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Lo Piccolo L, Wongkummool W, Jantaree P, Daroontum T, Chaowattanapanit S, Choonhakarn C, Amornpinyo W, Chaiwarith R, Kiratikanon S, Rujiwetpongstorn R, Tovanabutra N, Chiewchanvit S, Ngamphiw C, Intachai W, Kantaputra P, Chuamanochan M. Rare Filaggrin Variants Are Associated with Pustular Skin Diseases in Asians. Int J Mol Sci 2024; 25:6466. [PMID: 38928170 PMCID: PMC11203790 DOI: 10.3390/ijms25126466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Reactive pustular eruptions (RPEs) can manifest in a variety of conditions, including pustular psoriasis (PP) and adult-onset immunodeficiency syndrome due to anti-interferon-γ autoantibody (AOID). These RPEs can be attributed to different causes, one of which is genetic factors. However, the genetic basis for pustular skin diseases remains poorly understood. In our study, we conducted whole-exome sequencing on a cohort of 17 AOID patients with pustular reactions (AOID-PR) and 24 PP patients. We found that 76% and 58% of the AOID-PR and PP patients, respectively, carried rare genetic variations within the filaggrin (FLG) gene family. A total of 12 out of 21 SNPs on FLG had previously received clinical classifications, with only p.Ser2706Ter classified as pathogenic. In contrast, none of the FLG3 SNPs identified in this study had prior clinical classifications. Overall, these variations had not been previously documented in cases of pustular disorders, and two of them were entirely novel discoveries. Immunohistochemical analysis of skin biopsies revealed that FLG variants like p.Ser860Trp, p.Gly3903Ter, p.Gly2440Glu, and p.Glu2133Asp caused reductions in FLG levels similar to the pathogenic FLG p.Ser2706Ter. These results highlight rare FLG variants as potential novel genetic risk factors contributing to pustule formation in both AOID and PP.
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Affiliation(s)
- Luca Lo Piccolo
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.P.); (W.W.); (P.J.)
| | - Wasinee Wongkummool
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.P.); (W.W.); (P.J.)
| | - Phatcharida Jantaree
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (L.L.P.); (W.W.); (P.J.)
| | - Teerada Daroontum
- Department of Pathology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Suteeraporn Chaowattanapanit
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (C.C.)
| | - Charoen Choonhakarn
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (C.C.)
| | - Warayuwadee Amornpinyo
- Division of Dermatology, Department of Internal Medicine, Khon Kaen Hospital, Ministry of Public Health, Khon Kaen 40002, Thailand;
| | - Romanee Chaiwarith
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Salin Kiratikanon
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Rujira Rujiwetpongstorn
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Napatra Tovanabutra
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Siri Chiewchanvit
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand;
| | - Worrachet Intachai
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand; (W.I.); (P.K.)
| | - Piranit Kantaputra
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand; (W.I.); (P.K.)
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Mati Chuamanochan
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
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Inborn Errors of Immunity Predisposing to Herpes Simplex Virus Infections of the Central Nervous System. Pathogens 2023; 12:pathogens12020310. [PMID: 36839582 PMCID: PMC9961685 DOI: 10.3390/pathogens12020310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
Herpesvirus infections can lead to a number of severe clinical manifestations, particularly when involving the central nervous system (CNS), causing encephalitis and meningitis. However, understanding of the host factors conferring increased susceptibility to these diseases and their complications remains incomplete. Previous studies have uncovered defects in the innate Toll-like receptor 3 pathway and production of type I interferon (IFN-I) in children and adults that predispose them to herpes simplex encephalitis. More recently, there is accumulating evidence for an important role of IFN-independent cell-autonomous intrinsic mechanisms, including small nucleolar RNAs, RNA lariat metabolism, and autophagy, in restricting herpesvirus replication and conferring protection against CNS infection. The present review first describes clinical manifestations of HSV infection with a focus on neurological complications and then summarizes the host-pathogen interactions and innate immune pathways responsible for sensing herpesviruses and triggering antiviral responses and immunity. Next, we review the current landscape of inborn errors of immunity and the underlying genetic defects and disturbances of cellular immune pathways that confer increased susceptibility to HSV infection in CNS. Ultimately, we discuss some of the present outstanding unanswered questions relating to inborn errors of immunity and HSV CNS infection together with some perspectives and future directions for research in the pathogenesis of these severe diseases in humans.
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Genetic Variants in Epidermal Differentiation Complex Genes as Predictive Biomarkers for Atopic Eczema, Allergic Sensitization, and Eczema-Associated Asthma in a 6-Year Follow-Up Case-Control Study in Children. J Clin Med 2022; 11:jcm11164865. [PMID: 36013110 PMCID: PMC9410399 DOI: 10.3390/jcm11164865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Atopic eczema is the most common chronic inflammatory skin disease of early childhood and is often the first manifestation of atopic march. Therefore, one challenge is to identify the risk factors associated with atopic eczema that may also be predictors of atopic disease progression. The aim of this study was to investigate the association of SNPs in hornerin (HRNR) and filaggrin-2 (FLG2) genes with childhood atopic eczema, as well as other atopic phenotypes. Genotyping for HRNR and FLG2 was performed in 188 children younger than 2 years of age, previously screened for the FLG null mutations, and followed at yearly intervals until the age of 6. We demonstrated that risk variants of HRNR rs877776[C] and FLG2 rs12568784[T] were associated with atopic eczema, allergic sensitization, and susceptibility to the complex phenotype—asthma plus eczema. These effects seem to be supplementary to the well-known associations for FLG mutations and may be modulated by gene–gene interactions. Additionally, in children with eczema, these genetic variants may also be considered, along with FLG mutations, as predictive biomarkers for eczema-associated asthma. In conclusion, our results indicate that genetic variants in the epidermal differentiation complex gene could contribute to the pathogenesis of atopic eczema and progression to subsequent allergic disease.
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Vaseghi-Shanjani M, Snow AL, Margolis DJ, Latrous M, Milner JD, Turvey SE, Biggs CM. Atopy as Immune Dysregulation: Offender Genes and Targets. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1737-1756. [PMID: 35680527 DOI: 10.1016/j.jaip.2022.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Allergic diseases are a heterogeneous group of disorders resulting from exaggerated type 2 inflammation. Although typically viewed as polygenic multifactorial disorders caused by the interaction of several genes with the environment, we have come to appreciate that allergic diseases can also be caused by monogenic variants affecting the immune system and the skin epithelial barrier. Through a myriad of genetic association studies and high-throughput sequencing tools, many monogenic and polygenic culprits of allergic diseases have been described. Identifying the genetic causes of atopy has shaped our understanding of how these conditions occur and how they may be treated and even prevented. Precision diagnostic tools and therapies that address the specific molecular pathways implicated in allergic inflammation provide exciting opportunities to improve our care for patients across the field of allergy and immunology. Here, we highlight offender genes implicated in polygenic and monogenic allergic diseases and list targeted therapeutic approaches that address these disrupted pathways.
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Affiliation(s)
- Maryam Vaseghi-Shanjani
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Experimental Medicine Program, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew L Snow
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - David J Margolis
- Department of Dermatology and Dermatologic Surgery, University of Pennsylvania Medical Center, Philadelphia, Pa; Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Medical Center, Philadelphia, Pa
| | - Meriem Latrous
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Stuart E Turvey
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Experimental Medicine Program, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Catherine M Biggs
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; St Paul's Hospital, Vancouver, British Columbia, Canada.
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Starr I, Seiffert-Sinha K, Sinha AA, Gokcumen O. Evolutionary context of psoriatic immune skin response. Evol Med Public Health 2022; 9:474-486. [PMID: 35154781 PMCID: PMC8830311 DOI: 10.1093/emph/eoab042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/22/2021] [Indexed: 12/18/2022] Open
Abstract
The skin is vital for protecting the body and perceiving external stimuli in the environment. Ability to adapt between environments is in part based on skin phenotypic plasticity, indicating evolved homeostasis between skin and environment. This homeostasis reflects the greater relationship between the body and the environment, and disruptions in this balance may lead to accumulation of susceptibility factors for autoimmune conditions like psoriasis. In this study, we examined the relationship between rapid, lineage-specific evolution of human skin and formation of psoriatic skin responses at the transcriptome level. We collected skin tissue biopsies from individuals with psoriasis and compared gene expression in psoriatic plaques to non-plaque psoriatic skin. We then compared these data with non-psoriatic skin transcriptome data from multiple primate species. We found 67 genes showing human-specific skin expression that are also differentially regulated in psoriatic skin; these genes are significantly enriched for skin barrier function, immunity and neuronal development. We identified six gene clusters with differential expression in the context of human evolution and psoriasis, suggesting underlying regulatory mechanisms in these loci. Human and psoriasis-specific enrichment of neuroimmune genes shows the importance of the ongoing evolved homeostatic relationship between skin and external environment. These results have implications for both evolutionary medicine and public health, using transcriptomic data to acknowledge the importance of an individual’s surroundings on their overall health. The skin is important for protecting the body from the environment and perceiving external stimuli, creating an evolved balance between skin and the environment. We compare skin gene expression in humans with psoriasis to humans and non-human primates without psoriasis to better understand human-specific evolutionary changes in the skin. Our results suggest important evolutionary links between skin perception, human-specific skin development and immune response.
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Affiliation(s)
- Izzy Starr
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Kristina Seiffert-Sinha
- Department of Dermatology, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Animesh A Sinha
- Department of Dermatology, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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6
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Christophers E, Schröder JM. Evolution of innate defense in human skin. Exp Dermatol 2021; 31:304-311. [PMID: 34694661 DOI: 10.1111/exd.14482] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/01/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022]
Abstract
More often as compared to other barrier systems (gastrointestinal, urogenital, and respiratory linings) human skin over millions of years has been subject to fundamental changes in structure and function. When life on land started, the first changes consisted in the formation of a coherent impermeable stratum corneum. Two-legged locomotion was followed by loss of body hair and formation of sweat glands. Major changes took place after the agricultural revolution, investigating settlements with domestication of animals and plants. Living together after giving up nomadic life, hairless skin became a battlefield for pathogens, members of the skin microbiome, and arthropod visits. Human skin became exceptional in showing a boosted, highly developed immune system which is much more complex as compared to the "skins" of other species. A recently found skin disinfection system ("Cationic Intrinsically Disordered Antimicrobial Peptides, CIDAMPs") dates back to the origins of life and still is active in present-day integuments. As a skin-restricted and effective principle, keratinocyte- myeloid synergy (KMS) is recognized. As a consequence of such highly developed immune defense, the basic contributions of KMS - cells (keratinocytes, neutrophils, macrophages) in regulating innate immunity is emphasized. Antimicrobial peptides and chemokines became major keratinocyte products. The formation of impermeable str. corneum membrane has enabled KMS - cells to accumulate within upper skin levels and cause a special group of human skin diseases, pustular dermatoses.
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Affiliation(s)
- Enno Christophers
- Department of Dermatology, University-Hospital Schleswig-Holstein, Kiel, Germany
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Jablonski NG. The evolution of human skin pigmentation involved the interactions of genetic, environmental, and cultural variables. Pigment Cell Melanoma Res 2021; 34:707-729. [PMID: 33825328 PMCID: PMC8359960 DOI: 10.1111/pcmr.12976] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
The primary biological role of human skin pigmentation is as a mediator of penetration of ultraviolet radiation (UVR) into the deep layers of skin and the cutaneous circulation. Since the origin of Homo sapiens, dark, protective constitutive pigmentation and strong tanning abilities have been favored under conditions of high UVR and represent the baseline condition for modern humans. The evolution of partly depigmented skin and variable tanning abilities has occurred multiple times in prehistory, as populations have dispersed into environments with lower and more seasonal UVR regimes, with unique complements of genes and cultural practices. The evolution of extremes of dark pigmentation and depigmentation has been rare and occurred only under conditions of extremely high or low environmental UVR, promoted by positive selection on variant pigmentation genes followed by limited gene flow. Over time, the evolution of human skin pigmentation has been influenced by the nature and course of human dispersals and modifications of cultural practices, which have modified the nature and actions of skin pigmentation genes. Throughout most of prehistory and history, the evolution of human skin pigmentation has been a contingent and non-deterministic process.
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Affiliation(s)
- Nina G. Jablonski
- Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkPAUSA
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Zhu Y, Mitra N, Feng Y, Tishkoff S, Hoffstad O, Margolis D. FLG Variation Differs between European Americans and African Americans. J Invest Dermatol 2021; 141:1855-1857. [PMID: 33493532 PMCID: PMC8238796 DOI: 10.1016/j.jid.2020.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023]
Affiliation(s)
- Yaqian Zhu
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuanqing Feng
- Departments of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sarah Tishkoff
- Departments of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ole Hoffstad
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Margolis
- Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Mathyer ME, Brettmann EA, Schmidt AD, Goodwin ZA, Oh IY, Quiggle AM, Tycksen E, Ramakrishnan N, Matkovich SJ, Guttman-Yassky E, Edwards JR, de Guzman Strong C. Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa. Nat Commun 2021; 12:2557. [PMID: 33963188 PMCID: PMC8105351 DOI: 10.1038/s41467-021-22821-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
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Affiliation(s)
- Mary Elizabeth Mathyer
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Erin A. Brettmann
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Alina D. Schmidt
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zane A. Goodwin
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Inez Y. Oh
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Ashley M. Quiggle
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Eric Tycksen
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Natasha Ramakrishnan
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Scot J. Matkovich
- grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Emma Guttman-Yassky
- grid.59734.3c0000 0001 0670 2351Department of Dermatology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029 USA
| | - John R. Edwards
- grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Cristina de Guzman Strong
- grid.4367.60000 0001 2355 7002Division of Dermatology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for the Study of Itch & Sensory Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
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Abstract
Purpose of review Mutations in the Filaggrin gene can cause absent or reduced filaggrin protein, leading to impaired keratinization and skin barrier defect, which produce characteristic phenotypes. In this short review, we report current evidence on the topic with special reference to atopic dermatitis, suggest future directions, and discuss therapeutic implications. Recent findings Numerous candidate gene association studies, genome-wide association studies, studies on copy number variations and most recently, sequencing studies, have confirmed the robust association of mutations in the Filaggrin gene with atopic dermatitis, and have also linked these mutations with several other disorders. Summary Filaggrin gene defects remain the strongest identified genetic risk factors for atopic dermatitis. Taken in conjunction with other genes found to be associated with this condition, genetic screening and identification of individuals at risk for atopic dermatitis could lead to personalized therapy. Manipulation of genetic regulatory elements to increase the amount of filaggrin protein in deficient individuals is an attractive treatment option for the future.
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Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep 2020; 26:2241-2256.e4. [PMID: 30784602 DOI: 10.1016/j.celrep.2019.01.095] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 12/12/2018] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
We used whole-organ mapping to study the locoregional molecular changes in a human bladder containing multifocal cancer. Widespread DNA methylation changes were identified in the entire mucosa, representing the initial field effect. The field effect was associated with subclonal low-allele frequency mutations and a small number of DNA copy alterations. A founder mutation in the RNA splicing gene, ACIN1, was identified in normal mucosa and expanded clonally with an additional 21 mutations in progression to carcinoma. The patterns of mutations and copy number changes in carcinoma in situ and foci of carcinoma were almost identical, confirming their clonal origins. The pathways affected by the DNA copy alterations and mutations, including the Kras pathway, were preceded by the field changes in DNA methylation, suggesting that they reinforced mechanisms that had already been initiated by methylation. The results demonstrate that DNA methylation can serve as the initiator of bladder carcinogenesis.
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Margolis DJ, Mitra N, Berna R, Hoffstad O, Kim BS, Yan A, Zaenglein AL, Fuxench ZC, Quiggle AM, de Guzman Strong C, Wong XFCC, Common JE. Associating filaggrin copy number variation and atopic dermatitis in African-Americans: Challenges and opportunities. J Dermatol Sci 2020; 98:58-60. [PMID: 32037100 DOI: 10.1016/j.jdermsci.2020.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/16/2022]
Affiliation(s)
- David J Margolis
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, PA, United States; Department of Dermatology, Perlman School of Medicine, Philadelphia, PA, United States; Department of Medicine, Division of Translational Medicine and Human Genetics, Perlman School of Medicine, Philadelphia, PA, United States.
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, PA, United States
| | - Ron Berna
- Department of Dermatology, Perlman School of Medicine, Philadelphia, PA, United States; Department of Medicine, Division of Translational Medicine and Human Genetics, Perlman School of Medicine, Philadelphia, PA, United States
| | - Ole Hoffstad
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, PA, United States
| | - Brian S Kim
- Division of Dermatology, Department of Medicine, Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, United States
| | - Albert Yan
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Andrea L Zaenglein
- Departments of Dermatology and Pediatrics, Pennsylvania State University/Hershey Medical Center, PA, United States
| | - Zelma Chiesa Fuxench
- Department of Dermatology, Perlman School of Medicine, Philadelphia, PA, United States; Department of Medicine, Division of Translational Medicine and Human Genetics, Perlman School of Medicine, Philadelphia, PA, United States
| | - Ashley M Quiggle
- Division of Dermatology, Department of Medicine, Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, United States; Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Cristina de Guzman Strong
- Division of Dermatology, Department of Medicine, Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, United States; Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | | | - John E Common
- Skin Research Institute of Singapore, A⁎STAR, Singapore
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13
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Abuabara K, You Y, Margolis DJ, Hoffmann TJ, Risch N, Jorgenson E. Genetic ancestry does not explain increased atopic dermatitis susceptibility or worse disease control among African American subjects in 2 large US cohorts. J Allergy Clin Immunol 2020; 145:192-198.e11. [PMID: 31369801 PMCID: PMC6949407 DOI: 10.1016/j.jaci.2019.06.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is more common among African American children. Whether there are racial/ethnic difference among adults with AD and the causes for those disparities are unclear. OBJECTIVE We sought to examine the relationship between self-reported race/ethnicity and AD and determine whether African genetic ancestry is predictive of these outcomes among African American subjects. METHODS We analyzed data from 2 independent multiethnic longitudinal studies: 86,893 subjects aged 18 to 100 years from the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and 5467 subjects aged 2 to 26 years from the national Pediatric Eczema Elective Registry (PEER) cohort. The primary outcomes were physician-diagnosed AD in GERA and repeated measures of self-reported disease control among patients with physician-diagnosed AD at 6-month intervals in PEER. We examined whether self-identified African American race/ethnicity was predictive of these outcomes and then tested whether a continuous measure of African genetic ancestry was associated with outcomes within the African American group. RESULTS AD was more common among self-identified African American subjects than non-Hispanic white subjects in GERA (4.4% vs 2.1%; odds ratio, 2.06; 95% CI, 1.70-2.48) and less well-controlled in PEER subjects (odds of 1-level worse control, 1.91; 95% CI, 1.64-2.22). However, African genetic ancestry was not associated with AD risk or control among self-identified African American subjects in either cohort, nor did an AD polygenic risk score or genetic skin pigment score explain the AD disparities in patients with AD. CONCLUSION Ancestry-related genetic effects do not explain increased AD prevalence or poorer disease control among African American subjects.
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Affiliation(s)
- Katrina Abuabara
- Program for Clinical Research, Department of Dermatology, University of California, San Francisco, Calif.
| | - Yue You
- Division of Biostatistics and Epidemiology, University of California, Berkeley, Calif
| | - David J Margolis
- Department of Dermatology and Center for Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Thomas J Hoffmann
- Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California, San Francisco, Calif
| | - Neil Risch
- Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California, San Francisco, Calif; Division of Research, Kaiser Permanente, Oakland, Calif
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14
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Margolis DJ, Mitra N, Wubbenhorst B, D'Andrea K, Kraya AA, Hoffstad O, Shah S, Nathanson KL. Association of Filaggrin Loss-of-Function Variants With Race in Children With Atopic Dermatitis. JAMA Dermatol 2019; 155:1269-1276. [PMID: 31365035 DOI: 10.1001/jamadermatol.2019.1946] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Importance Atopic dermatitis (AD) is a common chronic illness that has been associated with variation in the filaggrin gene (FLG). Four variants are most often evaluated. Objectives To comprehensively describe and compare results from targeted sequencing of FLG loss-of-function (LoF) variants in children of African and European ancestry and the association of these variants with onset and persistence of AD. Design, Setting, and Participants This prospective US cohort study assessed the genetic subcohort of the Pediatric Eczema Elective Registry (PEER). Children with mild to moderate AD were included in the analysis. Massively parallel sequencing (MPS) was used to focus on FLG LoF variation in white and African American children. Patients were enrolled from June 2005 through July 2017. Data were analyzed from January 25 through May 10, 2019. Main Outcomes and Measures Associations of FLG LoF variation with white and African American ancestry and with the risk and persistence of AD. Results A total of 741 children were included in the analysis (394 [53.2%] female and 347 [46.8%] male; mean [SD] age at onset, 1.97 [2.72] years); of these, 394 (53.2%) were white, 326 (44.0%) were African American, and 21 (2.8%) were of other ancestries. Using MPS technology, 23 FLG LoF variants were found in children with AD. The prevalence of FLG LoF variants was 177 participants (23.9%) in the full cohort, 124 white participants (31.5%), and 50 African American participants (15.3%). The odds ratio for carrying any FLG LoF variant in a white child compared with an African American child with AD was 2.44 (95% CI, 1.76-3.39). Some FLG LoF variants are only found in children of a specific ancestry (eg, p.S3316* and p.R826* were not seen in white patients). Children with an FLG LoF were more likely to have persistent AD (odds ratio, 0.67; 95% CI, 0.56-0.80). Conclusions and Relevance The FLG LoF variants in a US cohort of children with mild to moderate AD differ significantly by race and their association with the persistence of AD. Conventional testing of the 4 frequently evaluated variants is inadequate. Any planned genetic diagnostic test for AD based on FLG LoF variants must be inclusive and not rely on the most frequently studied variants.
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Affiliation(s)
- David J Margolis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia.,Department of Dermatology, University of Pennsylvania, Philadelphia
| | - Nandita Mitra
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia
| | - Bradley Wubbenhorst
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia
| | - Kurt D'Andrea
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia
| | - Adam A Kraya
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia
| | - Ole Hoffstad
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Dermatology, University of Pennsylvania, Philadelphia
| | - Saloni Shah
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Dermatology, University of Pennsylvania, Philadelphia
| | - Katherine L Nathanson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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15
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An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. J Mol Evol 2019; 88:104-119. [PMID: 31522275 DOI: 10.1007/s00239-019-09911-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Copy number variants (CNVs), deletions and duplications of segments of DNA, account for at least five times more variable base pairs in humans than single-nucleotide variants. Several common CNVs were shown to change coding and regulatory sequences and thus dramatically affect adaptive phenotypes involving immunity, perception, metabolism, skin structure, among others. Some of these CNVs were also associated with susceptibility to cancer, infection, and metabolic disorders. These observations raise the possibility that CNVs are a primary contributor to human phenotypic variation and consequently evolve under selective pressures. Indeed, locus-specific haplotype-level analyses revealed signatures of natural selection on several CNVs. However, more traditional tests of selection which are often applied to single-nucleotide variation often have diminished statistical power when applied to CNVs because they often do not show strong linkage disequilibrium with nearby variants. Recombination-based formation mechanisms of CNVs lead to frequent recurrence and gene conversion events, breaking the linkage disequilibrium involving CNVs. Similar methodological challenges also prevent routine genome-wide association studies to adequately investigate the impact of CNVs on heritable human disease. Thus, we argue that the full relevance of CNVs to human health and evolution is yet to be elucidated. We further argue that a holistic investigation of formation mechanisms within an evolutionary framework would provide a powerful framework to understand the functional and biomedical impact of CNVs. In this paper, we review several cases where studies reveal diverse evolutionary histories and unexpected functional consequences of CNVs. We hope that this review will encourage further work on CNVs by both evolutionary and medical geneticists.
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16
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Filaggrin sequencing and bioinformatics tools. Arch Dermatol Res 2019; 312:155-158. [PMID: 31372728 DOI: 10.1007/s00403-019-01956-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/13/2019] [Indexed: 12/30/2022]
Abstract
Atopic dermatitis (AD) is a common illness that most commonly originates in childhood, but can be seen in all ages. Filaggrin (FLG) loss of function variants have been associated with the onset and severity of atopic dermatitis and are the most common genetic association with AD. Previous studies have shown variability in the frequency of FLG variants. We have recently demonstrated that previous FLG genotyping methods were inadequate for proper genotyping. In this concise report, we show that genotyping using a popular older informatics program is problematic. In fact, publications that used the older program likely do not properly capture all FLG variants.
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17
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Saitou M, Gokcumen O. Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection. Genome Biol Evol 2019; 11:1679-1690. [PMID: 31124564 PMCID: PMC6587411 DOI: 10.1093/gbe/evz107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2019] [Indexed: 12/18/2022] Open
Abstract
Polymorphic duplications in humans have been shown to contribute to phenotypic diversity. However, the evolutionary forces that maintain variable duplications across the human genome are largely unexplored. We developed a linkage-disequilibrium based method to detect insertion sites of polymorphic duplications not represented in reference genomes. This method also allows resolution of haplotypes harboring the duplications. Using this approach, we conducted genome-wide analyses and identified the insertion sites of 22 common polymorphic duplications. We found that the majority of these duplications is intrachromosomal and only one of them is an interchromosomal insertion. Further characterization of these duplications revealed significant associations to blood and skin phenotypes. On the basis of population genetics analyses, we found that the duplication of a well-characterized pigmentation-related region, including the HERC2 gene, may be selected against in European populations. We further demonstrated that the haplotype harboring this duplication significantly affects the expression of the HERC2P9 gene in multiple tissues. Our study sheds light onto the evolutionary impact of understudied polymorphic duplications in human populations and presents methodological insights for future studies.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, SUNY at Buffalo
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18
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Lin YL, Gokcumen O. Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. Genome Biol Evol 2019; 11:1136-1151. [PMID: 30887040 PMCID: PMC6475128 DOI: 10.1093/gbe/evz058] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2019] [Indexed: 12/25/2022] Open
Abstract
Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2,504 genomes to construct a refined map of 1,148 SV hotspots in human genomes. We confirmed that segmental duplication-related nonallelic homologous recombination is an important mechanistic driver of SV hotspot formation. However, to our surprise, we also found that a majority of SVs in hotspots do not form through such recombination-based mechanisms, suggesting diverse mechanistic and selective forces shaping hotspots. Indeed, our evolutionary analyses showed that the majority of SV hotspots are within gene-poor regions and evolve under relaxed negative selection or neutrality. However, we still found a small subset of SV hotspots harboring genes that are enriched for anthropologically crucial functions and evolve under geography-specific and balancing adaptive forces. These include two independent hotspots on different chromosomes affecting alpha and beta hemoglobin gene clusters. Biomedically, we found that the SV hotspots coincide with breakpoints of clinically relevant, large de novo SVs, significantly more often than genome-wide expectations. For example, we showed that the breakpoints of multiple large SVs, which lead to idiopathic short stature, coincide with SV hotspots. Therefore, the mutational instability in SV hotpots likely enables chromosomal breaks that lead to pathogenic structural variation formations. Overall, our study contributes to a better understanding of the mutational and adaptive landscape of the genome.
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Affiliation(s)
- Yen-Lung Lin
- Department of Biological Sciences, University at Buffalo
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo
- Corresponding author: E-mail: or
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19
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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20
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Abstract
The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here, we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations.
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Affiliation(s)
- Erin A. Brettmann
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
| | - Cristina de Guzman Strong
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
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21
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Mathyer ME, Quiggle AM, Wong XFCC, Denil SLIJ, Kumar MG, Ciliberto HM, Bayliss SJ, Common JE, de Guzman Strong C. Tiled array-based sequencing identifies enrichment of loss-of-function variants in the highly homologous filaggrin gene in African-American children with severe atopic dermatitis. Exp Dermatol 2018; 27:989-992. [PMID: 29791750 DOI: 10.1111/exd.13691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 12/27/2022]
Abstract
Filaggrin (FLG) loss-of-function (LOF) variants are a major risk factor for the common inflammatory skin disease, atopic dermatitis (AD) and are often population-specific. African-American (AA) children are disproportionately affected with AD, often later developing asthma and/or allergic rhinitis and comprise an atopy health disparity group for which the role of FLG LOF is not well known. Discovery of FLG LOF using exome sequencing is challenging given the known difficulties for accurate short-read alignment to FLG's high homology repeat variation. Here, we employed an array-based sequencing approach to tile across each FLG repeat and discover FLG LOF in a well-characterized cohort of AA children with moderate-to-severe AD. Five FLG LOF were identified in 23% of our cohort. Two novel FLG LOF singletons, c.488delG and p.S3101*, were discovered as well as p.R501*, p.R826* and p.S3316* previously reported for AD. p.S3316* (rs149484917) is likely an African ancestral FLG LOF, reported in African individuals in ExAC (Exome Aggregation Consortium), Exome Variant Server (ESP), and 4 African 1000G population databases (ESN, MSL, ASW, and ACB). The proportion of FLG LOF (11.5%) among the total FLG alleles in our cohort was significantly higher in comparisons with FLG LOF reported for African individuals in ExAC (2.5%; P = 4.3 × 10-4 ) and ESP (1.7%; P = 3.5 × 10-5 ) suggesting a disease-enrichment effect for FLG LOF. Our results demonstrate the utility of array-based sequencing in discovering FLG LOF, including novel and population-specific, which are of higher prevalence in our AA severe AD group than previously reported.
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Affiliation(s)
- Mary Elizabeth Mathyer
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashley M Quiggle
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Monique G Kumar
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Heather M Ciliberto
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan J Bayliss
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - John E Common
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Cristina de Guzman Strong
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Center for Pharmacogenomics, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
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22
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Abstract
Atopic dermatitis (AD) is driven by a complex gene-environment interaction. Many of the risk factors and genetic underpinning previously observed for pediatric AD may not apply to adult atopic dermatitis, suggesting that these may largely be different disorders. Whereas AD is classically thought of as a pediatric disease, recent studies have shown high rates of disease in adults as well. Risk factors for persistence of childhood-onset AD, as well as adult-onset AD, are reviewed. Adults with AD are particularly vulnerable to exogenous insults from the outside environment, including climate, ultraviolet exposure, pollution, irritants and pruritogens, and microbes. Finally, adult AD is associated with a substantial health care burden, with increased utilization, direct and indirect costs of care, and lost work productivity.
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Affiliation(s)
- Ryan Sacotte
- Department of Dermatology, Feinberg School of Medicine at Northwestern University, Chicago, Illinois, USA
| | - Jonathan I Silverberg
- Department of Dermatology, Preventive Medicine and Medical Social Sciences, Feinberg School of Medicine at Northwestern University, Chicago, Illinois, USA; Northwestern Medicine Multidisciplinary AD Center, Chicago, Illinois, USA.
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23
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Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol Biol Evol 2017; 34:2704-2715. [PMID: 28957509 PMCID: PMC5850612 DOI: 10.1093/molbev/msx206] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One of the most abundant proteins in human saliva, mucin-7, is encoded by the MUC7 gene, which harbors copy number variable subexonic repeats (PTS-repeats) that affect the size and glycosylation potential of this protein. We recently documented the adaptive evolution of MUC7 subexonic copy number variation among primates. Yet, the evolution of MUC7 genetic variation in humans remained unexplored. Here, we found that PTS-repeat copy number variation has evolved recurrently in the human lineage, thereby generating multiple haplotypic backgrounds carrying five or six PTS-repeat copy number alleles. Contrary to previous studies, we found no associations between the copy number of PTS-repeats and protection against asthma. Instead, we revealed a significant association of MUC7 haplotypic variation with the composition of the oral microbiome. Furthermore, based on in-depth simulations, we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans.
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Affiliation(s)
- Duo Xu
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Pavlos Pavlidis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Recep Ozgur Taskent
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Nikolaos Alachiotis
- Institute of Computer Science (ICS), Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Colin Flanagan
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Michael DeGiorgio
- Department of Biology and the Institute for CyberScience, Pennsylvania State University, University Park, PA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
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24
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Xu D, Jaber Y, Pavlidis P, Gokcumen O. VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. BMC Bioinformatics 2017; 18:426. [PMID: 28950836 PMCID: PMC5615795 DOI: 10.1186/s12859-017-1844-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/21/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. RESULTS Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. CONCLUSION VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .
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Affiliation(s)
- Duo Xu
- Department of Biological Sciences, State University of New York at Buffalo, New York, 14260, USA
| | - Yousef Jaber
- Department of Biological Sciences, State University of New York at Buffalo, New York, 14260, USA
| | - Pavlos Pavlidis
- Institute of Molecular Biology and biotechnology (IMBB), Foundation of Research and Technology--Hellas, Heraklion, Crete, Greece
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, New York, 14260, USA.
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Thyssen JP, Elias PM. It Remains Unknown Whether Filaggrin Gene Mutations Evolved to Increase Cutaneous Synthesis of Vitamin D. Genome Biol Evol 2017; 9:900-901. [PMID: 28338939 PMCID: PMC5387992 DOI: 10.1093/gbe/evx049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 02/07/2023] Open
Abstract
About 8-10% of normal Northern Europeans are heterozygous carriers of common FLG mutations, while only 1-4% of southern Europeans display these mutations, and only very rarely are mutations detected in African populations. Although mutations are found in Asians, they are different from those encountered in Northern Europeans. Importantly, FLG mutation carriers have 10% increased serum vitamin D concentrations compared to controls. Based on these observations, we have proposed that this latitude-dependent gradient of FLG mutations across Europe, Asia and Africa could have provided an evolutionary advantage for heterozygous FLG mutation carriers, residing at northern latitudes, depletion of the FLG downstream product, trans-urocanic acid, would facilitate the intracutaneous synthesis of vitamin D3 by allowing increased transcutaneous absorption of UVB photons. Such loss-of-function FLG mutations would have provided an evolutionary advantage for modern humans, living in the far North of Europe, where little UV-B penetrates the atomosphere. In a recent article, it was concluded not only that the UVB-Vitamin D3 hypothesis is invalid, but also that FLG genetic variations, including loss-of-function variants, provide little or no impact on the fitness of modern humans. While we welcome studies that reassess our hypothesis, their conclusions are not valid for reasons explained in this letter.
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Affiliation(s)
- Jacob P Thyssen
- Department of Dermatology and Allergy, Herlev and Gentofte University Hospital, University of Copenhagen, Hellerup, Denmark
| | - Peter M Elias
- Dermatology Service, Veterans Affairs Medical Center, and Department of Dermatology, UCSF, San Francisco, California
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Fernandez K, Asad S, Taylan F, Wahlgren CF, Bilcha KD, Nordenskjöld M, Winge MCG, Bradley M. Intragenic Copy Number Variation in the Filaggrin Gene in Ethiopian Patients with Atopic Dermatitis. Pediatr Dermatol 2017; 34:e140-e141. [PMID: 28295514 DOI: 10.1111/pde.13095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetic variants in filaggrin (FLG) involving truncating mutations or intragenic copy number variation are strongly associated with the risk of developing atopic dermatitis (AD) in European and Asian populations. Few loss-of-function mutations have been identified in Africans, although an association between FLG copy number variation and AD severity in a small African American cohort has been proposed. We studied the association between FLG copy number and AD in 132 Ethiopians and found no association between AD severity and FLG copy number, suggesting that other, still unidentified genetic factors are of more importance in predisposing Ethiopians to AD.
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Affiliation(s)
- Kerstin Fernandez
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Samina Asad
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Carl-Fredrik Wahlgren
- Dermatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Kassahun D Bilcha
- Department of Dermatovenereology, Faculty of Medicine, Gondar University, Gondar, Ethiopia
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Mårten C G Winge
- Program in Epithelial Biology, School of Medicine, Stanford University, Stanford, California
| | - Maria Bradley
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden.,Dermatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
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Pajic P, Lin YL, Xu D, Gokcumen O. The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence. BMC Evol Biol 2016; 16:265. [PMID: 27919236 PMCID: PMC5139038 DOI: 10.1186/s12862-016-0842-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A common, 32kb deletion of LCE3B and LCE3C genes is strongly associated with psoriasis. We recently found that this deletion is ancient, predating Human-Denisovan divergence. However, it was not clear why negative selection has not removed this deletion from the population. RESULTS Here, we show that the haplotype block that harbors the deletion (i) retains high allele frequency among extant and ancient human populations; (ii) harbors unusually high nucleotide variation (π, P < 4.1 × 10-3); (iii) contains an excess of intermediate frequency variants (Tajima's D, P < 3.9 × 10-3); and (iv) has an unusually long time to coalescence to the most recent common ancestor (TSel, 0.1 quantile). CONCLUSIONS Our results are most parsimonious with the scenario where the LCE3BC deletion has evolved under balancing selection in humans. More broadly, this is consistent with the hypothesis that a balance between autoimmunity and natural vaccination through increased exposure to pathogens maintains this deletion in humans.
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Affiliation(s)
- Petar Pajic
- Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA
| | - Yen-Lung Lin
- Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA
| | - Duo Xu
- Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Cooke 639, Buffalo, NY, 14260, USA.
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