1
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Jin SC, Dong W, Kundishora AJ, Panchagnula S, Moreno-De-Luca A, Furey CG, Allocco AA, Walker RL, Nelson-Williams C, Smith H, Dunbar A, Conine S, Lu Q, Zeng X, Sierant MC, Knight JR, Sullivan W, Duy PQ, DeSpenza T, Reeves BC, Karimy JK, Marlier A, Castaldi C, Tikhonova IR, Li B, Peña HP, Broach JR, Kabachelor EM, Ssenyonga P, Hehnly C, Ge L, Keren B, Timberlake AT, Goto J, Mangano FT, Johnston JM, Butler WE, Warf BC, Smith ER, Schiff SJ, Limbrick DD, Heuer G, Jackson EM, Iskandar BJ, Mane S, Haider S, Guclu B, Bayri Y, Sahin Y, Duncan CC, Apuzzo MLJ, DiLuna ML, Hoffman EJ, Sestan N, Ment LR, Alper SL, Bilguvar K, Geschwind DH, Günel M, Lifton RP, Kahle KT. Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus. Nat Med 2020; 26:1754-1765. [PMID: 33077954 PMCID: PMC7871900 DOI: 10.1038/s41591-020-1090-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/02/2020] [Indexed: 01/08/2023]
Abstract
Congenital hydrocephalus (CH), characterized by enlarged brain ventricles, is considered a disease of excessive cerebrospinal fluid (CSF) accumulation and thereby treated with neurosurgical CSF diversion with high morbidity and failure rates. The poor neurodevelopmental outcomes and persistence of ventriculomegaly in some post-surgical patients highlight our limited knowledge of disease mechanisms. Through whole-exome sequencing of 381 patients (232 trios) with sporadic, neurosurgically treated CH, we found that damaging de novo mutations account for >17% of cases, with five different genes exhibiting a significant de novo mutation burden. In all, rare, damaging mutations with large effect contributed to ~22% of sporadic CH cases. Multiple CH genes are key regulators of neural stem cell biology and converge in human transcriptional networks and cell types pertinent for fetal neuro-gliogenesis. These data implicate genetic disruption of early brain development, not impaired CSF dynamics, as the primary pathomechanism of a significant number of patients with sporadic CH.
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Affiliation(s)
- Sheng Chih Jin
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Weilai Dong
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Shreyas Panchagnula
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Andres Moreno-De-Luca
- Autism & Developmental Medicine Institute, Genomic Medicine Institute, Department of Radiology, Geisinger, Danville, PA, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - August A Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Rebecca L Walker
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Hannah Smith
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Dunbar
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sierra Conine
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Xue Zeng
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Michael C Sierant
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - James R Knight
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - William Sullivan
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Jason K Karimy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | | | - Irina R Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Helena Perez Peña
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, UK
| | - James R Broach
- Institute for Personalized Medicine, The Penn State College of Medicine, Hershey, PA, USA
| | | | | | - Christine Hehnly
- Departments of Neurosurgery, Engineering Science & Mechanics, and Physics; Center for Neural Engineering and Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
| | - Li Ge
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Boris Keren
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et GHUEP Hôpital Trousseau, Sorbonne Université, GRC "Déficience Intellectuelle et Autisme", Paris, France
| | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - June Goto
- Division of Pediatric Neurosurgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francesco T Mangano
- Division of Pediatric Neurosurgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - James M Johnston
- Department of Neurosurgery, University of Alabama School of Medicine, Birmingham, AL, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward R Smith
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven J Schiff
- Departments of Neurosurgery, Engineering Science & Mechanics, and Physics; Center for Neural Engineering and Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
| | - David D Limbrick
- Department of Neurological Surgery and Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory Heuer
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric M Jackson
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin Medical School, Madison, WI, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, UK
| | - Bulent Guclu
- Kartal Dr. Lutfi Kirdar Research and Training Hospital, Istanbul, Turkey
| | - Yasar Bayri
- Department of Neurosurgery, Marmara University School of Medicine, Istanbul, Turkey
| | - Yener Sahin
- Department of Neurosurgery, Marmara University School of Medicine, Istanbul, Turkey
| | - Charles C Duncan
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Michael L J Apuzzo
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Ellen J Hoffman
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Laura R Ment
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Murat Günel
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA.
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2
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Dong W, Jin SC, Allocco A, Zeng X, Sheth AH, Panchagnula S, Castonguay A, Lorenzo LÉ, Islam B, Brindle G, Bachand K, Hu J, Sularz A, Gaillard J, Choi J, Dunbar A, Nelson-Williams C, Kiziltug E, Furey CG, Conine S, Duy PQ, Kundishora AJ, Loring E, Li B, Lu Q, Zhou G, Liu W, Li X, Sierant MC, Mane S, Castaldi C, López-Giráldez F, Knight JR, Sekula RF, Simard JM, Eskandar EN, Gottschalk C, Moliterno J, Günel M, Gerrard JL, Dib-Hajj S, Waxman SG, Barker FG, Alper SL, Chahine M, Haider S, De Koninck Y, Lifton RP, Kahle KT. Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia. iScience 2020; 23:101552. [PMID: 33083721 PMCID: PMC7554653 DOI: 10.1016/j.isci.2020.101552] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Trigeminal neuralgia (TN) is a common, debilitating neuropathic face pain syndrome often resistant to therapy. The familial clustering of TN cases suggests that genetic factors play a role in disease pathogenesis. However, no unbiased, large-scale genomic study of TN has been performed to date. Analysis of 290 whole exome-sequenced TN probands, including 20 multiplex kindreds and 70 parent-offspring trios, revealed enrichment of rare, damaging variants in GABA receptor-binding genes in cases. Mice engineered with a TN-associated de novo mutation (p.Cys188Trp) in the GABAA receptor Cl− channel γ-1 subunit (GABRG1) exhibited trigeminal mechanical allodynia and face pain behavior. Other TN probands harbored rare damaging variants in Na+ and Ca+ channels, including a significant variant burden in the α-1H subunit of the voltage-gated Ca2+ channel Cav3.2 (CACNA1H). These results provide exome-level insight into TN and implicate genetically encoded impairment of GABA signaling and neuronal ion transport in TN pathogenesis. Genomic analysis of trigeminal neuralgia (TN) using exome sequencing Rare mutations in GABA signaling and ion transport genes are enriched in TN cases Generation of a genetic TN mouse model engineered with a patient-specific mutation
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Affiliation(s)
- Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - August Allocco
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Xue Zeng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Amar H Sheth
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Annie Castonguay
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada
| | | | - Barira Islam
- University College London, School of Pharmacy, London, England
| | | | - Karine Bachand
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada
| | - Jamie Hu
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Agata Sularz
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan Gaillard
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.,Department of Biomedical Sciences, Korea University College of Medicine, 02841 Seoul, Korea
| | - Ashley Dunbar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Sierra Conine
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Erin Loring
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Geyu Zhou
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Wei Liu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Xinyue Li
- School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Michael C Sierant
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, West Haven, CT, USA
| | | | | | | | - Raymond F Sekula
- Department of Neurological Surgery, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - J Marc Simard
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emad N Eskandar
- Department of Neurological Surgery, Albert Einstein College of Medicine, Montefiore Medical Center, New York
| | | | | | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jason L Gerrard
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Sulayman Dib-Hajj
- Center for Neuroscience & Regeneration Research, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Neurology; Yale University, New Haven, CT, USA
| | - Stephen G Waxman
- Center for Neuroscience & Regeneration Research, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Neurology; Yale University, New Haven, CT, USA
| | - Fred G Barker
- Harvard Medical School, Boston, MA, USA.,Cancer Center, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mohamed Chahine
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada.,Department of Medicine, Université Laval, Québec, QC, Canada
| | - Shozeb Haider
- University College London, School of Pharmacy, London, England
| | - Yves De Koninck
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada.,Department of Psychiatry and Neuroscience, Université Laval, Québec, QC, Canada
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.,Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
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3
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Sierant MC, Choi J. Single-Cell Ssequencing in Cancer: Recent Applications to Immunogenomics and Multi-omics Tools. Genomics Inform 2018; 16:e17. [PMID: 30602078 PMCID: PMC6440661 DOI: 10.5808/gi.2018.16.4.e17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 12/21/2018] [Indexed: 12/21/2022] Open
Abstract
Tumor heterogeneity, the cellular mosaic of multiple lineages arising from the process of clonal evolution, has continued to thwart multi-omics analyses using traditional bulk sequencing methods. The application of single-cell sequencing, in concert with existing genomics methods, has enabled high-resolution interrogation of the genome, transcriptome, epigenome, and proteome. Applied to cancers, these single-cell multi-omics methods bypass previous limitations on data resolution and have enabled a more nuanced understanding of the evolutionary dynamics of tumor progression, immune evasion, metastasis, and treatment resistance. This review details the growing number of novel single-cell multi-omics methods applied to tumors and further discusses recent discoveries emerging from these approaches, especially in regard to immunotherapy.
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Affiliation(s)
- Michael C Sierant
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jungmin Choi
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
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4
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Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet 2017; 49:1593-1601. [PMID: 28991257 PMCID: PMC5675000 DOI: 10.1038/ng.3970] [Citation(s) in RCA: 486] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/15/2017] [Indexed: 12/17/2022]
Abstract
Congenital heart disease (CHD) is the leading cause of mortality from birth defects. Exome sequencing of a single cohort of 2,871 CHD probands including 2,645 parent-offspring trios implicated rare inherited mutations in 1.8%, including a recessive founder mutation in GDF1 accounting for ~5% of severe CHD in Ashkenazim, recessive genotypes in MYH6 accounting for ~11% of Shone complex, and dominant FLT4 mutations accounting for 2.3% of Tetralogy of Fallot. De novo mutations (DNMs) accounted for 8% of cases, including ~3% of isolated CHD patients and ~28% with both neurodevelopmental and extra-cardiac congenital anomalies. Seven genes surpassed thresholds for genome-wide significance and 12 genes not previously implicated in CHD had > 70% probability of being disease-related; DNMs in ~440 genes are inferred to contribute to CHD. There was striking overlap between genes with damaging DNMs in probands with CHD and autism.
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Affiliation(s)
- Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Samir Zaidi
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qiongshi Lu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sarah Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Steven R DePalma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hongjian Qi
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York, USA
| | - Weni Chang
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Michael C Sierant
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Wei-Chien Hung
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shozeb Haider
- Department of Computational Chemistry, University College London School of Pharmacy, London, UK
| | - Junhui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James Knight
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Robert D Bjornson
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | | | - Irina R Tikhonoa
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Shrikant M Mane
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Stephan J Sanders
- Department of Psychiatry, University of California San Francisco, San Francisco, California, USA
| | - Seema Mital
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Mark W Russell
- Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Michigan, USA
| | - J William Gaynor
- Department of Pediatric Cardiac Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John Deanfield
- Department of Cardiology, University College London and Great Ormond Street Hospital, London, UK
| | - Alessandro Giardini
- Department of Cardiology, University College London and Great Ormond Street Hospital, London, UK
| | - George A Porter
- Department of Pediatrics, University of Rochester Medical Center, The School of Medicine and Dentistry, Rochester, New York, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA.,Roddenberry Stem Cell Center at Gladstone, San Francisco, California, USA.,Departments of Pediatrics and Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Cecelia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, New York, USA
| | - W Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA.,USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - H Joseph Yost
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, USA
| | | | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Amy E Roberts
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Richard Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, Los Angeles, California, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, Maryland, USA
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York, USA
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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5
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Shi L, Lin YH, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim KC, Engel JD. Developmental transcriptome analysis of human erythropoiesis. Hum Mol Genet 2014; 23:4528-42. [PMID: 24781209 DOI: 10.1093/hmg/ddu167] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To globally survey the changes in transcriptional landscape during terminal erythroid differentiation, we performed RNA sequencing (RNA-seq) on primary human CD34(+) cells after ex vivo differentiation from the earliest into the most mature erythroid cell stages. This analysis identified thousands of novel intergenic and intronic transcripts as well as novel alternative transcript isoforms. After rigorous data filtering, 51 (presumptive) novel protein-coding transcripts, 5326 long and 679 small non-coding RNA candidates remained. The analysis also revealed two clear transcriptional trends during terminal erythroid differentiation: first, the complexity of transcript diversity was predominantly achieved by alternative splicing, and second, splicing junctional diversity diminished during erythroid differentiation. Finally, 404 genes that were not known previously to be differentially expressed in erythroid cells were annotated. Analysis of the most extremely differentially expressed transcripts revealed that these gene products were all closely associated with hematopoietic lineage differentiation. Taken together, this study will serve as a comprehensive platform for future in-depth investigation of human erythroid development that, in turn, may reveal new insights into multiple layers of the transcriptional regulatory hierarchy that controls erythropoiesis.
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Affiliation(s)
- Lihong Shi
- Department of Cell and Developmental Biology and
| | - Yu-Hsuan Lin
- Department of Cell and Developmental Biology and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - M C Sierant
- Department of Cell and Developmental Biology and
| | - Fan Zhu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Osamu Tanabe
- Department of Cell and Developmental Biology and Department of Integrative Genomics, Tohoku Medical Megabank, Tohoku University, 2-1 Seiryo-machi, Sendai 980-8573, Japan
| | - Kim-Chew Lim
- Department of Cell and Developmental Biology and
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