1
|
Li S, Siengdee P, Hadlich F, Trakooljul N, Oster M, Reyer H, Wimmers K, Ponsuksili S. Dynamics of DNA methylation during osteogenic differentiation of porcine synovial membrane mesenchymal stem cells from two metabolically distinct breeds. Epigenetics 2024; 19:2375011. [PMID: 38956836 PMCID: PMC11225923 DOI: 10.1080/15592294.2024.2375011] [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: 01/12/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
Mesenchymal stem cells (MSCs), with the ability to differentiate into osteoblasts, adipocytes, or chondrocytes, show evidence that the donor cell's metabolic type influences the osteogenic process. Limited knowledge exists on DNA methylation changes during osteogenic differentiation and the impact of diverse donor genetic backgrounds on MSC differentiation. In this study, synovial membrane mesenchymal stem cells (SMSCs) from two pig breeds (Angeln Saddleback, AS; German Landrace, DL) with distinct metabolic phenotypes were isolated, and the methylation pattern of SMSCs during osteogenic induction was investigated. Results showed that most differentially methylated regions (DMRs) were hypomethylated in osteogenic-induced SMSC group. These DMRs were enriched with genes of different osteogenic signalling pathways at different time points including Wnt, ECM, TGFB and BMP signalling pathways. AS pigs consistently exhibited a higher number of hypermethylated DMRs than DL pigs, particularly during the peak of osteogenesis (day 21). Predicting transcription factor motifs in regions of DMRs linked to osteogenic processes and donor breeds revealed influential motifs, including KLF1, NFATC3, ZNF148, ASCL1, FOXI1, and KLF5. These findings contribute to understanding the pattern of methylation changes promoting osteogenic differentiation, emphasizing the substantial role of donor the metabolic type and epigenetic memory of different donors on SMSC differentiation.
Collapse
Affiliation(s)
- Shuaichen Li
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Puntita Siengdee
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, 906 Kamphaeng Phet 6 Road, Lak-Si, Bangkok, Thailand
| | - Frieder Hadlich
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Nares Trakooljul
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Michael Oster
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Henry Reyer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| |
Collapse
|
2
|
Bigdeli TB, Barr PB, Rajeevan N, Graham DP, Li Y, Meyers JL, Gorman BR, Peterson RE, Sayward F, Radhakrishnan K, Natarajan S, Nielsen DA, Wilkinson AV, Malhotra AK, Zhao H, Brophy M, Shi Y, O'Leary TJ, Gleason T, Przygodzki R, Pyarajan S, Muralidhar S, Gaziano JM, Huang GD, Concato J, Siever LJ, DeLisi LE, Kimbrel NA, Beckham JC, Swann AC, Kosten TR, Fanous AH, Aslan M, Harvey PD. Correlates of suicidal behaviors and genetic risk among United States veterans with schizophrenia or bipolar I disorder. Mol Psychiatry 2024:10.1038/s41380-024-02472-1. [PMID: 38491344 DOI: 10.1038/s41380-024-02472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 03/18/2024]
Abstract
Persons diagnosed with schizophrenia (SCZ) or bipolar I disorder (BPI) are at high risk for self-injurious behavior, suicidal ideation, and suicidal behaviors (SB). Characterizing associations between diagnosed health problems, prior pharmacological treatments, and polygenic scores (PGS) has potential to inform risk stratification. We examined self-reported SB and ideation using the Columbia Suicide Severity Rating Scale (C-SSRS) among 3,942 SCZ and 5,414 BPI patients receiving care within the Veterans Health Administration (VHA). These cross-sectional data were integrated with electronic health records (EHRs), and compared across lifetime diagnoses, treatment histories, follow-up screenings, and mortality data. PGS were constructed using available genomic data for related traits. Genome-wide association studies were performed to identify and prioritize specific loci. Only 20% of the veterans who reported SB had a corroborating ICD-9/10 EHR code. Among those without prior SB, more than 20% reported new-onset SB at follow-up. SB were associated with a range of additional clinical diagnoses, and with treatment with specific classes of psychotropic medications (e.g., antidepressants, antipsychotics, etc.). PGS for externalizing behaviors, smoking initiation, suicide attempt, and major depressive disorder were associated with SB. The GWAS for SB yielded no significant loci. Among individuals with a diagnosed mental illness, self-reported SB were strongly associated with clinical variables across several EHR domains. Analyses point to sequelae of substance-related and psychiatric comorbidities as strong correlates of prior and subsequent SB. Nonetheless, past SB was frequently not documented in health records, underscoring the value of regular screening with direct, in-person assessments, especially among high-risk individuals.
Collapse
Affiliation(s)
- Tim B Bigdeli
- VA New York Harbor Healthcare System, Brooklyn, NY, US.
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, US.
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US.
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US.
| | - Peter B Barr
- VA New York Harbor Healthcare System, Brooklyn, NY, US
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, US
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US
| | - Nallakkandi Rajeevan
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - David P Graham
- Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Yuli Li
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, US
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US
| | - Bryan R Gorman
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA, USA
| | - Roseann E Peterson
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, US
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, US
| | - Frederick Sayward
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Krishnan Radhakrishnan
- National Mental Health and Substance Use Policy Laboratory, Substance Abuse and Mental Health Services Administration, Rockville, MD, USA
| | | | - David A Nielsen
- Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Anna V Wilkinson
- Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Science, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anil K Malhotra
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, NY, USA
| | - Hongyu Zhao
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Mary Brophy
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Yunling Shi
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA, USA
| | - Timothy J O'Leary
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
| | - Theresa Gleason
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
| | - Ronald Przygodzki
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
| | - Saiju Pyarajan
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA, USA
| | | | - J Michael Gaziano
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA, USA
- Harvard University, Boston, MA, USA
| | - Grant D Huang
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
| | - John Concato
- Yale University School of Medicine, New Haven, CT, USA
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Larry J Siever
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - Lynn E DeLisi
- Department of Psychiatry, Cambridge Health Alliance, Cambridge, MA, USA
| | - Nathan A Kimbrel
- Durham VA Health Care System, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jean C Beckham
- Durham VA Health Care System, Durham, NC, USA
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Alan C Swann
- Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Thomas R Kosten
- Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Ayman H Fanous
- VA New York Harbor Healthcare System, Brooklyn, NY, US
- Department of Psychiatry, University of Arizona College of Medicine Phoenix, Phoenix, AZ, USA
| | - Mihaela Aslan
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Philip D Harvey
- Bruce W. Carter Miami Veterans Affairs (VA) Medical Center, Miami, FL, USA
- University of Miami School of Medicine, Miami, FL, USA
| |
Collapse
|
3
|
Pacot L, Girish M, Knight S, Spurlock G, Varghese V, Ye M, Thomas N, Pasmant E, Upadhyaya M. Correlation between large rearrangements and patient phenotypes in NF1 deletion syndrome: an update and review. BMC Med Genomics 2024; 17:73. [PMID: 38448973 PMCID: PMC10919053 DOI: 10.1186/s12920-024-01843-5] [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: 10/30/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
About 5-10% of neurofibromatosis type 1 (NF1) patients exhibit large genomic germline deletions that remove the NF1 gene and its flanking regions. The most frequent NF1 large deletion is 1.4 Mb, resulting from homologous recombination between two low copy repeats. This "type-1" deletion is associated with a severe clinical phenotype in NF1 patients, with several phenotypic manifestations including learning disability, a much earlier development of cutaneous neurofibromas, an increased tumour risk, and cardiovascular malformations. NF1 adjacent co-deleted genes could act as modifier loci for the specific clinical manifestations observed in deleted NF1 patients. Furthermore, other genetic modifiers (such as CNVs) not located at the NF1 locus could also modulate the phenotype observed in patients with large deletions. In this study, we analysed 22 NF1 deletion patients by genome-wide array-CGH with the aim (1) to correlate deletion length to observed phenotypic features and their severity in NF1 deletion syndrome, and (2) to identify whether the deletion phenotype could also be modulated by copy number variations elsewhere in the genome. We then review the role of co-deleted genes in the 1.4 Mb interval of type-1 deletions, and their possible implication in the main clinical features observed in this high-risk group of NF1 patients.
Collapse
Affiliation(s)
- Laurence Pacot
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Milind Girish
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Samantha Knight
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Vinod Varghese
- All Wales Medical Genomics Service, Cardiff, Great Britain
| | - Manuela Ye
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Nick Thomas
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eric Pasmant
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France.
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France.
| | - Meena Upadhyaya
- Division of Cancer and Genetics, Institute of Medical Genetics, Cardiff University, Heath Park, CF14 4XN, Cardiff, UK
| |
Collapse
|
4
|
Sun J, Noss S, Banerjee D, Das M, Girirajan S. Strategies for dissecting the complexity of neurodevelopmental disorders. Trends Genet 2024; 40:187-202. [PMID: 37949722 PMCID: PMC10872993 DOI: 10.1016/j.tig.2023.10.009] [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: 05/27/2023] [Revised: 09/20/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Neurodevelopmental disorders (NDDs) are associated with a wide range of clinical features, affecting multiple pathways involved in brain development and function. Recent advances in high-throughput sequencing have unveiled numerous genetic variants associated with NDDs, which further contribute to disease complexity and make it challenging to infer disease causation and underlying mechanisms. Herein, we review current strategies for dissecting the complexity of NDDs using model organisms, induced pluripotent stem cells, single-cell sequencing technologies, and massively parallel reporter assays. We further highlight single-cell CRISPR-based screening techniques that allow genomic investigation of cellular transcriptomes with high efficiency, accuracy, and throughput. Overall, we provide an integrated review of experimental approaches that can be applicable for investigating a broad range of complex disorders.
Collapse
Affiliation(s)
- Jiawan Sun
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Serena Noss
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Deepro Banerjee
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Maitreya Das
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Santhosh Girirajan
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
5
|
Abstract
Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.
Collapse
Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
6
|
Clairmont CD, Gell JJ, Lau CC. Pediatric Tumors as Disorders of Development: The Case for In Vitro Modeling Based on Human Stem Cells. Cancer Control 2024; 31:10732748241270564. [PMID: 39118322 PMCID: PMC11311176 DOI: 10.1177/10732748241270564] [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: 11/30/2023] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 08/10/2024] Open
Abstract
Despite improvements in patient outcomes, pediatric cancer remains a leading cause of non-accidental death in children. Recent genetic analysis of patients with pediatric cancers indicates an important role for both germline genetic predisposition and cancer-specific somatic driver mutations. Increasingly, evidence demonstrates that the developmental timepoint at which the cancer cell-of-origin transforms is critical to tumor identity and therapeutic response. Therefore, future therapeutic development would be bolstered by the use of disease models that faithfully recapitulate the genetic context, cell-of-origin, and developmental window of vulnerability in pediatric cancers. Human stem cells have the potential to incorporate all of these characteristics into a pediatric cancer model, while serving as a platform for rapid genetic and pharmacological testing. In this review, we describe how human stem cells have been used to model pediatric cancers and how these models compare to other pediatric cancer model modalities.
Collapse
Affiliation(s)
- Cullen D. Clairmont
- University of Connecticut School of Medicine, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joanna J. Gell
- University of Connecticut School of Medicine, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Connecticut Children’s Medical Center, Center for Cancer and Blood Disorders, Hartford, CT, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, UConn Health, Farmington, CT, USA
| | - Ching C. Lau
- University of Connecticut School of Medicine, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Connecticut Children’s Medical Center, Center for Cancer and Blood Disorders, Hartford, CT, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, UConn Health, Farmington, CT, USA
| |
Collapse
|
7
|
Wilson AF, Barakat R, Mu R, Karush LL, Gao Y, Hartigan KA, Chen JK, Shu H, Turner TN, Maloney SE, Mennerick SJ, Gutmann DH, Anastasaki C. A common single nucleotide variant in the cytokine receptor-like factor-3 (CRLF3) gene causes neuronal deficits in human and mouse cells. Hum Mol Genet 2023; 32:3342-3352. [PMID: 37712888 PMCID: PMC10695679 DOI: 10.1093/hmg/ddad155] [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: 06/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Single nucleotide variants in the general population are common genomic alterations, where the majority are presumed to be silent polymorphisms without known clinical significance. Using human induced pluripotent stem cell (hiPSC) cerebral organoid modeling of the 1.4 megabase Neurofibromatosis type 1 (NF1) deletion syndrome, we previously discovered that the cytokine receptor-like factor-3 (CRLF3) gene, which is co-deleted with the NF1 gene, functions as a major regulator of neuronal maturation. Moreover, children with NF1 and the CRLF3L389P variant have greater autism burden, suggesting that this gene might be important for neurologic function. To explore the functional consequences of this variant, we generated CRLF3L389P-mutant hiPSC lines and Crlf3L389P-mutant genetically engineered mice. While this variant does not impair protein expression, brain structure, or mouse behavior, CRLF3L389P-mutant human cerebral organoids and mouse brains exhibit impaired neuronal maturation and dendrite formation. In addition, Crlf3L389P-mutant mouse neurons have reduced dendrite lengths and branching, without any axonal deficits. Moreover, Crlf3L389P-mutant mouse hippocampal neurons have decreased firing rates and synaptic current amplitudes relative to wild type controls. Taken together, these findings establish the CRLF3L389P variant as functionally deleterious and suggest that it may be a neurodevelopmental disease modifier.
Collapse
Affiliation(s)
- Anna F Wilson
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Rasha Barakat
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Rui Mu
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Leah L Karush
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Yunqing Gao
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Kelly A Hartigan
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Ji-Kang Chen
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Hongjin Shu
- Department of Psychiatry, Washington University School of Medicine, Box 8134, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, Box 8232, 660 South Euclid Avenue, St. Louis, MO 63110, United States
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Box 8504, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, Box 8134, 660 South Euclid Avenue, St. Louis, MO 63110, United States
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Box 8504, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Steven J Mennerick
- Department of Psychiatry, Washington University School of Medicine, Box 8134, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Corina Anastasaki
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| |
Collapse
|
8
|
Kilpatrick S, Irwin C, Singh KK. Human pluripotent stem cell (hPSC) and organoid models of autism: opportunities and limitations. Transl Psychiatry 2023; 13:217. [PMID: 37344450 DOI: 10.1038/s41398-023-02510-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/09/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder caused by genetic or environmental perturbations during early development. Diagnoses are dependent on the identification of behavioral abnormalities that likely emerge well after the disorder is established, leaving critical developmental windows uncharacterized. This is further complicated by the incredible clinical and genetic heterogeneity of the disorder that is not captured in most mammalian models. In recent years, advancements in stem cell technology have created the opportunity to model ASD in a human context through the use of pluripotent stem cells (hPSCs), which can be used to generate 2D cellular models as well as 3D unguided- and region-specific neural organoids. These models produce profoundly intricate systems, capable of modeling the developing brain spatiotemporally to reproduce key developmental milestones throughout early development. When complemented with multi-omics, genome editing, and electrophysiology analysis, they can be used as a powerful tool to profile the neurobiological mechanisms underlying this complex disorder. In this review, we will explore the recent advancements in hPSC-based modeling, discuss present and future applications of the model to ASD research, and finally consider the limitations and future directions within the field to make this system more robust and broadly applicable.
Collapse
Affiliation(s)
- Savannah Kilpatrick
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada
| | - Courtney Irwin
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karun K Singh
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
9
|
Wang L, Owusu-Hammond C, Sievert D, Gleeson JG. Stem Cell-Based Organoid Models of Neurodevelopmental Disorders. Biol Psychiatry 2023; 93:622-631. [PMID: 36759260 PMCID: PMC10022535 DOI: 10.1016/j.biopsych.2023.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The past decade has seen an explosion in the identification of genetic causes of neurodevelopmental disorders, including Mendelian, de novo, and somatic factors. These discoveries provide opportunities to understand cellular and molecular mechanisms as well as potential gene-gene and gene-environment interactions to support novel therapies. Stem cell-based models, particularly human brain organoids, can capture disease-associated alleles in the context of the human genome, engineered to mirror disease-relevant aspects of cellular complexity and developmental timing. These models have brought key insights into neurodevelopmental disorders as diverse as microcephaly, autism, and focal epilepsy. However, intrinsic organoid-to-organoid variability, low levels of certain brain-resident cell types, and long culture times required to reach maturity can impede progress. Several recent advances incorporate specific morphogen gradients, mixtures of diverse brain cell types, and organoid engraftment into animal models. Together with nonhuman primate organoid comparisons, mechanisms of human neurodevelopmental disorders are emerging.
Collapse
Affiliation(s)
- Lu Wang
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - Charlotte Owusu-Hammond
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - David Sievert
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - Joseph G Gleeson
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California.
| |
Collapse
|
10
|
Bigdeli TB, Barr PB, Rajeevan N, Graham DP, Li Y, Meyers JL, Gorman BR, Peterson RE, Sayward F, Radhakrishnan K, Natarajan S, Nielsen DA, Wilkinson AV, Malhotra AK, Zhao H, Brophy M, Shi Y, O’Leary TJ, Gleason T, Przygodzki R, Pyarajan S, Muralidhar S, Gaziano JM, Huang GD, Concato J, Siever LJ, DeLisi LE, Kimbrel NA, Beckham JC, Swann AC, Kosten TR, Fanous AH, Aslan M, Harvey PD. Correlates of suicidal behaviors and genetic risk among United States veterans with schizophrenia or bipolar I disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.06.23286866. [PMID: 36945597 PMCID: PMC10029042 DOI: 10.1101/2023.03.06.23286866] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Objective Persons diagnosed with schizophrenia (SCZ) or bipolar I disorder (BPI) are at high risk for self-injurious behavior, suicidal ideation, and suicidal behaviors (SB). Characterizing associations between diagnosed mental and physical health problems, prior pharmacological treatments, and aggregate genetic factors has potential to inform risk stratification and mitigation strategies. Methods In this study of 3,942 SCZ and 5,414 BPI patients receiving VA care, self-reported SB and ideation were assessed using the Columbia Suicide Severity Rating Scale (C-SSRS). These cross-sectional data were integrated with electronic health records (EHR), and compared by lifetime diagnoses, treatment histories, follow-up screenings, and mortality data. Polygenic scores (PGS) for traits related to psychiatric disorders, substance use, and cognition were constructed using available genomic data, and exploratory genome-wide association studies were performed to identify and prioritize specific loci. Results Only 20% of veterans who self-reported SB had a corroborating ICD-9/10 code in their EHR; and among those who denied prior behaviors, more than 20% reported new-onset SB at follow-up. SB were associated with a range of psychiatric and non-psychiatric diagnoses, and with treatment with specific classes of psychotropic medications (e.g., antidepressants, antipsychotics, etc.). PGS for externalizing behaviors, smoking, suicide attempt, and major depressive disorder were also associated with attempt and ideation. Conclusions Among individuals with a diagnosed mental illness, a GWAS for SB did not yield any significant loci. Self-reported SB were strongly associated with clinical variables across several EHR domains. Overall, clinical and polygenic analyses point to sequelae of substance-use related behaviors and other psychiatric comorbidities as strong correlates of prior and subsequent SB. Nonetheless, past SB was frequently not documented in clinical settings, underscoring the value of regular screening based on direct, in-person assessments, especially among high-risk individuals.
Collapse
Affiliation(s)
- Tim B. Bigdeli
- VA New York Harbor Healthcare System, Brooklyn, NY
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Peter B. Barr
- VA New York Harbor Healthcare System, Brooklyn, NY
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Nallakkandi Rajeevan
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT
- Yale University School of Medicine, New Haven, CT
| | - David P. Graham
- Michael E. DeBakey VA Medical Center, Houston, TX
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX
| | - Yuli Li
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT
- Yale University School of Medicine, New Haven, CT
| | - Jacquelyn L. Meyers
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Bryan R. Gorman
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA
| | - Roseann E. Peterson
- VA New York Harbor Healthcare System, Brooklyn, NY
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA
| | - Frederick Sayward
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT
- Yale University School of Medicine, New Haven, CT
| | - Krishnan Radhakrishnan
- National Mental Health and Substance Use Policy Laboratory, Substance Abuse and Mental Health Services Administration, Rockville, MD
| | | | - David A. Nielsen
- Michael E. DeBakey VA Medical Center, Houston, TX
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX
| | - Anna V. Wilkinson
- Michael E. DeBakey VA Medical Center, Houston, TX
- National Mental Health and Substance Use Policy Laboratory, Substance Abuse and Mental Health Services Administration, Rockville, MD
| | - Anil K. Malhotra
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY
- Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, NY
| | - Hongyu Zhao
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT
- Yale University School of Medicine, New Haven, CT
| | - Mary Brophy
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA
- Boston University School of Medicine, Boston, MA
| | - Yunling Shi
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA
| | - Timothy J. O’Leary
- Office of Research and Development, Veterans Health Administration, Washington, DC
| | - Theresa Gleason
- Office of Research and Development, Veterans Health Administration, Washington, DC
| | - Ronald Przygodzki
- Office of Research and Development, Veterans Health Administration, Washington, DC
| | - Saiju Pyarajan
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA
| | - Sumitra Muralidhar
- Office of Research and Development, Veterans Health Administration, Washington, DC
| | - J. Michael Gaziano
- Massachusetts Area Veterans Epidemiology, Research and Information Center (MAVERIC), Jamaica Plain, MA
- Harvard University, Boston, MA
| | | | | | - Grant D. Huang
- Office of Research and Development, Veterans Health Administration, Washington, DC
| | - John Concato
- Yale University School of Medicine, New Haven, CT
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Larry J. Siever
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY
- James J. Peters Veterans Affairs Medical Center, Bronx, NY
| | - Lynn E. DeLisi
- Department of Psychiatry, Cambridge Health Alliance, Cambridge, MA
| | - Nathan A. Kimbrel
- Durham VA Health Care System, Durham, NC
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC
| | - Jean C. Beckham
- Durham VA Health Care System, Durham, NC
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC
| | - Alan C. Swann
- Michael E. DeBakey VA Medical Center, Houston, TX
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX
| | - Thomas R. Kosten
- Michael E. DeBakey VA Medical Center, Houston, TX
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX
- Departments of Neuroscience, Pharmacology, and Immunology and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Ayman H. Fanous
- VA New York Harbor Healthcare System, Brooklyn, NY
- Department of Psychiatry, University of Arizona College of Medicine Phoenix, Phoenix, AZ
| | - Mihaela Aslan
- Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT
- Yale University School of Medicine, New Haven, CT
| | - Philip D. Harvey
- Bruce W. Carter Miami Veterans Affairs (VA) Medical Center, Miami, FL
- University of Miami School of Medicine, Miami, FL
| |
Collapse
|
11
|
Modeling Autism Spectrum Disorders with Induced Pluripotent Stem Cell-Derived Brain Organoids. Biomolecules 2023; 13:biom13020260. [PMID: 36830629 PMCID: PMC9953447 DOI: 10.3390/biom13020260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Autism spectrum disorders (ASD) are a group of complex neurodevelopmental disorders that affect communication and social interactions and present with restricted interests and repetitive behavior patterns. The susceptibility to ASD is strongly influenced by genetic/heritable factors; however, there is still a large gap in understanding the cellular and molecular mechanisms underlying the neurobiology of ASD. Significant progress has been made in identifying ASD risk genes and the possible convergent pathways regulated by these gene networks during development. The breakthrough of cellular reprogramming technology has allowed the generation of induced pluripotent stem cells (iPSCs) from individuals with syndromic and idiopathic ASD, providing patient-specific cell models for mechanistic studies. In the past decade, protocols for developing brain organoids from these cells have been established, leading to significant advances in the in vitro reproducibility of the early steps of human brain development. Here, we reviewed the most relevant literature regarding the application of brain organoids to the study of ASD, providing the current state of the art, and discussing the impact of such models on the field, limitations, and opportunities for future development.
Collapse
|
12
|
Knorr DY, Rodriguez Polo I, Pies HS, Schwedhelm-Domeyer N, Pauls S, Behr R, Heinrich R. The cytokine receptor CRLF3 is a human neuroprotective EV-3 (Epo) receptor. Front Mol Neurosci 2023; 16:1154509. [PMID: 37168680 PMCID: PMC10165946 DOI: 10.3389/fnmol.2023.1154509] [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: 01/30/2023] [Accepted: 03/15/2023] [Indexed: 05/13/2023] Open
Abstract
The evolutionary conserved orphan cytokine receptor-like factor 3 (CRLF3) has been implicated in human disease, vertebrate hematopoiesis and insect neuroprotection. While its specific functions are elusive, experimental evidence points toward a general role in cell homeostasis. Erythropoietin (Epo) is a major regulator of vertebrate hematopoiesis and a general cytoprotective cytokine. Erythropoietic functions mediated by classical Epo receptor are understood in great detail whereas Epo-mediated cytoprotective mechanisms are more complex due to involvement of additional Epo receptors and a non-erythropoietic splice variant with selectivity for certain receptors. In the present study, we show that the human CRLF3 mediates neuroprotection upon activation with the natural Epo splice variant EV-3. We generated CRLF3 knock-out iPSC lines and differentiated them toward the neuronal lineage. While apoptotic death of rotenone-challenged wild type iPSC-derived neurons was prevented by EV-3, EV-3-mediated neuroprotection was absent in CRLF3 knock-out neurons. Rotenone-induced apoptosis and EV-3-mediated neuroprotection were associated with differential expression of pro-and anti-apoptotic genes. Our data characterize human CRLF3 as a receptor involved in Epo-mediated neuroprotection and identify CRLF3 as the first known receptor for EV-3.
Collapse
Affiliation(s)
- Debbra Y. Knorr
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August University Göttingen, Göttingen, Germany
- *Correspondence: Debbra Y. Knorr,
| | - Ignacio Rodriguez Polo
- Department of Developmental Biology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
- Research Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
- Developmental Models Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Hanna S. Pies
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August University Göttingen, Göttingen, Germany
| | - Nicola Schwedhelm-Domeyer
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August University Göttingen, Göttingen, Germany
| | - Stephanie Pauls
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August University Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Research Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Ralf Heinrich
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August University Göttingen, Göttingen, Germany
- Ralf Heinrich,
| |
Collapse
|
13
|
Identifying Genes that Affect Differentiation of Human Neural Stem Cells and Myelination of Mature Oligodendrocytes. Cell Mol Neurobiol 2022:10.1007/s10571-022-01313-5. [DOI: 10.1007/s10571-022-01313-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
AbstractHuman neural stem cells (NSCs) are self-renewing, multipotent cells of the central nervous system (CNS). They are characterized by their ability to differentiate into a range of cells, including oligodendrocytes (OLs), neurons, and astrocytes, depending on exogenous stimuli. An efficient and easy directional differentiation method was developed for obtaining large quantities of high-quality of human OL progenitor cells (OPCs) and OLs from NSCs. RNA sequencing, immunofluorescence staining, flow cytometry, western blot, label-free proteomic sequencing, and qPCR were performed in OL lines differentiated from NSC lines. The changes in the positive rate of typical proteins were analyzed expressed by NSCs, neurons, astrocytes, OPCs, and OLs. We assessed Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of differentially expressed (DE) messenger RNAs (mRNAs) related to the differentiation of NSCs and the maturation of OLs. The percentage of NSCs differentiated into neurons, astrocytes, and OLs was 82.13%, 80.19%, and 90.15%, respectively. We found that nestin, PAX6, Musashi, and vimentin were highly expressed in NSCs; PDGFR-α, A2B5, NG2, OLIG2, SOX10, and NKX2-2 were highly expressed in OPCs; and CNP, GALC, PLP1, and MBP were highly expressed in OLs. RNA sequencing, western blot and qPCR revealed that ERBB4 and SORL1 gradually increased during NSC–OL differentiation. In conclusion, NSCs can differentiate into neurons, astrocytes, and OLs efficiently. PDGFR-α, APC, ID4, PLLP, and other markers were related to NSC differentiation and OL maturation. Moreover, we refined a screening method for ERBB4 and SORL1, which may underlie NSC differentiation and OL maturation.
Graphical Abstract
Potential unreported genes and proteins may regulate differentiation of human neural stem cells into oligodendrocyte lineage. Neural stem cells (NSCs) can differentiate into neurons, astrocytes, and oligodendrocyte (OLs) efficiently. By analyzing the DE mRNAs and proteins of NSCs and OLs lineage, we could identify reported markers and unreported markers of ERBB4 and SORL1 that may underlie regulate NSC differentiation and OL maturation.
Collapse
|
14
|
Abstract
The current understanding of neurological diseases is derived mostly from direct analysis of patients and from animal models of disease. However, most patient studies do not capture the earliest stages of disease development and offer limited opportunities for experimental intervention, so rarely yield complete mechanistic insights. The use of animal models relies on evolutionary conservation of pathways involved in disease and is limited by an inability to recreate human-specific processes. In vitro models that are derived from human pluripotent stem cells cultured in 3D have emerged as a new model system that could bridge the gap between patient studies and animal models. In this Review, we summarize how such organoid models can complement classical approaches to accelerate neurological research. We describe our current understanding of neurodevelopment and how this process differs between humans and other animals, making human-derived models of disease essential. We discuss different methodologies for producing organoids and how organoids can be and have been used to model neurological disorders, including microcephaly, Zika virus infection, Alzheimer disease and other neurodegenerative disorders, and neurodevelopmental diseases, such as Timothy syndrome, Angelman syndrome and tuberous sclerosis. We also discuss the current limitations of organoid models and outline how organoids can be used to revolutionize research into the human brain and neurological diseases. In this Review, Eichmüller and Knoblich discuss how human brain organoids can recapitulate the unique processes that occur in human brain development and how they can complement classical approaches to revolutionize research into neurological diseases. Development of the human brain involves unique processes that are relevant to neurological disease but cannot be studied in animal models, so alternative model systems are required. Organoids are 3D human cell culture models that originate from pluripotent stem cells and recapitulate the hallmarks of human neurodevelopment, enabling studies of human brain development in vitro. Specific mutations can be introduced into organoids to study their effects on neurodevelopment; combined with high-throughput screening methods, this approach can determine the disease relevance of mutations in human tissue. To study specific diseases, brain organoids can be generated from induced pluripotent stem cells from individual patients, thereby preserving the specific genetic background of the individual and generating an insightful model. Through recapitulation of previously inaccessible periods of human brain development, brain organoids have enabled identification of novel mechanisms that underlie neurodevelopmental, neurodegenerative and infectious diseases. Combining organoids, patient research and animal models enables us to take full advantage of each of these systems and will provide unprecedented insights into neurodevelopment and neurological diseases.
Collapse
|
15
|
Taznin T, Perera K, Gibert Y, Ward AC, Liongue C. Cytokine Receptor-Like Factor 3 (CRLF3) Contributes to Early Zebrafish Hematopoiesis. Front Immunol 2022; 13:910428. [PMID: 35795682 PMCID: PMC9251315 DOI: 10.3389/fimmu.2022.910428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022] Open
Abstract
Cytokine receptor-like factor 3 (CRLF3) is an ancient protein conserved across metazoans that contains an archetypal cytokine receptor homology domain (CHD). This domain is found in cytokine receptors present in bilateria, including higher vertebrates, that play key roles in a variety of developmental and homeostatic processes, particularly relating to blood and immune cells. However, understanding of CRLF3 itself remains very limited. This study aimed to investigate this evolutionarily significant protein by studying its embryonic expression and function in early development, particularly of blood and immune cells, using zebrafish as a model. Expression of crlf3 was identified in mesoderm-derived tissues in early zebrafish embryos, including the somitic mesoderm and both anterior and posterior lateral plate mesoderm. Later expression was observed in the thymus, brain, retina and exocrine pancreas. Zebrafish crlf3 mutants generated by genome editing technology exhibited a significant reduction in primitive hematopoiesis and early definitive hematopoiesis, with decreased early progenitors impacting on multiple lineages. No other obvious phenotypes were observed in the crlf3 mutants.
Collapse
Affiliation(s)
- Tarannum Taznin
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | | | - Yann Gibert
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- *Correspondence: Clifford Liongue,
| |
Collapse
|
16
|
Tang XY, Wu S, Wang D, Chu C, Hong Y, Tao M, Hu H, Xu M, Guo X, Liu Y. Human organoids in basic research and clinical applications. Signal Transduct Target Ther 2022; 7:168. [PMID: 35610212 PMCID: PMC9127490 DOI: 10.1038/s41392-022-01024-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/26/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
Organoids are three-dimensional (3D) miniature structures cultured in vitro produced from either human pluripotent stem cells (hPSCs) or adult stem cells (AdSCs) derived from healthy individuals or patients that recapitulate the cellular heterogeneity, structure, and functions of human organs. The advent of human 3D organoid systems is now possible to allow remarkably detailed observation of stem cell morphogens, maintenance and differentiation resemble primary tissues, enhancing the potential to study both human physiology and developmental stage. As they are similar to their original organs and carry human genetic information, organoids derived from patient hold great promise for biomedical research and preclinical drug testing and is currently used for personalized, regenerative medicine, gene repair and transplantation therapy. In recent decades, researchers have succeeded in generating various types of organoids mimicking in vivo organs. Herein, we provide an update on current in vitro differentiation technologies of brain, retinal, kidney, liver, lung, gastrointestinal, cardiac, vascularized and multi-lineage organoids, discuss the differences between PSC- and AdSC-derived organoids, summarize the potential applications of stem cell-derived organoids systems in the laboratory and clinic, and outline the current challenges for the application of organoids, which would deepen the understanding of mechanisms of human development and enhance further utility of organoids in basic research and clinical studies.
Collapse
Affiliation(s)
- Xiao-Yan Tang
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Shanshan Wu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Da Wang
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Chu Chu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Yuan Hong
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Mengdan Tao
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Hao Hu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Min Xu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China
| | - Xing Guo
- Department of Neurobiology, School of Basic Medical Sciences; Nanjing Medical University, Nanjing, China.
| | - Yan Liu
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy; State Key Laboratory of Reproductive Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine; Nanjing Medical University, Nanjing, China.
| |
Collapse
|
17
|
Villa CE, Cheroni C, Dotter CP, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli MR, Lyudchik J, Sommer C, Gabitto M, Danzl JG, Testa G, Novarino G. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Rep 2022; 39:110615. [PMID: 35385734 DOI: 10.1016/j.celrep.2022.110615] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/18/2021] [Accepted: 03/13/2022] [Indexed: 12/13/2022] Open
Abstract
Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients' macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.
Collapse
Affiliation(s)
- Carlo Emanuele Villa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Christoph P Dotter
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Alejandro López-Tóbon
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Bárbara Oliveira
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Roberto Sacco
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Aysan Çerağ Yahya
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Jasmin Morandell
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Michele Gabriele
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy
| | - Mojtaba R Tavakoli
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Julia Lyudchik
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Christoph Sommer
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | | | - Johann G Danzl
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, 20139 Milan, Italy; Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.
| | - Gaia Novarino
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria.
| |
Collapse
|
18
|
Kehrer-Sawatzki H, Bäzner U, Krämer J, Lewerenz J, Pfeiffer C. Das NF1-Mikrodeletions-Syndrom: Die frühzeitige genetische Diagnose erleichtert den Umgang mit einer klinisch definierten Erkrankung. J Dtsch Dermatol Ges 2022; 20:273-278. [PMID: 35304941 DOI: 10.1111/ddg.14707_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/29/2021] [Indexed: 12/01/2022]
Abstract
Neurofibromatose Typ-1 (NF1) ist ein Genodermatose, die häufig in der Dermatologie behandelt wird. Bei vielen Patienten mit NF1 wird die Diagnose aufgrund klinischer Merkmale erstellt wie Café-au-Lait-Flecken, Freckling und plexiformen Neurofibromen, die schon während der frühen Kindheit auftreten können. Später im Leben sind oft kutane Neurofibrome weitere wichtige diagnostische Merkmale. Die NF1 ist durch ausgeprägte klinische Variabilität und eine breite Heterogenität der NF1-Genmutationen charakterisiert, was Genotyp/Phänotyp-Korrelationen erschwert. Wichtige Ausnahmen sind NF1-Mikrodeletionen, die bei 5-11 % aller NF1-Patienten auftreten. Patienten mit NF1-Mikrodeletionen zeigen häufig spezifische Merkmale wie Gesichtsdysmorphien und sind von großer Statur. Zudem sind früh auftretende kutane und subkutane Neurofibrome, schwere Entwicklungsverzögerungen in multiplen Bereichen sowie kognitive Einschränkungen pathognomonisch für das NF1-Mikrodeletions-Syndrom. Darüber hinaus sind NF1-Mikrodeletionen mit einem Risiko für maligne periphere Nervenscheidentumoren assoziiert, das etwa zweifach höher ist als bei intragenischen NF1-Mutationen. Die schweren klinischen Manifestationen bei Patienten mit NF1-Mikrodeletionen machen eine frühe multidisziplinäre klinische Betreuung und häufige Tumor-Überwachung der Patienten notwendig. Wenn bei einem Patienten Red-Flag-Symptome für das NF1-Mikrodeletions-Syndrom auftreten, ist eine frühzeitige genetische Untersuchung notwendig, um eine NF1-Mikrodeletion zu bestätigen oder auszuschließen.
Collapse
Affiliation(s)
| | - Ute Bäzner
- Klinik für Neurochirurgie, Bezirkskrankenhaus Günzburg, und Klinik für Neurochirurgie, Universitätsklinikum Ulm
| | - Johannes Krämer
- Klinik für Kinder- und Jugendmedizin, Sektion Sozialpädiatrisches Zentrum und Pädiatrische Neurologie/Stoffwechsel, Universitätsklinikum Ulm
| | | | | |
Collapse
|
19
|
Anastasaki C, Wilson AF, Chen AS, Wegscheid ML, Gutmann DH. Generation of human induced pluripotent stem cell-derived cerebral organoids for cellular and molecular characterization. STAR Protoc 2022; 3:101173. [PMID: 35199037 PMCID: PMC8844852 DOI: 10.1016/j.xpro.2022.101173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived cerebral organoids (COs) can serve as an in vitro model for studying normal and pathologic human brain development. Here, we optimized existing protocols to streamline the generation of forebrain COs from hiPSCs. We employ these COs to define the impact of disease-causing mutations on cell fate, differentiation, maturation, and morphology relevant to neurodevelopmental disorders. Although limited to forebrain CO identity, this schema requires minimal external interference and is amenable to low-throughput biochemical assays. For complete details on the use and execution of this profile, please refer to Anastasaki et al. (2020) and Wegscheid et al. (2021).
Collapse
Affiliation(s)
- Corina Anastasaki
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna F. Wilson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexander S. Chen
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michelle L. Wegscheid
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David H. Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
20
|
Kehrer-Sawatzki H, Bäzner U, Krämer J, Lewerenz J, Pfeiffer C. The NF1 microdeletion syndrome: early genetic diagnosis facilitates the management of a clinically defined disease. J Dtsch Dermatol Ges 2022; 20:273-277. [PMID: 35246941 DOI: 10.1111/ddg.14707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Neurofibromatosis type-1 (NF1) is a genodermatosis frequently encountered in general dermatology. In many patients, the diagnosis of NF1 is made clinically based on the presence of café-au-lait macules and skinfold freckling, as well as plexiform neurofibromas detectable during early childhood. Later in life, cutaneous neurofibromas often represent important diagnostic features. NF1 is characterized by extreme clinical variability and a broad heterogeneity of NF1 gene mutations which impede genotype/phenotype correlations. Notable exceptions are NF1 microdeletions observed in 5-11 % of all NF1 patients. Patients with NF1 microdeletions frequently exhibit facial dysmorphic features and a tall stature as rather specific clinical signs. Furthermore, cutaneous and subcutaneous neurofibromas present at an early age, severe global developmental delay and cognitive disability are pathognomonic for the "NF1 microdeletion syndrome". Importantly, NF1 microdeletions are associated with an approximately twofold higher risk for malignant peripheral nerve sheath tumors than intragenic NF1 gene mutations. The severe clinical manifestations of patients with NF1 microdeletions require early multidisciplinary clinical care and frequent tumor surveillance. Therefore, when red flag features for the "NF1 microdeletion syndrome" are present in a patient, genetic testing is necessary to confirm or exclude an NF1 microdeletion.
Collapse
Affiliation(s)
| | - Ute Bäzner
- Department of Neurosurgery, Ulm University Medical Center, Günzburg, Germany
| | - Johannes Krämer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Jan Lewerenz
- Department of Neurology, Ulm University Medical Center, Ulm, Germany
| | - Christiane Pfeiffer
- Department of Dermatology and Allergology, Ulm University Medical Center, Ulm, Germany
| |
Collapse
|
21
|
Mo J, Moye SL, McKay RM, Le LQ. Neurofibromin and suppression of tumorigenesis: beyond the GAP. Oncogene 2022; 41:1235-1251. [PMID: 35066574 PMCID: PMC9063229 DOI: 10.1038/s41388-021-02156-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/01/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disease and one of the most common inherited tumor predisposition syndromes, affecting 1 in 3000 individuals worldwide. The NF1 gene encodes neurofibromin, a large protein with RAS GTP-ase activating (RAS-GAP) activity, and loss of NF1 results in increased RAS signaling. Neurofibromin contains many other domains, and there is considerable evidence that these domains play a role in some manifestations of NF1. Investigating the role of these domains as well as the various signaling pathways that neurofibromin regulates and interacts with will provide a better understanding of how neurofibromin acts to suppress tumor development and potentially open new therapeutic avenues. In this review, we discuss what is known about the structure of neurofibromin, its interactions with other proteins and signaling pathways, its role in development and differentiation, and its function as a tumor suppressor. Finally, we discuss the latest research on potential therapeutics for neurofibromin-deficient neoplasms.
Collapse
Affiliation(s)
- Juan Mo
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA
| | - Stefanie L Moye
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA
| | - Renee M McKay
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA
| | - Lu Q Le
- Department of Dermatology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- UTSW Comprehensive Neurofibromatosis Clinic, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
- O'Donnell Brain Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390-9069, USA.
| |
Collapse
|
22
|
Ossola C, Kalebic N. Roots of the Malformations of Cortical Development in the Cell Biology of Neural Progenitor Cells. Front Neurosci 2022; 15:817218. [PMID: 35069108 PMCID: PMC8766818 DOI: 10.3389/fnins.2021.817218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
The cerebral cortex is a structure that underlies various brain functions, including cognition and language. Mammalian cerebral cortex starts developing during the embryonic period with the neural progenitor cells generating neurons. Newborn neurons migrate along progenitors’ radial processes from the site of their origin in the germinal zones to the cortical plate, where they mature and integrate in the forming circuitry. Cell biological features of neural progenitors, such as the location and timing of their mitoses, together with their characteristic morphologies, can directly or indirectly regulate the abundance and the identity of their neuronal progeny. Alterations in the complex and delicate process of cerebral cortex development can lead to malformations of cortical development (MCDs). They include various structural abnormalities that affect the size, thickness and/or folding pattern of the developing cortex. Their clinical manifestations can entail a neurodevelopmental disorder, such as epilepsy, developmental delay, intellectual disability, or autism spectrum disorder. The recent advancements of molecular and neuroimaging techniques, along with the development of appropriate in vitro and in vivo model systems, have enabled the assessment of the genetic and environmental causes of MCDs. Here we broadly review the cell biological characteristics of neural progenitor cells and focus on those features whose perturbations have been linked to MCDs.
Collapse
|
23
|
Notaras M, Lodhi A, Fang H, Greening D, Colak D. The proteomic architecture of schizophrenia iPSC-derived cerebral organoids reveals alterations in GWAS and neuronal development factors. Transl Psychiatry 2021; 11:541. [PMID: 34667143 PMCID: PMC8526592 DOI: 10.1038/s41398-021-01664-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/21/2022] Open
Abstract
Schizophrenia (Scz) is a brain disorder that has a typical onset in early adulthood but otherwise maintains unknown disease origins. Unfortunately, little progress has been made in understanding the molecular mechanisms underlying neurodevelopment of Scz due to ethical and technical limitations in accessing developing human brain tissue. To overcome this challenge, we have previously utilized patient-derived Induced Pluripotent Stem Cells (iPSCs) to generate self-developing, self-maturating, and self-organizing 3D brain-like tissue known as cerebral organoids. As a continuation of this prior work, here we provide an architectural map of the developing Scz organoid proteome. Utilizing iPSCs from n = 25 human donors (n = 8 healthy Ctrl donors, and n = 17 Scz patients), we generated 3D cerebral organoids, employed 16-plex isobaric sample-barcoding chemistry, and simultaneously subjected samples to comprehensive high-throughput liquid-chromatography/mass-spectrometry (LC/MS) quantitative proteomics. Of 3,705 proteins identified by high-throughput proteomic profiling, we identified that just ~2.62% of the organoid global proteomic landscape was differentially regulated in Scz organoids. In sum, just 43 proteins were up-regulated and 54 were down-regulated in Scz patient-derived organoids. Notably, a range of neuronal factors were depleted in Scz organoids (e.g., MAP2, TUBB3, SV2A, GAP43, CRABP1, NCAM1 etc.). Based on global enrichment analysis, alterations in key pathways that regulate nervous system development (e.g., axonogenesis, axon development, axon guidance, morphogenesis pathways regulating neuronal differentiation, as well as substantia nigra development) were perturbed in Scz patient-derived organoids. We also identified prominent alterations in two novel GWAS factors, Pleiotrophin (PTN) and Podocalyxin (PODXL), in Scz organoids. In sum, this work serves as both a report and a resource that researchers can leverage to compare, contrast, or orthogonally validate Scz factors and pathways identified in observational clinical studies and other model systems.
Collapse
Affiliation(s)
- Michael Notaras
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Aiman Lodhi
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Haoyun Fang
- Baker Institute for Heart and Diabetes, Melbourne, VIC, Australia
| | - David Greening
- Baker Institute for Heart and Diabetes, Melbourne, VIC, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
| | - Dilek Colak
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA.
- Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medical College, Cornell University, New York, NY, USA.
| |
Collapse
|
24
|
Kehrer-Sawatzki H, Wahlländer U, Cooper DN, Mautner VF. Atypical NF1 Microdeletions: Challenges and Opportunities for Genotype/Phenotype Correlations in Patients with Large NF1 Deletions. Genes (Basel) 2021; 12:genes12101639. [PMID: 34681033 PMCID: PMC8535936 DOI: 10.3390/genes12101639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Patients with neurofibromatosis type 1 (NF1) and type 1 NF1 deletions often exhibit more severe clinical manifestations than patients with intragenic NF1 gene mutations, including facial dysmorphic features, overgrowth, severe global developmental delay, severe autistic symptoms and considerably reduced cognitive abilities, all of which are detectable from a very young age. Type 1 NF1 deletions encompass 1.4 Mb and are associated with the loss of 14 protein-coding genes, including NF1 and SUZ12. Atypical NF1 deletions, which do not encompass all 14 protein-coding genes located within the type 1 NF1 deletion region, have the potential to contribute to the delineation of the genotype/phenotype relationship in patients with NF1 microdeletions. Here, we review all atypical NF1 deletions reported to date as well as the clinical phenotype observed in the patients concerned. We compare these findings with those of a newly identified atypical NF1 deletion of 698 kb which, in addition to the NF1 gene, includes five genes located centromeric to NF1. The atypical NF1 deletion in this patient does not include the SUZ12 gene but does encompass CRLF3. Comparative analysis of such atypical NF1 deletions suggests that SUZ12 hemizygosity is likely to contribute significantly to the reduced cognitive abilities, severe global developmental delay and facial dysmorphisms observed in patients with type 1 NF1 deletions.
Collapse
Affiliation(s)
- Hildegard Kehrer-Sawatzki
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
- Correspondence: ; Tel.: +49-731-500-65421
| | - Ute Wahlländer
- Kliniken des Bezirks Oberbayern (KBO), Children Clinical Center Munich, 81377 Munich, Germany;
| | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK;
| | - Victor-Felix Mautner
- Department of Neurology, University Hospital Hamburg Eppendorf, 20246 Hamburg, Germany;
| |
Collapse
|
25
|
Kehrer-Sawatzki H, Cooper DN. Classification of NF1 microdeletions and its importance for establishing genotype/phenotype correlations in patients with NF1 microdeletions. Hum Genet 2021; 140:1635-1649. [PMID: 34535841 PMCID: PMC8553723 DOI: 10.1007/s00439-021-02363-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/01/2021] [Indexed: 01/12/2023]
Abstract
An estimated 5–11% of patients with neurofibromatosis type-1 (NF1) harbour large deletions encompassing the NF1 gene and flanking regions. These NF1 microdeletions are subclassified into type 1, 2, 3 and atypical deletions which are distinguishable from each other by their extent and by the number of genes included within the deletion regions as well as the frequency of mosaicism with normal cells. Most common are type-1 NF1 deletions which encompass 1.4-Mb and 14 protein-coding genes. Type-1 deletions are frequently associated with overgrowth, global developmental delay, cognitive disability and dysmorphic facial features which are uncommon in patients with intragenic pathogenic NF1 gene variants. Further, patients with type-1 NF1 deletions frequently exhibit high numbers of neurofibromas and have an increased risk of malignant peripheral nerve sheath tumours. Genes located within the type-1 NF1 microdeletion interval and co-deleted with NF1 are likely to act as modifiers responsible for the severe disease phenotype in patients with NF1 microdeletions, thereby causing the NF1 microdeletion syndrome. Genotype/phenotype correlations in patients with NF1 microdeletions of different lengths are important to identify such modifier genes. However, these correlations are critically dependent upon the accurate characterization of the deletions in terms of their extent. In this review, we outline the utility as well as the shortcomings of multiplex ligation-dependent probe amplification (MLPA) to classify the different types of NF1 microdeletion and indicate the importance of high-resolution microarray analysis for correct classification, a necessary precondition to identify those genes responsible for the NF1 microdeletion syndrome.
Collapse
Affiliation(s)
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| |
Collapse
|