1
|
Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. Science 2024; 384:eadi5199. [PMID: 38781369 PMCID: PMC11365579 DOI: 10.1126/science.adi5199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
Collapse
Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Chicago, IL 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
2
|
Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585576. [PMID: 38562822 PMCID: PMC10983939 DOI: 10.1101/2024.03.18.585576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
Collapse
Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Opthalmology, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Inc., Chicago, IL, 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA, 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Michael Margolis
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Manman Shi
- Tempus Labs, Inc., Chicago, IL, 60654, USA
| | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT, 06520, USA
| |
Collapse
|
3
|
Abstract
Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.
Collapse
Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
4
|
Curry AR, Ooi L, Matosin N. How spatial omics approaches can be used to map the biological impacts of stress in psychiatric disorders: a perspective, overview and technical guide. Stress 2024; 27:2351394. [PMID: 38752853 DOI: 10.1080/10253890.2024.2351394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
Exposure to significant levels of stress and trauma throughout life is a leading risk factor for the development of major psychiatric disorders. Despite this, we do not have a comprehensive understanding of the mechanisms that explain how stress raises psychiatric disorder risk. Stress in humans is complex and produces variable molecular outcomes depending on the stress type, timing, and duration. Deciphering how stress increases disorder risk has consequently been challenging to address with the traditional single-target experimental approaches primarily utilized to date. Importantly, the molecular processes that occur following stress are not fully understood but are needed to find novel treatment targets. Sequencing-based omics technologies, allowing for an unbiased investigation of physiological changes induced by stress, are rapidly accelerating our knowledge of the molecular sequelae of stress at a single-cell resolution. Spatial multi-omics technologies are now also emerging, allowing for simultaneous analysis of functional molecular layers, from epigenome to proteome, with anatomical context. The technology has immense potential to transform our understanding of how disorders develop, which we believe will significantly propel our understanding of how specific risk factors, such as stress, contribute to disease course. Here, we provide our perspective of how we believe these technologies will transform our understanding of the neurobiology of stress, and also provided a technical guide to assist molecular psychiatry and stress researchers who wish to implement spatial omics approaches in their own research. Finally, we identify potential future directions using multi-omics technology in stress research.
Collapse
Affiliation(s)
- Amber R Curry
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Molecular Horizons, School of Chemistry and Molecular Bioscience, Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Lezanne Ooi
- Molecular Horizons, School of Chemistry and Molecular Bioscience, Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Natalie Matosin
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Molecular Horizons, School of Chemistry and Molecular Bioscience, Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| |
Collapse
|
5
|
de Klein N, Tsai EA, Vochteloo M, Baird D, Huang Y, Chen CY, van Dam S, Oelen R, Deelen P, Bakker OB, El Garwany O, Ouyang Z, Marshall EE, Zavodszky MI, van Rheenen W, Bakker MK, Veldink J, Gaunt TR, Runz H, Franke L, Westra HJ. Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases. Nat Genet 2023; 55:377-388. [PMID: 36823318 PMCID: PMC10011140 DOI: 10.1038/s41588-023-01300-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait locus (eQTL) meta-analyses in multiple brain region- and ancestry-specific datasets (n ≤ 2,759). Many of the 16,169 cortex cis-eQTLs were tissue-dependent when compared with blood cis-eQTLs. We inferred brain cell types for 3,549 cis-eQTLs by interaction analysis. We prioritized 186 cis-eQTLs for 31 brain-related traits using Mendelian randomization and co-localization including 40 cis-eQTLs with an inferred cell type, such as a neuron-specific cis-eQTL (CYP24A1) for multiple sclerosis. We further describe 737 trans-eQTLs for 526 unique variants and 108 unique genes. We used brain-specific gene-co-regulation networks to link GWAS loci and prioritize additional genes for five central nervous system diseases. This study represents a valuable resource for post-GWAS research on central nervous system diseases.
Collapse
Affiliation(s)
- Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Ellen A Tsai
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Martijn Vochteloo
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Denis Baird
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Yunfeng Huang
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Sipko van Dam
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Ancora Health, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Omar El Garwany
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Eric E Marshall
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Maria I Zavodszky
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Heiko Runz
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA.
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
| |
Collapse
|
6
|
Coleman JRI. Feasibility and application of polygenic score analysis to the morphology of human-induced pluripotent stem cells. Mol Genet Genomics 2022; 297:1111-1122. [PMID: 35633379 PMCID: PMC9250464 DOI: 10.1007/s00438-022-01905-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Genome-wide association studies have identified thousands of significant associations between genetic variants and complex traits. Inferring biological insights from these associations has been challenging. One approach attempted has been to examine the effects of individual variants in cellular models. Here, I demonstrate the feasibility of examining the aggregate effect of many variants on cellular phenotypes. I examine the effects of polygenic scores for cross-psychiatric disorder risk, schizophrenia, body mass index and height on cellular morphology, using 1.5 million induced pluripotent stem cells (iPSC) from 60 European-ancestry donors from the Human iPSC Initiative dataset. I show that measuring multiple cells per donor provides sufficient power for polygenic score analyses, and that cross-psychiatric disorder risk is associated with cell area (p = 0.004). Combined with emerging methods of high-throughput iPSC phenotyping, cellular polygenic scoring is a promising method for understanding potential biological effects of the polygenic component of complex traits.
Collapse
Affiliation(s)
- Jonathan R I Coleman
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience-PO80, King's College London, DeCrespigny Park, Denmark Hill, London, SE5 8AF, UK. .,National Institute for Health and Care Research Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK.
| |
Collapse
|
7
|
Flynn E, Lappalainen T. Functional Characterization of Genetic Variant Effects on Expression. Annu Rev Biomed Data Sci 2022; 5:119-139. [PMID: 35483347 DOI: 10.1146/annurev-biodatasci-122120-010010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thousands of common genetic variants in the human population have been associated with disease risk and phenotypic variation by genome-wide association studies (GWAS). However, the majority of GWAS variants fall into noncoding regions of the genome, complicating our understanding of their regulatory functions, and few molecular mechanisms of GWAS variant effects have been clearly elucidated. Here, we set out to review genetic variant effects, focusing on expression quantitative trait loci (eQTLs), including their utility in interpreting GWAS variant mechanisms. We discuss the interrelated challenges and opportunities for eQTL analysis, covering determining causal variants, elucidating molecular mechanisms of action, and understanding context variability. Addressing these questions can enable better functional characterization of disease-associated loci and provide insights into fundamental biological questions of the noncoding genetic regulatory code and its control of gene expression. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Elise Flynn
- New York Genome Center, New York, NY, USA; , .,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; , .,Department of Systems Biology, Columbia University, New York, NY, USA.,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
8
|
Functional genomics data: privacy risk assessment and technological mitigation. Nat Rev Genet 2022; 23:245-258. [PMID: 34759381 DOI: 10.1038/s41576-021-00428-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy challenges, some of which are analogous to those that occur when sharing genetic variant data. However, there are also unique privacy challenges that arise from cryptic information leakage during the processing and summarization of functional genomics data from raw reads to derived quantities, such as gene expression values. Here, we review these challenges and present potential solutions for mitigating privacy risks while allowing broad data dissemination and analysis.
Collapse
|
9
|
Privacy-preserving genotype imputation with fully homomorphic encryption. Cell Syst 2022; 13:173-182.e3. [PMID: 34758288 PMCID: PMC8857019 DOI: 10.1016/j.cels.2021.10.003] [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: 08/21/2020] [Revised: 06/28/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022]
Abstract
Genotype imputation is the inference of unknown genotypes using known population structure observed in large genomic datasets; it can further our understanding of phenotype-genotype relationships and is useful for QTL mapping and GWASs. However, the compute-intensive nature of genotype imputation can overwhelm local servers for computation and storage. Hence, many researchers are moving toward using cloud services, raising privacy concerns. We address these concerns by developing an efficient, privacy-preserving algorithm called p-Impute. Our method uses homomorphic encryption, allowing calculations on ciphertext, thereby avoiding the decryption of private genotypes in the cloud. It is similar to k-nearest neighbor approaches, inferring missing genotypes in a genomic block based on the SNP genotypes of genetically related individuals in the same block. Our results demonstrate accuracy in agreement with the state-of-the-art plaintext solutions. Moreover, p-Impute is scalable to real-world applications as its memory and time requirements increase linearly with the increasing number of samples. p-Impute is freely available for download here: https://doi.org/10.5281/zenodo.5542001.
Collapse
|
10
|
Rocks D, Jaric I, Tesfa L, Greally JM, Suzuki M, Kundakovic M. Cell type-specific chromatin accessibility analysis in the mouse and human brain. Epigenetics 2022; 17:202-219. [PMID: 33775205 PMCID: PMC8865312 DOI: 10.1080/15592294.2021.1896983] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/18/2021] [Accepted: 01/30/2021] [Indexed: 11/07/2022] Open
Abstract
The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using ATAC-seq include a small amount of material needed, fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. With increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs. Here we tested three protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescence-activated nuclei sorting (FANS) and ATAC-seq. Our study shows that the cryopreservation method impacts the number of open chromatin regions identified from frozen brain tissue using ATAC-seq. However, we show that all protocols generate consistent and robust data and enable the identification of functional regulatory elements in neuronal cells. Our study implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. We also reveal additional challenges of doing chromatin analysis on post-mortem human brain tissue. Overall, ATAC-seq coupled with FANS is a powerful method to capture cell-type-specific chromatin accessibility information in mouse and human brain. Our study provides alternative brain preservation methods that generate high-quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in the brain.
Collapse
Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Ivana Jaric
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Lydia Tesfa
- Flow Cytometry Core Facility, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John M. Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| |
Collapse
|
11
|
Lee B, Katsushima K, Pokhrel R, Yuan M, Stapleton S, Jallo G, Wechsler-Reya RJ, Eberhart CG, Ray A, Perera RJ. The long non-coding RNA SPRIGHTLY and its binding partner PTBP1 regulate exon 5 skipping of SMYD3 transcripts in group 4 medulloblastomas. Neurooncol Adv 2022; 4:vdac120. [PMID: 36267874 PMCID: PMC9569026 DOI: 10.1093/noajnl/vdac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Although some of the regulatory genes, signaling pathways, and gene regulatory networks altered in medulloblastomas (MB) are known, the roles of non-coding RNAs, particularly long non-coding RNAs (lncRNAs), are poorly described. Here we report that the lncRNA SPRIGHTLY (SPRY4-IT1) gene is upregulated in group 4 medulloblastoma (G4 MB). Methods SPRIGHTLY expression was assessed in MB subgroup patient-derived xenografts, cell lines, and patient samples. The effect of SPRIGHTLY hemizygous deletion on proliferation, invasion, apoptosis, and colony formation were assessed in vitro and on tumor growth in vivo. dChIRP pull-down assays were used to assess SPRIGHTLY-binding partners, confirmed by immunoprecipitation. SMYD3 ΔE5 transcripts were examined in cell lines and publicly available RNA-seq data. Pathway analysis was performed by phospho-kinase profiling and RNA-seq. Results CRISPR/Cas9 deletion of SPRIGHTLY reduced cell viability and invasion and increased apoptosis in G4 MB cell lines in vitro. SPRIGHTLY hemizygous-deleted G4 MB cells injected into mouse cerebellums produced smaller tumors than those derived from parental cells expressing both copies of SPRIGHTLY. SPRIGHTLY lncRNA bound to the intronic region of the SMYD3 pre-mRNA transcript. SPRIGHTLY also interacted with PTPB1 protein to regulate SMYD3 exon skipping to produce an aberrant protein. SPRIGHTLY-driven SMYD3 regulation enhanced the expression of EGFR pathway genes in G4 MB cell lines and activated cell coagulation/hemostasis-related gene expression, suggesting a novel oncogenic role in G4 MB. Conclusions These results demonstrate the importance of SPRIGHTLY lncRNA as a promoter of G4 MB and the role of the SPRIGHTLY-SMYD3-PTPB1 axis as an important oncogenic regulator in MB.
Collapse
Affiliation(s)
- Bongyong Lee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Rudramani Pokhrel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - George Jallo
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave – Ross Bldg 558, Baltimore, MD 21205, USA
| | - Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont CA, 91711, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| |
Collapse
|
12
|
Pagni S, Mills JD, Frankish A, Mudge JM, Sisodiya SM. Non-coding regulatory elements: Potential roles in disease and the case of epilepsy. Neuropathol Appl Neurobiol 2021; 48:e12775. [PMID: 34820881 DOI: 10.1111/nan.12775] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/04/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022]
Abstract
Non-coding DNA (ncDNA) refers to the portion of the genome that does not code for proteins and accounts for the greatest physical proportion of the human genome. ncDNA includes sequences that are transcribed into RNA molecules, such as ribosomal RNAs (rRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and un-transcribed sequences that have regulatory functions, including gene promoters and enhancers. Variation in non-coding regions of the genome have an established role in human disease, with growing evidence from many areas, including several cancers, Parkinson's disease and autism. Here, we review the features and functions of the regulatory elements that are present in the non-coding genome and the role that these regions have in human disease. We then review the existing research in epilepsy and emphasise the potential value of further exploring non-coding regulatory elements in epilepsy. In addition, we outline the most widely used techniques for recognising regulatory elements throughout the genome, current methodologies for investigating variation and the main challenges associated with research in the field of non-coding DNA.
Collapse
Affiliation(s)
- Susanna Pagni
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - James D Mills
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK.,Amsterdam UMC, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, Netherlands
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| |
Collapse
|
13
|
Lam M, Chen CY, Ge T, Xia Y, Hill DW, Trampush JW, Yu J, Knowles E, Davies G, Stahl EA, Huckins L, Liewald DC, Djurovic S, Melle I, Christoforou A, Reinvang I, DeRosse P, Lundervold AJ, Steen VM, Espeseth T, Räikkönen K, Widen E, Palotie A, Eriksson JG, Giegling I, Konte B, Hartmann AM, Roussos P, Giakoumaki S, Burdick KE, Payton A, Ollier W, Chiba-Falek O, Koltai DC, Need AC, Cirulli ET, Voineskos AN, Stefanis NC, Avramopoulos D, Hatzimanolis A, Smyrnis N, Bilder RM, Freimer NB, Cannon TD, London E, Poldrack RA, Sabb FW, Congdon E, Conley ED, Scult MA, Dickinson D, Straub RE, Donohoe G, Morris D, Corvin A, Gill M, Hariri AR, Weinberger DR, Pendleton N, Bitsios P, Rujescu D, Lahti J, Le Hellard S, Keller MC, Andreassen OA, Deary IJ, Glahn DC, Huang H, Liu C, Malhotra AK, Lencz T. Identifying nootropic drug targets via large-scale cognitive GWAS and transcriptomics. Neuropsychopharmacology 2021; 46:1788-1801. [PMID: 34035472 PMCID: PMC8357785 DOI: 10.1038/s41386-021-01023-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/22/2021] [Accepted: 04/12/2021] [Indexed: 02/05/2023]
Abstract
Broad-based cognitive deficits are an enduring and disabling symptom for many patients with severe mental illness, and these impairments are inadequately addressed by current medications. While novel drug targets for schizophrenia and depression have emerged from recent large-scale genome-wide association studies (GWAS) of these psychiatric disorders, GWAS of general cognitive ability can suggest potential targets for nootropic drug repurposing. Here, we (1) meta-analyze results from two recent cognitive GWAS to further enhance power for locus discovery; (2) employ several complementary transcriptomic methods to identify genes in these loci that are credibly associated with cognition; and (3) further annotate the resulting genes using multiple chemoinformatic databases to identify "druggable" targets. Using our meta-analytic data set (N = 373,617), we identified 241 independent cognition-associated loci (29 novel), and 76 genes were identified by 2 or more methods of gene identification. Actin and chromatin binding gene sets were identified as novel pathways that could be targeted via drug repurposing. Leveraging our transcriptomic and chemoinformatic databases, we identified 16 putative genes targeted by existing drugs potentially available for cognitive repurposing.
Collapse
Affiliation(s)
- Max Lam
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Institute of Mental Health, Singapore, Singapore
| | - Chia-Yen Chen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Biogen, Inc, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Yan Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Psychiatry Department, SUNY Upstate Medical University, Syracuse, NY, USA
| | - David W Hill
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland, UK
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Joey W Trampush
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jin Yu
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
| | - Emma Knowles
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Olin Neuropsychic Research Center, Institute of Living, Hartford Hospital, Hartford, CT, USA
| | - Gail Davies
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland, UK
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Eli A Stahl
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David C Liewald
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ingrid Melle
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Andrea Christoforou
- Spaulding Rehabilitation Hospital Boston, Charlestown, MA, USA
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ivar Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Pamela DeRosse
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Astri J Lundervold
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
| | - Vidar M Steen
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Thomas Espeseth
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - Johan G Eriksson
- Department of General Practice, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Folkhälsan Research Center, Helsinki, Finland
| | - Ina Giegling
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Bettina Konte
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Annette M Hartmann
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Katherine E Burdick
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2), James J. Peters VA Medical Center, Bronx, NY, USA
- Department of Psychiatry - Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Antony Payton
- Division of Informatics, Imaging & Data Sciences, School of Health Sciences, The University of Manchester, Manchester, UK
| | - William Ollier
- Centre for Epidemiology, Division of Population Health, Health Services Research & Primary Care, The University of Manchester, Manchester, UK
- School of Healthcare Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Bryan Alzheimer's Disease Research Center, and Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Deborah C Koltai
- Psychiatry and Behavioral Sciences, Division of Medical Psychology, and Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Anna C Need
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Aristotle N Voineskos
- Campbell Family Mental Health Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, ON, Canada
| | - Nikos C Stefanis
- 2nd Department of Psychiatry, National and Kapodistrian University of Athens Medical School, University General Hospital "ATTIKON", Athens, Greece
- University Mental Health Research Institute, Athens, Greece
- Neurobiology Research Institute, Theodor-Theohari Cozzika Foundation, Athens, Greece
| | - Dimitrios Avramopoulos
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex Hatzimanolis
- 2nd Department of Psychiatry, National and Kapodistrian University of Athens Medical School, University General Hospital "ATTIKON", Athens, Greece
- University Mental Health Research Institute, Athens, Greece
- Neurobiology Research Institute, Theodor-Theohari Cozzika Foundation, Athens, Greece
| | - Nikolaos Smyrnis
- 2nd Department of Psychiatry, National and Kapodistrian University of Athens Medical School, University General Hospital "ATTIKON", Athens, Greece
- University Mental Health Research Institute, Athens, Greece
| | - Robert M Bilder
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - Nelson B Freimer
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - Tyrone D Cannon
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychology, Yale University, New Haven, CT, USA
| | - Edythe London
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | | | - Fred W Sabb
- Robert and Beverly Lewis Center for Neuroimaging, University of Oregon, Eugene, OR, USA
| | - Eliza Congdon
- UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | | | - Matthew A Scult
- Weill Cornell Psychiatry at NewYork-Presbyterian, Weill Cornell Medical Center, New York, NY, USA
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Dwight Dickinson
- Clinical and Translational Neuroscience Branch, Intramural Research Program, National Institute of Mental Health, National Institute of Health, Bethesda, MD, USA
| | - Richard E Straub
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Gary Donohoe
- Neuroimaging, Cognition & Genomics (NICOG) Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Derek Morris
- Neuroimaging, Cognition & Genomics (NICOG) Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Michael Gill
- Neuropsychiatric Genetics Research Group, Department of Psychiatry and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Ahmad R Hariri
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Neil Pendleton
- Division of Neuroscience and Experimental Psychology/School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, Salford Royal NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Panos Bitsios
- Department of Psychiatry and Behavioral Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, GR, Greece
| | - Dan Rujescu
- Department of Psychiatry, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - Stephanie Le Hellard
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Ole A Andreassen
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ian J Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Scotland, UK
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - David C Glahn
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Olin Neuropsychic Research Center, Institute of Living, Hartford Hospital, Hartford, CT, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Psychiatry Department, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anil K Malhotra
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Todd Lencz
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA.
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA.
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.
| |
Collapse
|
14
|
Jayachandran J, Srinivasan H, Mani KP. Molecular mechanism involved in epithelial to mesenchymal transition. Arch Biochem Biophys 2021; 710:108984. [PMID: 34252392 DOI: 10.1016/j.abb.2021.108984] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/07/2023]
Abstract
Epithelial to mesenchymal transition (EMT) is a biological process that plays an important role during embryonic development. During this process, the epithelial cells lose their polarity and acquire mesenchymal properties. In addition to embryonic development, EMT is also well-known to participate in tissue repair, inflammation, fibrosis, and tumor metastasis. In the present review, we address the basics of epithelial to mesenchymal transition during both development and disease conditions and emphasize the role of various transcription factors and miRNAs involved in the process.
Collapse
Affiliation(s)
| | - Harini Srinivasan
- ASK-II, 212, Vascular Research Lab, SASTRA Deemed University, Thanjavur, India
| | - Krishna Priya Mani
- ASK-II, 212, Vascular Research Lab, SASTRA Deemed University, Thanjavur, India.
| |
Collapse
|
15
|
Human Pluripotent Stem-Cell-Derived Models as a Missing Link in Drug Discovery and Development. Pharmaceuticals (Basel) 2021; 14:ph14060525. [PMID: 34070895 PMCID: PMC8230131 DOI: 10.3390/ph14060525] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs), have the potential to accelerate the drug discovery and development process. In this review, by analyzing each stage of the drug discovery and development process, we identified the active role of hPSC-derived in vitro models in phenotypic screening, target-based screening, target validation, toxicology evaluation, precision medicine, clinical trial in a dish, and post-clinical studies. Patient-derived or genome-edited PSCs can generate valid in vitro models for dissecting disease mechanisms, discovering novel drug targets, screening drug candidates, and preclinically and post-clinically evaluating drug safety and efficacy. With the advances in modern biotechnologies and developmental biology, hPSC-derived in vitro models will hopefully improve the cost-effectiveness and the success rate of drug discovery and development.
Collapse
|
16
|
Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Data Sanitization to Reduce Private Information Leakage from Functional Genomics. Cell 2021; 183:905-917.e16. [PMID: 33186529 DOI: 10.1016/j.cell.2020.09.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 07/23/2020] [Accepted: 09/11/2020] [Indexed: 12/30/2022]
Abstract
The generation of functional genomics datasets is surging, because they provide insight into gene regulation and organismal phenotypes (e.g., genes upregulated in cancer). The intent behind functional genomics experiments is not necessarily to study genetic variants, yet they pose privacy concerns due to their use of next-generation sequencing. Moreover, there is a great incentive to broadly share raw reads for better statistical power and general research reproducibility. Thus, we need new modes of sharing beyond traditional controlled-access models. Here, we develop a data-sanitization procedure allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs. Our protocol works with traditional Illumina-based assays and newer technologies such as 10x single-cell RNA sequencing. It involves quantifying the privacy leakage in reads by statistically linking study participants to known individuals. We carried out these linkages using data from highly accurate reference genomes and more realistic environmental samples.
Collapse
Affiliation(s)
- Gamze Gürsoy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Prashant Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Charlotte M Brannon
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Otto A Jolanki
- Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA
| | - Arif Harmanci
- School of Biomedical Informatics, Center for Precision Health, University of Texas Health Sciences Center, Houston, TX 77030, USA
| | - J Seth Strattan
- Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA
| | - J Michael Cherry
- Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA
| | - Andrew D Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
17
|
Lee BH, Rhie SK. Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Epigenetics Chromatin 2021; 14:14. [PMID: 33741028 PMCID: PMC7980343 DOI: 10.1186/s13072-021-00390-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic marks do not change the sequence of DNA but affect gene expression in a cell-type specific manner by altering the activities of regulatory elements. Development of new molecular biology assays, sequencing technologies, and computational approaches enables us to profile the human epigenome in three-dimensional structure genome-wide. Here we describe various molecular biology techniques and bioinformatic tools that have been developed to measure the activities of regulatory elements and their chromatin interactions. Moreover, we list currently available three-dimensional epigenomic data sets that are generated in various human cell types and tissues to assist in the design and analysis of research projects.
Collapse
Affiliation(s)
- Beoung Hun Lee
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
| |
Collapse
|
18
|
Duong A, Evstratova A, Sivitilli A, Hernandez JJ, Gosio J, Wahedi A, Sondheimer N, Wrana JL, Beaulieu JM, Attisano L, Andreazza AC. Characterization of mitochondrial health from human peripheral blood mononuclear cells to cerebral organoids derived from induced pluripotent stem cells. Sci Rep 2021; 11:4523. [PMID: 33633238 PMCID: PMC7907388 DOI: 10.1038/s41598-021-84071-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/29/2021] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial health plays a crucial role in human brain development and diseases. However, the evaluation of mitochondrial health in the brain is not incorporated into clinical practice due to ethical and logistical concerns. As a result, the development of targeted mitochondrial therapeutics remains a significant challenge due to the lack of appropriate patient-derived brain tissues. To address these unmet needs, we developed cerebral organoids (COs) from induced pluripotent stem cells (iPSCs) derived from human peripheral blood mononuclear cells (PBMCs) and monitored mitochondrial health from the primary, reprogrammed and differentiated stages. Our results show preserved mitochondrial genetics, function and treatment responses across PBMCs to iPSCs to COs, and measurable neuronal activity in the COs. We expect our approach will serve as a model for more widespread evaluation of mitochondrial health relevant to a wide range of human diseases using readily accessible patient peripheral (PBMCs) and stem-cell derived brain tissue samples.
Collapse
Affiliation(s)
- Angela Duong
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Alesya Evstratova
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Adam Sivitilli
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - J Javier Hernandez
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, ON, M5G 1X5, Canada
| | - Jessica Gosio
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, ON, M5G 1X5, Canada
| | - Azizia Wahedi
- Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Neal Sondheimer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jeff L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Toronto, ON, M5G 1X5, Canada
| | - Jean-Martin Beaulieu
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Ana C Andreazza
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada. .,Department of Psychiatry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
19
|
Special Article: Translational Science Update. Pharmacological Implications of Emerging Schizophrenia Genetics: Can the Bridge From 'Genomics' to 'Therapeutics' be Defined and Traversed? J Clin Psychopharmacol 2021; 40:323-329. [PMID: 32433256 DOI: 10.1097/jcp.0000000000001215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent schizophrenia genome-wide association studies (GWAS) have identified genomic variants of common and rare frequency, significantly associated with schizophrenia. While numerous functional genomics efforts are ongoing to elucidate the biological effects of schizophrenia risk variants, a consideration of their therapeutic implications is timely and imperative, for patients as well as for an iterative effect on elucidating the underlying biology and pathophysiology of illness. The current article reviews efforts to translate emerging schizophrenia genomics into novel approaches to target discovery and therapeutic intervention. Though the path from 'genetic risk to therapy' is far from straightforward, there are provocative early possibilities that harbor the promise of treatment based on causation rather than phenomenology, as well as 'precision psychiatry,' a basis for stratifying patients to enable more precise and effective, personalized therapy.
Collapse
|
20
|
Wamsley B, Geschwind DH. Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease. Curr Opin Genet Dev 2020; 65:117-125. [PMID: 32634676 PMCID: PMC8171040 DOI: 10.1016/j.gde.2020.05.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/24/2020] [Indexed: 12/30/2022]
Abstract
Neurodegenerative and neuropsychiatric disorders are pervasive and debilitating conditions characterized by diverse clinical syndromes and comorbidities, whose origins are as complex and heterogeneous as their associated phenotypes. Risk for these disorders involves substantial genetic liability, which has fueled large-scale genetic studies that have led to a flood of discoveries. In turn, these discoveries have exposed substantial gaps in our knowledge with regards to the complicated genetic architecture of each disorder and the substantial amount of genetic overlap among disorders, which implies some degree of shared pathophysiology underlying these clinically distinct, multifactorial disorders. Understanding the role of specific genetic variants will involve resolving the connections between molecular pathways, heterogeneous cell types, specific circuits and disease pathogenesis at the tissue and patient level. We consider the current known genetic basis of these disorders and highlight the utility of molecular systems approaches that establish the function of genetic variation in the context of specific neurobiological networks, cell-types, and life stages. Beyond expanding our knowledge of disease mechanisms, understanding these relationships provides promise for early detection and potential therapeutic interventions.
Collapse
Affiliation(s)
- Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Program in Neurobehavioral Genetics and Center for Autism Research and Treatment Semel Institute and Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
21
|
Moyses-Oliveira M, Yadav R, Erdin S, Talkowski ME. New gene discoveries highlight functional convergence in autism and related neurodevelopmental disorders. Curr Opin Genet Dev 2020; 65:195-206. [PMID: 32846283 DOI: 10.1016/j.gde.2020.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023]
Abstract
Over the last two years, remarkable gene discovery efforts have implicated disruption of pathways involving gene regulatory functions and neuronal processes in autism spectrum disorder (ASD), and more broadly defined neurodevelopmental disorders (NDDs). Functional studies in the developing brain and across cell types demonstrate that the spatiotemporal expression patterns of many of these genes coalesce on subnetworks with distinct developmental trajectories. Here, we review the convergent biological processes derived from gene discovery and functional genomics in ASD and NDD from 2018-2020. We further probe the mechanistic insights that suggest these frequently perturbed pathways are interconnected and, ultimately, converge on specific functional deficits in human neurodevelopment.
Collapse
Affiliation(s)
- Mariana Moyses-Oliveira
- Center for Genomic Medicine, Massachusetts General Hospital, Boston MA, United States; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston MA, United States; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, United States; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston MA, United States; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston MA, United States; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, United States; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston MA, United States; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, United States; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston MA, United States; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston MA, United States; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge MA, United States; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States.
| |
Collapse
|
22
|
Nam KH, Yi SA, Jang HJ, Han JW, Lee J. In vitro modeling for inherited neurological diseases using induced pluripotent stem cells: from 2D to organoid. Arch Pharm Res 2020; 43:877-889. [PMID: 32761309 DOI: 10.1007/s12272-020-01260-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Stem cells are characterized by self-renewal and by their ability to differentiate into cells of various organs. With massive progress in 2D and 3D cell culture techniques, in vitro generation of various types of such organoids from patient-derived stem cells is now possible. As in vitro differentiation protocols are usually made to resemble human developmental processes, organogenesis of patient-derived stem cells can provide key information regarding a range of developmental diseases. Human stem cell-based in vitro modeling as opposed to using animal models can particularly benefit the evaluation of neurological diseases because of significant differences in structure and developmental processes between the human and the animal brain. This review focuses on stem cell-based in vitro modeling of neurodevelopmental disorders, more specifically, the fundamentals and technical advancements in monolayer neuron and brain organoid cultures. Furthermore, we discuss the drawbacks of the conventional culture method and explore the advanced, cutting edge 3D organoid models for several neurodevelopmental diseases, including genetic diseases such as Down syndrome, Rett syndrome, and Miller-Dieker syndrome, as well as brain malformations like macrocephaly and microcephaly. Finally, we discuss the limitations of the current organoid techniques and some potential solutions that pave the way for accurate modeling of neurological disorders in a dish.
Collapse
Affiliation(s)
- Ki Hong Nam
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sang Ah Yi
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Ji Jang
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea. .,Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon, 16419, Republic of Korea. .,Imnewrun Biosciences Inc., Suwon, 16419, Republic of Korea.
| |
Collapse
|
23
|
Rajarajan P, Akbarian S. Use of the epigenetic toolbox
to contextualize common variants associated with schizophrenia risk
. DIALOGUES IN CLINICAL NEUROSCIENCE 2020; 21:407-416. [PMID: 31949408 PMCID: PMC6952750 DOI: 10.31887/dcns.2019.21.4/sakbarian] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder with a complex genetic architecture and limited understanding of its neuropathology, reflected by the lack of diagnostic measures and effective pharmacological treatments. Geneticists have recently identified more than 145 risk loci comprising hundreds of common variants of small effect sizes, most of which lie in noncoding genomic regions. This review will discuss how the epigenetic toolbox can be applied to contextualize genetic findings in schizophrenia. Progress in next-generation sequencing, along with increasing methodological complexity, has led to the compilation of genome-wide maps of DNA methylation, histone modifications, RNA expression, and more. Integration of chromatin conformation datasets is one of the latest efforts in deciphering schizophrenia risk, allowing the identification of genes in contact with regulatory variants across 100s of kilobases. Large-scale multiomics studies will facilitate the prioritization of putative causal risk variants and gene networks that contribute to schizophrenia etiology, informing clinical diagnostics and treatment downstream.
.
Collapse
Affiliation(s)
- Prashanth Rajarajan
- Graduate School of Biomedical Sciences; Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
| |
Collapse
|
24
|
Wu Y, Li X, Liu J, Luo XJ, Yao YG. SZDB2.0: an updated comprehensive resource for schizophrenia research. Hum Genet 2020; 139:1285-1297. [DOI: 10.1007/s00439-020-02171-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/25/2020] [Indexed: 12/11/2022]
|
25
|
Lucassen PJ, Fitzsimons CP, Salta E, Maletic-Savatic M. Adult neurogenesis, human after all (again): Classic, optimized, and future approaches. Behav Brain Res 2020; 381:112458. [DOI: 10.1016/j.bbr.2019.112458] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/29/2019] [Accepted: 12/28/2019] [Indexed: 02/08/2023]
|
26
|
Reynolds RH, Hardy J, Ryten M, Gagliano Taliun SA. Informing disease modelling with brain-relevant functional genomic annotations. Brain 2019; 142:3694-3712. [PMID: 31603214 PMCID: PMC6885670 DOI: 10.1093/brain/awz295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
The past decade has seen a surge in the number of disease/trait-associated variants, largely because of the union of studies to share genetic data and the availability of electronic health records from large cohorts for research use. Variant discovery for neurological and neuropsychiatric genome-wide association studies, including schizophrenia, Parkinson's disease and Alzheimer's disease, has greatly benefitted; however, the translation of these genetic association results to interpretable biological mechanisms and models is lagging. Interpreting disease-associated variants requires knowledge of gene regulatory mechanisms and computational tools that permit integration of this knowledge with genome-wide association study results. Here, we summarize key conceptual advances in the generation of brain-relevant functional genomic annotations and amongst tools that allow integration of these annotations with association summary statistics, which together provide a new and exciting opportunity to identify disease-relevant genes, pathways and cell types in silico. We discuss the opportunities and challenges associated with these developments and conclude with our perspective on future advances in annotation generation, tool development and the union of the two.
Collapse
Affiliation(s)
- Regina H Reynolds
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - John Hardy
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
- UK Dementia Research Institute at University College London (UCL), London, UK
| | - Mina Ryten
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
27
|
Neurobiological functions of transcriptional enhancers. Nat Neurosci 2019; 23:5-14. [PMID: 31740812 DOI: 10.1038/s41593-019-0538-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/16/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional enhancers are regulatory DNA elements that underlie the specificity and dynamic patterns of gene expression. Over the past decade, large-scale functional genomics projects have driven transformative progress in our understanding of enhancers. These data have relevance for identifying mechanisms of gene regulation in the CNS, elucidating the function of non-coding regulatory sequences in neurobiology and linking sequence variation within enhancers to genetic risk for neurological and psychiatric disorders. However, the sheer volume and complexity of genomic data presents a challenge to interpreting enhancer function in normal and pathogenic neurobiological processes. Here, to advance the application of genome-scale enhancer data, we offer a primer on current models of enhancer function in the CNS, we review how enhancers regulate gene expression across the neuronal lifespan, and we suggest how emerging findings regarding the role of non-coding sequence variation offer opportunities for understanding brain disorders and developing new technologies for neuroscience.
Collapse
|
28
|
Abstract
Although recent years have seen large decreases in the overall global rate of suicide fatalities, this trend is not reflected everywhere. Suicide and suicidal behaviour continue to present key challenges for public policy and health services, with increasing suicide deaths in some countries such as the USA. The development of suicide risk is complex, involving contributions from biological (including genetics), psychological (such as certain personality traits), clinical (such as comorbid psychiatric illness), social and environmental factors. The involvement of multiple risk factors in conveying risk of suicide means that determining an individual's risk of suicide is challenging. Improving risk assessment, for example, by using computer testing and genetic screening, is an area of ongoing research. Prevention is key to reduce the number of suicide deaths and prevention efforts include universal, selective and indicated interventions, although these interventions are often delivered in combination. These interventions, combined with psychological (such as cognitive behavioural therapy, caring contacts and safety planning) and pharmacological treatments (for example, clozapine and ketamine) along with coordinated social and public health initiatives, should continue to improve the management of individuals who are suicidal and decrease suicide-associated morbidity.
Collapse
|
29
|
van den Heuvel MP, Scholtens LH, Kahn RS. Multiscale Neuroscience of Psychiatric Disorders. Biol Psychiatry 2019; 86:512-522. [PMID: 31320130 DOI: 10.1016/j.biopsych.2019.05.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/11/2022]
Abstract
The human brain comprises a multiscale network with multiple levels of organization. Neurons with dendritic and axonal connections form the microscale fabric of brain circuitry, and macroscale brain regions and white matter connections form the infrastructure for system-level brain communication and information integration. In this review, we discuss the emerging trend of multiscale neuroscience, the multidisciplinary field that brings together data from these different levels of nervous system organization to form a better understanding of between-scale relationships of brain structure, function, and behavior in health and disease. We provide a broad overview of this developing field and discuss recent findings of exemplary multiscale neuroscience studies that illustrate the importance of studying cross-scale interactions among the genetic, molecular, cellular, and macroscale levels of brain circuitry and connectivity and behavior. We particularly consider a central, overarching goal of these multiscale neuroscience studies of human brain connectivity: to obtain insight into how disease-related alterations at one level of organization may underlie alterations observed at other scales of brain network organization in mental disorders. We conclude by discussing the current limitations, challenges, and future directions of the field.
Collapse
Affiliation(s)
- Martijn P van den Heuvel
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands.
| | - Lianne H Scholtens
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - René S Kahn
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
30
|
Brady LS, Potter WZ, Gordon JA. Redirecting the revolution: new developments in drug development for psychiatry. Expert Opin Drug Discov 2019; 14:1213-1219. [PMID: 31545131 DOI: 10.1080/17460441.2019.1666102] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Linda S Brady
- Division of Neuroscience and Basic Behavioral Science, National Institute of Mental Health , Bethesda , MD , USA
| | | | | |
Collapse
|
31
|
Convergence in neuropsychiatric research. Nat Methods 2019; 16:961-964. [PMID: 31537909 DOI: 10.1038/s41592-019-0578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
32
|
Wei CL, Nicolis SK, Zhu Y, Pagin M. Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases. J Exp Neurosci 2019; 13:1179069519868224. [PMID: 31431802 PMCID: PMC6686325 DOI: 10.1177/1179069519868224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 11/16/2022] Open
Abstract
In our article, we asked whether Sox2, a transcription factor important in brain
development and disease, is involved in gene regulation through its action on
long-range interactions between promoters and distant enhancers. Our findings
highlight that Sox2 shapes a genome-wide network of promoter-enhancer
interactions, acting by direct binding to these elements. Sox2 loss affects the
three-dimensional (3D) genome and decreases the activity of a subset of genes
involved in Sox2-bound interactions. At least one of such downregulated genes,
Socs3, is critical for long-term neural stem cell
maintenance. These results point to the possibility of identifying a
transcriptional network downstream to Sox2, and involved in neural stem cell
maintenance. In addition, interacting Sox2-bound enhancers are often connected
to genes which are relevant, in man, to neurodevelopmental disease; this may
facilitate the detection of functionally relevant mutations in regulatory
elements in man, contributing to neural disease.
Collapse
Affiliation(s)
- Chia-Lin Wei
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Yanfen Zhu
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| |
Collapse
|
33
|
Sugrue LP, Desikan RS. Precision neuroradiology: mapping the nodes and networks that link genes to behaviour. Br J Radiol 2019; 92:20190093. [PMID: 31294609 PMCID: PMC6732927 DOI: 10.1259/bjr.20190093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
What is the future of neuroradiology in the era of precision medicine? As with any big change, this transformation in medicine presents both challenges and opportunities, and to flourish in this new environment we will have to adapt. It is difficult to predict exactly how neuroradiology will evolve in this shifting landscape, but there will be changes in both what we image and what we do. In terms of imaging, we will need to move beyond simply imaging brain anatomy and toward imaging function, both at the molecular and circuit level. In terms of what we do, we will need to move from the periphery of the clinical enterprise toward its center, with a new emphasis on integrating imaging with genetic and clinical data to form a comprehensive picture of the patient that can be used to direct further testing and care.The payoff is that these changes will align neuroradiology with the emerging field of precision psychiatry, which promises to replace symptom-based diagnosis and trial-and-error treatment of psychiatric disorders with diagnoses based on quantifiable genetic, imaging, physiologic, and behavioural criteria and therapies targeted to the particular pathophysiology of individual patients. Here we review some of the recent developments in behavioural genetics and neuroscience that are laying the foundation for precision psychiatry. By no means comprehensive, our goal is to introduce some of the perspectives and techniques that are likely to be relevant to the precision neuroradiologist of the future.
Collapse
Affiliation(s)
- Leo P Sugrue
- 1Departments of Radiology and Biomedical Imaging, University California, San Francisco, USA
| | - Rahul S Desikan
- 1Departments of Radiology and Biomedical Imaging, University California, San Francisco, USA.,2Department of Neurology, University California, San Francisco, USA
| |
Collapse
|
34
|
Sullivan PF, Geschwind DH. Defining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders. Cell 2019; 177:162-183. [PMID: 30901538 PMCID: PMC6432948 DOI: 10.1016/j.cell.2019.01.015] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 01/01/2023]
Abstract
Studies of the genetics of psychiatric disorders have become one of the most exciting and fast-moving areas in human genetics. A decade ago, there were few reproducible findings, and now there are hundreds. In this review, we focus on the findings that have illuminated the genetic architecture of psychiatric disorders and the challenges of using these findings to inform our understanding of pathophysiology. The evidence is now overwhelming that psychiatric disorders are "polygenic"-that many genetic loci contribute to risk. With the exception of a subset of those with ASD, few individuals with a psychiatric disorder have a single, deterministic genetic cause; rather, developing a psychiatric disorder is influenced by hundreds of different genetic variants, consistent with a polygenic model. As progressively larger studies have uncovered more about their genetic architecture, the need to elucidate additional architectures has become clear. Even if we were to have complete knowledge of the genetic architecture of a psychiatric disorder, full understanding requires deep knowledge of the functional genomic architecture-the implicated loci impact regulatory processes that influence gene expression and the functional coordination of genes that control biological processes. Following from this is cellular architecture: of all brain regions, cell types, and developmental stages, where and when are the functional architectures operative? Given that the genetic architectures of different psychiatric disorders often strongly overlap, we are challenged to re-evaluate and refine the diagnostic architectures of psychiatric disorders using fundamental genetic and neurobiological data.
Collapse
Affiliation(s)
- Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA.
| | - Daniel H Geschwind
- Departments of Neurology, Psychiatry, and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| |
Collapse
|