1
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Yun JH, Lee S, Srinivasa P, Morrow J, Chase R, Saferali A, Xu Z, Cho M, Castaldi P, Hersh CP. An interferon-inducible signature of airway disease from blood gene expression profiling. Eur Respir J 2022; 59:2100569. [PMID: 34649980 PMCID: PMC9245457 DOI: 10.1183/13993003.00569-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/24/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND The molecular basis of airway remodelling in chronic obstructive pulmonary disease (COPD) remains poorly understood. We identified gene expression signatures associated with chest computed tomography (CT) scan airway measures to understand molecular pathways associated with airway disease. METHODS In 2396 subjects in the COPDGene Study, we examined the relationship between quantitative CT airway phenotypes and blood transcriptomes to identify airway disease-specific genes and to define an airway wall thickness (AWT) gene set score. Multivariable regression analyses were performed to identify associations of the AWT score with clinical phenotypes, bronchial gene expression and genetic variants. RESULTS Type 1 interferon (IFN)-induced genes were consistently associated with AWT, square root wall area of a hypothetical airway with 10 mm internal perimeter (Pi10) and wall area percentage, with the strongest enrichment in AWT. A score derived from 18 genes whose expression was associated with AWT was associated with COPD-related phenotypes including reduced lung function (forced expiratory volume in 1 s percentage predicted β= -3.4; p<0.05) and increased exacerbations (incidence rate ratio 1.7; p<0.05). The AWT score was reproducibly associated with AWT in bronchial samples from 23 subjects (β=3.22; p<0.05). The blood AWT score was associated with genetic variant rs876039, an expression quantitative trait locus for IKZF1, a gene that regulates IFN signalling and is associated with inflammatory diseases. CONCLUSIONS A gene expression signature with IFN-stimulated genes from peripheral blood and bronchial brushings is associated with CT AWT, lung function and exacerbations. Shared genes and genetic associations suggest viral responses and/or autoimmune dysregulation as potential underlying mechanisms of airway disease in COPD.
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Affiliation(s)
- Jeong H Yun
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sool Lee
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pooja Srinivasa
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jarrett Morrow
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robert Chase
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Aadbida Saferali
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Zhonghui Xu
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Cho
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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2
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Ghosh AJ, Hobbs BD, Yun JH, Saferali A, Moll M, Xu Z, Chase RP, Morrow J, Ziniti J, Sciurba F, Barwick L, Limper AH, Flaherty K, Criner G, Brown KK, Wise R, Martinez FJ, McGoldrick D, Cho MH, DeMeo DL, Silverman EK, Castaldi PJ, Hersh CP. Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Respir Res 2022; 23:97. [PMID: 35449067 PMCID: PMC9026726 DOI: 10.1186/s12931-022-02013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/04/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. METHODS We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. RESULTS We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. CONCLUSIONS We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF.
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Affiliation(s)
- Auyon J. Ghosh
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Brian D. Hobbs
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Jeong H. Yun
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Aabida Saferali
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Matthew Moll
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Zhonghui Xu
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Robert P. Chase
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Jarrett Morrow
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - John Ziniti
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Frank Sciurba
- grid.21925.3d0000 0004 1936 9000Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Lucas Barwick
- grid.280434.90000 0004 0459 5494The Emmes Company, Rockville, MD USA
| | - Andrew H. Limper
- grid.66875.3a0000 0004 0459 167XDivision of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN USA
| | - Kevin Flaherty
- grid.214458.e0000000086837370Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Healthy System, Ann Arbor, MI USA
| | - Gerard Criner
- grid.264727.20000 0001 2248 3398Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA USA
| | - Kevin K. Brown
- grid.240341.00000 0004 0396 0728Department of Medicine, National Jewish Health, Denver, CO USA
| | - Robert Wise
- grid.21107.350000 0001 2171 9311Division of Pulmonary and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Fernando J. Martinez
- grid.5386.8000000041936877XDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Daniel McGoldrick
- grid.34477.330000000122986657Northwest Genomics Center, University of Washington, Seattle, WA USA
| | - Michael H. Cho
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Dawn L. DeMeo
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Edwin K. Silverman
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Peter J. Castaldi
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Craig P. Hersh
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
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Ghosh AJ, Saferali A, Lee S, Chase R, Moll M, Morrow J, Yun J, Castaldi PJ, Hersh CP. Blood RNA sequencing shows overlapping gene expression across COPD phenotype domains. Thorax 2022; 77:115-122. [PMID: 34168019 PMCID: PMC8711128 DOI: 10.1136/thoraxjnl-2020-216401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 05/21/2021] [Indexed: 02/03/2023]
Abstract
RATIONALE COPD can be assessed using multidimensional grading systems with components from three domains: pulmonary function tests, symptoms and systemic features. Clinically, measures may be used interchangeably, though it is not known if they share similar pathobiology. OBJECTIVE To use RNA sequencing (RNA-seq) to determine if there is an overlap in the underlying biological mechanisms and consequences driving different components of the multidimensional grading systems. METHODS Whole blood was collected for RNA-seq from current and former smokers in the Genetic Epidemiology of COPD study. We tested the overlap in gene expression and biological pathways associated with case-control status and quantitative COPD phenotypes within and between the three domains. RESULTS In 2647 subjects, there were 3030 genes differentially expressed in any of the three domains or case-control status. There were five genes that overlapped between the three domains and case-control status, including G protein-coupled receptor 15(GPR15), sestrin 1 (SESN1) and interferon-induced guanylate-binding protein 1 (GBP1), which were associated with longitudinal decline in FEV1. The overlap between the three domains was enriched for pathways related to cellular components. CONCLUSIONS We identified gene sets and pathways that overlap between 12 COPD-related phenotypes and case-control status. There were no pathways represented in the overlap between the three domains and case-control status, but we identified multiple genes that demonstrated a consistent pattern of expression across several of the phenotypes. Patterns of gene expression correlation were generally similar to the correlation of clinical phenotypes in the PFT and symptom domains but not the systemic features.
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Affiliation(s)
- Auyon J Ghosh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sool Lee
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Robert Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
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4
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Alobaidan A, Bugiardini E, Morrow J, Shah S, MacDonald S, Carr A, Machado P, Quinlivan R, Turner C, Yousry T, Parton M, Hanna M. FSHD. Neuromuscul Disord 2021. [DOI: 10.1016/j.nmd.2021.07.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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McCluskey G, Kinney MO, Russell A, Smithson WH, Parsons L, Morrison PJ, Bromley R, MacKillop L, Heath C, Liggan B, Murphy S, Delanty N, Irwin B, Campbell E, Morrow J, Hunt SJ, Craig JJ. Zonisamide safety in pregnancy: Data from the UK and Ireland epilepsy and pregnancy register. Seizure 2021; 91:311-315. [PMID: 34273670 DOI: 10.1016/j.seizure.2021.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Animal data suggest teratogenic effects with zonisamide use and risk of pregnancy losses. Human data following zonisamide exposure are presently limited, but suggest low risk of malformation with elevated risk of low birth weight. OBJECTIVE To calculate the major congenital malformation (MCM) rate of zonisamide in human pregnancy and assess for a signal of any specific malformation pattern and associations with birth weight. METHODS AND MATERIALS Data were obtained from the UK and Ireland Epilepsy and Pregnancy register (UKIEPR) which is an observational, registration, and follow up study from December 1996 to July 2020. Eligibility criteria were use of zonisamide and to have been referred to the UKIEPR before the outcome of the pregnancy was known. Primary outcome was evidence of MCM. RESULTS From December 1996 through July 2020 there were 112 cases of first trimester exposure to zonisamide, including 26 monotherapy cases. There were 3 MCM for monotherapy cases (MCM rate 13.0% (95% confidence interval 4.5-32.1)), and 5 MCM for polytherapy cases (MCM rate 6.9% (95% confidence interval 3.0-15.2)). While the median birth weight was on 71st and 44th centile for monotherapy and polytherapy cases respectively, there was a high rate of infants born small for gestational age (21% for both). CONCLUSION These data raise concerns about a signal for potential teratogenicity with zonisamide in human pregnancy. Given the low numbers reported, further data will be required to adequately counsel women who use zonisamide in pregnancy.
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Affiliation(s)
- G McCluskey
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom
| | - M O Kinney
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom
| | - A Russell
- Scottish Epilepsy Centre, Glasgow, United Kingdom
| | - W H Smithson
- Department of General Practice, University College Cork, Cork, Ireland
| | - L Parsons
- Neurology Department, Luton & Dunstable Hospitals NHS Trust, Luton, United Kingdom
| | - P J Morrison
- Department of Medical Genetics, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, United Kingdom
| | - R Bromley
- Royal Manchester Children's Hospital, Central Manchester University Foundation NHS Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - L MacKillop
- Women's Centre. Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - C Heath
- Department of Neurology, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - B Liggan
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - S Murphy
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - N Delanty
- Department of Neurology, Beaumont Hospital, Dublin, Ireland; Department of Neurology, Beaumont Hospital, and FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - B Irwin
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom
| | - E Campbell
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom
| | - J Morrow
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom
| | - S J Hunt
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom
| | - J J Craig
- Department of Neurology, Royal Victoria Hospital (Belfast Health and Social Care Trust), Grosvenor Road, Belfast BT12 6BA, United Kingdom.
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6
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Koo HK, Morrow J, Kachroo P, Tantisira K, Weiss ST, Hersh CP, Silverman EK, DeMeo DL. Sex-specific associations with DNA methylation in lung tissue demonstrate smoking interactions. Epigenetics 2021; 16:692-703. [PMID: 32962511 PMCID: PMC8143227 DOI: 10.1080/15592294.2020.1819662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/08/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cigarette smoking impacts DNA methylation, but the investigation of sex-specific features of lung tissue DNA methylation in smokers has been limited. Women appear more susceptible to cigarette smoke, and often develop more severe lung disease at an earlier age with less smoke exposure. We aimed to analyse whether there are sex differences in DNA methylation in lung tissue and whether these DNA methylation marks interact with smoking. We collected lung tissue samples from former smokers who underwent lung tissue resection. One hundred thirty samples from white subjects were included for this analysis. Regression models for sex as a predictor of methylation were adjusted for age, presence of COPD, smoking variables and technical batch variables revealed 710 associated sites. 294 sites demonstrated robust sex-specific methylation associations in foetal lung tissue. Pathway analysis identified 6 nominally significant pathways including the mitophagy pathway. Three CpG sites demonstrated a suggested interaction between sex and pack-years of smoking: GPR132, ANKRD44 and C19orf60. All of them were nominally significant in both male- and female-specific models, and the effect estimates were in opposite directions for male and female; GPR132 demonstrated significant association between DNA methylation and gene expression in lung tissue (P < 0.05). Sex-specific associations with DNA methylation in lung tissue are wide-spread and may reveal genes and pathways relevant to sex differences for lung damaging effects of cigarette smoking.
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Affiliation(s)
- Hyeon-Kyoung Koo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Ilsan Paik Hospital, Inje University College of Medicine, Ilsan, Republic of Korea
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
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7
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Robledo C, Machiorlatti M, Clark L, Morrow J. COVID-19 Impact on Health & Well-Being Survey: Measuring Depression and Anxiety Among Individuals Sheltering at Home. Ann Epidemiol 2020. [DOI: 10.1016/j.annepidem.2020.08.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Kneese G, Barrera S, Castillo J, Garcia M, Ryden A, White A, Vargas J, Morrow J. ScribeMD: Mixed-methods analysis of a pen pal program in undergraduate medical education. Med Teach 2020; 42:316-324. [PMID: 31747818 DOI: 10.1080/0142159x.2019.1686134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Introduction: A growing emphasis on humanistic medical care has led to the development of programs to imbue more humanistic values into training physicians. The ScribeMD intra-class pen pal program is a narrative medicine tool designed to meet this need with a focus on the journey through medical education. This study intends to evaluate the efficacy of this novel program on the participants' professional identity formation (PIF), emotional intelligence development (EID), and narrative competency improvement (NCI).Methods: This program evaluation involved quantitative and qualitative survey solicitations from first and second-year medical student participants and controls. An efficacy-triangulation model was developed as a quantitative outcome-measuring tool linking objective, writing prompts, and survey data.Results: The quantitative results showed statistically significant improvements in line with the Efficacy Triangulation Model in the participant group. Qualitatively, reflective and insight-driven gains were elicited, as were notable themes of personal and community improvements.Conclusion: ScribeMD poses a unique avenue for the development of more humanistic physicians during their medical education. We recommend additional development of the Efficacy Triangulation Model as well as the program design itself. We also recommend the piloting of this program in other healthcare-education settings both with medical education and other health professions.
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Affiliation(s)
- G Kneese
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - S Barrera
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - J Castillo
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - M Garcia
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - A Ryden
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - A White
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - J Vargas
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
| | - J Morrow
- Long School of Medicine, UT Health San Antonio (UTHSA), San Antonio, TX, USA
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9
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Paci P, Fiscon G, Conte F, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L. Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. Sci Rep 2020; 10:3361. [PMID: 32099002 PMCID: PMC7042269 DOI: 10.1038/s41598-020-60228-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called "switch genes" - for the disease. Genes contributing to common biological processes or defining given cell types are usually co-regulated and co-expressed, forming expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.
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Affiliation(s)
- Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
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10
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Scalco R, Morrow J, Manole A, Skorupinska I, Ricciardi F, Matthews E, Hanna M, Fialho D. P.98RCT of 2mg bumetanide for hypokalaemic periodic paralysis. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Bugiardini E, Khan A, Phadke R, Lynch D, Cortese A, Feng L, Gang Q, Pittman A, Morrow J, Turner C, Carr A, Quinlivan R, Rossor A, Holton J, Parton M, Blake J, Reilly M, Houlden H, Matthews E, Hanna M. EP.103Genetic and phenotypic characterisation of inherited myopathies in a tertiary neuromuscular centre. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Biabani M, Fornito A, Mutanen T, Morrow J, Rogasch N. Sensory contamination in TMS-EEG recordings: Can we isolate TMS-evoked neural activity? Brain Stimul 2019. [DOI: 10.1016/j.brs.2018.12.543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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13
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Rogasch N, Morrow J, Bailey N, Fitzgerald P, Fornito A. Assessing the role of prefrontal and parietal cortex in working memory using combined transcranial magnetic stimulation and electroencephalography. Brain Stimul 2019. [DOI: 10.1016/j.brs.2018.12.454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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14
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Conway R, Morrow J, Brennan R, Mulvey C, ÓhAiseadha C. The Current State of Cycling Infrastructure in Dublin and Copenhagen; A Comparison of Cycling Infrastructure in 8 Radial Routes into the City Centre of Dublin and Copenhagen. Ir Med J 2019; 112:856. [PMID: 30719897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- R Conway
- Department of Public Health East, Health Service Executive, Dublin
| | - J Morrow
- Department of Radiology, St Vincent’s University Hospital
| | - R Brennan
- Royal College of Physicians of Ireland, Dublin
| | - C Mulvey
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin
| | - C ÓhAiseadha
- Department of Public Health East, Health Service Executive, Dublin
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15
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Qiao D, Ameli A, Prokopenko D, Chen H, Kho AT, Parker MM, Morrow J, Hobbs BD, Liu Y, Beaty TH, Crapo JD, Barnes KC, Nickerson DA, Bamshad M, Hersh CP, Lomas DA, Agusti A, Make BJ, Calverley PMA, Donner CF, Wouters EF, Vestbo J, Paré PD, Levy RD, Rennard SI, Tal-Singer R, Spitz MR, Sharma A, Ruczinski I, Lange C, Silverman EK, Cho MH. Whole exome sequencing analysis in severe chronic obstructive pulmonary disease. Hum Mol Genet 2018; 27:3801-3812. [PMID: 30060175 PMCID: PMC6196654 DOI: 10.1093/hmg/ddy269] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/09/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), one of the leading causes of death worldwide, is substantially influenced by genetic factors. Alpha-1 antitrypsin deficiency demonstrates that rare coding variants of large effect can influence COPD susceptibility. To identify additional rare coding variants in patients with severe COPD, we conducted whole exome sequencing analysis in 2543 subjects from two family-based studies (Boston Early-Onset COPD Study and International COPD Genetics Network) and one case-control study (COPDGene). Applying a gene-based segregation test in the family-based data, we identified significant segregation of rare loss of function variants in TBC1D10A and RFPL1 (P-value < 2x10-6), but were unable to find similar variants in the case-control study. In single-variant, gene-based and pathway association analyses, we were unable to find significant findings that replicated or were significant in meta-analysis. However, we found that the top results in the two datasets were in proximity to each other in the protein-protein interaction network (P-value = 0.014), suggesting enrichment of these results for similar biological processes. A network of these association results and their neighbors was significantly enriched in the transforming growth factor beta-receptor binding and cilia-related pathways. Finally, in a more detailed examination of candidate genes, we identified individuals with putative high-risk variants, including patients harboring homozygous mutations in genes associated with cutis laxa and Niemann-Pick Disease Type C. Our results likely reflect heterogeneity of genetic risk for COPD along with limitations of statistical power and functional annotation, and highlight the potential of network analysis to gain insight into genetic association studies.
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Affiliation(s)
- Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Asher Ameli
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Alvin T Kho
- Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James D Crapo
- National Jewish Health, Denver, Colorado, United States of America
| | - Kathleen C Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, Washington , United States of America
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Barcelona, Spain
| | - Barry J Make
- National Jewish Health, Denver, Colorado, United States of America
| | | | - Claudio F Donner
- Mondo Medico di I.F.I.M. srl, Multidisciplinary and Rehabilitation Outpatient Clinic, Borgomanero, Novara, Italy
| | - Emiel F Wouters
- Department of Respiratory Medicine, Maastricht University Medical Center, AZ Maastricht, The Netherlands
| | - Jørgen Vestbo
- University of Manchester, Manchester, United Kingdom
| | - Peter D Paré
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T, Canada
| | - Robert D Levy
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T, Canada
| | - Stephen I Rennard
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- AstraZeneca, Cambridge CB2 0RE, United Kingdom
| | - Ruth Tal-Singer
- GSK Research and Development, KingOf Prussia, Pennsylvania, United States of America
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Longwood Avenue, Boston, MA, USA
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16
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Bugiardini E, Phadke R, Maas R, Pittman A, Kusters B, Morrow J, Parton M, Nunes A, Akhtar M, Syrris P, Lopes L, Fotelonga T, Houlden H, Elliott P, Hanna M, Raaphorst J, Burkin D, Matthews E. CONGENITAL MUSCULAR DYSTROPHIES. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Scalco R, Morrow J, Manole A, Skorupinska I, Bellin A, Ricciardi F, Matthews E, Hanna M, Fialho D. RCT of bumetanide in hypokalaemic periodic paralysis (HypoPP) using abductor digiti minimi compound muscle action potential (CMAP) as an objective outcome measure. Neuromuscul Disord 2018. [DOI: 10.1016/s0960-8966(18)30370-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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van Schaik IN, Bril V, van Geloven N, Hartung HP, Lewis RA, Sobue G, Lawo JP, Praus M, Mielke O, Durn BL, Cornblath DR, Merkies ISJ, Sabet A, George K, Roberts L, Carne R, Blum S, Henderson R, Van Damme P, Demeestere J, Larue S, D'Amour C, Bril V, Breiner A, Kunc P, Valis M, Sussova J, Kalous T, Talab R, Bednar M, Toomsoo T, Rubanovits I, Gross-Paju K, Sorro U, Saarela M, Auranen M, Pouget J, Attarian S, Le Masson G, Wielanek-Bachelet A, Desnuelle C, Delmont E, Clavelou P, Aufauvre D, Schmidt J, Zschuentssch J, Sommer C, Kramer D, Hoffmann O, Goerlitz C, Haas J, Chatzopoulos M, Yoon R, Gold R, Berlit P, Jaspert-Grehl A, Liebetanz D, Kutschenko A, Stangel M, Trebst C, Baum P, Bergh F, Klehmet J, Meisel A, Klostermann F, Oechtering J, Lehmann H, Schroeter M, Hagenacker T, Mueller D, Sperfeld A, Bethke F, Drory V, Algom A, Yarnitsky D, Murinson B, Di Muzio A, Ciccocioppo F, Sorbi S, Mata S, Schenone A, Grandis M, Lauria G, Cazzato D, Antonini G, Morino S, Cocito D, Zibetti M, Yokota T, Ohkubo T, Kanda T, Kawai M, Kaida K, Onoue H, Kuwabara S, Mori M, Iijima M, Ohyama K, Baba M, Tomiyama M, Nishiyama K, Akutsu T, Yokoyama K, Kanai K, van Schaik I, Eftimov F, Notermans N, Visser N, Faber C, Hoeijmakers J, Rejdak K, Chyrchel-Paszkiewicz U, Casanovas Pons C, Alberti Aguiló M, Gamez J, Figueras M, Marquez Infante C, Benitez Rivero S, Lunn M, Morrow J, Gosal D, Lavin T, Melamed I, Testori A, Ajroud-Driss S, Menichella D, Simpson E, Chi-Ho Lai E, Dimachkie M, Barohn R, Beydoun S, Johl H, Lange D, Shtilbans A, Muley S, Ladha S, Freimer M, Kissel J, Latov N, Chin R, Ubogu E, Mumfrey S, Rao T, MacDonald P, Sharma K, Gonzalez G, Allen J, Walk D, Hobson-Webb L, Gable K. Subcutaneous immunoglobulin for maintenance treatment in chronic inflammatory demyelinating polyneuropathy (PATH): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Neurol 2018; 17:35-46. [DOI: 10.1016/s1474-4422(17)30378-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
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19
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Scalco R, Morrow J, Booth S, Chatfield S, Godfrey R, Quinlivan R. Misdiagnosis and diagnostic delay in McArdle disease. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Durmus H, Scalco R, Gardiner A, Manole A, Schapira A, Morrow J, Houlden H, Holton J, Johnson K, Töpf A, Phillips L, Deymeer F, Parman Y, Straub V, Quinlivan R, Oflazer-Serdaoglu P. Anoctamin 5 muscular dystrophy mimicking metabolic myopathy. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Scalco R, Morrow J, Skorupinska I, Manole A, Federico R, Matthews E, Hanna M, Fialho D. RCT of Bumetanide in Hypokalaemic Periodic Paralysis (HypoPP) using abductor digiti minimi compound muscle action potential (CMAP) as an objective outcome measure. Muscle Nerve 2017. [DOI: 10.1002/mus.25769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- R.S. Scalco
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - J. Morrow
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - I. Skorupinska
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - A. Manole
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - R. Federico
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - E. Matthews
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - M.G. Hanna
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
| | - D. Fialho
- MRC Centre for Neuromuscular Diseases; Institute of Neurology, UCL; London United Kingdom
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22
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Yun JH, Morrow J, Owen CA, Qiu W, Glass K, Lao T, Jiang Z, Perrella MA, Silverman EK, Zhou X, Hersh CP. Transcriptomic Analysis of Lung Tissue from Cigarette Smoke-Induced Emphysema Murine Models and Human Chronic Obstructive Pulmonary Disease Show Shared and Distinct Pathways. Am J Respir Cell Mol Biol 2017; 57:47-58. [PMID: 28248572 DOI: 10.1165/rcmb.2016-0328oc] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although cigarette smoke (CS) is the primary risk factor for chronic obstructive pulmonary disease (COPD), the underlying molecular mechanisms for the significant variability in developing COPD in response to CS are incompletely understood. We performed lung gene expression profiling of two different wild-type murine strains (C57BL/6 and NZW/LacJ) and two genetic models with mutations in COPD genome-wide association study genes (HHIP and FAM13A) after 6 months of chronic CS exposure and compared the results to human COPD lung tissues. We identified gene expression patterns that correlate with severity of emphysema in murine and human lungs. Xenobiotic metabolism and nuclear erythroid 2-related factor 2-mediated oxidative stress response were commonly regulated molecular response patterns in C57BL/6, Hhip+/-, and Fam13a-/- murine strains exposed chronically to CS. The CS-resistant Fam13a-/- mouse and NZW/LacJ strain revealed gene expression response pattern differences. The Fam13a-/- strain diverged in gene expression compared with C57BL/6 control only after CS exposure. However, the NZW/LacJ strain had a unique baseline expression pattern, enriched for nuclear erythroid 2-related factor 2-mediated oxidative stress response and xenobiotic metabolism, and converged to a gene expression pattern similar to the more susceptible wild-type C57BL/6 after CS exposure. These results suggest that distinct molecular pathways may account for resistance to emphysema. Surprisingly, there were few genes commonly modulated in mice and humans. Our study suggests that gene expression responses to CS may be largely species and model dependent, yet shared pathways could provide biologically significant insights underlying individual susceptibility to CS.
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Affiliation(s)
- Jeong H Yun
- 1 Channing Division of Network Medicine, and.,2 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Caroline A Owen
- 2 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,3 The Lovelace Respiratory Research Institute, Albuquerque, New Mexico; and
| | | | | | - Taotao Lao
- 1 Channing Division of Network Medicine, and
| | | | - Mark A Perrella
- 2 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,4 Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edwin K Silverman
- 1 Channing Division of Network Medicine, and.,2 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Xiaobo Zhou
- 1 Channing Division of Network Medicine, and.,2 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Craig P Hersh
- 1 Channing Division of Network Medicine, and.,2 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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23
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Qiao D, Lange C, Beaty TH, Crapo JD, Barnes KC, Bamshad M, Hersh CP, Morrow J, Pinto-Plata VM, Marchetti N, Bueno R, Celli BR, Criner GJ, Silverman EK, Cho MH. Exome Sequencing Analysis in Severe, Early-Onset Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2017; 193:1353-63. [PMID: 26736064 DOI: 10.1164/rccm.201506-1223oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RATIONALE Genomic regions identified by genome-wide association studies explain only a small fraction of heritability for chronic obstructive pulmonary disease (COPD). Alpha-1 antitrypsin deficiency shows that rare coding variants of large effect also influence COPD susceptibility. We hypothesized that exome sequencing in families identified through a proband with severe, early-onset COPD would identify additional rare genetic determinants of large effect. OBJECTIVES To identify rare genetic determinants of severe COPD. METHODS We applied filtering approaches to identify potential causal variants for COPD in whole exomes from 347 subjects in 49 extended pedigrees from the Boston Early-Onset COPD Study. We assessed the power of this approach under different levels of genetic heterogeneity using simulations. We tested genes identified in these families using gene-based association tests in exomes of 204 cases with severe COPD and 195 resistant smokers from the COPDGene study. In addition, we examined previously described loci associated with COPD using these datasets. MEASUREMENTS AND MAIN RESULTS We identified 69 genes with predicted deleterious nonsynonymous, stop, or splice variants that segregated with severe COPD in at least two pedigrees. Four genes (DNAH8, ALCAM, RARS, and GBF1) also demonstrated an increase in rare nonsynonymous, stop, and/or splice mutations in cases compared with resistant smokers from the COPDGene study; however, these results were not statistically significant. We demonstrate the limitations of the power of this approach under genetic heterogeneity through simulation. CONCLUSIONS Rare deleterious coding variants may increase risk for COPD, but multiple genes likely contribute to COPD susceptibility.
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Affiliation(s)
| | - Christoph Lange
- 2 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Terri H Beaty
- 3 Johns Hopkins Bloomberg School of Public Health, and
| | | | - Kathleen C Barnes
- 5 Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Michael Bamshad
- 6 Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Washington
| | - Craig P Hersh
- 1 Channing Division of Network Medicine.,7 Division of Pulmonary and Critical Care Medicine, and
| | | | - Victor M Pinto-Plata
- 8 Department of Critical Care Medicine and Pulmonary Disease, Baystate Medical Center, Springfield, Massachusetts
| | | | - Raphael Bueno
- 10 Division of Thoracic Surgery, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Gerald J Criner
- 11 Division of Pulmonary and Critical Care Medicine Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Edwin K Silverman
- 1 Channing Division of Network Medicine.,7 Division of Pulmonary and Critical Care Medicine, and
| | - Michael H Cho
- 1 Channing Division of Network Medicine.,7 Division of Pulmonary and Critical Care Medicine, and
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24
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Li Y, Morrow J, Raby B, Tantisira K, Weiss ST, Huang W, Qiu W. Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data. PLoS One 2017; 12:e0174602. [PMID: 28358896 PMCID: PMC5373614 DOI: 10.1371/journal.pone.0174602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/10/2017] [Indexed: 12/02/2022] Open
Abstract
Detecting disease-associated genomic outcomes is one of the key steps in precision medicine research. Cutting-edge high-throughput technologies enable researchers to unbiasedly test if genomic outcomes are associated with disease of interest. However, these technologies also include the challenges associated with the analysis of genome-wide data. Two big challenges are (1) how to reduce the effects of technical noise; and (2) how to handle the curse of dimensionality (i.e., number of variables are way larger than the number of samples). To tackle these challenges, we propose a constrained mixture of Bayesian hierarchical models (MBHM) for detecting disease-associated genomic outcomes for data obtained from paired/matched designs. Paired/matched designs can effectively reduce effects of confounding factors. MBHM does not involve multiple testing, hence does not have the problem of the curse of dimensionality. It also could borrow information across genes so that it can be used for whole genome data with small sample sizes.
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Affiliation(s)
- Yunfeng Li
- School of Mathematical Sciences, Zhejiang University, HongZhou, Zhejiang, China
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, United States of America
| | - Benjamin Raby
- Channing Division of Network Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, United States of America
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, United States of America
| | - Wei Huang
- School of Mathematical Sciences, Zhejiang University, HongZhou, Zhejiang, China
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, United States of America
- * E-mail:
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25
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Naqvi S, Tan I, Rasmussen J, Aldrich M, Morrow J, Blanco A, Gutierrez C, Jain K, Sevick-Muraca E, Karni R. PO-111: Dermal backflow: NIRFLI pattern associated multimodality therapy in patients with oropharynx cancer. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)30245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Qiao D, Lange C, Laird NM, Won S, Hersh CP, Morrow J, Hobbs BD, Lutz SM, Ruczinski I, Beaty TH, Silverman EK, Cho MH. Gene-based segregation method for identifying rare variants in family-based sequencing studies. Genet Epidemiol 2017; 41:309-319. [PMID: 28191685 DOI: 10.1002/gepi.22037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/30/2016] [Accepted: 12/09/2016] [Indexed: 11/11/2022]
Abstract
Whole-exome sequencing using family data has identified rare coding variants in Mendelian diseases or complex diseases with Mendelian subtypes, using filters based on variant novelty, functionality, and segregation with the phenotype within families. However, formal statistical approaches are limited. We propose a gene-based segregation test (GESE) that quantifies the uncertainty of the filtering approach. It is constructed using the probability of segregation events under the null hypothesis of Mendelian transmission. This test takes into account different degrees of relatedness in families, the number of functional rare variants in the gene, and their minor allele frequencies in the corresponding population. In addition, a weighted version of this test allows incorporating additional subject phenotypes to improve statistical power. We show via simulations that the GESE and weighted GESE tests maintain appropriate type I error rate, and have greater power than several commonly used region-based methods. We apply our method to whole-exome sequencing data from 49 extended pedigrees with severe, early-onset chronic obstructive pulmonary disease (COPD) in the Boston Early-Onset COPD study (BEOCOPD) and identify several promising candidate genes. Our proposed methods show great potential for identifying rare coding variants of large effect and high penetrance for family-based sequencing data. The proposed tests are implemented in an R package that is available on CRAN (https://cran.r-project.org/web/packages/GESE/).
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Affiliation(s)
- Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Nan M Laird
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sungho Won
- Department of Public Health Science, Seoul National University, Seoul, Republic of Korea
| | - Craig P Hersh
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jarrett Morrow
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sharon M Lutz
- Department of Biostatistics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.,University of Washington Center for Mendelian Genomics, Seattle, Washington, United States of America
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Rinsky JL, Berl E, Greene V, Morrow J, Didomenico A, MacFarquhar J, Gómez G, Lúquez C, Williams C. Notes from the Field: Clostridium perfringensGastroenteritis Outbreak Associated with a Catered Lunch — North Carolina, November 2015. MMWR Morb Mortal Wkly Rep 2016; 65:1300-1301. [DOI: 10.15585/mmwr.mm6546a5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Busch R, Qiu W, Lasky-Su J, Morrow J, Criner G, DeMeo D. Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations. Respir Res 2016; 17:143. [PMID: 27814717 PMCID: PMC5097392 DOI: 10.1186/s12931-016-0459-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is the third-leading cause of death worldwide. Identifying COPD-associated DNA methylation marks in African-Americans may contribute to our understanding of racial disparities in COPD susceptibility. We determined differentially methylated genes and co-methylation network modules associated with COPD in African-Americans recruited during exacerbations of COPD and smoking controls from the Pennsylvania Study of Chronic Obstructive Pulmonary Exacerbations (PA-SCOPE) cohort. Methods We assessed DNA methylation from whole blood samples in 362 African-American smokers in the PA-SCOPE cohort using the Illumina Infinium HumanMethylation27 BeadChip Array. Final analysis included 19302 CpG probes annotated to the nearest gene transcript after quality control. We tested methylation associations with COPD case-control status using mixed linear models. Weighted gene comethylation networks were constructed using weighted gene coexpression network analysis (WGCNA) and network modules were analyzed for association with COPD. Results There were five differentially methylated CpG probes significantly associated with COPD among African-Americans at an FDR less than 5 %, and seven additional probes that approached significance at an FDR less than 10 %. The top ranked gene association was MAML1, which has been shown to affect NOTCH-dependent angiogenesis in murine lung. Network modeling yielded the “yellow” and “blue” comethylation modules which were significantly associated with COPD (p-value 4 × 10-10 and 4 × 10-9, respectively). The yellow module was enriched for gene sets related to inflammatory pathways known to be relevant to COPD. The blue module contained the top ranked genes in the concurrent differential methylation analysis (FXYD1/LGI4, gene significance p-value 1.2 × 10-26; MAML1, p-value 2.0 × 10-26; CD72, p-value 2.1 × 10-25; and LPO, p-value 7.2 × 10-25), and was significantly associated with lung development processes in Gene Ontology gene-set enrichment analysis. Conclusion We identified 12 differentially methylated CpG sites associated with COPD that mapped to biologically plausible genes. Network module comethylation patterns have identified candidate genes that may be contributing to racial differences in COPD susceptibility and severity. COPD-associated comethylation modules contained genes previously associated with lung disease and inflammation and recapitulated known COPD-associated genes. The genes implicated by differential methylation and WGCNA analysis may provide mechanistic targets contributing to COPD susceptibility, exacerbations, and outcomes among African-Americans. Trial registration Trial Registration: NCT00774176, Registry: ClinicalTrials.gov, URL: www.clinicaltrials.gov, Date of Enrollment of First Participant: June 2004, Date Registered: 04 January 2008 (retrospectively registered). Electronic supplementary material The online version of this article (doi:10.1186/s12931-016-0459-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert Busch
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Room 449, Boston, 02111, MA, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Room 449, Boston, 02111, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Room 449, Boston, 02111, MA, USA
| | - Jarrett Morrow
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Room 449, Boston, 02111, MA, USA
| | - Gerard Criner
- Temple Lung Center, Temple University Health System, Philadelphia, PA, USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Room 449, Boston, 02111, MA, USA.
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Qiu W, Wan E, Morrow J, Cho MH, Crapo JD, Silverman EK, DeMeo DL. The impact of genetic variation and cigarette smoke on DNA methylation in current and former smokers from the COPDGene study. Epigenetics 2016; 10:1064-73. [PMID: 26646902 DOI: 10.1080/15592294.2015.1106672] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
DNA methylation can be affected by systemic exposures, such as cigarette smoking and genetic sequence variation; however, the relative impact of each on the epigenome is unknown. We aimed to assess if cigarette smoking and genetic variation are associated with overlapping or distinct sets of DNA methylation marks and pathways. We selected 85 Caucasian current and former smokers with genome-wide single nucleotide polymorphism (SNP) genotyping available from the COPDGene study. Genome-wide methylation was obtained on DNA from whole blood using the Illumina HumanMethylation27 platform. To determine the impact of local sequence variation on DNA methylation (mQTL), we examined the association between methylation and SNPs within 50 kb of each CpG site. To examine the impact of cigarette smoking on DNA methylation, we examined the differences in methylation by current cigarette smoking status. We detected 770 CpG sites annotated to 708 genes associated at an FDR < 0.05 in the cis-mQTL analysis and 1,287 CpG sites annotated to 1,242 genes, which were nominally associated in the smoking-CpG association analysis (P(unadjusted) < 0.05). Forty-three CpG sites annotated to 40 genes were associated with both SNP variation and current smoking; this overlap was not greater than that expected by chance. Our results suggest that cigarette smoking and genetic variants impact distinct sets of DNA methylation marks, the further elucidation of which may partially explain the variable susceptibility to the health effects of cigarette smoking. Ascertaining how genetic variation and systemic exposures differentially impact the human epigenome has relevance for both biomarker identification and therapeutic target development for smoking-related diseases.
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Affiliation(s)
- Weiliang Qiu
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Emily Wan
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Jarrett Morrow
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Michael H Cho
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | | | - Edwin K Silverman
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
| | - Dawn L DeMeo
- a Channing Division of Network Medicine; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA.,b Division of Pulmonary/Critical Care; Brigham and Women's Hospital/Harvard Medical School ; Boston , MA USA
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Al-Garawi A, Carey VJ, Chhabra D, Mirzakhani H, Morrow J, Lasky-Su J, Qiu W, Laranjo N, Litonjua AA, Weiss ST. The Role of Vitamin D in the Transcriptional Program of Human Pregnancy. PLoS One 2016; 11:e0163832. [PMID: 27711190 PMCID: PMC5053446 DOI: 10.1371/journal.pone.0163832] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood transcriptomes were measured longitudinally on 30 women and used to characterize gene co-expression networks. Objective Studies suggest that increased maternal Vitamin D levels may reduce the risk of asthma in early life, yet the underlying mechanisms have not been examined. In this study, we used a network-based approach to examine changes in gene expression profiles during the course of normal pregnancy and evaluated their association with maternal Vitamin D levels. Design The VDAART study is a randomized clinical trial of vitamin D supplementation in pregnancy for reduction of pediatric asthma risk. The trial enrolled 881 women at 10–18 weeks of gestation. Longitudinal gene expression measures were obtained on thirty pregnant women, using RNA isolated from peripheral blood samples obtained in the first and third trimesters. Differentially expressed genes were identified using significance of analysis of microarrays (SAM), and clustered using a weighted gene co-expression network analysis (WGCNA). Gene-set enrichment was performed to identify major biological pathways. Results Comparison of transcriptional profiles between first and third trimesters of pregnancy identified 5839 significantly differentially expressed genes (FDR<0.05). Weighted gene co-expression network analysis clustered these transcripts into 14 co-expression modules of which two showed significant correlation with maternal vitamin D levels. Pathway analysis of these two modules revealed genes enriched in immune defense pathways and extracellular matrix reorganization as well as genes enriched in notch signaling and transcription factor networks. Conclusion Our data show that gene expression profiles of healthy pregnant women change during the course of pregnancy and suggest that maternal Vitamin D levels influence transcriptional profiles. These alterations of the maternal transcriptome may contribute to fetal immune imprinting and reduce allergic sensitization in early life. Trial Registration clinicaltrials.gov NCT00920621
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Affiliation(s)
- Amal Al-Garawi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Vincent J. Carey
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Divya Chhabra
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Nancy Laranjo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Augusto A. Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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Scalco R, Skorupinska I, Blochet C, Habib M, Matthews E, Morrow J, Hanna M, Fialho D. Bumetanide in hypokalaemic periodic paralysis: a randomised, double-blind, placebo controlled phase II clinical trial with a crossover design. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Nastasi L, Desikan M, Turner C, Parton M, Morrow J, Carr A, Manji H, Hanna M, Quinlivan R. Quality of care in the first neuromuscular complex care centre in the UK from the patients' perspective. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Hobbs BD, Parker MM, Chen H, Lao T, Hardin M, Qiao D, Hawrylkiewicz I, Sliwinski P, Yim JJ, Kim WJ, Kim DK, Castaldi PJ, Hersh CP, Morrow J, Celli BR, Pinto-Plata VM, Criner GJ, Marchetti N, Bueno R, Agustí A, Make BJ, Crapo JD, Calverley PM, Donner CF, Lomas DA, Wouters EFM, Vestbo J, Paré PD, Levy RD, Rennard SI, Zhou X, Laird NM, Lin X, Beaty TH, Silverman EK, Cho MH. Exome Array Analysis Identifies a Common Variant in IL27 Associated with Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2016; 194:48-57. [PMID: 26771213 PMCID: PMC4960630 DOI: 10.1164/rccm.201510-2053oc] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/15/2016] [Indexed: 12/14/2022] Open
Abstract
RATIONALE Chronic obstructive pulmonary disease (COPD) susceptibility is in part related to genetic variants. Most genetic studies have been focused on genome-wide common variants without a specific focus on coding variants, but common and rare coding variants may also affect COPD susceptibility. OBJECTIVES To identify coding variants associated with COPD. METHODS We tested nonsynonymous, splice, and stop variants derived from the Illumina HumanExome array for association with COPD in five study populations enriched for COPD. We evaluated single variants with a minor allele frequency greater than 0.5% using logistic regression. Results were combined using a fixed effects meta-analysis. We replicated novel single-variant associations in three additional COPD cohorts. MEASUREMENTS AND MAIN RESULTS We included 6,004 control subjects and 6,161 COPD cases across five cohorts for analysis. Our top result was rs16969968 (P = 1.7 × 10(-14)) in CHRNA5, a locus previously associated with COPD susceptibility and nicotine dependence. Additional top results were found in AGER, MMP3, and SERPINA1. A nonsynonymous variant, rs181206, in IL27 (P = 4.7 × 10(-6)) was just below the level of exome-wide significance but attained exome-wide significance (P = 5.7 × 10(-8)) when combined with results from other cohorts. Gene expression datasets revealed an association of rs181206 and the surrounding locus with expression of multiple genes; several were differentially expressed in COPD lung tissue, including TUFM. CONCLUSIONS In an exome array analysis of COPD, we identified nonsynonymous variants at previously described loci and a novel exome-wide significant variant in IL27. This variant is at a locus previously described in genome-wide associations with diabetes, inflammatory bowel disease, and obesity and appears to affect genes potentially related to COPD pathogenesis.
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Affiliation(s)
- Brian D. Hobbs
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | - Han Chen
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - Megan Hardin
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | | | - Pawel Sliwinski
- National Tuberculosis and Lung Disease Research Institute, Warsaw, Poland
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Woo Jin Kim
- Kangwon National University, Chuncheon, South Korea
| | - Deog Kyeom Kim
- Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Peter J. Castaldi
- Channing Division of Network Medicine
- Division of General Medicine and Primary Care, and
| | - Craig P. Hersh
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | | | - Victor M. Pinto-Plata
- Department of Critical Care Medicine and Pulmonary Disease, Baystate Medical Center, Springfield, Massachusetts
| | | | - Nathaniel Marchetti
- Department of Thoracic Medicine and Surgery, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Alvar Agustí
- Thorax Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Barcelona, Spain
| | | | | | | | - Claudio F. Donner
- Mondo Medico di I.F.I.M. srl, Multidisciplinary and Rehabilitation Outpatient Clinic, Borgomanero (NO), Italy
| | | | | | - Jorgen Vestbo
- University of Manchester, Manchester, United Kingdom
| | - Peter D. Paré
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert D. Levy
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen I. Rennard
- Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Clinical Discovery Unit, AstraZeneca, Cambridge, United Kingdom; and
| | | | - Nan M. Laird
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Edwin K. Silverman
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
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Naqvi S, Karni R, Tan I, Rasmussen J, Aldrich M, Morrow J, Sevick E. Dermal Backflow Seen Through Near-Infrared Fluorescence Imaging: An Early Response to Cancer Treatments in Head and Neck for the Detection of Lymphedema. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2015.12.184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Li X, Qiu W, Morrow J, DeMeo DL, Weiss ST, Fu Y, Wang X. A Comparative Study of Tests for Homogeneity of Variances with Application to DNA Methylation Data. PLoS One 2015; 10:e0145295. [PMID: 26683022 PMCID: PMC4684215 DOI: 10.1371/journal.pone.0145295] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/02/2015] [Indexed: 12/18/2022] Open
Abstract
Variable DNA methylation has been associated with cancers and complex diseases. Researchers have identified many DNA methylation markers that have different mean methylation levels between diseased subjects and normal subjects. Recently, researchers found that DNA methylation markers with different variabilities between subject groups could also have biological meaning. In this article, we aimed to help researchers choose the right test of equal variance in DNA methylation data analysis. We performed systematic simulation studies and a real data analysis to compare the performances of 7 equal-variance tests, including 2 tests recently proposed in the DNA methylation analysis literature. Our results showed that the Brown-Forsythe test and trimmed-mean-based Levene's test had good performance in testing for equality of variance in our simulation studies and real data analyses. Our results also showed that outlier profiles could be biologically very important.
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Affiliation(s)
- Xuan Li
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, ON, M3J1P3, Canada
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, United States of America
- * E-mail:
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, United States of America
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, United States of America
| | - Yuejiao Fu
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, ON, M3J1P3, Canada
| | - Xiaogang Wang
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, ON, M3J1P3, Canada
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Wan ES, Qiu W, Carey VJ, Morrow J, Bacherman H, Foreman MG, Hokanson JE, Bowler RP, Crapo JD, DeMeo DL. Smoking-Associated Site-Specific Differential Methylation in Buccal Mucosa in the COPDGene Study. Am J Respir Cell Mol Biol 2015; 53:246-54. [PMID: 25517428 DOI: 10.1165/rcmb.2014-0103oc] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is a complex, tissue-specific phenomenon that can reflect both endogenous factors and exogenous exposures. Buccal brushings represent an easily accessible source of DNA, which may be an appropriate surrogate tissue in the study of environmental exposures and chronic respiratory diseases. Buccal brushings were obtained from a subset of current and former smokers from the COPDGene study. Genome-wide DNA methylation data were obtained in the discovery cohort (n = 82) using the Illumina HumanMethylation450K array. Empirical Bayes methods were used to test for differential methylation by current smoking status at 468,219 autosomal CpG sites using linear models adjusted for age, sex, and race. Pyrosequencing was performed in a nonoverlapping replication cohort (n = 130). Current smokers were significantly younger than former smokers in both the discovery and replication cohorts. Seven CpG sites were associated with current smoking at a false discovery rate less than 0.05 in the discovery cohort. Six of the seven significant sites were pyrosequenced in the replication cohort; five CpG sites, including sites annotated to CYP1B1 and PARVA, were replicated. Correlations between cumulative smoke exposure and time since smoking cessation were observed in a subset of the significantly associated CpG sites. A significant correlation between reduced lung function and increased radiographic emphysema with methylation at cg02162897 (CYP1B1) was observed among female subjects. Site-specific methylation of DNA isolated from buccal mucosa is associated with exposure to cigarette smoke, and may provide insights into the mechanisms underlying differential susceptibility toward the development of smoking-related chronic respiratory diseases.
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Affiliation(s)
- Emily S Wan
- 1 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Weiliang Qiu
- 1 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Vincent J Carey
- 1 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jarrett Morrow
- 1 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Helene Bacherman
- 1 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - John E Hokanson
- 3 Colorado School of Public Health, University of Colorado, Aurora, Colorado; and
| | | | | | - Dawn L DeMeo
- 1 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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Chhabra D, Sharma S, Kho AT, Gaedigk R, Vyhlidal CA, Leeder JS, Morrow J, Carey VJ, Weiss ST, Tantisira KG, DeMeo DL. Fetal lung and placental methylation is associated with in utero nicotine exposure. Epigenetics 2015; 9:1473-84. [PMID: 25482056 DOI: 10.4161/15592294.2014.971593] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the PKP3 (P = 2.94 × 10(-03)), ANKRD33B (P = 3.12 × 10(-03)), CNTD2 (P = 4.9 × 10(-03)) and DPP10 (P = 5.43 × 10(-03)) genes. In the placental methylome, the most significant CpG sites mapped to the GTF2H2C and GTF2H2D genes (P = 2.87 × 10(-06) - 3.48 × 10(-05)). One hundred and one unique CpG sites with P-values < 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
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Affiliation(s)
- Divya Chhabra
- a Channing Division of Network Medicine; Brigham and Women's Hospital ; Boston , MA USA
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Wan ES, Qiu W, Morrow J, Beaty TH, Hetmanski J, Make BJ, Lomas DA, Silverman EK, DeMeo DL. Genome-wide site-specific differential methylation in the blood of individuals with Klinefelter syndrome. Mol Reprod Dev 2015; 82:377-86. [PMID: 25988574 DOI: 10.1002/mrd.22483] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/30/2015] [Indexed: 12/25/2022]
Abstract
Klinefelter syndrome (KS) (47 XXY) is a common sex-chromosome aneuploidy with an estimated prevalence of one in every 660 male births. Investigations into the associations between DNA methylation and the highly variable clinical manifestations of KS have largely focused on the supernumerary X chromosome; systematic investigations of the epigenome have been limited. We obtained genome-wide DNA methylation data from peripheral blood using the Illumina HumanMethylation450K platform in 5 KS (47 XXY) versus 102 male (46 XY) and 113 female (46 XX) control subjects participating in the COPDGene Study. Empirical Bayes-mediated models were used to test for differential methylation by KS status. CpG sites with a false-discovery rate < 0.05 in the discovery cohort which were available on the first-generation HumanMethylation 27 K platform were further examined in an independent replication cohort of 2 KS subjects, 590 male, and 495 female controls drawn from the International COPD Genetics Network (ICGN). Differential methylation at sites throughout the genome were identified, including 86 CpG sites that were differentially methylated in KS subjects relative to both male and female controls. CpG sites annotated to the HEN1 methyltransferase homolog 1 (HENMT1), calcyclin-binding protein (CACYBP), and GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) genes were among the "KS-specific" loci that were replicated in ICGN. We conclude that site-specific differential methylation exists throughout the genome in KS. The functional impact and clinical relevance of these differentially methylated loci should be explored in future studies.
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Affiliation(s)
- Emily S Wan
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Terri H Beaty
- Department of Biostatistics and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Jacqueline Hetmanski
- Department of Biostatistics and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Barry J Make
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado
| | - David A Lomas
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
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Loor G, Radosevich D, Cich I, Lyon C, Morrow J, Grabowski T, Holley C, Kelly R, Hertz M. The University of Minnesota Lung Donor Quality Index (UMN-DLQI): A Consensus-Based Scoring Tool for Lung Donor Evaluations. J Heart Lung Transplant 2015. [DOI: 10.1016/j.healun.2015.01.787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Keogh S, McDonald P, Lawthom C, Brodie MJ, McLean B, Damodaran D, Morrow J, Tittensor P, Bagary M. SAFETY AND EFFICACY OF ESLICARBAZEPINE ACETATE (ZEBINIX) IN EVERYDAY CLINICAL PRACTICE USING A RETROSPECTIVE MULTICENTRE AUDIT. J Neurol Neurosurg Psychiatry 2014. [DOI: 10.1136/jnnp-2014-309236.67] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Campbell E, Kennedy F, Russell A, Smithson WH, Parsons L, Morrison PJ, Liggan B, Irwin B, Delanty N, Hunt SJ, Craig J, Morrow J. Malformation risks of antiepileptic drug monotherapies in pregnancy: updated results from the UK and Ireland Epilepsy and Pregnancy Registers. J Neurol Neurosurg Psychiatry 2014; 85:1029-34. [PMID: 24444855 DOI: 10.1136/jnnp-2013-306318] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Antiepileptic drug (AED) exposure during pregnancy increases the risk of major congenital malformations (MCMs). The magnitude of this risk varies by AED exposure. Here we provide updated results from the UK Epilepsy and Pregnancy Register of the risk of MCMs after monotherapy exposure to valproate, carbamazepine and lamotrigine. METHODS Fifteen-year prospective observational study from 1996 until 2012. The main outcome measure is the MCM rate. RESULTS Informative outcomes were available for 5206 cases. 1290 women were exposed to valproate monotherapy, 1718 to carbamazepine monotherapy and 2198 to lamotrigine monotherapy. The MCM risk with valproate monotherapy exposure in utero was 6.7% (95% CI 5.5% to 8.3%) compared with 2.6% with carbamazepine (95% CI 1.9% to 3.5%) and 2.3% with lamotrigine (95% CI 1.8% to 3.1%). A significant dose effect was seen with valproate (p=0.0006) and carbamazepine (p=0.03) exposed pregnancies. A non-significant trend towards higher MCM rate with increasing dose was found with lamotrigine. MCM rate for high-dose lamotrigine (>400 mg daily) was lower than the MCM rate for pregnancies exposed to <600 mg daily of valproate, but this was not significant (3.4% vs 5.0%, p=0.31). CONCLUSIONS In utero exposure to valproate carries a significantly higher MCM risk than lamotrigine (p=0.0001) and carbamazepine (p=0.0001) monotherapy. In contrast to prior findings, high-dose lamotrigine was associated with fewer MCMs than all doses of valproate. While lamotrigine has a favourable profile compared with valproate for adverse pregnancy outcomes, the requirements for seizure control should not be overlooked.
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Affiliation(s)
- E Campbell
- Neurology Department, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, Co Antrim, UK
| | - F Kennedy
- Institute of Neurology, University College London
| | - A Russell
- Department of Clinical Neurophysiology, Institute of Neurological Sciences, Southern General Hospital, Glasgow, UK
| | - W H Smithson
- Academic Unit of Primary Medical Care, Samuel Fox House, University of Sheffield, Northern General Hospital, Sheffield, UK
| | - L Parsons
- Neurology Department, Luton & Dunstable Hospitals NHS Trust, Luton, UK
| | - P J Morrison
- Department of Medical Genetics, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, Co Antrim, UK
| | - B Liggan
- RSCI, Beaumont Hospital, Dublin, Ireland
| | - B Irwin
- Neurology Department, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, Co Antrim, UK
| | - N Delanty
- Department of Neurology, Beaumont Hospital, Dublin, UK
| | - S J Hunt
- Neurology Department, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, Co Antrim, UK
| | - J Craig
- Neurology Department, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, Co Antrim, UK
| | - J Morrow
- Neurology Department, Belfast Health and Social Care Trust, Royal Victoria Hospital, Belfast, Co Antrim, UK
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Shallcross R, Bromley RL, Cheyne CP, Garcia-Finana M, Irwin B, Morrow J, Baker GA. In utero exposure to levetiracetam vs valproate: Development and language at 3 years of age. Neurology 2014; 82:213-21. [DOI: 10.1212/wnl.0000000000000030] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Campbell E, Hunt S, Kinney MO, Guthrie E, Smithson WH, Parsons L, Irwin B, Morrison PJ, Morrow J, Craig J, Russell AJ. The effect of socioeconomic status on treatment and pregnancy outcomes in women with epilepsy in Scotland. Epilepsy Behav 2013; 28:354-7. [PMID: 23827318 DOI: 10.1016/j.yebeh.2013.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 11/30/2022]
Abstract
Compared to the background population, people with epilepsy tend to have lower rates of education and employment, lower rates of marriage and childbearing, and lower overall socioeconomic status (SES). Disparities in epilepsy care based on sociodemographic factors have been observed in the literature, but it is not known whether any such disparities exist in the UK. The UK Epilepsy and Pregnancy Register is a prospective, observational, registration and follow-up study that was set up to determine the relative safety of all AEDs taken in pregnancy. Here, we report outcomes of registered pregnancies to women with epilepsy living in Scotland from December 1996 to June 2012, based on the degree of socioeconomic deprivation of their postcode area. The Scottish Index of Multiple Deprivation (SIMD) quintile scores from 2006 were used to determine degree of socioeconomic deprivation, and group 1 (most deprived) and group 5 (least deprived) were compared. There were 1526 pregnancies with complete outcome data to women living in Scotland. Of these, 1453 (95.1%) resulted in a live birth and 68 (4.7%) had a major congenital malformation (MCM). Postcodes could not be reliably identified or verified for an additional three women, who have been excluded from SIMD group analysis. Of all women included in this study, 32.4% were in group 1 and 13.2% in group 5. No difference in MCM rate was observed between the two groups (4.4% in group 1 compared to 4.7% in group 5, p=0.84). Women in group 5 were more likely to take preconceptual folic acid (56.8% compared to 14.0%, relative risk: 4.1; 95% CI: 3.1-5.2) and less likely to have generalized tonic-clonic seizures in pregnancy (13.0% compared to 29.2%, relative risk: 0.4; 95% CI: 0.3-0.7) than those in group 1. Women in group 5 were more likely to be on monotherapy regimens (80.2% compared to 65.9%, relative risk: 1.2; 95% CI: 1.1-1.3), less likely to be on valproate (19.5% compared to 28.0%, p=0.05), and more likely to be on lower doses of the drug (825.9mg/day compared to 1012.0mg/day, p=0.05) compared to those in group 1. Although no change in MCM rate was seen based on SES, differences in treatment between socioeconomic groups do exist, particularly for preconceptual folic acid consumption, AED regimen, and seizure frequency. Greater emphasis on the importance of preconceptual counseling, both to discuss AED choice and folic acid intake, would be of benefit, particularly to those living in areas of high socioeconomic deprivation, to improve equity of healthcare delivery for women with epilepsy in Scotland.
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Affiliation(s)
- E Campbell
- Neurology Department, Belfast Health and Social Care Trust, Royal Victoria Hospital, Grosvenor Road, Belfast, UK
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Garan A, Han J, Nahumi N, Yuzefpolskaya M, Colombo P, Whang W, Morrow J, Garan H, Jorde U, Uriel N. Catheter Ablation of Ventricular Arrhythmias in Patients Supported by Left Ventricular Assist Device. J Heart Lung Transplant 2013. [DOI: 10.1016/j.healun.2013.01.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Hoeritzauer A, Mawhinney E, Irwin B, Hunt S, Morrow J, Craig J. INCREASED LEVETIRACETAM CLEARANCE IN PREGNANCY: IS SEIZURE FREQUENCY AFFECTED? J Neurol Neurosurg Psychiatry 2012. [DOI: 10.1136/jnnp-2012-304200a.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Hoeritzauer I, Mawhinney E, Irwin B, Hunt SJ, Morrow J, Craig J. Increased levetiracetam clearance in pregnancy: is seizure frequency affected? Seizure 2012; 21:559-60. [PMID: 22658454 DOI: 10.1016/j.seizure.2012.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 10/28/2022] Open
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Mawhinney E, Campbell J, Craig J, Russell A, Smithson W, Parsons L, Robertson I, Irwin B, Morrison P, Liggan B, Delanty N, Hunt S, Morrow J. Valproate and the risk for congenital malformations: Is formulation and dosage regime important? Seizure 2012; 21:215-8. [DOI: 10.1016/j.seizure.2012.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 01/16/2012] [Accepted: 01/18/2012] [Indexed: 10/28/2022] Open
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Machado P, Hudson J, Miller A, Morrow J, Parton M, Bushby K, Hanna M. 097 Valosin Containing Protein (VCP) and Myofibrillar Myopathies (MFM) genes' mutations are not associated with sporadic Inclusion Body Myositis (sIBM). J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2011-301993.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Cortese A, Machado P, Morrow J, Dewar L, Hiscock A, Miller A, Brady S, Hilton-Jones D, Parton M, Hanna M. P73 The natural history of sporadic inclusion body myositis: data from the IBM-Net prospective cohort study. Neuromuscul Disord 2012. [DOI: 10.1016/s0960-8966(12)70081-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mawhinney E, Campbell J, Craig J, Russell A, Smithson W, Parsons L, Robertson I, Irwin B, Morrison P, Liggan B, Delanty N, Hunt S, Morrow J. 051 Valproate and the risk for congenital malformations; is formulation and dosage regime important? J Neurol Neurosurg Psychiatry 2012. [DOI: 10.1136/jnnp-2011-301993.93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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