1
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Steyn C, Mishi R, Fillmore S, Verhoog MB, More J, Rohlwink UK, Melvill R, Butler J, Enslin JMN, Jacobs M, Sauka-Spengler T, Greco M, Quiñones S, Dulla CG, Raimondo JV, Figaji A, Hockman D. Cell type-specific gene expression dynamics during human brain maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560114. [PMID: 37808657 PMCID: PMC10557738 DOI: 10.1101/2023.09.29.560114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The human brain undergoes protracted post-natal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell type-specific gene expression dynamics. Here, using single nucleus (sn)RNA-seq on temporal lobe tissue, including samples of African ancestry, we build a joint paediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between paediatric and adult cell types, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in paediatric tissue. The new resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map.
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Affiliation(s)
- Christina Steyn
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ruvimbo Mishi
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fillmore
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Matthijs B Verhoog
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jessica More
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ursula K Rohlwink
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Roger Melvill
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - James Butler
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Johannes M N Enslin
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Muazzam Jacobs
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Immunology, Department of Pathology University of Cape Town
- National Health Laboratory Service, South Africa
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Maria Greco
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sadi Quiñones
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Graduate School of Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Joseph V Raimondo
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anthony Figaji
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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2
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Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
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Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
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3
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Adkins-Threats M, Huang YZ, Mills JC. Highlights of how single-cell analyses are illuminating differentiation and disease in the gastric corpus. Am J Physiol Gastrointest Liver Physiol 2024; 326:G205-G215. [PMID: 38193187 DOI: 10.1152/ajpgi.00164.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024]
Abstract
Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful technique to identify novel cell markers, developmental trajectories, and transcriptional changes during cell differentiation and disease onset and progression. In this review, we highlight recent scRNA-seq studies of the gastric corpus in both human and murine systems that have provided insight into gastric organogenesis, identified novel markers for the various gastric lineages during development and in adults, and revealed transcriptional changes during regeneration and tumorigenesis. Overall, by elucidating transcriptional states and fluctuations at the cellular level in healthy and disease contexts, scRNA-seq may lead to better, more personalized clinical treatments for disease progression.
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Affiliation(s)
- Mahliyah Adkins-Threats
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
| | - Yang-Zhe Huang
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
- Graduate School of Biomedical Sciences, Cancer and Cell Biology Program, Baylor College of Medicine, Houston, Texas, United States
| | - Jason C Mills
- Section of Gastroenterology, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States
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4
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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.
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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.
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5
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Blain R, Couly G, Shotar E, Blévinal J, Toupin M, Favre A, Abjaghou A, Inoue M, Hernández-Garzón E, Clarençon F, Chalmel F, Mazaud-Guittot S, Giacobini P, Gitton Y, Chédotal A. A tridimensional atlas of the developing human head. Cell 2023; 186:5910-5924.e17. [PMID: 38070509 PMCID: PMC10783631 DOI: 10.1016/j.cell.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/01/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023]
Abstract
The evolution and development of the head have long captivated researchers due to the crucial role of the head as the gateway for sensory stimuli and the intricate structural complexity of the head. Although significant progress has been made in understanding head development in various vertebrate species, our knowledge of early human head ontogeny remains limited. Here, we used advanced whole-mount immunostaining and 3D imaging techniques to generate a comprehensive 3D cellular atlas of human head embryogenesis. We present detailed developmental series of diverse head tissues and cell types, including muscles, vasculature, cartilage, peripheral nerves, and exocrine glands. These datasets, accessible through a dedicated web interface, provide insights into human embryogenesis. We offer perspectives on the branching morphogenesis of human exocrine glands and unknown features of the development of neurovascular and skeletomuscular structures. These insights into human embryology have important implications for understanding craniofacial defects and neurological disorders and advancing diagnostic and therapeutic strategies.
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Affiliation(s)
- Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Gérard Couly
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eimad Shotar
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Interventional Neuroradiology, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | | | - Maryne Toupin
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Anais Favre
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Ali Abjaghou
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Megumi Inoue
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Frédéric Clarençon
- Department of Interventional Neuroradiology, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Frédéric Chalmel
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Séverine Mazaud-Guittot
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Paolo Giacobini
- University of Lille, INSERM, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, 59000 Lille, France
| | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Institut de pathologie, Groupe Hospitalier Est, Hospices Civils de Lyon, Lyon, France; University Claude Bernard Lyon 1, MeLiS, CNRS UMR 5284, INSERM U1314, 69008 Lyon, France.
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6
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Stabile AM, Pistilli A, Mariangela R, Rende M, Bartolini D, Di Sante G. New Challenges for Anatomists in the Era of Omics. Diagnostics (Basel) 2023; 13:2963. [PMID: 37761332 PMCID: PMC10529314 DOI: 10.3390/diagnostics13182963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.
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Affiliation(s)
- Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Ruggirello Mariangela
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Desirée Bartolini
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
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7
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Knoppers BM, Bernier A, Bowers S, Kirby E. Open Data in the Era of the GDPR: Lessons from the Human Cell Atlas. Annu Rev Genomics Hum Genet 2023; 24:369-391. [PMID: 36791787 DOI: 10.1146/annurev-genom-101322-113255] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Human Cell Atlas (HCA) is striving to build an open community that is inclusive of all researchers adhering to its principles and as open as possible with respect to data access and use. However, open data sharing can pose certain challenges. For instance, being a global initiative, the HCA must contend with a patchwork of local and regional privacy rules. A notable example is the implementation of the European Union General Data Protection Regulation (GDPR), which caused some concern in the biomedical and genomic data-sharing community. We examine how the HCA's large, international group of researchers is investing tremendous efforts into ensuring appropriate sharing of data. We describe the HCA's objectives and governance, how it defines open data sharing, and ethico-legal challenges encountered early in its development; in particular, we describe the challenges prompted by the GDPR. Finally, we broaden the discussion to address tools and strategies that can be used to address ethical data governance.
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Affiliation(s)
- Bartha Maria Knoppers
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; , ,
| | - Alexander Bernier
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; , ,
| | | | - Emily Kirby
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; , ,
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8
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Kana O, Nault R, Filipovic D, Marri D, Zacharewski T, Bhattacharya S. Generative modeling of single-cell gene expression for dose-dependent chemical perturbations. PATTERNS (NEW YORK, N.Y.) 2023; 4:100817. [PMID: 37602218 PMCID: PMC10436058 DOI: 10.1016/j.patter.2023.100817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/07/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023]
Abstract
Single-cell sequencing reveals the heterogeneity of cellular response to chemical perturbations. However, testing all relevant combinations of cell types, chemicals, and doses is a daunting task. A deep generative learning formalism called variational autoencoders (VAEs) has been effective in predicting single-cell gene expression perturbations for single doses. Here, we introduce single-cell variational inference of dose-response (scVIDR), a VAE-based model that predicts both single-dose and multiple-dose cellular responses better than existing models. We show that scVIDR can predict dose-dependent gene expression across mouse hepatocytes, human blood cells, and cancer cell lines. We biologically interpret the latent space of scVIDR using a regression model and use scVIDR to order individual cells based on their sensitivity to chemical perturbation by assigning each cell a "pseudo-dose" value. We envision that scVIDR can help reduce the need for repeated animal testing across tissues, chemicals, and doses.
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Affiliation(s)
- Omar Kana
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Rance Nault
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology Michigan State University, Michigan State University, East Lansing, MI 48824, USA
| | - David Filipovic
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel Marri
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Tim Zacharewski
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology Michigan State University, Michigan State University, East Lansing, MI 48824, USA
| | - Sudin Bhattacharya
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
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9
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Yang MC, Wu ZC, Huang LL, Abbas F, Wang HC. Systematic Methods for Isolating High Purity Nuclei from Ten Important Plants for Omics Interrogation. Cells 2022; 11:cells11233919. [PMID: 36497177 PMCID: PMC9740283 DOI: 10.3390/cells11233919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/23/2022] [Accepted: 12/01/2022] [Indexed: 12/07/2022] Open
Abstract
Recent advances in developmental biology have been made possible by using multi-omic studies at single cell resolution. However, progress in plants has been slowed, owing to the tremendous difficulty in protoplast isolation from most plant tissues and/or oversize protoplasts during flow cytometry purification. Surprisingly, rapid innovations in nucleus research have shed light on plant studies in single cell resolution, which necessitates high quality and efficient nucleus isolation. Herein, we present efficient nuclei isolation protocols from the leaves of ten important plants including Arabidopsis, rice, maize, tomato, soybean, banana, grape, citrus, apple, and litchi. We provide a detailed procedure for nucleus isolation, flow cytometry purification, and absolute nucleus number quantification. The nucleus isolation buffer formula of the ten plants tested was optimized, and the results indicated a high nuclei yield. Microscope observations revealed high purity after flow cytometry sorting, and the DNA and RNA quality extract from isolated nuclei were monitored by using the nuclei in cell division cycle and single nucleus RNA sequencing (snRNA-seq) studies, with detailed procedures provided. The findings indicated that nucleus yield and quality meet the requirements of snRNA-seq, cell division cycle, and likely other omic studies. The protocol outlined here makes it feasible to perform plant omic studies at single cell resolution.
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Affiliation(s)
- Ming-Chao Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Chen Wu
- Becton Dickinson Medical Devices (Shanghai) Co., Ltd., Guangzhou 510180, China
| | - Liang-Liang Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Farhat Abbas
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hui-Cong Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Litchi Engineering Research Center, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Department of Life Sciences and Technology, Yangtze Normal University, Chongqing 408100, China
- Correspondence:
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10
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Childs CJ, Eiken MK, Spence JR. Approaches to benchmark and characterize in vitro human model systems. Development 2022; 149:dev200641. [PMID: 36214410 PMCID: PMC10906492 DOI: 10.1242/dev.200641] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
In vitro human models, such as gastruloids and organoids, are complex three-dimensional (3D) structures often consist of cells from multiple germ layers that possess some attributes of a developing embryo or organ. To use these models to interrogate human development and organogenesis, these 3D models must accurately recapitulate aspects of their in vivo counterparts. Recent advances in single-cell technologies, including sequencing and spatial approaches, have enabled efforts to better understand and directly compare organoids with native tissues. For example, single-cell genomic efforts have created cell and organ atlases that enable benchmarking of in vitro models and can also be leveraged to gain novel biological insights that can be used to further improve in vitro models. This Spotlight discusses the state of current in vitro model systems, the efforts to create large publicly available atlases of the developing human and how these data are being used to improve organoids. Limitations and perspectives on future efforts are also discussed.
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Affiliation(s)
- Charlie J. Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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11
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Koczwara KE, Lake NJ, DeSimone AM, Lek M. Neuromuscular disorders: finding the missing genetic diagnoses. Trends Genet 2022; 38:956-971. [PMID: 35908999 DOI: 10.1016/j.tig.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022]
Abstract
Neuromuscular disorders (NMDs) are a wide-ranging group of diseases that seriously affect the quality of life of affected individuals. The development of next-generation sequencing revolutionized the diagnosis of NMD, enabling the discovery of hundreds of NMD genes and many more pathogenic variants. However, the diagnostic yield of genetic testing in NMD cohorts remains incomplete, indicating a large number of genetic diagnoses are not identified through current methods. Fortunately, recent advancements in sequencing technologies, analytical tools, and high-throughput functional screening provide an opportunity to circumvent current challenges. Here, we discuss reasons for missing genetic diagnoses in NMD, how emerging technologies and tools can overcome these hurdles, and examine future approaches to improving diagnostic yields in NMD.
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Affiliation(s)
- Katherine E Koczwara
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Nicole J Lake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alec M DeSimone
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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12
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Mauracher AA, Henrickson SE. Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:910243. [PMID: 37670772 PMCID: PMC10477056 DOI: 10.3389/fsysb.2022.910243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Inborn errors of immunity (IEI) are monogenic disorders that can cause diverse symptoms, including recurrent infections, autoimmunity and malignancy. While many factors have contributed, the increased availability of next-generation sequencing has been central in the remarkable increase in identification of novel monogenic IEI over the past years. Throughout this phase of disease discovery, it has also become evident that a given gene variant does not always yield a consistent phenotype, while variants in seemingly disparate genes can lead to similar clinical presentations. Thus, it is increasingly clear that the clinical phenotype of an IEI patient is not defined by genetics alone, but is also impacted by a myriad of factors. Accordingly, we need methods to amplify our current diagnostic algorithms to better understand mechanisms underlying the variability in our patients and to optimize treatment. In this review, we will explore how systems immunology can contribute to optimizing both diagnosis and treatment of IEI patients by focusing on identifying and quantifying key dysregulated pathways. To improve mechanistic understanding in IEI we must deeply evaluate our rare IEI patients using multimodal strategies, allowing both the quantification of altered immune cell subsets and their functional evaluation. By studying representative controls and patients, we can identify causative pathways underlying immune cell dysfunction and move towards functional diagnosis. Attaining this deeper understanding of IEI will require a stepwise strategy. First, we need to broadly apply these methods to IEI patients to identify patterns of dysfunction. Next, using multimodal data analysis, we can identify key dysregulated pathways. Then, we must develop a core group of simple, effective functional tests that target those pathways to increase efficiency of initial diagnostic investigations, provide evidence for therapeutic selection and contribute to the mechanistic evaluation of genetic results. This core group of simple, effective functional tests, targeting key pathways, can then be equitably provided to our rare patients. Systems biology is thus poised to reframe IEI diagnosis and therapy, fostering research today that will provide streamlined diagnosis and treatment choices for our rare and complex patients in the future, as well as providing a better understanding of basic immunology.
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Affiliation(s)
- Andrea A. Mauracher
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah E. Henrickson
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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13
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Li Z, Sau-Wai Ngan E. New insights empowered by single-cell sequencing: from neural crest to enteric nervous system. Comput Struct Biotechnol J 2022; 20:2464-2472. [PMID: 35664232 PMCID: PMC9133688 DOI: 10.1016/j.csbj.2022.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/03/2022] Open
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14
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Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med 2022; 24:784-797. [PMID: 35148959 PMCID: PMC9119004 DOI: 10.1016/j.gim.2021.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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Affiliation(s)
- Samantha M Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lisa H Chadwick
- Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Kimberly F Doheny
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colleen P Davis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT
| | | | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA.
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
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15
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Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nat Neurosci 2022; 25:306-316. [PMID: 35260865 DOI: 10.1038/s41593-022-01022-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples.
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16
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Syrimi E, Fennell E, Richter A, Vrljicak P, Stark R, Ott S, Murray PG, Al-Abadi E, Chikermane A, Dawson P, Hackett S, Jyothish D, Kanthimathinathan HK, Monaghan S, Nagakumar P, Scholefield BR, Welch S, Khan N, Faustini S, Davies K, Zelek WM, Kearns P, Taylor GS. The immune landscape of SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Children (MIS-C) from acute disease to recovery. iScience 2021; 24:103215. [PMID: 34632327 PMCID: PMC8487319 DOI: 10.1016/j.isci.2021.103215] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/10/2021] [Accepted: 09/26/2021] [Indexed: 01/08/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening disease occurring several weeks after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Deep immune profiling showed acute MIS-C patients had highly activated neutrophils, classical monocytes and memory CD8+ T-cells, with increased frequencies of B-cell plasmablasts and double-negative B-cells. Post treatment samples from the same patients, taken during symptom resolution, identified recovery-associated immune features including increased monocyte CD163 levels, emergence of a new population of immature neutrophils and, in some patients, transiently increased plasma arginase. Plasma profiling identified multiple features shared by MIS-C, Kawasaki Disease and COVID-19 and that therapeutic inhibition of IL-6 may be preferable to IL-1 or TNF-α. We identified several potential mechanisms of action for IVIG, the most commonly used drug to treat MIS-C. Finally, we showed systemic complement activation with high plasma C5b-9 levels is common in MIS-C suggesting complement inhibitors could be used to treat the disease.
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Affiliation(s)
- Eleni Syrimi
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Eanna Fennell
- Health Research Institute and the Bernal Institute, University of Limerick, Limerick, Ireland
| | - Alex Richter
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Pavle Vrljicak
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Richard Stark
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry, UK
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Paul G. Murray
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
- Health Research Institute and the Bernal Institute, University of Limerick, Limerick, Ireland
| | - Eslam Al-Abadi
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Ashish Chikermane
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Pamela Dawson
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Scott Hackett
- Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Deepthi Jyothish
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Sean Monaghan
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Prasad Nagakumar
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Barnaby R. Scholefield
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Steven Welch
- Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Naeem Khan
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Sian Faustini
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
| | - Kate Davies
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Wioleta M. Zelek
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Pamela Kearns
- NIHR Birmingham Biomedical Research Centre and Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Graham S. Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, B15 2TT Birmingham, UK
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17
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Weber LM, Hippen AA, Hickey PF, Berrett KC, Gertz J, Doherty JA, Greene CS, Hicks SC. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. Gigascience 2021; 10:giab062. [PMID: 34553212 PMCID: PMC8458035 DOI: 10.1093/gigascience/giab062] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Pooling cells from multiple biological samples prior to library preparation within the same single-cell RNA sequencing experiment provides several advantages, including lower library preparation costs and reduced unwanted technological variation, such as batch effects. Computational demultiplexing tools based on natural genetic variation between individuals provide a simple approach to demultiplex samples, which does not require complex additional experimental procedures. However, to our knowledge these tools have not been evaluated in cancer, where somatic variants, which could differ between cells from the same sample, may obscure the signal in natural genetic variation. RESULTS Here, we performed in silico benchmark evaluations by combining raw sequencing reads from multiple single-cell samples in high-grade serous ovarian cancer, which has a high copy number burden, and lung adenocarcinoma, which has a high tumor mutational burden. Our results confirm that genetic demultiplexing tools can be effectively deployed on cancer tissue using a pooled experimental design, although high proportions of ambient RNA from cell debris reduce performance. CONCLUSIONS This strategy provides significant cost savings through pooled library preparation. To facilitate similar analyses at the experimental design phase, we provide freely accessible code and a reproducible Snakemake workflow built around the best-performing tools found in our in silico benchmark evaluations, available at https://github.com/lmweber/snp-dmx-cancer.
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Affiliation(s)
- Lukas M Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ariel A Hippen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter F Hickey
- Advanced Technology & Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Kristofer C Berrett
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
| | - Jason Gertz
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
| | - Jennifer Anne Doherty
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84108, USA
| | - Casey S Greene
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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18
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A roadmap for the Human Developmental Cell Atlas. Nature 2021; 597:196-205. [PMID: 34497388 DOI: 10.1038/s41586-021-03620-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
The Human Developmental Cell Atlas (HDCA) initiative, which is part of the Human Cell Atlas, aims to create a comprehensive reference map of cells during development. This will be critical to understanding normal organogenesis, the effect of mutations, environmental factors and infectious agents on human development, congenital and childhood disorders, and the cellular basis of ageing, cancer and regenerative medicine. Here we outline the HDCA initiative and the challenges of mapping and modelling human development using state-of-the-art technologies to create a reference atlas across gestation. Similar to the Human Genome Project, the HDCA will integrate the output from a growing community of scientists who are mapping human development into a unified atlas. We describe the early milestones that have been achieved and the use of human stem-cell-derived cultures, organoids and animal models to inform the HDCA, especially for prenatal tissues that are hard to acquire. Finally, we provide a roadmap towards a complete atlas of human development.
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19
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Li H, Huang Q, Liu Y, Garmire LX. Single cell transcriptome research in human placenta. Reproduction 2021; 160:R155-R167. [PMID: 33112783 PMCID: PMC7707799 DOI: 10.1530/rep-20-0231] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/22/2020] [Indexed: 12/30/2022]
Abstract
Human placenta is a complex and heterogeneous organ interfacing between the mother and the fetus that supports fetal development. Alterations to placental structural components are associated with various pregnancy complications. To reveal the heterogeneity among various placenta cell types in normal and diseased placentas, as well as elucidate molecular interactions within a population of placental cells, a new genomics technology called single cell RNA-seq (or scRNA-seq) has been employed in the last couple of years. Here we review the principles of scRNA-seq technology, and summarize the recent human placenta studies at scRNA-seq level across gestational ages as well as in pregnancy complications, such as preterm birth and preeclampsia. We list the computational analysis platforms and resources available for the public use. Lastly, we discuss the future areas of interest for placenta single cell studies, as well as the data analytics needed to accomplish them.
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Affiliation(s)
- Hui Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Qianhui Huang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Yu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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20
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Abstract
Genetic testing has yielded major advances in our understanding of the causes of epilepsy. Seizures remain resistant to treatment in a significant proportion of cases, particularly in severe, childhood-onset epilepsy, the patient population in which an underlying causative genetic variant is most likely to be identified. A genetic diagnosis can be explanatory as to etiology, and, in some cases, might suggest a therapeutic approach; yet, a clear path from genetic diagnosis to treatment remains unclear in most cases. Here, we discuss theoretical considerations behind the attempted use of small molecules for the treatment of genetic epilepsies, which is but one among various approaches currently under development. We explore a few salient examples and consider the future of the small molecule approach for genetic epilepsies. We conclude that significant additional work is required to understand how genetic variation leads to dysfunction of epilepsy-associated protein targets, and how this impacts the function of diverse subtypes of neurons embedded within distributed brain circuits to yield epilepsy and epilepsy-associated comorbidities. A syndrome- or even variant-specific approach may be required to achieve progress. Advances in the field will require improved methods for large-scale target validation, compound identification and optimization, and the development of accurate model systems that reflect the core features of human epilepsy syndromes, as well as novel approaches towards clinical trials of such compounds in small rare disease cohorts.
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Affiliation(s)
- Ethan M Goldberg
- Department of Pediatrics, Division of Neurology, Abramson Research Center, The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Abramson Research Center Room 502A, 19104, Philadelphia, PA, USA.
- Departments of Neurology and Neuroscience, The University of Pennsylvania Perelman School of Medicine, 19104, Philadelphia, PA, USA.
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21
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Yu Q, Kilik U, Holloway EM, Tsai YH, Harmel C, Wu A, Wu JH, Czerwinski M, Childs CJ, He Z, Capeling MM, Huang S, Glass IA, Higgins PDR, Treutlein B, Spence JR, Camp JG. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 2021; 184:3281-3298.e22. [PMID: 34019796 PMCID: PMC8208823 DOI: 10.1016/j.cell.2021.04.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022]
Abstract
Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity during human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract. We illuminate cell states, transcription factors, and organ-specific epithelial stem cell and mesenchyme interactions across lineages. We implement the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions. We show that HIOs recapitulate reference cell states and use HIOs to reconstruct the molecular dynamics of intestinal epithelium and mesenchyme emergence. We show that the mesenchyme-derived niche cue NRG1 enhances intestinal stem cell maturation in vitro and that the homeobox transcription factor CDX2 is required for regionalization of intestinal epithelium and mesenchyme in humans. This work combines cell atlases and organoid technologies to understand how human organ development is orchestrated.
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Affiliation(s)
- Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Umut Kilik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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22
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Schlieben LD, Prokisch H, Yépez VA. How Machine Learning and Statistical Models Advance Molecular Diagnostics of Rare Disorders Via Analysis of RNA Sequencing Data. Front Mol Biosci 2021; 8:647277. [PMID: 34141720 PMCID: PMC8204083 DOI: 10.3389/fmolb.2021.647277] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Rare diseases, although individually rare, collectively affect approximately 350 million people worldwide. Currently, nearly 6,000 distinct rare disorders with a known molecular basis have been described, yet establishing a specific diagnosis based on the clinical phenotype is challenging. Increasing integration of whole exome sequencing into routine diagnostics of rare diseases is improving diagnostic rates. Nevertheless, about half of the patients do not receive a genetic diagnosis due to the challenges of variant detection and interpretation. During the last years, RNA sequencing is increasingly used as a complementary diagnostic tool providing functional data. Initially, arbitrary thresholds have been applied to call aberrant expression, aberrant splicing, and mono-allelic expression. With the application of RNA sequencing to search for the molecular diagnosis, the implementation of robust statistical models on normalized read counts allowed for the detection of significant outliers corrected for multiple testing. More recently, machine learning methods have been developed to improve the normalization of RNA sequencing read count data by taking confounders into account. Together the methods have increased the power and sensitivity of detection and interpretation of pathogenic variants, leading to diagnostic rates of 10-35% in rare diseases. In this review, we provide an overview of the methods used for RNA sequencing and illustrate how these can improve the diagnostic yield of rare diseases.
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Affiliation(s)
- Lea D. Schlieben
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vicente A. Yépez
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
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Gout AM, Arunachalam S, Finkelstein DB, Zhang J. Data-driven approaches to advance research and clinical care for pediatric cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188571. [PMID: 34051287 DOI: 10.1016/j.bbcan.2021.188571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022]
Abstract
Pediatric cancer is a rare disease with a distinct etiology and mutational landscape compared with adult cancer. Multi-omics profiling of retrospective and prospective cohorts coupled with innovative computational analysis have been instrumental in uncovering mechanisms of tumorigenesis and drug resistance that are now informing pediatric cancer clinical therapy. In this review we present the major data resources of pediatric cancer and actionable insights into pediatric cancer etiology stemming from the identification of oncogenic gene fusions, mutational signature analysis, systems biology, cancer predisposition and survivorship studies - that have led to improved clinical diagnosis, discovery of new drug-targets, pharmacological therapy, and screening for genetic predisposition. Ultimately, integration of large-scale omics datasets generated through international collaboration is required to maximize the power of data-driven approaches to advance pediatric cancer research informing clinical therapy.
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Affiliation(s)
- Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sasi Arunachalam
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David B Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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24
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Conde D, Triozzi PM, Balmant KM, Doty AL, Miranda M, Boullosa A, Schmidt HW, Pereira WJ, Dervinis C, Kirst M. A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus. PLoS One 2021; 16:e0251149. [PMID: 33974645 PMCID: PMC8112699 DOI: 10.1371/journal.pone.0251149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/21/2021] [Indexed: 02/01/2023] Open
Abstract
Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover key regulatory elements that determine cell fate during developmental programs. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues' secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available. Here we present a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. We developed the protocol using two different plant materials with varying cellular complexity levels and cell wall structure, Populus shoot apices, and more lignified stems. Using the 10× Genomics Chromium technology, we show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.
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Affiliation(s)
- Daniel Conde
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Paolo M. Triozzi
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Kelly M. Balmant
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Andria L. Doty
- Interdisciplinary Center for Biotechnology, Flow Cytometry & Imaging Core, University of Florida, Gainesville, Florida, United States of America
| | - Mariza Miranda
- Interdisciplinary Center for Biotechnology, Flow Cytometry & Imaging Core, University of Florida, Gainesville, Florida, United States of America
| | - Anthony Boullosa
- Interdisciplinary Center for Biotechnology, Flow Cytometry & Imaging Core, University of Florida, Gainesville, Florida, United States of America
| | - Henry W. Schmidt
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Wendell J. Pereira
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Matias Kirst
- School of Forest, Fisheries and Geomatic Sciences, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida, Gainesville, Florida, United States of America
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25
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Malone CF, Dharia NV, Kugener G, Forman AB, Rothberg MV, Abdusamad M, Gonzalez A, Kuljanin M, Robichaud AL, Conway AS, Dempster JM, Paolella BR, Dumont N, Hovestadt V, Mancias JD, Younger ST, Root DE, Golub TR, Vazquez F, Stegmaier K. Selective Modulation of a Pan-Essential Protein as a Therapeutic Strategy in Cancer. Cancer Discov 2021; 11:2282-2299. [PMID: 33883167 DOI: 10.1158/2159-8290.cd-20-1213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/12/2021] [Accepted: 03/26/2021] [Indexed: 12/26/2022]
Abstract
Cancer dependency maps, which use CRISPR/Cas9 depletion screens to profile the landscape of genetic dependencies in hundreds of cancer cell lines, have identified context-specific dependencies that could be therapeutically exploited. An ideal therapy is both lethal and precise, but these depletion screens cannot readily distinguish between gene effects that are cytostatic or cytotoxic. Here, we use a diverse panel of functional genomic screening assays to identify NXT1 as a selective and rapidly lethal in vivo relevant genetic dependency in MYCN-amplified neuroblastoma. NXT1 heterodimerizes with NXF1, and together they form the principal mRNA nuclear export machinery. We describe a previously unrecognized mechanism of synthetic lethality between NXT1 and its paralog NXT2: their common essential binding partner NXF1 is lost only in the absence of both. We propose a potential therapeutic strategy for tumor-selective elimination of a protein that, if targeted directly, is expected to cause widespread toxicity. SIGNIFICANCE: We provide a framework for identifying new therapeutic targets from functional genomic screens. We nominate NXT1 as a selective lethal target in neuroblastoma and propose a therapeutic approach where the essential protein NXF1 can be selectively eliminated in tumor cells by exploiting the NXT1-NXT2 paralog relationship.See related commentary by Wang and Abdel-Wahab, p. 2129.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | | | - Alexandra B Forman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Mai Abdusamad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amanda L Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Nancy Dumont
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott T Younger
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Todd R Golub
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | | | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
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26
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27
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Reilly J, Gallagher L, Leader G, Shen S. Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation. PLoS One 2020; 15:e0242773. [PMID: 33338084 PMCID: PMC7748153 DOI: 10.1371/journal.pone.0242773] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous disorder that is often accompanied with many co-morbidities. Recent genetic studies have identified various pathways from hundreds of candidate risk genes with varying levels of association to ASD. However, it is unknown which pathways are specific to the core symptoms or which are shared by the co-morbidities. We hypothesised that critical ASD candidates should appear widely across different scoring systems, and that comorbidity pathways should be constituted by genes expressed in the relevant tissues. We analysed the Simons Foundation for Autism Research Initiative (SFARI) database and four independently published scoring systems and identified 292 overlapping genes. We examined their mRNA expression using the Genotype-Tissue Expression (GTEx) database and validated protein expression levels using the human protein atlas (HPA) dataset. This led to clustering of the overlapping ASD genes into 2 groups; one with 91 genes primarily expressed in the central nervous system (CNS geneset) and another with 201 genes expressed in both CNS and peripheral tissues (CNS+PT geneset). Bioinformatic analyses showed a high enrichment of CNS development and synaptic transmission in the CNS geneset, and an enrichment of synapse, chromatin remodelling, gene regulation and endocrine signalling in the CNS+PT geneset. Calcium signalling and the glutamatergic synapse were found to be highly interconnected among pathways in the combined geneset. Our analyses demonstrate that 2/3 of ASD genes are expressed beyond the brain, which may impact peripheral function and involve in ASD co-morbidities, and relevant pathways may be explored for the treatment of ASD co-morbidities.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, Biomedical Science Building, National University of Ireland (NUI) Galway, Galway, Ireland
- * E-mail: (JR); (SS)
| | - Louise Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity Centre for Health Sciences—Trinity College Dublin, St. James’s Hospital, Dublin, Ireland
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland (NUI) Galway, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, Biomedical Science Building, National University of Ireland (NUI) Galway, Galway, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
- * E-mail: (JR); (SS)
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28
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Giangreco NP, Elias JE, Tatonetti NP. No population left behind: Improving paediatric drug safety using informatics and systems biology. Br J Clin Pharmacol 2020; 88:1464-1470. [PMID: 33332641 PMCID: PMC8209126 DOI: 10.1111/bcp.14705] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/26/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
Adverse drugs effects (ADEs) in children are common and may result in disability and death. The current paediatric drug safety landscape, including clinical trials, is limited as it rarely includes children and relies on extrapolation from adults. Children are not small adults but go through an evolutionarily conserved and physiologically dynamic process of growth and maturation. Novel quantitative approaches, integrating observations from clinical trials and drug safety databases with dynamic mechanisms, can be used to systematically identify ADEs unique to childhood. In this perspective, we discuss three critical research directions using systems biology methodologies and novel informatics to improve paediatric drug safety, namely child versus adult drug safety profiles, age-dependent drug toxicities and genetic susceptibility of ADEs across childhood. We argue that a data-driven framework that leverages observational data, biomedical knowledge and systems biology modelling will reveal previously unknown mechanisms of pediatric adverse drug events and lead to improved paediatric drug safety.
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Affiliation(s)
- Nicholas P Giangreco
- Department of Biomedical Informatics and Systems Biology, Columbia University, New York, NY, USA
| | - Jonathan E Elias
- Department of Pediatrics, Instructor in Pediatrics, Assistant Medical Director of Information Services, Weill Cornell Medical & NYP Weill Cornell Medical Center, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics and Systems Biology, Columbia University, New York, NY, USA
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29
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Dhaundiyal A, Kumari P, Jawalekar SS, Chauhan G, Kalra S, Navik U. Is highly expressed ACE 2 in pregnant women "a curse" in times of COVID-19 pandemic? Life Sci 2020; 264:118676. [PMID: 33129880 PMCID: PMC7598563 DOI: 10.1016/j.lfs.2020.118676] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
Angiotensin-converting enzyme 2 (ACE 2) is a membrane-bound enzyme that cleaves angiotensin II (Ang II) into angiotensin (1-7). It also serves as an important binding site for SARS-CoV-2, thereby, facilitating viral entry into target host cells. ACE 2 is abundantly present in the intestine, kidney, heart, lungs, and fetal tissues. Fetal ACE 2 is involved in myocardium growth, lungs and brain development. ACE 2 is highly expressed in pregnant women to compensate preeclampsia by modulating angiotensin (1-7) which binds to the Mas receptor, having vasodilator action and maintain fluid homeostasis. There are reports available on Zika, H1N1 and SARS-CoV where these viruses have shown to produce fetal defects but very little is known about SARS-CoV-2 involvement in pregnancy, but it might have the potential to interact with fetal ACE 2 and enhance COVID-19 transmission to the fetus, leading to fetal morbidity and mortality. This review sheds light on a path of SARS-CoV-2 transmission risk in pregnancy and its possible link with fetal ACE 2.
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Affiliation(s)
- Ankit Dhaundiyal
- Senior Data Analyst at Private Organization, Gurugram, Haryana 122001,M.S. (Pharma) in Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar, Punjab 160 062, India
| | - Puja Kumari
- Principal Research Analyst at Private Organization Jaipur, Rajasthan 302021, M.S. (Pharma) in Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar, Punjab 160 062, India
| | - Snehal Sainath Jawalekar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar, Punjab-160 062, India
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849, Monterrey, NL, Mexico
| | - Sourav Kalra
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar, Punj, ab-160 062, India.
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, Punj, ab-151001, India.
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30
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Rahimzadeh V, Knoppers BM, Bartlett G. Ethical, Legal, and Social Issues (ELSI) of Responsible Data Sharing Involving Children in Genomics: A Systematic Literature Review of Reasons. AJOB Empir Bioeth 2020; 11:233-245. [PMID: 32975491 DOI: 10.1080/23294515.2020.1818875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Progress in precision medicine relies on the access to, use of, and exchange of genomic and associated clinical data, including from children. The ethical, legal, and social issues (ELSI) of such data access, use, and exchange may be accentuated in the pediatric context due in part to the highly sensitive nature of genomic data, children's consent-related vulnerabilities, and uncertain risks of reidentification. Systematic analyses of the ELSI and scientific reasons for why and how genomic data may be shared responsibly are, however, limited. Methods: We conducted a modified systematic review of reasons according to Sofaer and Strech to examine the ELSI and scientific reasons for "responsible" sharing of children's genomic and associated clinical data. Empirical articles, commentaries, and data-sharing policies indexed in Medline, Scopus, Web of Science, and BIOSIS were included in the analysis if they discussed ELSI and were published between 2003 and 2017 in English. Results: One hundred and fifty-one records met our inclusion criteria. We identified 11 unique reasons and 8 subreasons for why children's genomic data should or should not be shared. Enhancing the prospect of direct and indirect benefits and maximizing the utility of children's data were top reasons why data should be shared. Inadequate data privacy protection was the leading reason why it should not. We furthermore identified 8 reasons and 30 subreasons that support conditional data sharing, in which recontact for the continued use of children's data once they reach the age of majority was the most frequently endorsed condition. Conclusions: The complete list of ELSI reasons and responsible conditions provides an evidentiary basis upon which institutions can develop data-sharing policies. Institutions should encourage the sharing of children's data to advance genomic research, while heeding special reconsent and data protection mechanisms that may help mitigate uncertain longitudinal risks for children and families.
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Affiliation(s)
- Vasiliki Rahimzadeh
- Center for Biomedical Ethics, Stanford University, Stanford, California, USA
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31
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Molaei H, Khedmat L, Nemati E, Rostami Z, Saadat SH. Iranian kidney transplant recipients with COVID-19 infection: Clinical outcomes and cytomegalovirus coinfection. Transpl Infect Dis 2020; 23:e13455. [PMID: 32881220 DOI: 10.1111/tid.13455] [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: 06/16/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND There is a high risk of COVID-19 in kidney transplant recipients (KTRs) because of chronic immunosuppression and severe cytomegalovirus (CMV) pneumonitis. CASE PRESENTATION A case series of 10 KTRs with COVID-19 in Iran was developed. Participants consisted of two female and eight male patients, aged 46-68 years old. The data related to clinical laboratory tests, outcomes, diagnosis, and drug treatments were collected. The RT-PCR confirmed the COVID-19 infection in KTRs. The assessment of serum biochemical and blood hematological factors showed that there was a strong correlation between COVID-19 intensity and high serum Cr, BUN, and ALT levels, high CRP concentration, and lower lymphocyte and platelet counts in male KTRs. Ground-glass opacity (GGO) was the main radiologic pattern visible on both chest radiographs of computed tomography scans. The COVID-19 and CMV coinfection in KTRs resulted in large-size kidneys with severe parenchymal echogenicity and hydronephrosis. The combined use of effective antibiotic and antiviral drugs was suitable to prevent COVID-19 progression in KTRs. CONCLUSIONS The coincidence of COVID-19 and CMV in KTRs may potentially increase the mortality risk of patients. The levels of Cr, BUN, ALT, and CRP as well as lymphocytes count in these patients should be continuously controlled.
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Affiliation(s)
- Hamideh Molaei
- Trauma Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Leila Khedmat
- Health Management Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Eghlim Nemati
- Nephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Zohreh Rostami
- Nephrology and Urology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Hassan Saadat
- Behavioral Sciences Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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32
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Conklin LS, Hoffman EP, van den Anker J. Developmental Pharmacodynamics and Modeling in Pediatric Drug Development. J Clin Pharmacol 2020; 59 Suppl 1:S87-S94. [PMID: 31502687 DOI: 10.1002/jcph.1482] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Challenges in pediatric drug development include small patient numbers, limited outcomes research, ethical barriers, and sparse biosamples. Increasingly, pediatric drug development is focusing on extrapolation: leveraging knowledge about adult disease and drug responses to inform projections of drug and clinical trial performance in pediatric subpopulations. Pharmacokinetic-pharmacodynamic (PK-PD) modeling and extrapolation aim to reduce the numbers of patients and data points needed to establish efficacy. Planning for PK-PD and biomarker studies should begin early in the adult drug development program. Extrapolation relies on the assumption that both the underlying disease and the mechanism of action of the drug used to treat that disease are similar in adults and pediatric subpopulations. Clearly, developmental changes in PK and PD need to be considered to enhance the quality of PK-PD modeling and, therefore, increase the success of extrapolation. This article focuses on the influence of differences in PD between adults and pediatric subpopulations that are highly relevant for the use of extrapolation.
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Affiliation(s)
- Laurie S Conklin
- Division of Gastroenterology, Hepatology, and Nutrition, Children's National Health System, Washington, DC, USA.,ReveraGen BioPharma, Rockville, MD, USA
| | - Eric P Hoffman
- ReveraGen BioPharma, Rockville, MD, USA.,Binghamton University-SUNY, School of Pharmacy and Pharmaceutical Sciences, Binghamton, NY, USA
| | - John van den Anker
- ReveraGen BioPharma, Rockville, MD, USA.,Division of Clinical Pharmacology, Children's National Health System, Washington, DC, USA
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33
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Ando Y, Kwon ATJ, Shin JW. An era of single-cell genomics consortia. Exp Mol Med 2020; 52:1409-1418. [PMID: 32929222 PMCID: PMC8080593 DOI: 10.1038/s12276-020-0409-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 12/24/2022] Open
Abstract
The human body consists of 37 trillion single cells represented by over 50 organs that are stitched together to make us who we are, yet we still have very little understanding about the basic units of our body: what cell types and states make up our organs both compositionally and spatially. Previous efforts to profile a wide range of human cell types have been attempted by the FANTOM and GTEx consortia. Now, with the advancement in genomic technologies, profiling the human body at single-cell resolution is possible and will generate an unprecedented wealth of data that will accelerate basic and clinical research with tangible applications to future medicine. To date, several major organs have been profiled, but the challenges lie in ways to integrate single-cell genomics data in a meaningful way. In recent years, several consortia have begun to introduce harmonization and equity in data collection and analysis. Herein, we introduce existing and nascent single-cell genomics consortia, and present benefits to necessitate single-cell genomic consortia in a regional environment to achieve the universal human cell reference dataset.
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Affiliation(s)
- Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan
| | - Andrew Tae-Jun Kwon
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan.
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34
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Fan J, Slowikowski K, Zhang F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Exp Mol Med 2020; 52:1452-1465. [PMID: 32929226 PMCID: PMC8080633 DOI: 10.1038/s12276-020-0422-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/26/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Intratumor heterogeneity is a common characteristic across diverse cancer types and presents challenges to current standards of treatment. Advancements in high-throughput sequencing and imaging technologies provide opportunities to identify and characterize these aspects of heterogeneity. Notably, transcriptomic profiling at a single-cell resolution enables quantitative measurements of the molecular activity that underlies the phenotypic diversity of cells within a tumor. Such high-dimensional data require computational analysis to extract relevant biological insights about the cell types and states that drive cancer development, pathogenesis, and clinical outcomes. In this review, we highlight emerging themes in the computational analysis of single-cell transcriptomics data and their applications to cancer research. We focus on downstream analytical challenges relevant to cancer research, including how to computationally perform unified analysis across many patients and disease states, distinguish neoplastic from nonneoplastic cells, infer communication with the tumor microenvironment, and delineate tumoral and microenvironmental evolution with trajectory and RNA velocity analysis. We include discussions of challenges and opportunities for future computational methodological advancements necessary to realize the translational potential of single-cell transcriptomic profiling in cancer.
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Affiliation(s)
- Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
| | - Kamil Slowikowski
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA
| | - Fan Zhang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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35
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Abstract
Organ constructs are organ-like structures grown in vitro or in vivo that harbor the components, architecture, and function of in vivo organs, in part or in toto. The convergence of stem cell biology, bioengineering, and gene editing tools have substantially broadened our ability to generate various types of organ constructs for regenerative medicine as well as to address pressing biomedical questions. In this Review, we highlight prevailing approaches for generating organ constructs, from organoids to chimeric organ engineering. We also discuss design principles of different approaches, their utility and limitations, and propose strategies to resolve existing hurdles.
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Affiliation(s)
- Yun Xia
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore.
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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36
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Takahashi K, Jeong D, Wang S, Narita M, Jin X, Iwasaki M, Perli SD, Conklin BR, Yamanaka S. Critical Roles of Translation Initiation and RNA Uridylation in Endogenous Retroviral Expression and Neural Differentiation in Pluripotent Stem Cells. Cell Rep 2020; 31:107715. [PMID: 32492424 PMCID: PMC8195978 DOI: 10.1016/j.celrep.2020.107715] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 02/06/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Previous studies have suggested that the loss of the translation initiation factor eIF4G1 homolog NAT1 induces excessive self-renewability of naive pluripotent stem cells (PSCs); yet the role of NAT1 in the self-renewal and differentiation of primed PSCs is still unclear. Here, we generate a conditional knockout of NAT1 in primed PSCs and use the cells for the functional analyses of NAT1. Our results show that NAT1 is required for the self-renewal and neural differentiation of primed PSCs. In contrast, NAT1 deficiency in naive pluripotency attenuates the differentiation to all cell types. We also find that NAT1 is involved in efficient protein expression of an RNA uridyltransferase, TUT7. TUT7 is involved in the neural differentiation of primed PSCs via the regulation of human endogenous retrovirus accumulation. These data demonstrate the essential roles of NAT1 and TUT7 in the precise transition of stem cell fate.
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Affiliation(s)
- Kazutoshi Takahashi
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
| | - Daeun Jeong
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Songnan Wang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Megumi Narita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Xuemei Jin
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Samuel D Perli
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Bruce R Conklin
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Departments of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shinya Yamanaka
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
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37
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Anderson M, Youngner S, Smith RD, Nandyal RR, Orlowski JP, Jessie Hill B, Barsman SG. Neonatal Organ and Tissue Donation for Research: Options Following Death by Natural Causes. Cell Tissue Bank 2020; 21:289-302. [PMID: 32166424 PMCID: PMC7223177 DOI: 10.1007/s10561-020-09822-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
The donation of organs and tissues from neonates (birth to 28 days) for transplantation has been a relatively infrequent occurrence. Less common has been the use of neonatal organs and tissues for research. Specific ethical and legal questions beg for rational and transparent guidelines with which to evaluate referrals of potential donors. Donation of organs and tissues from a neonate can play a key role in the care and support provided to families by health care professionals around the time of a neonate's death. We report on the recovery of neonatal organs and tissues for research. A working group made up of bioethicists, neonatologists, lawyers, obstetric practioners as well as organ procurement and tissue banking professionals evaluated legal, ethical and medical issues. Neonatal donor family members were also consulted. Our primary goals were (a) to ensure that referrals were made in compliance with all applicable federal and state laws, regulations and institutional protocols, and (b) to follow acceptable ethical standards. Algorithms and policies designed to assist in the evaluation of potential neonatal donors were developed. Neonatal donation is proving increasingly valuable for research into areas including diabetes, pulmonary, gastrointestinal, genitourinary and neurological development, rheumatoid arthritis, autism, childhood psychiatric and neurologic disorders, treatment of MRSA infection and pediatric emergency resuscitation. The development of policies and procedures will assist medical professionals who wish to offer the option of donation to family members anticipating the death of a neonate.
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Affiliation(s)
| | - Stuart Youngner
- Department of Bioethics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4976 USA
| | - Regina Dunne Smith
- International Institute for Advancement of Medicine, Romansville, PA USA
| | - Raja R. Nandyal
- Department of Neonatology, Oklahoma University Health Sciences Center, Oklahoma City, OK USA
| | | | - B. Jessie Hill
- School of Law, Case Western Reserve University, Cleveland, OH USA
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38
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Wilbrey-Clark A, Roberts K, Teichmann SA. Cell Atlas technologies and insights into tissue architecture. Biochem J 2020; 477:1427-1442. [PMID: 32339226 PMCID: PMC7200628 DOI: 10.1042/bcj20190341] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/17/2022]
Abstract
Since Robert Hooke first described the existence of 'cells' in 1665, scientists have sought to identify and further characterise these fundamental units of life. While our understanding of cell location, morphology and function has expanded greatly; our understanding of cell types and states at the molecular level, and how these function within tissue architecture, is still limited. A greater understanding of our cells could revolutionise basic biology and medicine. Atlasing initiatives like the Human Cell Atlas aim to identify all cell types at the molecular level, including their physical locations, and to make this reference data openly available to the scientific community. This is made possible by a recent technology revolution: both in single-cell molecular profiling, particularly single-cell RNA sequencing, and in spatially resolved methods for assessing gene and protein expression. Here, we review available and upcoming atlasing technologies, the biological insights gained to date and the promise of this field for the future.
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39
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Li M, Chen L, Zhang J, Xiong C, Li X. The SARS-CoV-2 receptor ACE2 expression of maternal-fetal interface and fetal organs by single-cell transcriptome study. PLoS One 2020; 15:e0230295. [PMID: 32298273 PMCID: PMC7161957 DOI: 10.1371/journal.pone.0230295] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/31/2020] [Indexed: 12/16/2022] Open
Abstract
The new type of pneumonia caused by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) has been declared as a global public health concern by WHO. As of April 3, 2020, more than 1,000,000 human infections have been diagnosed around the world, which exhibited apparent person-to-person transmission characteristics of this virus. The capacity of vertical transmission in SARS-CoV-2 remains controversial recently. Angiotensin-converting enzyme 2 (ACE2) is now confirmed as the receptor of SARS-CoV-2 and plays essential roles in human infection and transmission. In present study, we collected the online available single-cell RNA sequencing (scRNA-seq) data to evaluate the cell specific expression of ACE2 in maternal-fetal interface as well as in multiple fetal organs. Our results revealed that ACE2 was highly expressed in maternal-fetal interface cells including stromal cells and perivascular cells of decidua, and cytotrophoblast and syncytiotrophoblast in placenta. Meanwhile, ACE2 was also expressed in specific cell types of human fetal heart, liver and lung, but not in kidney. And in a study containing series fetal and post-natal mouse lung, we observed ACE2 was dynamically changed over the time, and ACE2 was extremely high in neonatal mice at post-natal day 1~3. In summary, this study revealed that the SARS-CoV-2 receptor was widely spread in specific cell types of maternal-fetal interface and fetal organs. And thus, both the vertical transmission and the placenta dysfunction/abortion caused by SARS-CoV-2 need to be further carefully investigated in clinical practice.
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Affiliation(s)
- Mengmeng Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Liang Chen
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Jingxiao Zhang
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Chenglong Xiong
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai, China
- * E-mail: (CX); (XL)
| | - Xiangjie Li
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
- * E-mail: (CX); (XL)
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40
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Basil MC, Morrisey EE. Lung regeneration: a tale of mice and men. Semin Cell Dev Biol 2020; 100:88-100. [PMID: 31761445 PMCID: PMC7909713 DOI: 10.1016/j.semcdb.2019.11.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 01/11/2023]
Abstract
The respiratory system is the main site of gas exchange with the external environment in complex terrestrial animals. Within the trachea and lungs are multiple different tissue niches each consisting of a myriad of cells types with critical roles in air conduction, gas exchange, providing important niche specific cell-cell interactions, connection to the cardiovascular system, and immune surveillance. How the respiratory system responds to external insults and executes the appropriate regenerative response remains challenging to study given the plethora of cell and tissue interactions for this to occur properly. This review will examine the various cell types and tissue niches found within the respiratory system and provide a comparison between mouse and human lungs and trachea to highlight important similarities and differences. Defining the critical gaps in knowledge in human lung and tracheal regeneration is critical for future development of therapies directed towards respiratory diseases.
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Affiliation(s)
- Maria C Basil
- Department of Medicine; Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Edward E Morrisey
- Department of Medicine; Department of Cell and Developmental Biology; Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA 19104, United States.
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41
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Camp JG, Platt R, Treutlein B. Mapping human cell phenotypes to genotypes with single-cell genomics. Science 2020; 365:1401-1405. [PMID: 31604266 DOI: 10.1126/science.aax6648] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cumulative activity of all of the body's cells, with their myriad interactions, life histories, and environmental experiences, gives rise to a condition that is distinctly human and specific to each individual. It is an enduring goal to catalog our human cell types, to understand how they develop, how they vary between individuals, and how they fail in disease. Single-cell genomics has revolutionized this endeavor because sequencing-based methods provide a means to quantitatively annotate cell states on the basis of high-information content and high-throughput measurements. Together with advances in stem cell biology and gene editing, we are in the midst of a fascinating journey to understand the cellular phenotypes that compose human bodies and how the human genome is used to build and maintain each cell. Here, we will review recent advances into how single-cell genomics is being used to develop personalized phenotyping strategies that cross subcellular, cellular, and tissue scales to link our genome to our cumulative cellular phenotypes.
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Affiliation(s)
- J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Randall Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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42
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Jin S, Zhang L, Nie Q. scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles. Genome Biol 2020; 21:25. [PMID: 32014031 PMCID: PMC6996200 DOI: 10.1186/s13059-020-1932-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Simultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide an unprecedented opportunity to understand cell fates. However, effective approaches for the integrative analysis of such data are lacking. Here, we present a single-cell aggregation and integration (scAI) method to deconvolute cellular heterogeneity from parallel transcriptomic and epigenomic profiles. Through iterative learning, scAI aggregates sparse epigenomic signals in similar cells learned in an unsupervised manner, allowing coherent fusion with transcriptomic measurements. Simulation studies and applications to three real datasets demonstrate its capability of dissecting cellular heterogeneity within both transcriptomic and epigenomic layers and understanding transcriptional regulatory mechanisms.
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Affiliation(s)
- Suoqin Jin
- Department of Mathematics, University of California, Irvine, CA 92697 USA
| | - Lihua Zhang
- Department of Mathematics, University of California, Irvine, CA 92697 USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697 USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA 92697 USA
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697 USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697 USA
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43
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Lignelli E, Palumbo F, Myti D, Morty RE. Recent advances in our understanding of the mechanisms of lung alveolarization and bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol 2019; 317:L832-L887. [PMID: 31596603 DOI: 10.1152/ajplung.00369.2019] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) is the most common cause of morbidity and mortality in preterm infants. A key histopathological feature of BPD is stunted late lung development, where the process of alveolarization-the generation of alveolar gas exchange units-is impeded, through mechanisms that remain largely unclear. As such, there is interest in the clarification both of the pathomechanisms at play in affected lungs, and the mechanisms of de novo alveoli generation in healthy, developing lungs. A better understanding of normal and pathological alveolarization might reveal opportunities for improved medical management of affected infants. Furthermore, disturbances to the alveolar architecture are a key histopathological feature of several adult chronic lung diseases, including emphysema and fibrosis, and it is envisaged that knowledge about the mechanisms of alveologenesis might facilitate regeneration of healthy lung parenchyma in affected patients. To this end, recent efforts have interrogated clinical data, developed new-and refined existing-in vivo and in vitro models of BPD, have applied new microscopic and radiographic approaches, and have developed advanced cell-culture approaches, including organoid generation. Advances have also been made in the development of other methodologies, including single-cell analysis, metabolomics, lipidomics, and proteomics, as well as the generation and use of complex mouse genetics tools. The objective of this review is to present advances made in our understanding of the mechanisms of lung alveolarization and BPD over the period 1 January 2017-30 June 2019, a period that spans the 50th anniversary of the original clinical description of BPD in preterm infants.
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Affiliation(s)
- Ettore Lignelli
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
| | - Francesco Palumbo
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
| | - Despoina Myti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
| | - Rory E Morty
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center, member of the German Center for Lung Research, Giessen, Germany
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44
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Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga FA, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. Am J Respir Cell Mol Biol 2019; 61:31-41. [PMID: 30995076 PMCID: PMC6604220 DOI: 10.1165/rcmb.2018-0416tr] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Lung disease accounts for every sixth death globally. Profiling the molecular state of all lung cell types in health and disease is currently revolutionizing the identification of disease mechanisms and will aid the design of novel diagnostic and personalized therapeutic regimens. Recent progress in high-throughput techniques for single-cell genomic and transcriptomic analyses has opened up new possibilities to study individual cells within a tissue, classify these into cell types, and characterize variations in their molecular profiles as a function of genetics, environment, cell-cell interactions, developmental processes, aging, or disease. Integration of these cell state definitions with spatial information allows the in-depth molecular description of cellular neighborhoods and tissue microenvironments, including the tissue resident structural and immune cells, the tissue matrix, and the microbiome. The Human Cell Atlas consortium aims to characterize all cells in the healthy human body and has prioritized lung tissue as one of the flagship projects. Here, we present the rationale, the approach, and the expected impact of a Human Lung Cell Atlas.
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Affiliation(s)
- Herbert B. Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Daniel T. Montoro
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Lukas M. Simon
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Emma L. Rawlins
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Maximilian Strunz
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Wim Timens
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, and
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - G. R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Janette K. Burgess
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Maarten van den Berge
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Fabian J. Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Department of Biology, Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts; and
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jayaraj Rajagopal
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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