9 high-constrained genes in the JAGUAR cohort, including the gene NAV2, when data were compared with NFE. Moreover, LSVs in constrained regions overlapping CACNA1E, NAV2, and TMEM132D genes were observed in TIGER and SEVTIN.
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Affiliation(s)
- Alvaro Gallego-Martinez
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Alba Escalera-Balsera
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Natalia Trpchevska
- grid.4714.60000 0004 1937 0626Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Paula Robles-Bolivar
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Pablo Roman-Naranjo
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Lidia Frejo
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
| | - Patricia Perez-Carpena
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain ,grid.4489.10000000121678994Department of Surgery, Division of Otolaryngology, University of Granada, 18016 Granada, Spain
| | - Jan Bulla
- grid.7914.b0000 0004 1936 7443Department of Mathematics, University of Bergen, 5020 Bergen, Norway ,grid.7727.50000 0001 2190 5763Department of Psychiatry and Psychotherapy, University of Regensburg, 93053 Regensburg, Germany
| | - Silvano Gallus
- grid.4527.40000000106678902Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Barbara Canlon
- grid.4714.60000 0004 1937 0626Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christopher R. Cederroth
- grid.4714.60000 0004 1937 0626Section of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden ,grid.240404.60000 0001 0440 1889National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Ropewalk House, Nottingham, NG1 5DU UK ,grid.4563.40000 0004 1936 8868Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, NG7 2UH UK
| | - Jose A. Lopez-Escamez
- grid.470860.d0000 0004 4677 7069Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain ,grid.411380.f0000 0000 8771 3783Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain ,grid.452372.50000 0004 1791 1185Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain ,grid.4489.10000000121678994Department of Surgery, Division of Otolaryngology, University of Granada, 18016 Granada, Spain
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19
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O'Neil-Pirozzi TM, Pinto SM, Sevigny M, Hammond FM, Juengst SB, Bombardier CH. Factors Associated With High and Low Life Satisfaction 10 Years After Traumatic Brain Injury. Arch Phys Med Rehabil 2022; 103:2164-2173. [PMID: 35202582 PMCID: PMC9484051 DOI: 10.1016/j.apmr.2022.01.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To identify correlates of life satisfaction at 10 years after moderate to severe traumatic brain injury (TBI) using an extreme phenotyping approach. DESIGN Effect sizes were calculated in this observational cohort study to estimate relationships of 10-year postinjury extremely high, extremely low, and moderate life satisfaction with (1) pre-injury demographics, injury-related factors, and functional characteristics at inpatient rehabilitation admission and discharge; and (2) postinjury demographics and clinical and functional measures at 10 years postinjury. SETTING Multicenter longitudinal database study. PARTICIPANTS People identified from the National Institute on Disability, Independent Living, and Rehabilitation Research TBI Database with life satisfaction data at 10 years post TBI (N=4800). INTERVENTIONS Not applicable. MAIN OUTCOME MEASURE Satisfaction With Life Scale. RESULTS Although few pre-injury factors or clinical and functional factors shortly after injury were associated with 10-year life satisfaction groups, the following 10-year postinjury factors were associated with extremely high vs extremely low life satisfaction group membership: greater independent functioning, less disability, more frequent community participation, being employed, and having fewer depressive and anxiety symptoms. Those with extremely high life satisfaction were distinctly different from those with moderate and extremely low satisfaction. Extremely high life satisfaction was underrepresented among non-Hispanic Black persons relative to non-Hispanic White persons. Relationships between life satisfaction and independent functioning, disability, and participation were attenuated among non-Hispanic Black persons. CONCLUSIONS Extreme phenotyping analysis complements existing knowledge regarding life satisfaction after moderate to severe TBI and may inform acute and postacute clinical service delivery by comparing extremely high and extremely low life satisfaction subgroups. Findings suggest little association among personal, clinical, and functional characteristics early post TBI and life satisfaction 10 years later. Contemporaneous correlates of extremely high life satisfaction exist at 10 years post TBI, although the positive relationship of these variables to life satisfaction may be attenuated for non-Hispanic Black persons.
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Affiliation(s)
- Therese M O'Neil-Pirozzi
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Boston, MA; Department of Communication Sciences and Disorders, Northeastern University, Boston, MA.
| | - Shanti M Pinto
- Department of Physical Medicine and Rehabilitation, Carolinas Rehabilitation, Charlotte, NC
| | | | - Flora M Hammond
- Department of Physical Medicine and Rehabilitation, Indiana University School of Medicine, Rehabilitation Hospital of Indiana, Indianapolis, IN
| | - Shannon B Juengst
- Department of Physical Medicine and Rehabilitation, Indiana University School of Medicine, Rehabilitation Hospital of Indiana, Indianapolis, IN; Department of Applied Clinical Research, UT Southwestern Medical Center, Dallas, TX
| | - Charles H Bombardier
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA, United States
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20
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Wu T, Liu Z, Mak TSH, Sham PC. Polygenic power calculator: Statistical power and polygenic prediction accuracy of genome-wide association studies of complex traits. Front Genet 2022; 13:989639. [PMID: 36299579 PMCID: PMC9589038 DOI: 10.3389/fgene.2022.989639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Power calculation is a necessary step when planning genome-wide association studies (GWAS) to ensure meaningful findings. Statistical power of GWAS depends on the genetic architecture of phenotype, sample size, and study design. While several computer programs have been developed to perform power calculation for single SNP association testing, it might be more appropriate for GWAS power calculation to address the probability of detecting any number of associated SNPs. In this paper, we derive the statistical power distribution across causal SNPs under the assumption of a point-normal effect size distribution. We demonstrate how key outcome indices of GWAS are related to the genetic architecture (heritability and polygenicity) of the phenotype through the power distribution. We also provide a fast, flexible and interactive power calculation tool which generates predictions for key GWAS outcomes including the number of independent significant SNPs, the phenotypic variance explained by these SNPs, and the predictive accuracy of resulting polygenic scores. These results could also be used to explore the future behaviour of GWAS as sample sizes increase further. Moreover, we present results from simulation studies to validate our derivation and evaluate the agreement between our predictions and reported GWAS results.
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Affiliation(s)
- Tian Wu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Zipeng Liu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Timothy Shin Heng Mak
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Fano Labs, Hong Kong, Hong Kong SAR, China
| | - Pak Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- *Correspondence: Pak Chung Sham,
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21
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Biscontin A, Zarantonello L, Russo A, Costa R, Montagnese S. Toward a Molecular Approach to Chronotype Assessment. J Biol Rhythms 2022; 37:272-282. [PMID: 35583112 DOI: 10.1177/07487304221099365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of the present study was to develop a Polygenic Score-based model for molecular chronotype assessment. Questionnaire-based phenotypical chronotype assessment was used as a reference. In total, 54 extremely morning/morning (MM/M; 35 females, 39.7 ± 3.8 years) and 44 extremely evening/evening (EE/E; 20 females, 27.3 ± 7.7 years) individuals donated a buccal DNA sample for genotyping by sequencing of the entire genetic variability of 19 target genes known to be involved in circadian rhythmicity and/or sleep duration. Targeted genotyping was performed using the single primer enrichment technology and a specifically designed panel of 5526 primers. Among 2868 high-quality polymorphisms, a cross-validation approach lead to the identification of 83 chronotype predictive variants, including previously known and also novel chronotype-associated polymorphisms. A large (35 single-nucleotide polymorphisms [SNPs]) and also a small (13 SNPs) panel were obtained, both with an estimated predictive validity of approximately 80%. Potential mechanistic hypotheses for the role of some of the newly identified variants in modulating chronotype are formulated. Once validated in independent populations encompassing the whole range of chronotypes, the identified panels might become useful within the setting of both circadian public health initiatives and precision medicine.
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Affiliation(s)
| | | | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy.,Institute of Neuroscience, National Research Council, Padova, Italy.,Chronobiology Section, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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22
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Boussaty EC, Friedman RA, Clifford RE. Hearing loss and tinnitus: association studies for complex-hearing disorders in mouse and man. Hum Genet 2022; 141:981-990. [PMID: 34318347 PMCID: PMC8792513 DOI: 10.1007/s00439-021-02317-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022]
Abstract
Genome-wide association studies (GWAS) provide an unbiased first look at genetic loci involved in aging and noise-induced sensorineural hearing loss and tinnitus. The hearing phenotype, whether audiogram-based or self-report, is regressed against genotyped information at representative single nucleotide polymorphisms (SNPs) across the genome. Findings include the fact that both hearing loss and tinnitus are polygenic disorders, with up to thousands of genes, each of effect size of < 0.02. Smaller human GWAS' were able to use objective measures and identified a few loci; however, hundreds of thousands of participants have been required for the statistical power to identify significant variants, and GWAS is unable to assess rare variants with mean allele frequency < 1%. Animal studies are required as well because of inability to access the human cochlea. Mouse GWAS builds on linkage techniques and the known phenotypic differences in auditory function between inbred strains. With the advantage that the laboratory environment can be controlled for noise and aging, the Hybrid Mouse Diversity Panel (HDMP) combines 100 strains sequenced at high resolution. Lift-over regions between mice and humans have identified over 17,000 homologous genes. Since most significant SNPs are either intergenic or in introns, and binding sites between species are poorly preserved between species, expression quantitative trait locus information is required to bring humans and mice into agreement. Transcriptome-wide analysis studies (TWAS) can prioritize putative causal genes and tissues. Diverse species, each making a distinct contribution, carry a synergistic advantage in the quest for treatment and ultimate cure of sensorineural hearing difficulties.
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Affiliation(s)
- Ely Cheikh Boussaty
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Rick Adam Friedman
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Royce E Clifford
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA.
- Research Department, VA Hospitals San Diego, San Diego, CA, USA.
- Visiting Scientist, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA.
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23
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Liyanage JSS, Estepp JH, Srivastava K, Li Y, Mori M, Kang G. GMEPS: a fast and efficient likelihood approach for genome-wide mediation analysis under extreme phenotype sequencing. Stat Appl Genet Mol Biol 2022; 21:sagmb-2021-0071. [PMID: 35266368 DOI: 10.1515/sagmb-2021-0071] [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: 09/14/2021] [Accepted: 02/17/2022] [Indexed: 11/15/2022]
Abstract
Due to many advantages such as higher statistical power of detecting the association of genetic variants in human disorders and cost saving, extreme phenotype sequencing (EPS) is a rapidly emerging study design in epidemiological and clinical studies investigating how genetic variations associate with complex phenotypes. However, the investigation of the mediation effect of genetic variants on phenotypes is strictly restrictive under the EPS design because existing methods cannot well accommodate the non-random extreme tails sampling process incurred by the EPS design. In this paper, we propose a likelihood approach for testing the mediation effect of genetic variants through continuous and binary mediators on a continuous phenotype under the EPS design (GMEPS). Besides implementing in EPS design, it can also be utilized as a general mediation analysis procedure. Extensive simulations and two real data applications of a genome-wide association study of benign ethnic neutropenia under EPS design and a candidate-gene study of neurocognitive performance in patients with sickle cell disease under random sampling design demonstrate the superiority of GMEPS under the EPS design over widely used mediation analysis procedures, while demonstrating compatible capabilities under the general random sampling framework.
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Affiliation(s)
- Janaka S S Liyanage
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Jeremie H Estepp
- Departments of Global Pediatric Medicine and Hematology, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Kumar Srivastava
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Yun Li
- Department of Biostatistics, Department of Genetics, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill 27599, NC, USA
| | - Motomi Mori
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
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24
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Frejo L, Lopez-Escamez JA. Cytokines and Inflammation in Meniere Disease. Clin Exp Otorhinolaryngol 2022; 15:49-59. [PMID: 35124944 PMCID: PMC8901949 DOI: 10.21053/ceo.2021.00920] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/20/2021] [Indexed: 12/05/2022] Open
Abstract
Meniere disease (MD) is a rare set of conditions associated with the accumulation of endolymph in the cochlear duct and the vestibular labyrinth with a decrease of endocochlear potential. It is considered a chronic inflammatory disorder of the inner ear with a multifactorial origin. The clinical syndrome includes several groups of patients with a core phenotype: sensorineural hearing loss, episodes of vertigo, and tinnitus with a non-predictable course. Genetic factors and the innate immune response seem to play a central role in the pathophysiology of the condition. Autoimmune MD should be diagnosed if a patient fulfills the diagnostic criteria for MD and one of the following autoimmune disorders: autoimmune thyroid disease, psoriasis, autoimmune arthritis, ankylosing spondylitis, or systemic lupus erythematosus. We summarize the evidence to support autoimmune MD as an endophenotype in bilateral MD associated with the allelic variant rs4947296 and nuclear factor-kappa B (NF-κB)-mediated inflammation, the role of cytokines (particularly interleukin-1β and tumor necrosis factor-α) in defining a subset of patients with autoinflammation, and the potential role of cytokines as biomarkers to distinguish between patients with MD and vestibular migraine. Finally, we also introduce a list of potential drugs that could regulate the immune response in MD with potential for repurposing in clinical trials.
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Affiliation(s)
- Lidia Frejo
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, PTS, Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs. Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Jose Antonio Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, PTS, Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs. Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.,Department of Surgery, Division of Otolaryngology, Universidad de Granada, Granada, Spain
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25
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Zuo Y, Wei D, Zhu C, Naveed O, Hong W, Yang X. Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models. Genes (Basel) 2021; 12:1101. [PMID: 34356117 PMCID: PMC8304351 DOI: 10.3390/genes12071101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Psychiatric disorders are complex brain disorders with a high degree of genetic heterogeneity, affecting millions of people worldwide. Despite advances in psychiatric genetics, the underlying pathogenic mechanisms of psychiatric disorders are still largely elusive, which impedes the development of novel rational therapies. There has been accumulating evidence suggesting that the genetics of complex disorders can be viewed through an omnigenic lens, which involves contextualizing genes in highly interconnected networks. Thus, applying network-based multi-omics integration methods could cast new light on the pathophysiology of psychiatric disorders. In this review, we first provide an overview of the recent advances in psychiatric genetics and highlight gaps in translating molecular associations into mechanistic insights. We then present an overview of network methodologies and review previous applications of network methods in the study of psychiatric disorders. Lastly, we describe the potential of such methodologies within a multi-tissue, multi-omics approach, and summarize the future directions in adopting diverse network approaches.
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Affiliation(s)
- Yanning Zuo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Don Wei
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Carissa Zhu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Ormina Naveed
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Weizhe Hong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Tambi R, Abdel Hameid R, Bankapur A, Nassir N, Begum G, Alsheikh-Ali A, Uddin M, Berdiev BK. Single-cell transcriptomics trajectory and molecular convergence of clinically relevant mutations in Brugada syndrome. Am J Physiol Heart Circ Physiol 2021; 320:H1935-H1948. [PMID: 33797273 DOI: 10.1152/ajpheart.00061.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Brugada syndrome (BrS) is a rare, inherited arrhythmia with high risk of sudden cardiac death. To evaluate the molecular convergence of clinically relevant mutations and to identify developmental cardiac cell types that are associated with BrS etiology, we collected 733 mutations represented by 16 sodium, calcium, potassium channels, and regulatory and structural genes related to BrS. Among the clinically relevant mutations, 266 are unique singletons and 88 mutations are recurrent. We observed an over-representation of clinically relevant mutations (∼80%) in SCN5A gene and also identified several candidate genes, including GPD1L, TRPM4, and SCN10A. Furthermore, protein domain enrichment analysis revealed that a large proportion of the mutations impacted ion transport domains in multiple genes, including SCN5A, TRPM4, and SCN10A. A comparative protein domain analysis of SCN5A further established a significant (P = 0.04) enrichment of clinically relevant mutations within ion transport domain, including a significant (P = 0.02) mutation hotspot within 1321-1380 residue. The enrichment of clinically relevant mutations within SCN5A ion transport domain is stronger (P = 0.00003) among early onset of BrS. Our spatiotemporal cellular heart developmental (prenatal to adult) trajectory analysis applying single-cell transcriptome identified the most frequently BrS-mutated genes (SCN5A and GPD1L) are significantly upregulated in the prenatal cardiomyocytes. A more restrictive cellular expression trajectory is prominent in the adult heart ventricular cardiomyocytes compared to prenatal. Our study suggests that genomic and proteomic hotspots in BrS converge into ion transport pathway and cardiomyocyte as a major BrS-associated cell type that provides insight into the complex genetic etiology of BrS.NEW & NOTEWORTHY Brugada syndrome is a rare inherited arrhythmia with high risk of sudden cardiac death. We present the findings for a molecular convergence of clinically relevant mutations and identification of a single-cell transcriptome-derived cardiac cell types that are associated with the etiology of BrS. Our study suggests that genomic and proteomic hotspots in BrS converge into ion transport pathway and cardiomyocyte as a major BrS-associated cell type that provides insight into the complex genetic etiology of BrS.
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Affiliation(s)
- Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Reem Abdel Hameid
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Asma Bankapur
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ghausia Begum
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alawi Alsheikh-Ali
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Bakhrom K Berdiev
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Amanat S, Gallego-Martinez A, Sollini J, Perez-Carpena P, Espinosa-Sanchez JM, Aran I, Soto-Varela A, Batuecas-Caletrio A, Canlon B, May P, Cederroth CR, Lopez-Escamez JA. Burden of rare variants in synaptic genes in patients with severe tinnitus: An exome based extreme phenotype study. EBioMedicine 2021; 66:103309. [PMID: 33813136 PMCID: PMC8047463 DOI: 10.1016/j.ebiom.2021.103309] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND tinnitus is a heterogeneous condition associated with audiological and/or mental disorders. Chronic, severe tinnitus is reported in 1% of the population and it shows a relevant heritability, according to twins, adoptees and familial aggregation studies. The genetic contribution to severe tinnitus is unknown since large genomic studies include individuals with self-reported tinnitus and large heterogeneity in the phenotype. The aim of this study was to identify genes for severe tinnitus in patients with extreme phenotype. METHODS for this extreme phenotype study, we used three different cohorts with European ancestry (Spanish with Meniere disease (MD), Swedes tinnitus and European generalized epilepsy). In addition, four independent control datasets were also used for comparisons. Whole-exome sequencing was performed for the MD and epilepsy cohorts and whole-genome sequencing was carried out in Swedes with tinnitus. FINDINGS we found an enrichment of rare missense variants in 24 synaptic genes in a Spanish cohort, the most significant being PRUNE2, AKAP9, SORBS1, ITGAX, ANK2, KIF20B and TSC2 (p < 2E-04), when they were compared with reference datasets. This burden was replicated for ANK2 gene in a Swedish cohort with 97 tinnitus individuals, and in a subset of 34 Swedish patients with severe tinnitus for ANK2, AKAP9 and TSC2 genes (p < 2E-02). However, these associations were not significant in a third cohort of 701 generalized epilepsy individuals without tinnitus. Gene ontology (GO) and gene-set enrichment analyses revealed several pathways and biological processes involved in severe tinnitus, including membrane trafficking and cytoskeletal protein binding in neurons. INTERPRETATION a burden of rare variants in ANK2, AKAP9 and TSC2 is associated with severe tinnitus. ANK2, encodes a cytoskeleton scaffolding protein that coordinates the assembly of several proteins, drives axonal branching and influences connectivity in neurons.
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Affiliation(s)
- Sana Amanat
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain
| | - Joseph Sollini
- Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
| | - Patricia Perez-Carpena
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain; Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Juan M Espinosa-Sanchez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain; Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Ismael Aran
- Department of Otolaryngology, Complexo Hospitalario de Pontevedra, Pontevedra, Spain
| | - Andres Soto-Varela
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | | | - Barbara Canlon
- Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for System Biomedicine, University of Luxemburg, Esch-sur-Alzette, Luxembourg
| | - Christopher R Cederroth
- Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK; Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden; National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Ropewalk House, Nottingham, UK
| | - Jose A Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain; Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain; Department of Surgery, Division of Otolaryngology, University of Granada, Granada, Spain.
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28
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Patiño-García A, Guruceaga E, Segura V, Sánchez Bayona R, Andueza MP, Tamayo Uria I, Serrano G, Fusco JP, Pajares MJ, Gurpide A, Ocón M, Sanmamed MF, Rodriguez Ruiz M, Melero I, Lozano MD, de Andrea C, Pita G, Gonzalez-Neira A, Gonzalez A, Zulueta JJ, Montuenga LM, Pio R, Perez-Gracia JL. Whole exome sequencing characterization of individuals presenting extreme phenotypes of high and low risk of developing tobacco-induced lung adenocarcinoma. Transl Lung Cancer Res 2021; 10:1327-1337. [PMID: 33889513 PMCID: PMC8044482 DOI: 10.21037/tlcr-20-1197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Background Tobacco is the main risk factor for developing lung cancer. Yet, some heavy smokers do not develop lung cancer at advanced ages while others develop it at young ages. Here, we assess for the first time the genetic background of these clinically relevant extreme phenotypes using whole exome sequencing (WES). Methods We performed WES of germline DNA from heavy smokers who either developed lung adenocarcinoma at an early age (extreme cases, n=50) or did not present lung adenocarcinoma or other tumors at an advanced age (extreme controls, n=50). We selected non-synonymous variants located in exonic regions and consensus splice sites of the genes that showed significantly different allelic frequencies between both cohorts. We validated our results in all the additional extreme cases (i.e., heavy smokers who developed lung adenocarcinoma at an early age) available from The Cancer Genome Atlas (TCGA). Results The mean age for the extreme cases and controls was respectively 49.7 and 77.5 years. Mean tobacco consumption was 43.6 and 56.8 pack-years. We identified 619 significantly different variants between both cohorts, and we validated 108 of these in extreme cases selected from TCGA. Nine validated variants, located in relevant cancer related genes, such as PARP4, HLA-A or NQO1, among others, achieved statistical significance in the False Discovery Rate test. The most significant validated variant (P=4.48×10−5) was located in the tumor-suppressor gene ALPK2. Conclusions We describe genetic variants associated with extreme phenotypes of high and low risk for the development of tobacco-induced lung adenocarcinoma. Our results and our strategy may help to identify high-risk subjects and to develop new therapeutic approaches.
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Affiliation(s)
- Ana Patiño-García
- Department of Pediatrics and Clinical Genetics, Clinica Universidad de Navarra, Pamplona, Spain.,Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Program in Solid Tumors, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | - Elizabeth Guruceaga
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Bioinformatics Platform, CIMA, Universidad de Navarra, Pamplona, Spain
| | - Victor Segura
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Bioinformatics Platform, CIMA, Universidad de Navarra, Pamplona, Spain
| | - Rodrigo Sánchez Bayona
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Oncology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Maria Pilar Andueza
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Oncology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Ibon Tamayo Uria
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Bioinformatics Platform, CIMA, Universidad de Navarra, Pamplona, Spain
| | - Guillermo Serrano
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Program in Solid Tumors, Center for Applied Medical Research (CIMA), Pamplona, Spain
| | | | - María José Pajares
- Biochemistry Area, Department of Health Science, Public University of Navarre, Pamplona, Spain
| | - Alfonso Gurpide
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Oncology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Marimar Ocón
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Pulmonary, Clinica Universidad de Navarra, Pamplona, Spain
| | - Miguel F Sanmamed
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Oncology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Maria Rodriguez Ruiz
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Oncology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Melero
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Division of Immunology and Immunotherapy, CIMA, Universidad de Navarra and Instituto de Investigación Sanitaria de Navarra (IdisNA), Pamplona, Spain.,Department of Immunology, Clinica Universidad de Navarra and CIMA, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Maria Dolores Lozano
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain.,Department of Pathology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Carlos de Andrea
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Pathology, Clinica Universidad de Navarra, Pamplona, Spain
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Anna Gonzalez-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alvaro Gonzalez
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Biochemistry, Clinica Universidad de Navarra, Pamplona, Spain
| | - Javier J Zulueta
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Division of Immunology and Immunotherapy, CIMA, Universidad de Navarra and Instituto de Investigación Sanitaria de Navarra (IdisNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Luis M Montuenga
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Program in Solid Tumors, Center for Applied Medical Research (CIMA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain.,Department of Pathology, Anatomy and Physiology, Schools of Medicine and Sciences, University of Navarra, Pamplona, Spain
| | - Ruben Pio
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Program in Solid Tumors, Center for Applied Medical Research (CIMA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Jose Luis Perez-Gracia
- Health Research Institute of Navarra (IdisNA), Pamplona, Spain.,Department of Oncology, Clinica Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
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29
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Germenis AE, Rijavec M, Veronez CL. Leveraging Genetics for Hereditary Angioedema: A Road Map to Precision Medicine. Clin Rev Allergy Immunol 2021; 60:416-428. [PMID: 33507496 DOI: 10.1007/s12016-021-08836-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/25/2022]
Abstract
Biochemical studies performed during the last decades resulted in the development of various innovative medicinal products for hereditary angioedema (HAE). These therapeutic agents target the production or the function of bradykinin-the main mediator of HAE due to C1-inhibitor (C1-INH) deficiency. However, despite these remarkable achievements, current knowledge cannot provide convincing explanations for the clinical variability of the disease. As a consequence, treatment indications apply for drugs available for C1-INH deficiency. The advent of high-throughput next-generation sequencing technologies may assist in covering the missing part of our understanding of HAE pathogenesis. During the last 3 years alone, several new entities were added to the already described genotypes. The recent discovery of four novel target genes expands our understanding of other causes which may explain recurrent angioedema in individuals and families with normal C1-INH activity. Furthermore, new genetic technologies allowed the recognition of deep intronic variants associated with the disease, and elegant functional studies characterized new variants for the C1-INH gene. Thus, evidence has been provided regarding pathogenetic aspects remaining obscure for many years, such as the defective intracellular transport of mutant C1-INH, and environmental effect on the disease expression. Therefore, it seems that the stage for Precision Medicine era in HAE management is ready. Disease endotypes are expected to be uncovered and specified targets for therapeutic intervention will be detected, promising a more effective, individualized management of the disease.
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Affiliation(s)
- Anastasios E Germenis
- Department of Immunology and Histocompatibility, School of Medicine, University of Thessaly, 3 Panepistimiou Street, GR-41500, Biopolis Larissa, Greece.
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Camila Lopes Veronez
- Department of Medicine, Division of Rheumatology, Allergy and Immunology, University of California San Diego, San Diego, CA, USA.,Research Service, San Diego Veterans Affairs Healthcare, San Diego, CA, USA
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30
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Paz-Tamayo A, Perez-Carpena P, Lopez-Escamez JA. Systematic Review of Prevalence Studies and Familial Aggregation in Vestibular Migraine. Front Genet 2020; 11:954. [PMID: 33110417 PMCID: PMC7489493 DOI: 10.3389/fgene.2020.00954] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Background: Vestibular migraine (VM) is complex disorder consisting of episodes of migraine and vertigo with an estimated prevalence of 1–3%. As migraine, it is considered that VM has genetic predisposition; however, evidence to support a genetic contribution has not been critically appraised. Objective: The aim of this systematic review is to assess available evidence in scientific publications to determine the role of inheritance in VM. Methods: After performing the quality assessment of the retrieved records, 31 studies were included (24 epidemiological reports and 7 genetic association studies in families or case-control in candidate genes). We gathered data about prevalence of VM in different populations and in families, and also about the genetic findings reported. In addition, other variables were considered to assess the heritability of VM, such as the ancestry, the age of onset or the familial history of vertigo and migraine. Results: The estimated prevalence of VM was different between black (3.13%), white (2.64%) and Asian (1.07%) ethnicities. The reported prevalence of VM in migraine patients is higher in European countries (21%) than in Asian countries (10%). Moreover, the prevalence of the migraine-vertigo association in families is 4–10 times higher than the prevalence reported in the general population (sibling recurrence risk ratio λs = 4.31–10.42). We also found that the age of onset is lower in patients with simultaneous onset of symptoms and in those who have familial history for migraine and/or vertigo, suggesting anticipation. Although some genetic studies have reported few allelic variants associated to MV, replication studies are needed to validate these results. Conclusions: The available evidence to support heritability in VM is limited. Variability in prevalence depending on ethnicity and geographic location suggests a combined genetic and environmental contribution to VM. However, the familial aggregation observed in VM support genetic and shared familial environmental effects that remarks the necessity of twins and adoptees-based epidemiological studies to estimate its heritability.
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Affiliation(s)
- Ana Paz-Tamayo
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, Granada, Spain
| | - Patricia Perez-Carpena
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario San Cecilio, Granada, Spain.,Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer/University of Granada/Junta de Andalucía, PTS, Granada, Spain
| | - Jose A Lopez-Escamez
- Division of Otolaryngology, Department of Surgery, Universidad de Granada, Granada, Spain.,Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer/University of Granada/Junta de Andalucía, PTS, Granada, Spain.,Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain
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