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Yurkovich JT, Evans SJ, Rappaport N, Boore JL, Lovejoy JC, Price ND, Hood LE. The transition from genomics to phenomics in personalized population health. Nat Rev Genet 2024; 25:286-302. [PMID: 38093095 DOI: 10.1038/s41576-023-00674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 03/21/2024]
Abstract
Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.
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Affiliation(s)
- James T Yurkovich
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
| | - Simon J Evans
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Noa Rappaport
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Jeffrey L Boore
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Jennifer C Lovejoy
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy E Hood
- Phenome Health, Seattle, WA, USA.
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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Lombardi L, Le Clerc S, Wu CL, Bouassida J, Boukouaci W, Sugusabesan S, Richard JR, Lajnef M, Tison M, Le Corvoisier P, Barau C, Banaschewski T, Holt R, Durston S, Persico AM, Oakley B, Loth E, Buitelaar J, Murphy D, Leboyer M, Zagury JF, Tamouza R. A human leukocyte antigen imputation study uncovers possible genetic interplay between gut inflammatory processes and autism spectrum disorders. Transl Psychiatry 2023; 13:244. [PMID: 37407551 DOI: 10.1038/s41398-023-02550-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental conditions that are for subsets of individuals, underpinned by dysregulated immune processes, including inflammation, autoimmunity, and dysbiosis. Consequently, the major histocompatibility complex (MHC)-hosted human leukocyte antigen (HLA) has been implicated in ASD risk, although seldom investigated. By utilizing a GWAS performed by the EU-AIMS consortium (LEAP cohort), we compared HLA and MHC genetic variants, single nucleotide polymorphisms (SNP), and haplotypes in ASD individuals, versus typically developing controls. We uncovered six SNPs, namely rs9268528, rs9268542, rs9268556, rs14004, rs9268557, and rs8084 that crossed the Bonferroni threshold, which form the underpinnings of 3 independent genetic pathways/blocks that differentially associate with ASD. Block 1 (rs9268528-G, rs9268542-G, rs9268556-C, and rs14004-A) afforded protection against ASD development, whilst the two remaining blocks, namely rs9268557-T, and rs8084-A, associated with heightened risk. rs8084 and rs14004 mapped to the HLA-DRA gene, whilst the four other SNPs located in the BTNL2 locus. Different combinations amongst BTNL2 SNPs and HLA amino acid variants or classical alleles were found either to afford protection from or contribute to ASD risk, indicating a genetic interplay between BTNL2 and HLA. Interestingly, the detected variants had transcriptional and/or quantitative traits loci implications. As BTNL2 modulates gastrointestinal homeostasis and the identified HLA alleles regulate the gastrointestinal tract in celiac disease, it is proposed that the data on ASD risk may be linked to genetically regulated gut inflammatory processes. These findings might have implications for the prevention and treatment of ASD, via the targeting of gut-related processes.
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Affiliation(s)
- Laura Lombardi
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Sigrid Le Clerc
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Ching-Lien Wu
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Jihène Bouassida
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Wahid Boukouaci
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Sobika Sugusabesan
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Jean-Romain Richard
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Mohamed Lajnef
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
| | - Maxime Tison
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Philippe Le Corvoisier
- Université Paris Est Créteil, Inserm, Centre Investigation Clinique, CIC 1430, Henri Mondor, Créteil, F94010, France
| | - Caroline Barau
- Plateforme de Ressources Biologiques, HU Henri Mondor, Créteil, F94010, France
| | - Tobias Banaschewski
- Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Rosemary Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Sarah Durston
- Education Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Antonio M Persico
- Child and Adolescent Neuropsychiatry Program at Modena University Hospital, & Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Bethany Oakley
- Department of Forensic and Neurodevelopemental Science, Institute of Psychatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Eva Loth
- Department of Forensic and Neurodevelopemental Science, Institute of Psychatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jan Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Declan Murphy
- Department of Forensic and Neurodevelopemental Science, Institute of Psychatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Marion Leboyer
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, AP-HP, Hôpital Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision (FHU ADAPT) and Fondation FondaMental, Créteil, F-94010, France
| | - Jean-François Zagury
- Laboratoire Génomique, Bio-informatique et Chimie Moléculaire (EA7528), Conservatoire National des Arts et Métiers, 292, rue Saint Martin, 75003, Paris, France
- HESAM Université, Paris, France
| | - Ryad Tamouza
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, F-94010, Créteil, France.
- Université Paris Est Créteil, INSERM U955, IMRB, Laboratoire Neuro-Psychiatrie translationnelle, AP-HP, Hôpital Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision (FHU ADAPT) and Fondation FondaMental, Créteil, F-94010, France.
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Collier AE, Piekos SN, Liu A, Pattison JM, Felix F, Bailetti AA, Sedov E, Gaddam S, Zhen H, Oro AE. GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. iScience 2023; 26:106125. [PMID: 36843855 PMCID: PMC9950457 DOI: 10.1016/j.isci.2023.106125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.
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Affiliation(s)
- Ann E. Collier
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Samantha N. Piekos
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | - Angela Liu
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Franco Felix
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Egor Sedov
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Hanson Zhen
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
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Harley ITW, Allison K, Scofield RH. Polygenic autoimmune disease risk alleles impacting B cell tolerance act in concert across shared molecular networks in mouse and in humans. Front Immunol 2022; 13:953439. [PMID: 36090990 PMCID: PMC9450536 DOI: 10.3389/fimmu.2022.953439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Most B cells produced in the bone marrow have some level of autoreactivity. Despite efforts of central tolerance to eliminate these cells, many escape to periphery, where in healthy individuals, they are rendered functionally non-responsive to restimulation through their antigen receptor via a process termed anergy. Broad repertoire autoreactivity may reflect the chances of generating autoreactivity by stochastic use of germline immunoglobulin gene segments or active mechanisms may select autoreactive cells during egress to the naïve peripheral B cell pool. Likewise, it is unclear why in some individuals autoreactive B cell clones become activated and drive pathophysiologic changes in autoimmune diseases. Both of these remain central questions in the study of the immune system(s). In most individuals, autoimmune diseases arise from complex interplay of genetic risk factors and environmental influences. Advances in genome sequencing and increased statistical power from large autoimmune disease cohorts has led to identification of more than 200 autoimmune disease risk loci. It has been observed that autoantibodies are detectable in the serum years to decades prior to the diagnosis of autoimmune disease. Thus, current models hold that genetic defects in the pathways that control autoreactive B cell tolerance set genetic liability thresholds across multiple autoimmune diseases. Despite the fact these seminal concepts were developed in animal (especially murine) models of autoimmune disease, some perceive a disconnect between human risk alleles and those identified in murine models of autoimmune disease. Here, we synthesize the current state of the art in our understanding of human risk alleles in two prototypical autoimmune diseases - systemic lupus erythematosus (SLE) and type 1 diabetes (T1D) along with spontaneous murine disease models. We compare these risk networks to those reported in murine models of these diseases, focusing on pathways relevant to anergy and central tolerance. We highlight some differences between murine and human environmental and genetic factors that may impact autoimmune disease development and expression and may, in turn, explain some of this discrepancy. Finally, we show that there is substantial overlap between the molecular networks that define these disease states across species. Our synthesis and analysis of the current state of the field are consistent with the idea that the same molecular networks are perturbed in murine and human autoimmune disease. Based on these analyses, we anticipate that murine autoimmune disease models will continue to yield novel insights into how best to diagnose, prognose, prevent and treat human autoimmune diseases.
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Affiliation(s)
- Isaac T. W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
- Rheumatology Section, Medicine Service, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
| | - Kristen Allison
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
| | - R. Hal Scofield
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Medical/Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
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