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Lee GB, Mazli WNAB, Hao L. Multiomics Evaluation of Human iPSCs and iPSC-Derived Neurons. J Proteome Res 2024; 23:3149-3160. [PMID: 38415376 DOI: 10.1021/acs.jproteome.3c00790] [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] [Indexed: 02/29/2024]
Abstract
Human induced pluripotent stem cells (iPSCs) can be differentiated into neurons, providing living human neurons to model brain diseases. However, it is unclear how different types of molecules work together to regulate stem cell and neuron biology in healthy and disease states. In this study, we conducted integrated proteomics, lipidomics, and metabolomics analyses with confident identification, accurate quantification, and reproducible measurements to compare the molecular profiles of human iPSCs and iPSC-derived neurons. Proteins, lipids, and metabolites related to mitosis, DNA replication, pluripotency, glycosphingolipids, and energy metabolism were highly enriched in iPSCs, whereas synaptic proteins, neurotransmitters, polyunsaturated fatty acids, cardiolipins, and axon guidance pathways were highly enriched in neurons. Mutations in the GRN gene lead to the deficiency of the progranulin (PGRN) protein, which has been associated with various neurodegenerative diseases. Using this multiomics platform, we evaluated the impact of PGRN deficiency on iPSCs and neurons at the whole-cell level. Proteomics, lipidomics, and metabolomics analyses implicated PGRN's roles in neuroinflammation, purine metabolism, and neurite outgrowth, revealing commonly altered pathways related to neuron projection, synaptic dysfunction, and brain metabolism. Multiomics data sets also pointed toward the same hypothesis that neurons seem to be more susceptible to PGRN loss compared to iPSCs, consistent with the neurological symptoms and cognitive impairment from patients carrying inherited GRN mutations.
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Affiliation(s)
- Gwang Bin Lee
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
| | - Wan Nur Atiqah Binti Mazli
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, 800 22nd St. NW, Washington, D.C. 20052, United States
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2
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Guo G, Chen J, Shen Q, Chen Z. Single-cell transcriptome analysis reveals distinct cell populations in dorsal root ganglia and their potential roles in diabetic peripheral neuropathy. PLoS One 2024; 19:e0306424. [PMID: 39083491 PMCID: PMC11290642 DOI: 10.1371/journal.pone.0306424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Diabetic peripheral neuropathy (DPN) is a common complication associated with diabetes, and can affect quality of life considerably. Dorsal root ganglion (DRG) plays an important role in the development of DPN. However, the relationship between DRG and the pathogenesis of DPN still lacks a thorough exploration. Besides, a more in-depth understanding of the cell type composition of DRG, and the roles of different cell types in mediating DPN are needed. Here we conducted single-cell RNA-seq (scRNA-seq) for DRG tissues isolated from healthy control and DPN rats. Our results demonstrated DRG includes eight cell-type populations (e.g., neurons, satellite glial cells (SGCs), Schwann cells (SCs), endothelial cells, fibroblasts). In the heterogeneity analyses of cells, six neuron sub-types, three SGC sub-types and three SC sub-types were identified, additionally, biological functions related to cell sub-types were further revealed. Cell communication analysis showed dynamic interactions between neurons, SGCs and SCs. We also found that the aberrantly expressed transcripts in sub-types of neurons, SGCs and SCs with DPN were associated with diabetic neuropathic pain, cell apoptosis, oxidative stress, etc. In conclusion, this study provides a systematic perspective of the cellular composition and interactions of DRG tissues, and suggests that neurons, SGCs and SCs play vital roles in the progression of DPN. Our data may provide a valuable resource for future studies regarding the pathophysiological effect of particular cell type in DPN.
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Affiliation(s)
- Guojun Guo
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jing Chen
- Department of Dermatology, Traditional Chinese and Western Medicine Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qixiao Shen
- Department of Orthopedics, Yangxin People’s Hospital, Huangshi, Hubei, China
| | - Zhenbing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Oliviero G, Wynne K, Andrews D, Crean J, Kolch W, Cagney G. Expression Proteomics and Histone Analysis Reveal Extensive Chromatin Network Changes and a Role for Histone Tail Trimming during Cellular Differentiation. Biomolecules 2024; 14:747. [PMID: 39062462 PMCID: PMC11274982 DOI: 10.3390/biom14070747] [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: 05/22/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
In order to understand the coordinated proteome changes associated with differentiation of a cultured cell pluripotency model, protein expression changes induced by treatment of NT2 embryonal carcinoma cells with retinoic acid were monitored by mass spectrometry. The relative levels of over 5000 proteins were mapped across distinct cell fractions. Analysis of the chromatin fraction revealed major abundance changes among chromatin proteins and epigenetic pathways between the pluripotent and differentiated states. Protein complexes associated with epigenetic regulation of gene expression, chromatin remodelling (e.g., SWI/SNF, NuRD) and histone-modifying enzymes (e.g., Polycomb, MLL) were found to be extensively regulated. We therefore investigated histone modifications before and after differentiation, observing changes in the global levels of lysine acetylation and methylation across the four canonical histone protein families, as well as among variant histones. We identified the set of proteins with affinity to peptides housing the histone marks H3K4me3 and H3K27me3, and found increased levels of chromatin-associated histone H3 tail trimming following differentiation that correlated with increased expression levels of cathepsin proteases. We further found that inhibition of cathepsins B and D reduces histone H3 clipping. Overall, the work reveals a global reorganization of the cell proteome congruent with differentiation, highlighting the key role of multiple epigenetic pathways, and demonstrating a direct link between cathepsin B and D activity and histone modification.
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Affiliation(s)
- Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - Darrell Andrews
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - John Crean
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - Gerard Cagney
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
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4
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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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Djalali-Cuevas A, Rettel M, Stein F, Savitski M, Kearns S, Kelly J, Biggs M, Skoufos I, Tzora A, Prassinos N, Diakakis N, Zeugolis DI. Macromolecular crowding in human tenocyte and skin fibroblast cultures: A comparative analysis. Mater Today Bio 2024; 25:100977. [PMID: 38322661 PMCID: PMC10846491 DOI: 10.1016/j.mtbio.2024.100977] [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: 10/04/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Although human tenocytes and dermal fibroblasts have shown promise in tendon engineering, no tissue engineered medicine has been developed due to the prolonged ex vivo time required to develop an implantable device. Considering that macromolecular crowding has the potential to substantially accelerate the development of functional tissue facsimiles, herein we compared human tenocyte and dermal fibroblast behaviour under standard and macromolecular crowding conditions to inform future studies in tendon engineering. Basic cell function analysis made apparent the innocuousness of macromolecular crowding for both cell types. Gene expression analysis of the without macromolecular crowding groups revealed expression of tendon related molecules in human dermal fibroblasts and tenocytes. Protein electrophoresis and immunocytochemistry analyses showed significantly increased and similar deposition of collagen fibres by macromolecular crowding in the two cell types. Proteomics analysis demonstrated great similarities between human tenocyte and dermal fibroblast cultures, as well as the induction of haemostatic, anti-microbial and tissue-protective proteins by macromolecular crowding in both cell populations. Collectively, these data rationalise the use of either human dermal fibroblasts or tenocytes in combination with macromolecular crowding in tendon engineering.
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Affiliation(s)
- Adrian Djalali-Cuevas
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikhail Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jack Kelly
- Galway University Hospital, Galway, Ireland
| | - Manus Biggs
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Athina Tzora
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios I. Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
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6
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Buczyńska A, Sidorkiewicz I, Niemira M, Krętowski AJ, Węgrzyn P, Kosiński P, Zbucka-Krętowska M. Identification of MicroRNA Profiles in Fetal Spina Bifida: The Role in Pathomechanism and Diagnostic Significance. Int J Mol Sci 2024; 25:2896. [PMID: 38474143 DOI: 10.3390/ijms25052896] [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: 01/19/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Distinct miRNA expression patterns may reflect anomalies related to fetal congenital malformations such as spinal bifida (SB). The aim of this preliminary study was to determine the maternal miRNA expression profile of women carrying fetuses with SB. Therefore, six women carrying fetuses with SB and twenty women with euploid healthy fetuses were enrolled in this study. Using NanoString technology, we evaluated the expression level of 798 miRNAs in both plasma and amniotic fluid samples. A downregulation of miR-1253, miR-1290, miR-194-5p, miR-302d-3p, miR-3144-3p, miR-4536-5p, miR-548aa + miR-548t-3p, miR-548ar-5p, miR-548n, miR-590-5p, miR-612, miR-627-5p, miR-644a, and miR-122-5p, and an upregulation of miR-320e, let-7b-5p, miR-23a-3p, miR-873-3p, and miR-30d-5p were identified in maternal amniotic fluid samples in SB when compared to the control group. The target genes of these miRNAs play a predominant role in regulating the synthesis of several biological compounds related to signaling pathways such as those regulating the pluripotency of stem cells. Moreover, the maternal plasma expression of miR-320e was increased in pregnancies with SB, and this marker could serve as a valuable non-invasive screening tool. Our results highlight the SB-specific miRNA signature and the differentially expressed miRNAs that may be involved in SB pathogenesis. Our findings emphasize the role of miRNA as a predictive factor that could potentially be useful in prenatal genetic screening for SB.
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Affiliation(s)
- Angelika Buczyńska
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Iwona Sidorkiewicz
- Clinical Research Support Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Adam Jacek Krętowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
| | - Piotr Węgrzyn
- Department of Obstetrics, Perinatology and Gynecology, Medical University of Warsaw, 63A Zwirki i Wigury, 02-091 Warsaw, Poland
| | - Przemysław Kosiński
- Department of Obstetrics, Perinatology and Gynecology, Medical University of Warsaw, 63A Zwirki i Wigury, 02-091 Warsaw, Poland
| | - Monika Zbucka-Krętowska
- Department of Gynecological Endocrinology and Adolescent Gynecology, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
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7
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Steiner JP, Bachani M, Malik N, Li W, Tyagi R, Sampson K, Abrams RPM, Kousa Y, Solis J, Johnson TP, Nath A. Neurotoxic properties of the Zika virus envelope protein. Exp Neurol 2023; 367:114469. [PMID: 37327963 PMCID: PMC10527427 DOI: 10.1016/j.expneurol.2023.114469] [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: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
Prenatal Zika virus (ZIKV) infection is a serious global concern as it can lead to brain injury and many serious birth defects, collectively known as congenital Zika syndrome. Brain injury likely results from viral mediated toxicity in neural progenitor cells. Additionally, postnatal ZIKV infections have been linked to neurological complications, yet the mechanisms driving these manifestations are not well understood. Existing data suggest that the ZIKV envelope protein can persist in the central nervous system for extended periods of time, but it is unknown if this protein can independently contribute to neuronal toxicity. Here we find that the ZIKV envelope protein is neurotoxic, leading to overexpression of poly adenosine diphosphate -ribose polymerase 1, which can induce parthanatos. Together, these data suggest that neuronal toxicity resulting from the envelope protein may contribute to the pathogenesis of post-natal ZIKV-related neurologic complications.
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Affiliation(s)
- Joseph P Steiner
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Muznabanu Bachani
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Nasir Malik
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Richa Tyagi
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Kevon Sampson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Rachel P M Abrams
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Youssef Kousa
- Division of Neurology, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA
| | - Jamie Solis
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Tory P Johnson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Avindra Nath
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America; Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America.
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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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Yde Ohki CM, Walter NM, Bender A, Rickli M, Ruhstaller S, Walitza S, Grünblatt E. Growth rates of human induced pluripotent stem cells and neural stem cells from attention-deficit hyperactivity disorder patients: a preliminary study. J Neural Transm (Vienna) 2023; 130:243-252. [PMID: 36800023 PMCID: PMC10033475 DOI: 10.1007/s00702-023-02600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental polygenic disorder that affects more than 5% of children and adolescents around the world. Genetic and environmental factors play important roles in ADHD etiology, which leads to a wide range of clinical outcomes and biological phenotypes across the population. Brain maturation delays of a 4-year lag are commonly found in patients, when compared to controls of the same age. Possible differences in cellular growth rates might reflect the clinical observations in ADHD patients. However, the cellular mechanisms are still not elucidated. To test this hypothesis, we analysed the proliferation of induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) derived from male children and adolescents diagnosed with ADHD and with genetic predisposition to it (assessed using polygenic risk scores), as well as their respective matched controls. In the current pilot study, it was noticeable that NSCs from the ADHD group proliferate less than controls, while no differences were seen at the iPSC developmental stage. Our results from two distinct proliferation methods indicate that the functional and structural delays found in patients might be associated with these in vitro phenotypic differences, but start at a distinct neurodevelopmental stage. These findings are the first ones in the field of disease modelling of ADHD and might be crucial to better understand the pathophysiology of this disorder.
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Affiliation(s)
- Cristine Marie Yde Ohki
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Biomedicine PhD Program, University of Zurich, Zurich, Switzerland
| | - Natalie Monet Walter
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Audrey Bender
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michelle Rickli
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sina Ruhstaller
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland.
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zurich, Switzerland.
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
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10
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Neves D, Goodfellow BJ, Vieira SI, Silva RM. The role of NAD metabolism in neuronal differentiation. Neurochem Int 2022; 159:105402. [PMID: 35843422 DOI: 10.1016/j.neuint.2022.105402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/17/2022] [Accepted: 07/09/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Nicotinamide adenine dinucleotide (NAD) metabolism is involved in redox and non-redox reactions that regulate several processes including differentiation of cells of different origins. Here, the role of NAD metabolism in neuronal differentiation, which remains elusive so far, was investigated. MATERIAL AND METHODS A protein-protein interaction network between neurotrophin signaling and NAD metabolic pathways was built. Expression of NAD biosynthetic enzymes in SH-SY5Y cells during retinoic acid (RA)/brain derived neurotrophic factor (BDNF) differentiation, was evaluated. The effects of NAD biosynthetic enzymes QPRT and NAPRT inhibition in neurite outgrowth, cell viability, NAD availability and histone deacetylase (HDAC) activity, were analysed in RA- and BDNF-differentiated cells. RESULTS Bioinformatics analysis revealed the interaction between NAD biosynthetic enzyme NMNAT1 and NTRK2, a receptor activated by RA/BDNF sequential treatment. Differences were found in the expression of NAD biosynthetic enzymes during neuronal differentiation, namely, increased QPRT gene expression along the course of RA/BDNF treatment and NAPRT protein expression after a 5-day treatment with RA. QPRT inhibition in BDNF-differentiated SH-SY5Y cells resulted in less neuritic length per cell, decreased expression of the neuronal marker β-III Tubulin and also decreased NAD+ levels and HDAC activity. NAPRT inhibition had no effect in neuritic length per cell, NAD+ levels and HDAC activity. Of note, NAD supplementation along with RA, but not with BDNF, resulted in considerable cell death. CONCLUSIONS Taken together, our results show the involvement of NAD metabolism in neuronal differentiation, specifically, the importance of QPRT-mediated NAD biosynthesis in BDNF-associated SH-SY5Y differentiation and suggest additional roles for NAPRT beyond NAD production in RA-differentiated cells.
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Affiliation(s)
- Diogo Neves
- Departamento de Ciências Médicas & Institute of Biomedicine (iBiMED), Universidade de Aveiro, Portugal.
| | | | - Sandra I Vieira
- Departamento de Ciências Médicas & Institute of Biomedicine (iBiMED), Universidade de Aveiro, Portugal
| | - Raquel M Silva
- Departamento de Ciências Médicas & Institute of Biomedicine (iBiMED), Universidade de Aveiro, Portugal; Universidade Católica Portuguesa, Faculdade de Medicina Dentária, Centro de Investigação Interdisciplinar em Saúde, Viseu, Portugal
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Inflammation: A New Look at an Old Problem. Int J Mol Sci 2022; 23:ijms23094596. [PMID: 35562986 PMCID: PMC9100490 DOI: 10.3390/ijms23094596] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
Pro-inflammatory stress is inherent in any cells that are subject to damage or threat of damage. It is defined by a number of universal components, including oxidative stress, cellular response to DNA damage, unfolded protein response to mitochondrial and endoplasmic reticulum stress, changes in autophagy, inflammasome formation, non-coding RNA response, formation of an inducible network of signaling pathways, and epigenetic changes. The presence of an inducible receptor and secretory phenotype in many cells is the cause of tissue pro-inflammatory stress. The key phenomenon determining the occurrence of a classical inflammatory focus is the microvascular inflammatory response (exudation, leukocyte migration to the alteration zone). This same reaction at the systemic level leads to the development of life-critical systemic inflammation. From this standpoint, we can characterize the common mechanisms of pathologies that differ in their clinical appearance. The division of inflammation into alternative variants has deep evolutionary roots. Evolutionary aspects of inflammation are also described in the review. The aim of the review is to provide theoretical arguments for the need for an up-to-date theory of the relationship between key human pathological processes based on the integrative role of the molecular mechanisms of cellular and tissue pro-inflammatory stress.
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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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13
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Varderidou-Minasian S, Verheijen BM, Harschnitz O, Kling S, Karst H, van der Pol WL, Pasterkamp RJ, Altelaar M. Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Display Altered Proteomes at Early Stages of Differentiation. ACS OMEGA 2021; 6:35375-35388. [PMID: 34984269 PMCID: PMC8717385 DOI: 10.1021/acsomega.1c04688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/24/2021] [Indexed: 05/08/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder characterized by loss of motor neurons (MN) in the spinal cord leading to progressive muscle atrophy and weakness. SMA is caused by mutations in the survival motor neuron 1 (SMN1) gene, resulting in reduced levels of survival motor neuron (SMN) protein. The mechanisms that link SMN deficiency to selective motor neuron dysfunction in SMA remain largely unknown. We present here, for the first time, a comprehensive quantitative TMT-10plex proteomics analysis that covers the development of induced pluripotent stem cell-derived MNs from both healthy individuals and SMA patients. We show that the proteomes of SMA samples segregate from controls already at early stages of neuronal differentiation. The altered proteomic signature in SMA MNs is associated with mRNA splicing, ribonucleoprotein biogenesis, organelle organization, cellular biogenesis, and metabolic processes. We highlight several known SMN-binding partners and evaluate their expression changes during MN differentiation. In addition, we compared our study to human and mouse in vivo proteomic studies revealing distinct and similar signatures. Altogether, our work provides a comprehensive resource of molecular events during early stages of MN differentiation, containing potentially therapeutically interesting protein expression profiles for SMA.
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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
- Department
of Neurology and Neurosurgery, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Oliver Harschnitz
- Department
of Translational Neuroscience, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
- Department
of Neurology and Neurosurgery, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Sandra Kling
- Department
of Translational Neuroscience, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
- Department
of Neurology and Neurosurgery, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Henk Karst
- Department
of Translational Neuroscience, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - W. Ludo van der Pol
- Department
of Neurology and Neurosurgery, UMC Utrecht Brain Center, University
Medical Center Utrecht, Utrecht University, 3584 CX 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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14
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van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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15
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Cui ZK, Li SY, Liao K, Wang ZJ, Guo YL, Tang LS, Tang SB, Ma JH, Chen JS. Characteristics of neural growth and cryopreservation of the dorsal root ganglion using three-dimensional collagen hydrogel culture versus conventional culture. Neural Regen Res 2021; 16:1856-1864. [PMID: 33510093 PMCID: PMC8328787 DOI: 10.4103/1673-5374.306097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In vertebrates, most somatosensory pathways begin with the activation of dorsal root ganglion (DRG) neurons. The development of an appropriate DRG culture method is a prerequisite for establishing in vitro peripheral nerve disease models and for screening therapeutic drugs. In this study, we compared the changes in morphology, molecular biology, and transcriptomics of chicken embryo DRG cultured on tissue culture plates (T-DRG) versus three-dimensional collagen hydrogels (C-DRG). Our results showed that after 7 days of culture, the transcriptomics of T-DRG and C-DRG were quite different. The upregulated genes in C-DRG were mainly related to neurogenesis, axon guidance, and synaptic plasticity, whereas the downregulated genes in C-DRG were mainly related to cell proliferation and cell division. In addition, the genes related to cycles/pathways such as the synaptic vesicle cycle, cyclic adenosine monophosphate signaling pathway, and calcium signaling pathway were activated, while those related to cell-cycle pathways were downregulated. Furthermore, neurogenesis- and myelination-related genes were highly expressed in C-DRG, while epithelial–mesenchymal transition-, apoptosis-, and cell division-related genes were suppressed. Morphological results indicated that the numbers of branches, junctions, and end-point voxels per C-DRG were significantly greater than those per T-DRG. Furthermore, cells were scattered in T-DRG and more concentrated in C-DRG, with a higher ratio of 5-ethynyl-2′-deoxyuridine (EdU)-positive cells in T-DRG compared with C-DRG. C-DRG also had higher S100 calcium-binding protein B (S100B) and lower α-smooth muscle actin (α-SMA) expression than T-DRG, and contained fewer terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells after 48 hours of serum starvation. After cryopreservation, C-DRG maintained more intact morphological characteristics, and had higher viability and less TUNEL-positive cells than T-DRG. Furthermore, newly formed nerve bundles were able to grow along the existing Schwann cells in C-DRG. These results suggest that C-DRG may be a promising in vitro culture model, with better nerve growth and anti-apoptotic ability, quiescent Schwann cells, and higher viability. Results from this study provide a reference for the construction, storage, and transportation of tissue-engineered nerves. The study was approved by the Ethics Committee of Aier School of Ophthalmology, Central South University, China (approval No. 2020-IRB16), on March 15, 2020.
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Affiliation(s)
- Ze-Kai Cui
- Department of Ophthalmology, the Second Xiangya Hospital, Central South University; Aier Eye Institute; Aier School of Ophthalmology, Central South University, Changsha, Hunan Province, China
| | - Shen-Yang Li
- Aier School of Ophthalmology, Central South University, Changsha, Hunan Province, China
| | - Kai Liao
- Aier School of Ophthalmology, Central South University, Changsha, Hunan Province, China
| | - Zhi-Jie Wang
- Aier School of Ophthalmology, Central South University, Changsha, Hunan Province, China
| | - Yong-Long Guo
- Institute of Ophthalmology, Medical College, Jinan University; Department of Ophthalmology, First Affiliated Hospital of Jinan University; Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Luo-Sheng Tang
- Department of Ophthalmology, the Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Shi-Bo Tang
- Aier Eye Institute; Aier School of Ophthalmology, Central South University, Changsha, Hunan Province; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Jacey Hongjie Ma
- Department of Ophthalmology, the Second Xiangya Hospital, Central South University; Aier Eye Institute, Changsha, Hunan Province; Imaging and Functional Center, Guangzhou Aier Eye Hospital, Guangzhou, Guangdong Province, China
| | - Jian-Su Chen
- Aier Eye Institute; Aier School of Ophthalmology, Central South University, Changsha, Hunan Province; Institute of Ophthalmology, Medical College, Jinan University; Department of Ophthalmology, First Affiliated Hospital of Jinan University; Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
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