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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [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: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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2
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Krontira AC, Cruceanu C, Dony L, Kyrousi C, Link MH, Rek N, Pöhlchen D, Raimundo C, Penner-Goeke S, Schowe A, Czamara D, Lahti-Pulkkinen M, Sammallahti S, Wolford E, Heinonen K, Roeh S, Sportelli V, Wölfel B, Ködel M, Sauer S, Rex-Haffner M, Räikkönen K, Labeur M, Cappello S, Binder EB. Human cortical neurogenesis is altered via glucocorticoid-mediated regulation of ZBTB16 expression. Neuron 2024; 112:1426-1443.e11. [PMID: 38442714 DOI: 10.1016/j.neuron.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 08/15/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
Glucocorticoids are important for proper organ maturation, and their levels are tightly regulated during development. Here, we use human cerebral organoids and mice to study the cell-type-specific effects of glucocorticoids on neurogenesis. We show that glucocorticoids increase a specific type of basal progenitors (co-expressing PAX6 and EOMES) that has been shown to contribute to cortical expansion in gyrified species. This effect is mediated via the transcription factor ZBTB16 and leads to increased production of neurons. A phenome-wide Mendelian randomization analysis of an enhancer variant that moderates glucocorticoid-induced ZBTB16 levels reveals causal relationships with higher educational attainment and altered brain structure. The relationship with postnatal cognition is also supported by data from a prospective pregnancy cohort study. This work provides a cellular and molecular pathway for the effects of glucocorticoids on human neurogenesis that relates to lasting postnatal phenotypes.
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Affiliation(s)
- Anthi C Krontira
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany.
| | - Cristiana Cruceanu
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Leander Dony
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany; Department for Computational Health, Helmholtz Munich, Neuherberg 85764, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising 85354, Germany
| | - Christina Kyrousi
- Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich 80804, Germany; First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, Athens 15784, Greece; University Mental Health, Neurosciences and Precision Medicine Research Institute "Costas Stefanis", Athens 15601, Greece
| | - Marie-Helen Link
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Nils Rek
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany
| | - Dorothee Pöhlchen
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; International Max Planck Research School for Translational Psychiatry, Munich 80804, Germany
| | - Catarina Raimundo
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Signe Penner-Goeke
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Alicia Schowe
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany; Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University, Munich 82152, Germany
| | - Darina Czamara
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Marius Lahti-Pulkkinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland; Finnish Institute for Health and Welfare, Helsinki 00271, Finland; Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Sara Sammallahti
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki 00014, Finland
| | - Elina Wolford
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Kati Heinonen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland; Psychology/Welfare, Faculty of Social Sciences, University of Tampere, Tampere 33014, Finland; Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, ON M5T 1P8, Canada
| | - Simone Roeh
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Vincenza Sportelli
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Wölfel
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Maik Ködel
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Susann Sauer
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Monika Rex-Haffner
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Marta Labeur
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Silvia Cappello
- Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich 80804, Germany; Physiological Genomics, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU), Munich 82152, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich 80804, Germany.
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Manda V, Pavelka J, Lau E. Proteomics applications in next generation induced pluripotent stem cell models. Expert Rev Proteomics 2024; 21:217-228. [PMID: 38511670 PMCID: PMC11065590 DOI: 10.1080/14789450.2024.2334033] [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: 06/14/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Induced pluripotent stem (iPS) cell technology has transformed biomedical research. New opportunities now exist to create new organoids, microtissues, and body-on-a-chip systems for basic biology investigations and clinical translations. AREAS COVERED We discuss the utility of proteomics for attaining an unbiased view into protein expression changes during iPS cell differentiation, cell maturation, and tissue generation. The ability to discover cell-type specific protein markers during the differentiation and maturation of iPS-derived cells has led to new strategies to improve cell production yield and fidelity. In parallel, proteomic characterization of iPS-derived organoids is helping to realize the goal of bridging in vitro and in vivo systems. EXPERT OPINIONS We discuss some current challenges of proteomics in iPS cell research and future directions, including the integration of proteomic and transcriptomic data for systems-level analysis.
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Affiliation(s)
- Vyshnavi Manda
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jay Pavelka
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Edward Lau
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
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4
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Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. MASS SPECTROMETRY REVIEWS 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
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Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
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5
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Lear BP, Moore DL. Moving CNS axon growth and regeneration research into human model systems. Front Neurosci 2023; 17:1198041. [PMID: 37425013 PMCID: PMC10324669 DOI: 10.3389/fnins.2023.1198041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
Axon regeneration is limited in the adult mammalian central nervous system (CNS) due to both intrinsic and extrinsic factors. Rodent studies have shown that developmental age can drive differences in intrinsic axon growth ability, such that embryonic rodent CNS neurons extend long axons while postnatal and adult CNS neurons do not. In recent decades, scientists have identified several intrinsic developmental regulators in rodents that modulate growth. However, whether this developmentally programmed decline in CNS axon growth is conserved in humans is not yet known. Until recently, there have been limited human neuronal model systems, and even fewer age-specific human models. Human in vitro models range from pluripotent stem cell-derived neurons to directly reprogrammed (transdifferentiated) neurons derived from human somatic cells. In this review, we discuss the advantages and disadvantages of each system, and how studying axon growth in human neurons can provide species-specific knowledge in the field of CNS axon regeneration with the goal of bridging basic science studies to clinical trials. Additionally, with the increased availability and quality of 'omics datasets of human cortical tissue across development and lifespan, scientists can mine these datasets for developmentally regulated pathways and genes. As there has been little research performed in human neurons to study modulators of axon growth, here we provide a summary of approaches to begin to shift the field of CNS axon growth and regeneration into human model systems to uncover novel drivers of axon growth.
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Affiliation(s)
| | - Darcie L. Moore
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, United States
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Schäfer M, Schneider M, Müller T, Franz N, Braspenning-Wesch I, Stephan S, Schmidt G, Krijgsveld J, Helm D, Rösl F, Hasche D. Spatial tissue proteomics reveals distinct landscapes of heterogeneity in cutaneous papillomavirus-induced keratinocyte carcinomas. J Med Virol 2023; 95:e28850. [PMID: 37322807 DOI: 10.1002/jmv.28850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
Infection with certain cutaneous human papillomaviruses (HPV), in conjunction with chronic ultraviolet (UV) exposure, are the major cofactors of non-melanoma skin cancer (NMSC), the most frequent cancer type worldwide. Cutaneous squamous cell carcinomas (SCCs) as well as tumors in general represent three-dimensional entities determined by both temporal and spatial constraints. Whole tissue proteomics is a straightforward approach to understand tumorigenesis in better detail, but studies focusing on different progression states toward a dedifferentiated SCC phenotype on a spatial level are rare. Here, we applied an innovative proteomic workflow on formalin-fixed, paraffin-embedded (FFPE) epithelial tumors derived from the preclinical animal model Mastomys coucha. This rodent is naturally infected with its genuine cutaneous papillomavirus and closely mimics skin carcinogenesis in the context of cutaneous HPV infections in humans. We deciphered cellular networks by comparing diverse epithelial tissues with respect to their differentiation level and infection status. Our study reveals novel regulatory proteins and pathways associated with virus-induced tumor initiation and progression of SCCs. This approach provides the basis to better comprehend the multistep process of skin carcinogenesis.
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Affiliation(s)
- Miriam Schäfer
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Torsten Müller
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natascha Franz
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilona Braspenning-Wesch
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sonja Stephan
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriele Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division Proteomics of Stem Cells and Cancer, Research Program "Functional and Structural Genomics", German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center (DKFZ), Heidelberg, Germany
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Rodrigues DC, Mufteev M, Yuki KE, Narula A, Wei W, Piekna A, Liu J, Pasceri P, Rissland OS, Wilson MD, Ellis J. Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models. Nat Commun 2023; 14:1896. [PMID: 37019888 PMCID: PMC10076348 DOI: 10.1038/s41467-023-37339-6] [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: 01/26/2022] [Accepted: 03/13/2023] [Indexed: 04/07/2023] Open
Abstract
Transcriptional changes in Rett syndrome (RTT) are assumed to directly correlate with steady-state mRNA levels, but limited evidence in mice suggests that changes in transcription can be compensated by post-transcriptional regulation. We measure transcription rate and mRNA half-life changes in RTT patient neurons using RATEseq, and re-interpret nuclear and whole-cell RNAseq from Mecp2 mice. Genes are dysregulated by changing transcription rate or half-life and are buffered when both change. We utilized classifier models to predict the direction of transcription rate changes and find that combined frequencies of three dinucleotides are better predictors than CA and CG. MicroRNA and RNA-binding Protein (RBP) motifs are enriched in 3'UTRs of genes with half-life changes. Nuclear RBP motifs are enriched on buffered genes with increased transcription rate. We identify post-transcriptional mechanisms in humans and mice that alter half-life or buffer transcription rate changes when a transcriptional modulator gene is mutated in a neurodevelopmental disorder.
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Affiliation(s)
- Deivid C Rodrigues
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyoko E Yuki
- Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Ashrut Narula
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jiajie Liu
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Peter Pasceri
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Olivia S Rissland
- Molecular Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- RNA Bioscience Initiative and Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - James Ellis
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Sidhaye J, Trepte P, Sepke N, Novatchkova M, Schutzbier M, Dürnberger G, Mechtler K, Knoblich JA. Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids. eLife 2023; 12:85135. [PMID: 36989136 PMCID: PMC10059687 DOI: 10.7554/elife.85135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. However, the posttranscriptional control of gene expression and protein abundance during human corticogenesis remains poorly understood. We addressed this issue by using human telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons and performed cell class and developmental stage-specific transcriptome and proteome analysis. Integrating the two datasets revealed modules of gene expression during human corticogenesis. Investigation of one such module uncovered mTOR-mediated regulation of translation of the 5'TOP element-enriched translation machinery in early progenitor cells. We show that in early progenitors partial inhibition of the translation of ribosomal genes prevents precocious translation of differentiation markers. Overall, our multiomics approach proposes novel posttranscriptional regulatory mechanisms crucial for the fidelity of cortical development.
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Affiliation(s)
- Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Philipp Trepte
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Natalie Sepke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | | | | | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Neurology, Medical University of Vienna, Vienna, Austria
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9
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Lam KHB, Faust K, Yin R, Fiala C, Diamandis P. The Brain Protein Atlas: A conglomerate of proteomics datasets of human neural tissue. Proteomics 2022; 22:e2200127. [PMID: 35971647 DOI: 10.1002/pmic.202200127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/09/2022] [Accepted: 08/03/2022] [Indexed: 11/06/2022]
Abstract
The human brain represents one of the most complex biological structures with significant spatiotemporal molecular plasticity occurring through early development, learning, aging, and disease. While much progress has been made in mapping its transcriptional architecture, more downstream phenotypic readouts are relatively scarce due to limitations with tissue heterogeneity and accessibility, as well as an inability to amplify protein species prior to global -OMICS analysis. To address some of these barriers, our group has recently focused on using mass-spectrometry workflows compatible with small amounts of formalin-fixed paraffin-embedded tissue samples. This has enabled exploration into spatiotemporal proteomic signatures of the brain and disease across otherwise inaccessible neurodevelopmental timepoints and anatomical niches. Given the similar theme and approaches, we introduce an integrated online portal, "The Brain Protein Atlas (BPA)" (www.brainproteinatlas.org), representing a public resource that allows users to access and explore these amalgamated datasets. Specifically, this portal contains a growing set of peer-reviewed mass-spectrometry-based proteomic datasets, including spatiotemporal profiles of human cerebral development, diffuse gliomas, clinically aggressive meningiomas, and a detailed anatomic atlas of glioblastoma. One barrier to entry in mass spectrometry-based proteomics data analysis is the steep learning curve required to extract biologically relevant data. BPA, therefore, includes several built-in analytical tools to generate relevant plots (e.g., volcano plots, heatmaps, boxplots, and scatter plots) and evaluate the spatiotemporal patterns of proteins of interest. Future iterations aim to expand available datasets, including those generated by the community at large, and analytical tools for exploration. Ultimately, BPA aims to improve knowledge dissemination of proteomic information across the neuroscience community in hopes of accelerating the biological understanding of the brain and various maladies.
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Affiliation(s)
- K H Brian Lam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, United States of America
| | - Kevin Faust
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Richard Yin
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Clare Fiala
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Phedias Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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10
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Generation of cell-type-specific proteomes of neurodevelopment from human cerebral organoids. STAR Protoc 2022; 3:101774. [PMID: 36313540 PMCID: PMC9597183 DOI: 10.1016/j.xpro.2022.101774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Characterization of cerebral organoids has been challenging due to their heterogeneous nature. Here, we optimized a protocol to streamline the generation of FACS-purified cell populations from human cerebral organoids for proteomic analysis with liquid chromatography tandem mass spectrometry (LC-MS/MS). We describe the procedures for enzymatic dissociation of organoids into single-cell suspension, the generation of cell-type-specific lysates, peptide extraction, and proteomic analysis. This generalizable approach can be used to study temporal and cell-type-specific protein dynamics in developing cerebral organoids. For complete details on the use and execution of this protocol, please refer to Melliou et al. (2022). A streamlined protocol covering human organoid cell sorting, lysis, and LC-MS/MS analysis Enzymatic dissociation of organoids into single-cell suspension for downstream analysis Generation of FACS-purified cell populations derived from cerebral organoids Label-free quantification of cell-type-specific populations within organoid cultures
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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11
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Melliou S, Sangster KT, Kao J, Zarrei M, Lam KHB, Howe J, Papaioannou MD, Tsang QPL, Borhani OA, Sajid RS, Bonnet C, Leheup B, Shannon P, Scherer SW, Stavropoulos DJ, Djuric U, Diamandis P. Regionally defined proteomic profiles of human cerebral tissue and organoids reveal conserved molecular modules of neurodevelopment. Cell Rep 2022; 39:110846. [PMID: 35613588 DOI: 10.1016/j.celrep.2022.110846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/01/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022] Open
Abstract
Cerebral organoids have emerged as robust models for neurodevelopmental and pathological processes, as well as a powerful discovery platform for less-characterized neurobiological programs. Toward this prospect, we leverage mass-spectrometry-based proteomics to molecularly profile precursor and neuronal compartments of both human-derived organoids and mid-gestation fetal brain tissue to define overlapping programs. Our analysis includes recovery of precursor-enriched transcriptional regulatory proteins not found to be differentially expressed in previous transcriptomic datasets. To highlight the discovery potential of this resource, we show that RUVBL2 is preferentially expressed in the SOX2-positive compartment of organoids and that chemical inactivation leads to precursor cell displacement and apoptosis. To explore clinicopathological correlates of this cytoarchitectural disruption, we interrogate clinical datasets and identify rare de novo genetic variants involving RUVBL2 in patients with neurodevelopmental impairments. Together, our findings demonstrate how cell-type-specific profiling of organoids can help nominate previously unappreciated genes in neurodevelopment and disease.
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Affiliation(s)
- Sofia Melliou
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kevin T Sangster
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Jennifer Kao
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mehdi Zarrei
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - K H Brian Lam
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jennifer Howe
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Queenie P L Tsang
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Okty Abbasi Borhani
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Rifat Shahriar Sajid
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Céline Bonnet
- Department of Clinical Genetics, Nancy University Hospital, Nancy, France
| | - Bruno Leheup
- Department of Clinical Genetics, Nancy University Hospital, Nancy, France
| | - Patrick Shannon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON M5G 1X5, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dimitri James Stavropoulos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ugljesa Djuric
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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12
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Dent A, Diamandis P. Integrating computational pathology and proteomics to address tumor heterogeneity. J Pathol 2022; 257:445-453. [DOI: 10.1002/path.5905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Anglin Dent
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario M5S 1A8 Canada
- Princess Margaret Cancer Center University Health Network, Toronto, Ontario, 610 University Avenue, M5G 2C1 Canada
| | - Phedias Diamandis
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario M5S 1A8 Canada
- Princess Margaret Cancer Center University Health Network, Toronto, Ontario, 610 University Avenue, M5G 2C1 Canada
- Laboratory Medicine Program University Health Network, 200 Elizabeth Street, Toronto, ON Toronto Ontario M5G 2C4 Canada
- Department of Medical Biophysics University of Toronto Toronto Ontario M5S 1A8 Canada
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13
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Di Fraia D, Anitei M, Mackmull MT, Parca L, Behrendt L, Andres-Pons A, Gilmour D, Helmer Citterich M, Kaether C, Beck M, Ori A. Conserved exchange of paralog proteins during neuronal differentiation. Life Sci Alliance 2022; 5:5/6/e202201397. [PMID: 35273078 PMCID: PMC8917807 DOI: 10.26508/lsa.202201397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
Paralog proteins promote fine tuning of protein complexes. The author identified a specific paralog signature conserved across vertebrate neuronal differentiation. Altering the ratio of SEC23 paralogs in the COPII complex influences neuronal differentiation in a opposite way. Gene duplication enables the emergence of new functions by lowering the evolutionary pressure that is posed on the ancestral genes. Previous studies have highlighted the role of specific paralog genes during cell differentiation, for example, in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological functions and whether the regulation of paralog genes is conserved across species. Here, we analyze the expression of paralogs across human tissues, during development and neuronal differentiation in fish, rodents and humans. Whereas ∼80% of paralog genes are co-regulated, a subset of paralogs shows divergent expression profiles, contributing to variability of protein complexes. We identify 78 substitutions of paralog pairs that occur during neuronal differentiation and are conserved across species. Among these, we highlight a substitution between the paralogs SEC23A and SEC23B members of the COPII complex. Altering the ratio between these two genes via RNAi-mediated knockdown is sufficient to influence neuron differentiation. We propose that remodeling of the vesicular transport system via paralog substitutions is an evolutionary conserved mechanism enabling neuronal differentiation.
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Affiliation(s)
| | - Mihaela Anitei
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Marie-Therese Mackmull
- Eidgenössische Technische Hochschule (ETH) Zürich Inst. f. Molekulare Systembiologie, Zürich, Switzerland
| | - Luca Parca
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Laura Behrendt
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | | | - Darren Gilmour
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | | | | | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
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14
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Melliou S, Sangster KT, Djuric U, Diamandis P. The promise of organoids for unraveling the proteomic landscape of the developing human brain. Mol Psychiatry 2022; 27:73-80. [PMID: 34703024 DOI: 10.1038/s41380-021-01354-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022]
Abstract
Cerebral organoids offer an opportunity to bioengineer experimental avatars of the developing human brain and have already begun garnering relevant insights into complex neurobiological processes and disease. Thus far, investigations into their heterogeneous cellular composition and developmental trajectories have been largely limited to transcriptional readouts. Recent advances in global proteomic technologies have enabled a new range of techniques to explore dynamic and non-overlapping spatiotemporal protein-level programs operational in these humanoid neural structures. Here we discuss these early protein-based studies and their potentially essential role for unraveling critical secreted paracrine signals, processes with poor proteogenomic correlations, or neurodevelopmental proteins requiring post-translational modification for biological activity. Integrating emerging proteomic tools with these faithful human-derived neurodevelopmental models could transform our understanding of complex neural cell phenotypes and neurobiological processes, not exclusively driven by transcriptional regulation. These insights, less accessible by exclusive RNA-based approaches, could reveal new knowledge into human brain development and guide improvements in neural regenerative medicine efforts.
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Affiliation(s)
- Sofia Melliou
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kevin T Sangster
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Ugljesa Djuric
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, M5G 2C4, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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15
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Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F, Mertins P. Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Nat Commun 2021; 12:3576. [PMID: 34117251 PMCID: PMC8196151 DOI: 10.1038/s41467-021-23855-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
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Affiliation(s)
- Corinna Friedrich
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), MDC graduate school, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Simon Schallenberg
- grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marieluise Kirchner
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Ziehm
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Niquet
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Christin Beier
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Jens Neudecker
- grid.6363.00000 0001 2218 4662Department of Surgery - Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.5252.00000 0004 1936 973XInstitute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philipp Mertins
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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16
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Matos B, Publicover SJ, Castro LFC, Esteves PJ, Fardilha M. Brain and testis: more alike than previously thought? Open Biol 2021; 11:200322. [PMID: 34062096 PMCID: PMC8169208 DOI: 10.1098/rsob.200322] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several strands of evidence indicate the presence of marked similarities between human brain and testis. Understanding these similarities and their implications has become a topic of interest among the scientific community. Indeed, an association of intelligence with some semen quality parameters has been reported and a relation between dysfunctions of the human brain and testis has also been evident. Numerous common molecular features are evident when these tissues are compared, which is reflected in the huge number of common proteins. At the functional level, human neurons and sperm share a number of characteristics, including the importance of the exocytotic process and the presence of similar receptors and signalling pathways. The common proteins are mainly involved in exocytosis, tissue development and neuron/brain-associated biological processes. With this analysis, we conclude that human brain and testis share several biochemical characteristics which, in addition to their involvement in the speciation process, could, at least in part, be responsible for the expression of a huge number of common proteins. Nonetheless, this is an underexplored topic, and the connection between these tissues needs to be clarified, which could help to understand the dysfunctions affecting brain and testis, as well as to develop improved therapeutic strategies.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Stephen J Publicover
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Luis Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- Department of Biology, FCUP-Faculty of Sciences, University of Porto, Porto, Portugal.,CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, Campus Agrico de Vairão, University of Porto, 4485-661 Vairão, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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17
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Goto-Silva L, Martins M, Murillo JR, Souza LRQ, Vitória G, Oliveira JT, Nascimento JM, Loiola EC, Nogueira FCS, Domont GB, Guimarães MZP, Tovar-Moll F, Rehen SK, Junqueira M. Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140656. [PMID: 33857633 DOI: 10.1016/j.bbapap.2021.140656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022]
Abstract
Axon guidance is required for the establishment of brain circuits. Whether much of the molecular basis of axon guidance is known from animal models, the molecular machinery coordinating axon growth and pathfinding in humans remains to be elucidated. The use of induced pluripotent stem cells (iPSC) from human donors has revolutionized in vitro studies of the human brain. iPSC can be differentiated into neuronal stem cells which can be used to generate neural tissue-like cultures, known as neurospheres, that reproduce, in many aspects, the cell types and molecules present in the brain. Here, we analyzed quantitative changes in the proteome of neurospheres during differentiation. Relative quantification was performed at early time points during differentiation using iTRAQ-based labeling and LC-MS/MS analysis. We identified 6438 proteins, from which 433 were downregulated and 479 were upregulated during differentiation. We show that human neurospheres have a molecular profile that correlates to the fetal brain. During differentiation, upregulated pathways are related to neuronal development and differentiation, cell adhesion, and axonal guidance whereas cell proliferation pathways were downregulated. We developed a functional assay to check for neurite outgrowth in neurospheres and confirmed that neurite outgrowth potential is increased after 10 days of differentiation and is enhanced by increasing cyclic AMP levels. The proteins identified here represent a resource to monitor neurosphere differentiation and coupled to the neurite outgrowth assay can be used to functionally explore neurological disorders using human neurospheres as a model.
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Affiliation(s)
- Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil
| | - Michele Martins
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos, 149 - bloco A 5° andar - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Jimmy Rodriguez Murillo
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos, 149 - bloco A 5° andar - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Leticia R Q Souza
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil
| | - Gabriela Vitória
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil
| | - Júlia T Oliveira
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil
| | - Juliana M Nascimento
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil; Department of Biosciences, Institute Science and Society, Federal University of São Paulo (Unifesp), Rua Silva Jardim, 136, Santos, SP 11015-020, Brazil
| | - Erick Correia Loiola
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil
| | - Fabio C S Nogueira
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos, 149 - bloco A 5° andar - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Gilberto B Domont
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos, 149 - bloco A 5° andar - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Marília Zaluar P Guimarães
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil; Institute of Biomedical Sciences, Federal University of Rio de Janeiro (UFRJ), Rua Manoel Frota Moreira - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Fernanda Tovar-Moll
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil
| | - Stevens Kastrup Rehen
- D'Or Institute for Research and Education (IDOR), Rua Diniz Cordeiro, 30 - Botafogo, Rio de Janeiro, RJ 22281-100, Brazil; Institute of Biomedical Sciences, Federal University of Rio de Janeiro (UFRJ), Rua Manoel Frota Moreira - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.
| | - Magno Junqueira
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro (UFRJ), Av. Athos da Silveira Ramos, 149 - bloco A 5° andar - Cidade Universitária da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil.
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18
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Rodrigues DC, Mufteev M, Weatheritt RJ, Djuric U, Ha KCH, Ross PJ, Wei W, Piekna A, Sartori MA, Byres L, Mok RSF, Zaslavsky K, Pasceri P, Diamandis P, Morris Q, Blencowe BJ, Ellis J. Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome. Cell Rep 2021; 30:4179-4196.e11. [PMID: 32209477 DOI: 10.1016/j.celrep.2020.02.107] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 12/30/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022] Open
Abstract
Regulation of translation during human development is poorly understood, and its dysregulation is associated with Rett syndrome (RTT). To discover shifts in mRNA ribosomal engagement (RE) during human neurodevelopment, we use parallel translating ribosome affinity purification sequencing (TRAP-seq) and RNA sequencing (RNA-seq) on control and RTT human induced pluripotent stem cells, neural progenitor cells, and cortical neurons. We find that 30% of transcribed genes are translationally regulated, including key gene sets (neurodevelopment, transcription and translation factors, and glycolysis). Approximately 35% of abundant intergenic long noncoding RNAs (lncRNAs) are ribosome engaged. Neurons translate mRNAs more efficiently and have longer 3' UTRs, and RE correlates with elements for RNA-binding proteins. RTT neurons have reduced global translation and compromised mTOR signaling, and >2,100 genes are translationally dysregulated. NEDD4L E3-ubiquitin ligase is translationally impaired, ubiquitinated protein levels are reduced, and protein targets accumulate in RTT neurons. Overall, the dynamic translatome in neurodevelopment is disturbed in RTT and provides insight into altered ubiquitination that may have therapeutic implications.
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Affiliation(s)
- Deivid C Rodrigues
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Marat Mufteev
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert J Weatheritt
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ugljesa Djuric
- Laboratory Medicine and Pathology Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Kevin C H Ha
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - P Joel Ross
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wei Wei
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Alina Piekna
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria A Sartori
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Loryn Byres
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rebecca S F Mok
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kirill Zaslavsky
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter Pasceri
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Phedias Diamandis
- Laboratory Medicine and Pathology Program, University Health Network, Toronto, ON M5G 2C4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada; Department of Pathology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - James Ellis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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19
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Rodrigues DC, Mufteev M, Ellis J. Quantification of mRNA ribosomal engagement in human neurons using parallel translating ribosome affinity purification (TRAP) and RNA sequencing. STAR Protoc 2021; 2:100229. [PMID: 33364619 PMCID: PMC7753199 DOI: 10.1016/j.xpro.2020.100229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Translation regulation is a fundamental step in gene regulation with critical roles in neurodevelopment. Here, we describe three protocols to calculate the ribosomal-engagement levels of the transcriptome from in vitro-derived neuronal cells. The protocols described here include enrichment of in vitro-generated pluripotent-derived neurons, immunoaffinity purification of ribosome-bound RNAs, and calculation of the fraction of ribosome-engaged mRNAs. The ribosome-engaged RNA fraction is a measurement of the translation activity, and differences between genotype or growth conditions report change in translational regulation. For complete details on the use and execution of this protocol, please refer to Rodrigues et al. (2020).
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Affiliation(s)
- Deivid Carvalho Rodrigues
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Corresponding author
| | - Marat Mufteev
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - James Ellis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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20
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Basu A, Ash PEA, Wolozin B, Emili A. Protein Interaction Network Biology in Neuroscience. Proteomics 2021; 21:e1900311. [PMID: 33314619 PMCID: PMC7900949 DOI: 10.1002/pmic.201900311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/27/2020] [Indexed: 01/04/2023]
Abstract
Mapping the intricate networks of cellular proteins in the human brain has the potential to address unsolved questions in molecular neuroscience, including the molecular basis of cognition, synaptic plasticity, long-term potentiation, learning, and memory. Perturbations to the protein-protein interaction networks (PPIN) present in neurons, glia, and other cell-types have been linked to multifactorial neurological disorders. Yet while knowledge of brain PPINs is steadily improving, the complexity and dynamic nature of the heterogeneous central nervous system in normal and disease contexts poses a formidable experimental challenge. In this review, the recent applications of functional proteomics and systems biology approaches to study PPINs central to normal neuronal function, during neurodevelopment, and in neurodegenerative disorders are summarized. How systematic PPIN analysis offers a unique mechanistic framework to explore intra- and inter-cellular functional modules governing neuronal activity and brain function is also discussed. Finally, future technological advancements needed to address outstanding questions facing neuroscience are outlined.
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Affiliation(s)
- Avik Basu
- Center for Network Systems BiologyBoston UniversityBostonMA02118USA
- Department of BiochemistryBoston University School of MedicineBostonMA02118USA
| | - Peter EA Ash
- Department of Pharmacology and Experimental TherapeuticsBoston University School of MedicineBostonMA02118USA
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental TherapeuticsBoston University School of MedicineBostonMA02118USA
| | - Andrew Emili
- Center for Network Systems BiologyBoston UniversityBostonMA02118USA
- Department of BiochemistryBoston University School of MedicineBostonMA02118USA
- Department of BiologyBoston UniversityBostonMA02215USA
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21
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Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
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22
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Di Meo A, Sohaei D, Batruch I, Alexandrou P, Prassas I, Diamandis EP. Proteomic Profiling of the Human Tissue and Biological Fluid Proteome. J Proteome Res 2020; 20:444-452. [PMID: 33107741 DOI: 10.1021/acs.jproteome.0c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In-depth analysis of the human genome sequence has led to the annotation of approximately 20,000 human protein-coding genes. Although mass spectrometry (MS)-based workflows have made a great headway in achieving near genome-wide coverage, an equivalent complete map of the human proteome remains elusive. Delineating the spatial distribution of all human proteins at the organ, tissue, and cellular level can offer insight into health and disease and represents an excellent reference for the discovery of biomarkers and therapeutic targets. Here, we performed label-free liquid chromatography coupled to tandem MS (LC-MS/MS) to profile the normal human proteome. In total, we analyzed 117 samples from 46 normal tissues and organs at autopsy. Our high-resolution MS approach allowed for the quantification of 10,438 unique proteins. In order to expand our coverage of the human proteome, we combined our previously published biological fluid proteomic data from healthy individuals. We considered data from seven biological fluids, including urine, cerebrospinal fluid, synovial fluid, seminal plasma, sweat, cervical vaginal fluid, and nipple aspirate fluid. Overall, we generated tandem mass spectra corresponding to 13,028 unique human protein-coding genes. Although our analysis did not accomplish complete proteome coverage, it should be an important complementary resource for future biomarker discovery.
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Affiliation(s)
- Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Dorsa Sohaei
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Pantelis Alexandrou
- Department of Forensic Medicine and Toxicology, School of Medicine, University of Athens, Athens 157 72, Greece
| | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto M5G 2C4, Canada
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23
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Malcolm J, Fiala C, Djuric U, Diamandis P. Can gliomas provide insights into promoting synaptogenesis? Mol Psychiatry 2020; 25:1920-1925. [PMID: 32457425 DOI: 10.1038/s41380-020-0795-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Jessica Malcolm
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Clare Fiala
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Ugljesa Djuric
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, 101 College Street, Toronto, ON, M5G 1L7, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, ON, M5G 2C4, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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24
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Varderidou-Minasian S, Verheijen BM, Schätzle P, Hoogenraad CC, Pasterkamp RJ, Altelaar M. Deciphering the Proteome Dynamics during Development of Neurons Derived from Induced Pluripotent Stem Cells. J Proteome Res 2020; 19:2391-2403. [PMID: 32357013 PMCID: PMC7281779 DOI: 10.1021/acs.jproteome.0c00070] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Neuronal development is a complex
multistep process that shapes
neurons by progressing though several typical stages, including axon
outgrowth, dendrite formation, and synaptogenesis. Knowledge of the
mechanisms of neuronal development is mostly derived from the study
of animal models. Advances in stem cell technology now enable us to
generate neurons from human induced pluripotent stem cells (iPSCs).
Here we provide a mass spectrometry-based quantitative proteomic signature
of human iPSC-derived neurons, i.e., iPSC-derived induced glutamatergic
neurons and iPSC-derived motor neurons, throughout neuronal differentiation.
Tandem mass tag 10-plex labeling was carried out to perform proteomic
profiling of cells at different time points. Our analysis reveals
significant expression changes (FDR < 0.001) of several key proteins
during the differentiation process, e.g., proteins involved in the
Wnt and Notch signaling pathways. Overall, our data provide a rich
resource of information on protein expression during human iPSC neuron
differentiation.
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Affiliation(s)
- Suzy Varderidou-Minasian
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bert M Verheijen
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Philipp Schätzle
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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25
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Ross PJ, Mok RSF, Smith BS, Rodrigues DC, Mufteev M, Scherer SW, Ellis J. Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells. Mol Autism 2020; 11:33. [PMID: 32398033 PMCID: PMC7218542 DOI: 10.1186/s13229-020-00333-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
Genetic factors contribute to the development of autism spectrum disorder (ASD), and although non-protein-coding regions of the genome are being increasingly implicated in ASD, the functional consequences of these variants remain largely uncharacterized. Induced pluripotent stem cells (iPSCs) enable the production of personalized neurons that are genetically matched to people with ASD and can therefore be used to directly test the effects of genomic variation on neuronal gene expression, synapse function, and connectivity. The combined use of human pluripotent stem cells with genome editing to introduce or correct specific variants has proved to be a powerful approach for exploring the functional consequences of ASD-associated variants in protein-coding genes and, more recently, long non-coding RNAs (lncRNAs). Here, we review recent studies that implicate lncRNAs, other non-coding mutations, and regulatory variants in ASD susceptibility. We also discuss experimental design considerations for using iPSCs and genome editing to study the role of the non-protein-coding genome in ASD.
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Affiliation(s)
- P Joel Ross
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Rebecca S F Mok
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Brandon S Smith
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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26
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Grenier K, Kao J, Diamandis P. Three-dimensional modeling of human neurodegeneration: brain organoids coming of age. Mol Psychiatry 2020; 25:254-274. [PMID: 31444473 DOI: 10.1038/s41380-019-0500-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/04/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023]
Abstract
The prevalence of dementia and other neurodegenerative diseases is rapidly increasing in aging nations. These relentless and progressive diseases remain largely without disease-modifying treatments despite decades of research and investments. It is becoming clear that traditional two-dimensional culture and animal model systems, while providing valuable insights on the major pathophysiological pathways associated with these diseases, have not translated well to patients' bedside. Fortunately, the advent of induced-pluripotent stem cells and three-dimensional cell culture now provide tools that are revolutionizing the study of human diseases by permitting analysis of patient-derived human tissue with non-invasive procedures. Specifically, brain organoids, self-organizing neural structures that can mimic human fetal brain development, have now been harnessed to develop alternative models of Alzheimer's disease, Parkinson's disease, motor neuron disease, and Frontotemporal dementia by recapitulating important neuropathological hallmarks found in these disorders. Despite these early breakthroughs, several limitations need to be vetted in brain organoid models in order to more faithfully match human tissue qualities, including relative tissue immaturity, lack of vascularization and incomplete cellular diversity found in this culture system. Here, we review current brain organoid protocols, the pathophysiology of neurodegenerative disorders, and early studies with brain organoid neurodegeneration models. We then discuss the multiple engineering and conceptual challenges surrounding their use and provide possible solutions and exciting avenues to be pursued. Altogether, we believe that brain organoids models, improved with classical and emerging molecular and analytic tools, have the potential to unravel the opaque pathophysiological mechanisms of neurodegeneration and devise novel treatments for an array of neurodegenerative disorders.
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Affiliation(s)
- Karl Grenier
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jennifer Kao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Laboratory Medicine Program, Department of Pathology, University Health Network, 200 Elizabeth Street, Toronto, ON, M5G 2C4, Canada
| | - Phedias Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Laboratory Medicine Program, Department of Pathology, University Health Network, 200 Elizabeth Street, Toronto, ON, M5G 2C4, Canada. .,Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, 101 College Street, Toronto, ON, M5G 1L7, Canada.
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27
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Ross PJ, Zhang WB, Mok RS, Zaslavsky K, Deneault E, D’Abate L, Rodrigues DC, Yuen RK, Faheem M, Mufteev M, Piekna A, Wei W, Pasceri P, Landa RJ, Nagy A, Varga B, Salter MW, Scherer SW, Ellis J. Synaptic Dysfunction in Human Neurons With Autism-Associated Deletions in PTCHD1-AS. Biol Psychiatry 2020; 87:139-149. [PMID: 31540669 PMCID: PMC6948145 DOI: 10.1016/j.biopsych.2019.07.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 06/23/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The Xp22.11 locus that encompasses PTCHD1, DDX53, and the long noncoding RNA PTCHD1-AS is frequently disrupted in male subjects with autism spectrum disorder (ASD), but the functional consequences of these genetic risk factors for ASD are unknown. METHODS To evaluate the functional consequences of PTCHD1 locus deletions, we generated induced pluripotent stem cells (iPSCs) from unaffected control subjects and 3 subjects with ASD with microdeletions affecting PTCHD1-AS/PTCHD1, PTCHD1-AS/DDX53, or PTCHD1-AS alone. Function of iPSC-derived cortical neurons was assessed using molecular approaches and electrophysiology. We also compiled novel and known genetic variants of the PTCHD1 locus to explore the roles of PTCHD1 and PTCHD1-AS in genetic risk for ASD and other neurodevelopmental disorders. Finally, genome editing was used to explore the functional consequences of deleting a single conserved exon of PTCHD1-AS. RESULTS iPSC-derived neurons from subjects with ASD exhibited reduced miniature excitatory postsynaptic current frequency and N-methyl-D-aspartate receptor hypofunction. We found that 35 ASD-associated deletions mapping to the PTCHD1 locus disrupted exons of PTCHD1-AS. We also found a novel ASD-associated deletion of PTCHD1-AS exon 3 and showed that exon 3 loss altered PTCHD1-AS splicing without affecting expression of the neighboring PTCHD1 coding gene. Finally, targeted disruption of PTCHD1-AS exon 3 recapitulated diminished miniature excitatory postsynaptic current frequency, supporting a role for the long noncoding RNA in the etiology of ASD. CONCLUSIONS Our genetic findings provide strong evidence that PTCHD1-AS deletions are risk factors for ASD, and human iPSC-derived neurons implicate these deletions in the neurophysiology of excitatory synapses and in ASD-associated synaptic impairment.
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Affiliation(s)
- P. Joel Ross
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,These authors contributed equally to this work,Present address: Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Wen-Bo Zhang
- Neuroscience & Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada,These authors contributed equally to this work
| | - Rebecca S.F. Mok
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Kirill Zaslavsky
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric Deneault
- Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lia D’Abate
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Deivid C. Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K.C. Yuen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Muhammad Faheem
- Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peter Pasceri
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebecca J. Landa
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD, USA,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andras Nagy
- Lunenfeld-Tenenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada,Institute of Medical Science and Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Balazs Varga
- Lunenfeld-Tenenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada,Present address: Wellcome Trust MRC Stem Cell Institute, University of Cambridge, Cambridge UK
| | - Michael W. Salter
- Neuroscience & Mental Health Program, The Hospital for Sick Children, Toronto, ON, Canada,Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Stephen W. Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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28
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Nascimento JM, Saia-Cereda VM, Sartore RC, da Costa RM, Schitine CS, Freitas HR, Murgu M, de Melo Reis RA, Rehen SK, Martins-de-Souza D. Human Cerebral Organoids and Fetal Brain Tissue Share Proteomic Similarities. Front Cell Dev Biol 2019; 7:303. [PMID: 31850342 PMCID: PMC6893972 DOI: 10.3389/fcell.2019.00303] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022] Open
Abstract
The limited access to functional human brain tissue has led to the development of stem cell-based alternative models. The differentiation of human pluripotent stem cells into cerebral organoids with self-organized architecture has created novel opportunities to study the early stages of the human cerebral formation. Here we applied state-of-the-art label-free shotgun proteomics to compare the proteome of stem cell-derived cerebral organoids to the human fetal brain. We identified 3,073 proteins associated with different developmental stages, from neural progenitors to neurons, astrocytes, or oligodendrocytes. The major protein groups are associated with neurogenesis, axon guidance, synaptogenesis, and cortical brain development. Glial cell proteins related to cell growth and maintenance, energy metabolism, cell communication, and signaling were also described. Our data support the variety of cells and neural network functional pathways observed within cell-derived cerebral organoids, confirming their usefulness as an alternative model. The characterization of brain organoid proteome is key to explore, in a dish, atypical and disrupted processes during brain development or neurodevelopmental, neurodegenerative, and neuropsychiatric diseases.
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Affiliation(s)
- Juliana Minardi Nascimento
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Verônica M Saia-Cereda
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafaela C Sartore
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil.,National Institute of Traumatology and Orthopedics, Rio de Janeiro, Brazil
| | | | - Clarissa S Schitine
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Hercules Rezende Freitas
- Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,School of Health Sciences, IBMR - University Center, Rio de Janeiro, Brazil
| | | | - Ricardo A de Melo Reis
- Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Stevens K Rehen
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil.,Institute of Biomedical Sciences, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.,Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil.,Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, Brazil
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29
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Djuric U, Lam KHB, Kao J, Batruch I, Jevtic S, Papaioannou MD, Diamandis P. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry. Mol Cell Proteomics 2019; 18:2029-2043. [PMID: 31353322 PMCID: PMC6773564 DOI: 10.1074/mcp.ra119.001521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/09/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular characterization of diffuse gliomas has thus far largely focused on genomic and transcriptomic interrogations. Here, we utilized mass spectrometry and overlay protein-level information onto genomically defined cohorts of diffuse gliomas to improve our downstream molecular understanding of these lethal malignancies. Bulk and macrodissected tissues were utilized to quantitate 5,496 unique proteins over three glioma cohorts subclassified largely based on their IDH and 1p19q codeletion status (IDH wild type (IDHwt), n = 7; IDH mutated (IDHmt), 1p19q non-codeleted, n = 7; IDH mutated, 1p19q-codeleted, n = 10). Clustering analysis highlighted proteome and systems-level pathway differences in gliomas according to IDH and 1p19q-codeletion status, including 287 differentially abundant proteins in macrodissection-enriched tumor specimens. IDHwt tumors were enriched for proteins involved in invasiveness and epithelial to mesenchymal transition (EMT), while IDHmt gliomas had increased abundances of proteins involved in mRNA splicing. Finally, these abundance changes were compared with IDH-matched GBM stem-like cells (GSCs) to better pinpoint protein patterns enriched in putative cellular drivers of gliomas. Using this integrative approach, we outline specific proteins involved in chloride transport (e.g. chloride intracellular channel 1, CLIC1) and EMT (e.g. procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, PLOD3, and serpin peptidase inhibitor clade H member 1, SERPINH1) that showed concordant IDH-status-dependent abundance differences in both primary tissue and purified GSC cultures. Given the downstream position proteins occupy in driving biology and phenotype, understanding the proteomic patterns operational in distinct glioma subtypes could help propose more specific, personalized, and effective targets for the management of patients with these aggressive malignancies.
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Affiliation(s)
- Ugljesa Djuric
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - K H Brian Lam
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jennifer Kao
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Stefan Jevtic
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada
| | - Michail-Dimitrios Papaioannou
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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30
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Molnár Z, Clowry GJ, Šestan N, Alzu'bi A, Bakken T, Hevner RF, Hüppi PS, Kostović I, Rakic P, Anton ES, Edwards D, Garcez P, Hoerder‐Suabedissen A, Kriegstein A. New insights into the development of the human cerebral cortex. J Anat 2019; 235:432-451. [PMID: 31373394 PMCID: PMC6704245 DOI: 10.1111/joa.13055] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The cerebral cortex constitutes more than half the volume of the human brain and is presumed to be responsible for the neuronal computations underlying complex phenomena, such as perception, thought, language, attention, episodic memory and voluntary movement. Rodent models are extremely valuable for the investigation of brain development, but cannot provide insight into aspects that are unique or highly derived in humans. Many human psychiatric and neurological conditions have developmental origins but cannot be studied adequately in animal models. The human cerebral cortex has some unique genetic, molecular, cellular and anatomical features, which need to be further explored. The Anatomical Society devoted its summer meeting to the topic of Human Brain Development in June 2018 to tackle these important issues. The meeting was organized by Gavin Clowry (Newcastle University) and Zoltán Molnár (University of Oxford), and held at St John's College, Oxford. The participants provided a broad overview of the structure of the human brain in the context of scaling relationships across the brains of mammals, conserved principles and recent changes in the human lineage. Speakers considered how neuronal progenitors diversified in human to generate an increasing variety of cortical neurons. The formation of the earliest cortical circuits of the earliest generated neurons in the subplate was discussed together with their involvement in neurodevelopmental pathologies. Gene expression networks and susceptibility genes associated to neurodevelopmental diseases were discussed and compared with the networks that can be identified in organoids developed from induced pluripotent stem cells that recapitulate some aspects of in vivo development. New views were discussed on the specification of glutamatergic pyramidal and γ-aminobutyric acid (GABA)ergic interneurons. With the advancement of various in vivo imaging methods, the histopathological observations can be now linked to in vivo normal conditions and to various diseases. Our review gives a general evaluation of the exciting new developments in these areas. The human cortex has a much enlarged association cortex with greater interconnectivity of cortical areas with each other and with an expanded thalamus. The human cortex has relative enlargement of the upper layers, enhanced diversity and function of inhibitory interneurons and a highly expanded transient subplate layer during development. Here we highlight recent studies that address how these differences emerge during development focusing on diverse facets of our evolution.
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Affiliation(s)
- Zoltán Molnár
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Gavin J. Clowry
- Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Nenad Šestan
- Department of Neuroscience, Yale University School of MedicineNew HavenCTUSA
| | - Ayman Alzu'bi
- Department of Basic Medical SciencesFaculty of MedicineYarmouk UniversityIrbidJordan
| | | | | | - Petra S. Hüppi
- Dept. de l'enfant et de l'adolescentHôpitaux Universitaires de GenèveGenèveSwitzerland
| | - Ivica Kostović
- Croatian Institute for Brain ResearchSchool of MedicineUniversity of ZagrebZagrebCroatia
| | - Pasko Rakic
- Department of Neuroscience, Yale University School of MedicineNew HavenCTUSA
| | - E. S. Anton
- UNC Neuroscience CenterDepartment of Cell and Molecular PhysiologyThe University of North Carolina School of MedicineChapel HillNCUSA
| | - David Edwards
- Centre for the Developing BrainBiomedical Engineering and Imaging Sciences,King's College LondonLondonUK
| | - Patricia Garcez
- Federal University of Rio de Janeiro, UFRJInstitute of Biomedical SciencesRio de JaneiroBrazil
| | | | - Arnold Kriegstein
- Department of NeurologyUniversity of California, San Francisco (UCSF)San FranciscoCAUSA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUCSFSan FranciscoCAUSA
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31
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SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons. Nat Neurosci 2019; 22:556-564. [PMID: 30911184 PMCID: PMC6475597 DOI: 10.1038/s41593-019-0365-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Heterozygous loss-of-function mutations in SHANK2 are associated with autism spectrum disorder (ASD). We generated cortical neurons from induced pluripotent stem cells (iPSC) derived from neurotypic and ASD-affected donors. We developed Sparse coculture for Connectivity (SparCon) assays where SHANK2 and control neurons were differentially labeled and sparsely seeded together on a lawn of unlabeled control neurons. We observed increases in dendrite length, dendrite complexity, synapse number, and frequency of spontaneous excitatory postsynaptic currents. These findings were phenocopied in gene-edited homozygous SHANK2 knockout cells and rescued by gene correction of an ASD SHANK2 mutation. Dendrite length increases were exacerbated by IGF1, TG003, or BDNF, and suppressed by DHPG treatment. The transcriptome in isogenic SHANK2 neurons was perturbed in synapse, plasticity, and neuronal morphogenesis gene sets and ASD gene modules, and activity-dependent dendrite extension was impaired. Our findings provide evidence for hyperconnectivity and altered transcriptome in SHANK2 neurons derived from ASD subjects.
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32
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Xie Q, Faust K, Van Ommeren R, Sheikh A, Djuric U, Diamandis P. Deep learning for image analysis: Personalizing medicine closer to the point of care. Crit Rev Clin Lab Sci 2019; 56:61-73. [PMID: 30628494 DOI: 10.1080/10408363.2018.1536111] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The precision-based revolution in medicine continues to demand stratification of patients into smaller and more personalized subgroups. While genomic technologies have largely led this movement, diagnostic results can take days to weeks to generate. Management at, or closer to, the point of care still heavily relies on the subjective qualitative interpretation of clinical and diagnostic imaging findings. New and emerging technological advances in artificial intelligence (AI) now appear poised to help bring objectivity and precision to these traditionally qualitative analytic tools. In particular, one specific form of AI, known as deep learning, is achieving expert-level disease classifications in many areas of diagnostic medicine dependent on visual and image-based findings. Here, we briefly review concepts of deep learning, and more specifically recent developments in convolutional neural networks (CNNs), to highlight their transformative potential in personalized medicine and, in particular, diagnostic histopathology. Understanding the opportunities and challenges of these quantitative machine-based decision support tools is critical to their widespread introduction into routine diagnostics.
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Affiliation(s)
- Quin Xie
- a Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Canada.,b MacFeeters-Hamilton Brain Tumour Centre , Princess Margaret Cancer Centre , Toronto , Canada
| | - Kevin Faust
- b MacFeeters-Hamilton Brain Tumour Centre , Princess Margaret Cancer Centre , Toronto , Canada.,c Department of Computer Science , University of Toronto , Toronto , Canada
| | - Randy Van Ommeren
- a Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Canada.,b MacFeeters-Hamilton Brain Tumour Centre , Princess Margaret Cancer Centre , Toronto , Canada
| | - Adeel Sheikh
- b MacFeeters-Hamilton Brain Tumour Centre , Princess Margaret Cancer Centre , Toronto , Canada
| | - Ugljesa Djuric
- b MacFeeters-Hamilton Brain Tumour Centre , Princess Margaret Cancer Centre , Toronto , Canada
| | - Phedias Diamandis
- a Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Canada.,b MacFeeters-Hamilton Brain Tumour Centre , Princess Margaret Cancer Centre , Toronto , Canada.,d Laboratory Medicine Program , University Health Network , Toronto , Canada
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33
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Fernández-Irigoyen J, Corrales F, Santamaría E. The Human Brain Proteome Project: Biological and Technological Challenges. Methods Mol Biol 2019; 2044:3-23. [PMID: 31432403 DOI: 10.1007/978-1-4939-9706-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory,, Proteored-ISCIII, CIBERehd, Madrid, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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34
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Liu X, Chang C, Han M, Yin R, Zhan Y, Li C, Ge C, Yu M, Yang X. PPIExp: A Web-Based Platform for Integration and Visualization of Protein-Protein Interaction Data and Spatiotemporal Proteomics Data. J Proteome Res 2018; 18:633-641. [PMID: 30565464 DOI: 10.1021/acs.jproteome.8b00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Integrating spatiotemporal proteomics data with protein-protein interaction (PPI) data can help researchers make an in-depth exploration of their proteins of interest in a dynamic manner. However, there is still a lack of proper tools for the biologists who usually have few programming skills to construct a PPI network for a protein list, visualize active PPI subnetworks, and then select key nodes for further study. We propose a web-based platform named PPIExp that can automatically construct a PPI network, perform clustering analysis according to protein abundances, and perform functional enrichment analysis. More importantly, it provides multiple effective visualization interfaces, such as the interface to display the PPI network map, the interface to display a dendrogram and heatmap for the clustering result, and the interface to display the expression pattern of a selected protein. To visualize the active PPI subnetworks in specific space or time, it provides buttons to highlight the differentially expressed proteins under each condition on the network map. Additionally, to help researchers determine which proteins are worth further attention, PPIExp provides extensive one-click interactive operations to map node centrality measures to node size on the network and highlight three types of proteins, that is, the proteins in an enriched functional term, the coexpressed proteins selected from the dendgrogram and heatmap, and the proteins input by users. PPIExp is available at http://www.fgvis.com/expressvis/PPIExp .
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Affiliation(s)
- Xian Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Mingfei Han
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Ronghua Yin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Yiqun Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Changyan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Changhui Ge
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Miao Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
| | - Xiaoming Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Life Omics , Beijing 102206 , P. R. China
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35
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Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018; 6:51. [PMID: 30544872 PMCID: PMC6313874 DOI: 10.3390/proteomes6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations. Despite these challenges, methods to improve proteomic yield and increase resolution continue to develop at a rapid rate. In this review, we highlight the importance of cell-type-specific proteomics in neuroscience and the technical difficulties associated. Furthermore, current progress and technological advancements in cell-type-specific proteomics research are discussed with an emphasis in neuroscience.
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Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
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36
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Breen MS, Ozcan S, Ramsey JM, Wang Z, Ma’ayan A, Rustogi N, Gottschalk MG, Webster MJ, Weickert CS, Buxbaum JD, Bahn S. Temporal proteomic profiling of postnatal human cortical development. Transl Psychiatry 2018; 8:267. [PMID: 30518843 PMCID: PMC6281671 DOI: 10.1038/s41398-018-0306-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/28/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Healthy cortical development depends on precise regulation of transcription and translation. However, the dynamics of how proteins are expressed, function and interact across postnatal human cortical development remain poorly understood. We surveyed the proteomic landscape of 69 dorsolateral prefrontal cortex samples across seven stages of postnatal life and integrated these data with paired transcriptome data. We detected 911 proteins by liquid chromatography-mass spectrometry, and 83 were significantly associated with postnatal age (FDR < 5%). Network analysis identified three modules of co-regulated proteins correlated with age, including two modules with increasing expression involved in gliogenesis and NADH metabolism and one neurogenesis-related module with decreasing expression throughout development. Integration with paired transcriptome data revealed that these age-related protein modules overlapped with RNA modules and displayed collinear developmental trajectories. Importantly, RNA expression profiles that are dynamically regulated throughout cortical development display tighter correlations with their respective translated protein expression compared to those RNA profiles that are not. Moreover, the correspondence between RNA and protein expression significantly decreases as a function of cortical aging, especially for genes involved in myelination and cytoskeleton organization. Finally, we used this data resource to elucidate the functional impact of genetic risk loci for intellectual disability, converging on gliogenesis, myelination and ATP-metabolism modules in the proteome and transcriptome. We share all data in an interactive, searchable companion website. Collectively, our findings reveal dynamic aspects of protein regulation and provide new insights into brain development, maturation, and disease.
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Affiliation(s)
- Michael S. Breen
- 0000 0001 0670 2351grid.59734.3cDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,0000 0001 0670 2351grid.59734.3cDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,0000 0001 0670 2351grid.59734.3cSeaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Sureyya Ozcan
- 0000000121885934grid.5335.0Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, UK
| | - Jordan M. Ramsey
- 0000000121885934grid.5335.0Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, UK
| | - Zichen Wang
- 0000 0001 0670 2351grid.59734.3cDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center, Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Avi Ma’ayan
- 0000 0001 0670 2351grid.59734.3cDepartment of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center, Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Nitin Rustogi
- 0000000121885934grid.5335.0Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, UK
| | - Michael G. Gottschalk
- 0000000121885934grid.5335.0Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, UK ,grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg Germany, Freiburg, Germany
| | - Maree J. Webster
- Stanley Medical Research Institute, Laboratory of Brain Research, Rockville, MD 20850 USA
| | - Cynthia Shannon Weickert
- 0000 0000 8900 8842grid.250407.4Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031 Australia ,0000 0004 4902 0432grid.1005.4School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052 Australia ,0000 0000 9159 4457grid.411023.5Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY 13210 USA
| | - Joseph D. Buxbaum
- 0000 0001 0670 2351grid.59734.3cDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,0000 0001 0670 2351grid.59734.3cDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,0000 0001 0670 2351grid.59734.3cSeaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Sabine Bahn
- 0000000121885934grid.5335.0Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, UK
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