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Fumagalli SE, Smith S, Ghazanchyan T, Meyer D, Paul R, Campbell C, Santana-Quintero L, Golikov A, Ibla J, Bar H, Komar AA, Hunt RC, Lin B, DiCuccio M, Kimchi-Sarfaty C. Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages. BMC Bioinformatics 2024; 25:294. [PMID: 39242990 PMCID: PMC11380194 DOI: 10.1186/s12859-024-05906-3] [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: 05/06/2024] [Accepted: 08/20/2024] [Indexed: 09/09/2024] Open
Abstract
Mouse (Mus musculus) models have been heavily utilized in developmental biology research to understand mammalian embryonic development, as mice share many genetic, physiological, and developmental characteristics with humans. New explorations into the integration of temporal (stage-specific) and transcriptional (tissue-specific) data have expanded our knowledge of mouse embryo tissue-specific gene functions. To better understand the substantial impact of synonymous mutational variations in the cell-state-specific transcriptome on a tissue's codon and codon pair usage landscape, we have established a novel resource-Mouse Embryo Codon and Codon Pair Usage Tables (Mouse Embryo CoCoPUTs). This webpage not only offers codon and codon pair usage, but also GC, dinucleotide, and junction dinucleotide usage, encompassing four strains, 15 murine embryonic tissue groups, 18 Theiler stages, and 26 embryonic days. Here, we leverage Mouse Embryo CoCoPUTs and employ the use of heatmaps to depict usage changes over time and a comparison to human usage for each strain and embryonic time point, highlighting unique differences and similarities. The usage similarities found between mouse and human central nervous system data highlight the translation for projects leveraging mouse models. Data for this analysis can be directly retrieved from Mouse Embryo CoCoPUTs. This cutting-edge resource plays a crucial role in deciphering the complex interplay between usage patterns and embryonic development, offering valuable insights into variation across diverse tissues, strains, and stages. Its applications extend across multiple domains, with notable advantages for biotherapeutic development, where optimizing codon usage can enhance protein expression; one can compare strains, tissues, and mouse embryonic stages in one query. Additionally, Mouse Embryo CoCoPUTs holds great potential in the field of tissue-specific genetic engineering, providing insights for tailoring gene expression to specific tissues for targeted interventions. Furthermore, this resource may enhance our understanding of the nuanced connections between usage biases and tissue-specific gene function, contributing to the development of more accurate predictive models for genetic disorders.
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Affiliation(s)
- Sarah E Fumagalli
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Sean Smith
- High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Tigran Ghazanchyan
- High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Rahul Paul
- High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Collin Campbell
- High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Luis Santana-Quintero
- High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Anton Golikov
- High-performance Integrated Virtual Environment (HIVE), Office of Biostatistics and Pharmacovigilance (OBPV), Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Juan Ibla
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT, USA
| | - Anton A Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Ryan C Hunt
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Brian Lin
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | | | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research (CBER), US Food and Drug Administration (FDA), Silver Spring, MD, USA.
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Argun Karsli B, Demir E, Bilginer U, Dogru H, Karsli T, Kaya S. Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq. Sci Rep 2024; 14:20518. [PMID: 39227733 PMCID: PMC11371811 DOI: 10.1038/s41598-024-71617-7] [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: 06/11/2024] [Accepted: 08/29/2024] [Indexed: 09/05/2024] Open
Abstract
High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.
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Affiliation(s)
- Bahar Argun Karsli
- Department of Agricultural Biotechnology, Faculty of Agriculture, Eskişehir Osmangazi University, Eskişehir, 26160, Türkiye.
| | - Eymen Demir
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Türkiye
| | - Umit Bilginer
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Türkiye
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Huriye Dogru
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, 15100, Türkiye
| | - Taki Karsli
- Institution Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, Eskisehir, 26160, Türkiye
| | - Sarp Kaya
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, 15100, Türkiye
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Li Y, Wen S, Xiang W, Shen F, Jiang N, Zhang J, Ma D. Upregulation of NFE2L1 reduces ROS levels and α-synuclein aggregation caused by GBA1 knockdown. Biochem Biophys Res Commun 2024; 734:150640. [PMID: 39241620 DOI: 10.1016/j.bbrc.2024.150640] [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: 08/27/2024] [Accepted: 09/01/2024] [Indexed: 09/09/2024]
Abstract
Biallelic mutations in the GBA1 gene result in Gaucher disease (GD), and both patients with GD and carriers of a single GBA1 mutation have an increased susceptibility to Parkinson's disease (PD), but the underlying mechanisms of this association are not yet clear. In previous studies, we established Gba1 F213I point mutation mice and found that homozygous Gba1 F213I mutant mice died shortly after birth, while heterozygous mice could survive normally. In this study, we investigated the transcriptomic changes in the brain tissue of Gba1 F213I heterozygous mice, identifying 138 differentially expressed genes. Among them, Nfe2l1 was the most significantly downregulated gene. Inhibition or knockdown of GBA1 in BE(2)-M17 cells resulted in decreased expression levels of NFE2L1. Knockdown of GBA1 or NFE2L1 could lead to an elevation in intracellular aggregation of α-synuclein (α-syn) and reactive oxygen species (ROS) levels, while upregulation of NFE2L1 effectively mitigated those cellular manifestations induced by GBA1 knockdown. In summary, our in vitro results showed that upregulation of NFE2L1 may provide a therapeutic benefit for cellular phenotypes resulting from GBA1 knockdown, providing new insights for future research on GD and GBA1-associated PD.
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Affiliation(s)
- Yajun Li
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuxia Wen
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wanqing Xiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Fei Shen
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Nan Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Children's Hospital, Fudan University, Shanghai, 201102, China.
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Sangree AK, Angireddy R, Bryant LM, Layo-Carris DE, Lubin EE, Wang XM, Clark KJ, Durham EE, Bhoj EJ. A novel iPSC model of Bryant-Li-Bhoj neurodevelopmental syndrome demonstrates the role of histone H3.3 in neuronal differentiation and maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609745. [PMID: 39253491 PMCID: PMC11382994 DOI: 10.1101/2024.08.26.609745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Background Bryant-Li-Bhoj neurodevelopmental syndrome (BLBS) is neurogenetic disorder caused by variants in H3-3A and H3-3B, the two genes that encode the histone H3.3 protein. Ninety-nine percent of individuals with BLBS show developmental delay/intellectual disability, but the mechanism by which variants in H3.3 result in these phenotypes is not yet understood. As a result, only palliative interventions are available to individuals living with BLBS. Methods Here, we investigate how one BLBS-causative variant, H3-3B p.Leu48Arg (L48R), affects neurodevelopment using an induced pluripotent stem cell (iPSC) model differentiated to 2D neural progenitor cells (NPCs), 2D forebrain neurons (FBNs), and 3D dorsal forebrain organoids (DFBOs). We employ a multi-omic approach in the 2D models to quantify the resulting changes in gene expression and chromatin accessibility. We used immunofluorescence (IF) staining to define the identities of cells in the 3D DFBOs. Results In the 2D systems, we found dysregulation of both gene expression and chromatin accessibility of genes important for neuronal fate, maturation, and function in H3.3 L48R compared to control. Our work in 3D organoids corroborates these findings, demonstrating altered proportions of radial glia and mature neuronal cells. Conclusions These data provide the first mechanistic insights into the pathogenesis of BLBS from a human-derived model of neurodevelopment, which suggest that the L48R increases H3-3B expression, resulting in the hyper-deposition of H3.3 into the nucleosome which underlies changes in gene expression and chromatin accessibility. Functionally, this causes dysregulation of cell adhesion, neurotransmission, and the balance between excitatory and inhibitory signaling. These results are a crucial step towards preclinical development and testing of targeted therapies for this and related disorders.
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Liu M, Xing Y, Tan J, Chen X, Xue Y, Qu L, Ma J, Jin X. Comprehensive summary: the role of PBX1 in development and cancers. Front Cell Dev Biol 2024; 12:1442052. [PMID: 39129784 PMCID: PMC11310070 DOI: 10.3389/fcell.2024.1442052] [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: 06/01/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
PBX1 is a transcription factor that can promote the occurrence of various tumors and play a reg-ulatory role in tumor growth, metastasis, invasion, and drug resistance. Furthermore, a variant generated by fusion of E2A and PBX1, E2A-PBX1, has been found in 25% of patients with childhood acute lymphoblastic leukemia. Thus, PBX1 is a potential therapeutic target for many cancers. Here, we describe the structure of PBX1 and E2A-PBX1 as well as the molecular mecha-nisms whereby these proteins promote tumorigenesis to provide future research directions for developing new treatments. We show that PBX1 and E2A-PBX1 induce the development of highly malignant and difficult-to-treat solid and blood tumors. The development of specific drugs against their targets may be a good therapeutic strategy for PBX1-related cancers. Furthermore, we strongly recommend E2A-PBX1 as one of the genes for prenatal screening to reduce the incidence of childhood hematological malignancies.
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Affiliation(s)
- Mingsheng Liu
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Yan Xing
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Jiufeng Tan
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Xiaoliang Chen
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Yaming Xue
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Licheng Qu
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Jianchao Ma
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
| | - Xuefei Jin
- 2nd Inpatient Area of Urology Department, China-Japan Union Hospital, Jilin University, Changchun, China
- Jinlin Provincial Key Laboratory of Molecular Diagnosis of Urological Tumors, Changchun, China
- Jinlin Provincial Key Laboratory of Urological Tumors, Changchun, China
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Kim TW, Koo SY, Riessland M, Chaudhry F, Kolisnyk B, Cho HS, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons. Cell 2024; 187:3671-3689.e23. [PMID: 38866017 DOI: 10.1016/j.cell.2024.05.030] [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: 11/20/2022] [Revised: 12/15/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Ongoing, early-stage clinical trials illustrate the translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, an unresolved challenge is the extensive cell death following transplantation. Here, we performed a pooled CRISPR-Cas9 screen to enhance postmitotic dopamine neuron survival in vivo. We identified p53-mediated apoptotic cell death as a major contributor to dopamine neuron loss and uncovered a causal link of tumor necrosis factor alpha (TNF-α)-nuclear factor κB (NF-κB) signaling in limiting cell survival. As a translationally relevant strategy to purify postmitotic dopamine neurons, we identified cell surface markers that enable purification without the need for genetic reporters. Combining cell sorting and treatment with adalimumab, a clinically approved TNF-α inhibitor, enabled efficient engraftment of postmitotic dopamine neurons with extensive reinnervation and functional recovery in a preclinical PD mouse model. Thus, transient TNF-α inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic hPSC-derived dopamine neurons in PD.
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Affiliation(s)
- Tae Wan Kim
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Interdisciplinary Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - So Yeon Koo
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Markus Riessland
- Department of Neurobiology and Behavior, Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA
| | - Fayzan Chaudhry
- Tri-Institutional PhD program in Computational Biology, New York, NY, USA
| | - Benjamin Kolisnyk
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hyein S Cho
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Marco Vincenzo Russo
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Nathalie Saurat
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doron Betel
- Division of Hematology & Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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Yanagi KS, Jochim B, Kunjo SO, Breen P, Ruvkun G, Lehrbach N. Mutations in nucleotide metabolism genes bypass proteasome defects in png-1/NGLY1-deficient Caenorhabditis elegans. PLoS Biol 2024; 22:e3002720. [PMID: 38991033 PMCID: PMC11265709 DOI: 10.1371/journal.pbio.3002720] [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: 12/17/2023] [Revised: 07/23/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The conserved SKN-1A/Nrf1 transcription factor regulates the expression of proteasome subunit genes and is essential for maintenance of adequate proteasome function in animal development, aging, and stress responses. Unusual among transcription factors, SKN-1A/Nrf1 is a glycoprotein synthesized in the endoplasmic reticulum (ER). N-glycosylated SKN-1A/Nrf1 exits the ER and is deglycosylated in the cytosol by the PNG-1/NGLY1 peptide:N-glycanase. Deglycosylation edits the protein sequence of SKN-1A/Nrf1 by converting N-glycosylated asparagine residues to aspartate, which is necessary for SKN-1A/Nrf1 transcriptional activation of proteasome subunit genes. Homozygous loss-of-function mutations in the peptide:N-glycanase (NGLY1) gene cause NGLY1 deficiency, a congenital disorder of deglycosylation. There are no effective treatments for NGLY1 deficiency. Since SKN-1A/Nrf1 is a major client of NGLY1, the resulting proteasome deficit contributes to NGLY1 disease. We sought to identify targets for mitigation of proteasome dysfunction in NGLY1 deficiency that might indicate new avenues for treatment. We isolated mutations that suppress the sensitivity to proteasome inhibitors caused by inactivation of the NGLY1 ortholog PNG-1 in Caenorhabditis elegans. We identified multiple suppressor mutations affecting 3 conserved genes: rsks-1, tald-1, and ent-4. We show that the suppressors act through a SKN-1/Nrf-independent mechanism and confer proteostasis benefits consistent with amelioration of proteasome dysfunction. ent-4 encodes an intestinal nucleoside/nucleotide transporter, and we show that restriction of nucleotide availability is beneficial, whereas a nucleotide-rich diet exacerbates proteasome dysfunction in PNG-1/NGLY1-deficient C. elegans. Our findings suggest that dietary or pharmacological interventions altering nucleotide availability have the potential to mitigate proteasome insufficiency in NGLY1 deficiency and other diseases associated with proteasome dysfunction.
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Affiliation(s)
- Katherine S. Yanagi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Briar Jochim
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Sheikh Omar Kunjo
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nicolas Lehrbach
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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Pottmeier P, Nikolantonaki D, Lanner F, Peuckert C, Jazin E. Sex-biased gene expression during neural differentiation of human embryonic stem cells. Front Cell Dev Biol 2024; 12:1341373. [PMID: 38764741 PMCID: PMC11101176 DOI: 10.3389/fcell.2024.1341373] [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: 11/20/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Sex differences in the developing human brain are primarily attributed to hormonal influence. Recently however, genetic differences and their impact on the developing nervous system have attracted increased attention. To understand genetically driven sexual dimorphisms in neurodevelopment, we investigated genome-wide gene expression in an in vitro differentiation model of male and female human embryonic stem cell lines (hESC), independent of the effects of human sex hormones. Four male and four female-derived hESC lines were differentiated into a population of mixed neurons over 37 days. Differential gene expression and gene set enrichment analyses were conducted on bulk RNA sequencing data. While similar differentiation tendencies in all cell lines demonstrated the robustness and reproducibility of our differentiation protocol, we found sex-biased gene expression already in undifferentiated ESCs at day 0, but most profoundly after 37 days of differentiation. Male and female cell lines exhibited sex-biased expression of genes involved in neurodevelopment, suggesting that sex influences the differentiation trajectory. Interestingly, the highest contribution to sex differences was found to arise from the male transcriptome, involving both Y chromosome and autosomal genes. We propose 13 sex-biased candidate genes (10 upregulated in male cell lines and 3 in female lines) that are likely to affect neuronal development. Additionally, we confirmed gene dosage compensation of X/Y homologs escaping X chromosome inactivation through their Y homologs and identified a significant overexpression of the Y-linked demethylase UTY and KDM5D in male hESC during neuron development, confirming previous results in neural stem cells. Our results suggest that genetic sex differences affect neuronal differentiation trajectories, which could ultimately contribute to sex biases during human brain development.
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Affiliation(s)
- Philipp Pottmeier
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Danai Nikolantonaki
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fredrik Lanner
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Barvaux S, Okawa S, Del Sol A. SinCMat: A single-cell-based method for predicting functional maturation transcription factors. Stem Cell Reports 2024; 19:270-284. [PMID: 38215756 PMCID: PMC10874865 DOI: 10.1016/j.stemcr.2023.12.006] [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: 07/18/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
A major goal of regenerative medicine is to generate tissue-specific mature and functional cells. However, current cell engineering protocols are still unable to systematically produce fully mature functional cells. While existing computational approaches aim at predicting transcription factors (TFs) for cell differentiation/reprogramming, no method currently exists that specifically considers functional cell maturation processes. To address this challenge, here, we develop SinCMat, a single-cell RNA sequencing (RNA-seq)-based computational method for predicting cell maturation TFs. Based on a model of cell maturation, SinCMat identifies pairs of identity TFs and signal-dependent TFs that co-target genes driving functional maturation. A large-scale application of SinCMat to the Mouse Cell Atlas and Tabula Sapiens accurately recapitulates known maturation TFs and predicts novel candidates. We expect SinCMat to be an important resource, complementary to preexisting computational methods, for studies aiming at producing functionally mature cells.
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Affiliation(s)
- Sybille Barvaux
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg; University of Pittsburgh School of Medicine, Vascular Medicine Institute, Department of Computational and Systems Biology, McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg; CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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10
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Crisafulli L, Brindisi M, Liturri MG, Sobacchi C, Ficara F. PBX1: a TALE of two seasons-key roles during development and in cancer. Front Cell Dev Biol 2024; 12:1372873. [PMID: 38404687 PMCID: PMC10884236 DOI: 10.3389/fcell.2024.1372873] [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: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Pre-B cell leukemia factor 1 (PBX1) is a Three Aminoacid Loop Extension (TALE) homeodomain-containing transcription factor playing crucial roles in organ pattering during embryogenesis, through the formation of nuclear complexes with other TALE class and/or homeobox proteins to regulate target genes. Its contribution to the development of several organs has been elucidated mainly through the study of murine knockout models. A crucial role for human development has been recently highlighted through the discovery of different de novo pathogenic PBX1 variants in children affected by developmental defects. In the adult, PBX1 is expressed in selected tissues such as in the brain, in the gastro-intestinal and urinary systems, or in hematopoietic stem and progenitor cells, while in other organs is barely detectable. When involved in the t(1;19) chromosomal translocation it acts as an oncogene, since the resulting fusion protein drives pre-B cell leukemia, due to the induction of target genes not normally targeted by the native protein. Its aberrant expression has been associated to tumor development, progression, or therapy-resistance as in breast cancer, ovarian cancer or myeloproliferative neoplasm (MPN). On the other hand, in colorectal cancer PBX1 functions as a tumor suppressor, highlighting its context-dependent role. We here discuss differences and analogies of PBX1 roles during embryonic development and in cancer, focusing mainly on the most recent discoveries.
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Affiliation(s)
- Laura Crisafulli
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
| | - Matteo Brindisi
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
| | | | - Cristina Sobacchi
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
| | - Francesca Ficara
- IRCCS Humanitas Research Hospital, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council, Milan, Italy
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11
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Łuczyńska K, Zhang Z, Pietras T, Zhang Y, Taniguchi H. NFE2L1/Nrf1 serves as a potential therapeutical target for neurodegenerative diseases. Redox Biol 2024; 69:103003. [PMID: 38150994 PMCID: PMC10788251 DOI: 10.1016/j.redox.2023.103003] [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: 08/13/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/29/2023] Open
Abstract
The failure of the proper protein turnover in the nervous system is mainly linked to a variety of neurodegenerative disorders. Therefore, a better understanding of key protein degradation through the ubiquitin-proteasome system is critical for effective prevention and treatment of those disorders. The proteasome expression is tightly regulated by a CNC (cap'n'collar) family of transcription factors, amongst which the nuclear factor-erythroid 2-like bZIP factor 1 (NFE2L1, also known as Nrf1, with its long isoform TCF11 and short isoform LCR-F1) has been identified as an indispensable regulator of the transcriptional expression of the ubiquitin-proteasome system. However, much less is known about how the pivotal role of NFE2L1/Nrf1, as compared to its homologous NFE2L2 (also called Nrf2), is translated to its physiological and pathophysiological functions in the nervous system insomuch as to yield its proper cytoprotective effects against neurodegenerative diseases. The potential of NFE2L1 to fulfill its unique neuronal function to serve as a novel therapeutic target for neurodegenerative diseases is explored by evaluating the hitherto established preclinical and clinical studies of Alzheimer's and Parkinson's diseases. In this review, we have also showcased a group of currently available activators of NFE2L1, along with an additional putative requirement of this CNC-bZIP factor for healthy longevity based on the experimental evidence obtained from its orthologous SKN1-A in Caenorhabditis elegans.
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Affiliation(s)
- Kamila Łuczyńska
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, 05-552, Poland; The Second Department of Psychiatry, Institute of Psychiatry and Neurology in Warsaw, 02-957, Warsaw, Poland
| | - Zhengwen Zhang
- Laboratory of Neuroscience, Institute of Cognitive Neuroscience and School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, England, United Kingdom
| | - Tadeusz Pietras
- The Second Department of Psychiatry, Institute of Psychiatry and Neurology in Warsaw, 02-957, Warsaw, Poland; Department of Clinical Pharmacology, Medical University of Lodz, 90-153, Łódź, Poland
| | - Yiguo Zhang
- Chongqing University Jiangjin Hospital, School of Medicine, Chongqing University, No. 725 Jiangzhou Avenue, Dingshan Street, Jiangjin District, Chongqing, 402260, China; The Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering & Faculty of Medical Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing, 400044, China.
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, 05-552, Poland.
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12
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Gomez Ramos B, Ohnmacht J, de Lange N, Valceschini E, Ginolhac A, Catillon M, Ferrante D, Rakovic A, Halder R, Massart F, Arena G, Antony P, Bolognin S, Klein C, Krause R, Schulz MH, Sauter T, Krüger R, Sinkkonen L. Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation. EMBO Rep 2024; 25:254-285. [PMID: 38177910 PMCID: PMC10897179 DOI: 10.1038/s44319-023-00024-2] [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: 04/17/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Midbrain dopaminergic neurons (mDANs) control voluntary movement, cognition, and reward behavior under physiological conditions and are implicated in human diseases such as Parkinson's disease (PD). Many transcription factors (TFs) controlling human mDAN differentiation during development have been described, but much of the regulatory landscape remains undefined. Using a tyrosine hydroxylase (TH) human iPSC reporter line, we here generate time series transcriptomic and epigenomic profiles of purified mDANs during differentiation. Integrative analysis predicts novel regulators of mDAN differentiation and super-enhancers are used to identify key TFs. We find LBX1, NHLH1 and NR2F1/2 to promote mDAN differentiation and show that overexpression of either LBX1 or NHLH1 can also improve mDAN specification. A more detailed investigation of TF targets reveals that NHLH1 promotes the induction of neuronal miR-124, LBX1 regulates cholesterol biosynthesis, and NR2F1/2 controls neuronal activity.
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Affiliation(s)
- Borja Gomez Ramos
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Jochen Ohnmacht
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Nikola de Lange
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Elena Valceschini
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Aurélien Ginolhac
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Marie Catillon
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Daniele Ferrante
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - François Massart
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Giuseppe Arena
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Silvia Bolognin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590, Frankfurt, Germany
- German Centre for Cardiovascular Research, Partner site Rhein-Main, 60590, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University, Frankfurt am Main, Germany
| | - Thomas Sauter
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Belvaux, Luxembourg
- Centre Hospitalier de Luxembourg (CHL), L-1210, Luxembourg, Luxembourg
- Luxembourg Institute of Health (LIH), L-1445, Luxembourg, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L-4362, Belvaux, Luxembourg.
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13
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Chandran A, Oliver HJ, Rochet JC. Role of NFE2L1 in the Regulation of Proteostasis: Implications for Aging and Neurodegenerative Diseases. BIOLOGY 2023; 12:1169. [PMID: 37759569 PMCID: PMC10525699 DOI: 10.3390/biology12091169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
A hallmark of aging and neurodegenerative diseases is a disruption of proteome homeostasis ("proteostasis") that is caused to a considerable extent by a decrease in the efficiency of protein degradation systems. The ubiquitin proteasome system (UPS) is the major cellular pathway involved in the clearance of small, short-lived proteins, including amyloidogenic proteins that form aggregates in neurodegenerative diseases. Age-dependent decreases in proteasome subunit expression coupled with the inhibition of proteasome function by aggregated UPS substrates result in a feedforward loop that accelerates disease progression. Nuclear factor erythroid 2- like 1 (NFE2L1) is a transcription factor primarily responsible for the proteasome inhibitor-induced "bounce-back effect" regulating the expression of proteasome subunits. NFE2L1 is localized to the endoplasmic reticulum (ER), where it is rapidly degraded under basal conditions by the ER-associated degradation (ERAD) pathway. Under conditions leading to proteasome impairment, NFE2L1 is cleaved and transported to the nucleus, where it binds to antioxidant response elements (AREs) in the promoter region of proteasome subunit genes, thereby stimulating their transcription. In this review, we summarize the role of UPS impairment in aging and neurodegenerative disease etiology and consider the potential benefit of enhancing NFE2L1 function as a strategy to upregulate proteasome function and alleviate pathology in neurodegenerative diseases.
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Affiliation(s)
- Aswathy Chandran
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Haley Jane Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
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14
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Xie L, Liu H, You Z, Wang L, Li Y, Zhang X, Ji X, He H, Yuan T, Zheng W, Wu Z, Xiong M, Wei W, Chen Y. Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding. Nat Methods 2023; 20:1244-1255. [PMID: 37460718 DOI: 10.1038/s41592-023-01947-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/06/2023] [Indexed: 08/09/2023]
Abstract
A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.
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Affiliation(s)
- Lianshun Xie
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hengxin Liu
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Zhiwen You
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyue Wang
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yiwen Li
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyue Zhang
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoshan Ji
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Hui He
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Tingli Yuan
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Wenping Zheng
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Ziyan Wu
- UniXell Biotechnology, Shanghai, China
| | - Man Xiong
- State Key Laboratory of Medical Neurobiology-Ministry of Education Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
- Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.
- Lingang Laboratory, Shanghai, China.
| | - Yuejun Chen
- Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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15
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Catta-Preta R, Lindtner S, Ypsilanti A, Price J, Abnousi A, Su-Feher L, Wang Y, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel D, Rubenstein JLR, Nord AS. Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546894. [PMID: 37425940 PMCID: PMC10327028 DOI: 10.1101/2023.06.28.546894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.
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Affiliation(s)
- Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
- Current Address: Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Athena Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James Price
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
- Current Address: NovaSignal, Los Angeles, CA 90064, USA
| | - Linda Su-Feher
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Yurong Wang
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Ivan Juric
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Ian R Jones
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Yin Shen
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
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16
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Wang X, Chen X, Liu G, Cai H, Le W. The Crucial Roles of Pitx3 in Midbrain Dopaminergic Neuron Development and Parkinson's Disease-Associated Neurodegeneration. Int J Mol Sci 2023; 24:ijms24108614. [PMID: 37239960 DOI: 10.3390/ijms24108614] [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: 03/29/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The degeneration of midbrain dopaminergic (mDA) neurons, particularly in the substantia nigra pars compacta (SNc), is one of the most prominent pathological hallmarks of Parkinson's disease (PD). To uncover the pathogenic mechanisms of mDA neuronal death during PD may provide therapeutic targets to prevent mDA neuronal loss and slow down the disease's progression. Paired-like homeodomain transcription factor 3 (Pitx3) is selectively expressed in the mDA neurons as early as embryonic day 11.5 and plays a critical role in mDA neuron terminal differentiation and subset specification. Moreover, Pitx3-deficient mice exhibit some canonical PD-related features, including the profound loss of SNc mDA neurons, a dramatic decrease in striatal dopamine (DA) levels, and motor abnormalities. However, the precise role of Pitx3 in progressive PD and how this gene contributes to mDA neuronal specification during early stages remains unclear. In this review, we updated the latest findings on Pitx3 by summarizing the crosstalk between Pitx3 and its associated transcription factors in mDA neuron development. We further explored the potential benefits of Pitx3 as a therapeutic target for PD in the future. To better understand the transcriptional network of Pitx3 in mDA neuron development may provide insights into Pitx3-related clinical drug-targeting research and therapeutic approaches.
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Affiliation(s)
- Xin Wang
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 611731, China
| | - Xi Chen
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 611731, China
| | - Guangdong Liu
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 611731, China
| | - Huaibin Cai
- Transgenic Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Weidong Le
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 611731, China
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17
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Kim TW, Koo SY, Riessland M, Cho H, Chaudhry F, Kolisnyk B, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534819. [PMID: 37034664 PMCID: PMC10081262 DOI: 10.1101/2023.03.29.534819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ongoing, first-in-human clinical trials illustrate the feasibility and translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, a major unresolved challenge in the field is the extensive cell death following transplantation with <10% of grafted dopamine neurons surviving. Here, we performed a pooled CRISPR/Cas9 screen to enhance survival of postmitotic dopamine neurons in vivo . We identified p53-mediated apoptotic cell death as major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival. As a translationally applicable strategy to purify postmitotic dopamine neurons, we performed a cell surface marker screen that enabled purification without the need for genetic reporters. Combining cell sorting with adalimumab pretreatment, a clinically approved and widely used TNFa inhibitor, enabled efficient engraftment of postmitotic dopamine neurons leading to extensive re-innervation and functional recovery in a preclinical PD mouse model. Thus, transient TNFa inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic human PSC-derived dopamine neurons in PD. Highlights In vivo CRISPR-Cas9 screen identifies p53 limiting survival of grafted human dopamine neurons. TNFα-NFκB pathway mediates p53-dependent human dopamine neuron deathCell surface marker screen to enrich human dopamine neurons for translational use. FDA approved TNF-alpha inhibitor rescues in vivo dopamine neuron survival with in vivo function.
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18
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Spindle function and Wnt pathway inhibition by PBX1 to suppress tumor progression via downregulating DCDC2 in colorectal cancer. Oncogenesis 2023; 12:3. [PMID: 36739270 PMCID: PMC9899229 DOI: 10.1038/s41389-023-00448-4] [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: 09/27/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 02/06/2023] Open
Abstract
PBX1 is a transcription factor that regulates a variety of genes, involved in intracellular lipid metabolism, cell proliferation, and other pathways. The promoting and inhibiting function of PBX1 in various cancer types was extensively discussed, however, there have been no studies on PBX1 proteins in colorectal cancer (CRC). This study aimed to reveal the anti-tumor function of PBX1 in CRC and the underlying molecular mechanism. Bioinformatics analysis revealed that PBX1 is downregulated in CRC, indicating that is a potential antioncogene in CRC. Overexpression of PBX1 suppresses tumor growth and metastasis in vitro and in vivo. Mechanistically, we found that PBX1 acted as a transcription factor that suppressed DCDC2 expression and inhibited spindle function. Moreover, the PBX1-DCDC2 axis controlled the Wnt pathway in CRC cells. Overexpression of DCDC2 restored CRC proliferation, metastasis abilities and Wnt pathway. In conclusion, this study suggests that PBX1 acts as a transcription factor to suppress DCDC2 expression and inhibit cell proliferation and metastasis by disrupting spindle function and the Wnt pathway in CRC.
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Liu T, Feng J, Sun Z, He M, Sun L, Dong S, Guo Z, Zhang G. Inhibition of miR-141-3p attenuates apoptosis of neural stem cells via targeting PBX1 to regulate PROK2 transcription in MCAO mice. Cell Cycle 2023; 22:403-418. [PMID: 36548024 PMCID: PMC9879164 DOI: 10.1080/15384101.2022.2121358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/27/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNA-141-3p (miR-141-3p) has been found to be altered in the brain following a stroke. Herein, we investigate the impact of miR-141-3p on the apoptosis of neural stem cells (NSCs) in mice with middle cerebral artery occlusion (MCAO) and the potential mechanisms involved. Eight-week-old mice were injected intracerebroventricularly with miR-141-3p, antagomir-141-3p, or agomir negative control 2 h before MCAO, and animal behavior tests and infraction volume measurements were performed 24 h later. MCAO-mediated brain injury and NSCs apoptosis were observed by H&E, TTC, and TUNEL staining. The expression of cleaved caspase-3 and Ki67 was detected by western blotting. The luciferase reporter assay proved that miR-141-3p in combination with its target gene PBX homeobox 1 (PBX1). Exogenous miR-141-3p (agomir-141-3p) treatment increased infraction volume and brain edema and damaged neurological functions compared to control mice. Agomir-141-3p increased miR-141-3p expression in brain tissue of mice with MCAO and suppressed PBX1 expression. The effects of the agomir-141-3p-induced apoptosis in NSCs treated with oxygen-glucose deprivation (OGD)/reoxygenation (R) were abolished by PBX1 overexpression. The results from UCSC and JASPAR database showed that prokineticin 2 (PROK2) was a transcription factor of PBX1. The expression of PROK2 was transcriptionally regulated by PBX1 using RT-PCR and western blot assays. The effects of the apoptosis-promoting caused by PBX1 inhibition in NSCs treated with OGD/R were reversed by PROK2 inhibition. In conclusion, the miR-141-3p/PBX1/PROK2 axis might be a novel therapeutic target for the apoptosis of NSCs in MCAO.
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Affiliation(s)
- Tingting Liu
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
| | - Jinzhou Feng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhenjie Sun
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
| | - Mingli He
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
| | - Linlin Sun
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
| | - Shuangshuang Dong
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
| | - Zhenwei Guo
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
| | - Guanghui Zhang
- Department of Neurology, Lianyungang Hospital affiliated to Xuzhou Medical College, Lianyungang, Jiangsu Province, China
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20
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Functional Assessment of a New PBX1 Variant in a 46,XY Fetus with Severe Syndromic Difference of Sexual Development through CRISPR-Cas9 Gene Editing. Genes (Basel) 2023; 14:genes14020273. [PMID: 36833200 PMCID: PMC9956894 DOI: 10.3390/genes14020273] [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: 10/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Sexual development is a complex process relying on numerous genes. Disruptions in some of these genes are known to cause differences of sexual development (DSDs). Advances in genome sequencing allowed the discovery of new genes implicated in sexual development, such as PBX1. We present here a fetus with a new PBX1 NM_002585.3: c.320G>A,p.(Arg107Gln) variant, presenting with severe DSD along with renal and lung malformations. Using CRISPR-Cas9 gene editing on HEK293T cells, we generated a KD cell line for PBX1. The KD cell line showed reduced proliferation and adhesion properties compared with HEK293T cells. HEK293T and KD cells were then transfected plasmids coding either PBX1 WT or PBX1-320G>A (mutant). WT or mutant PBX1 overexpression rescued cell proliferation in both cell lines. RNA-seq analyses showed less than 30 differentially expressed genes, in ectopic mutant-PBX1-expressing cells compared with WT-PBX1. Among them, U2AF1, encoding a splicing factor subunit, is an interesting candidate. Overall, mutant PBX1 seems to have modest effects compared with WT PBX1 in our model. However, the recurrence of PBX1 Arg107 substitution in patients with closely related phenotypes calls for its impact in human diseases. Further functional studies are needed to explore its effects on cellular metabolism.
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21
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van den Oord EJCG, Xie LY, Zhao M, Aberg KA, Clark SL. A single-nucleus transcriptomics study of alcohol use disorder in the nucleus accumbens. Addict Biol 2023; 28:e13250. [PMID: 36577731 DOI: 10.1111/adb.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/29/2022] [Accepted: 10/13/2022] [Indexed: 11/14/2022]
Abstract
Gene expression studies offer promising opportunities to better understand the processes underlying alcohol use disorder (AUD). As cell types differ in their function, gene expression profiles will typically vary across cell types. When studying bulk tissue, failure to account for this cellular diversity has a detrimental impact on the ability to detect disease associations. We therefore assayed the transcriptomes of 32,531 individual nuclei extracted from the nucleus accumbens (NAc) of nine donors with AUD and nine controls (72% male). Our study identified 17 clearly delineated cell types. We detected 26 transcriptome-wide significant differentially expressed genes (DEGs) that mainly involved medium spiny neurons with both D1-type and D2-type dopamine receptors, microglia (MGL) and oligodendrocytes. A higher than expected number of DEGs replicated in an existing single nucleus gene expression study of alcohol dependence in the prefrontal cortex (enrichment ratio 1.91, p value 0.019) with two genes remaining significant after a Bonferroni correction. Our most compelling result involved CD53 in MGL that replicated in the same cell type in the prefrontal cortex and was previously implicated in studies of DNA methylation, bulk gene expression and genetic variants. Several DEGs were previously reported to be associated with AUD (e.g., PER1 and MGAT5). The DEGs for MSN.3 seemed involved in neurodegeneration, disruption of circadian rhythms, alterations in glucose metabolism and changes in synaptic plasticity. For MGL, the DEGs implicated neuroinflammation and immune-related processes and for OLI, disruptions in myelination. This identification of the specific cell-types from which the association signals originate will be key for designing proper follow-up experiments and, eventually, novel clinical interventions.
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Affiliation(s)
- Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shaunna L Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, Texas, USA
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22
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Chen H, Yu Z, Niu Y, Wang L, Xu K, Liu J. Research progress of PBX1 in developmental and regenerative medicine. Int J Med Sci 2023; 20:225-231. [PMID: 36794159 PMCID: PMC9925990 DOI: 10.7150/ijms.80262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023] Open
Abstract
Pre-B-cell leukemia transcription factor 1 (PBX1) proteins are a subfamily of evolutionarily conserved atypical homeodomain transcription factors belonging to the superfamily of triple amino acid loop extension homeodomain proteins. PBX family members play crucial roles in the regulation of various pathophysiological processes. This article reviews the research progress on PBX1 in terms of structure, developmental function, and regenerative medicine. The potential mechanisms of development and research targets in regenerative medicine are also summarized. It also suggests a possible link between PBX1 in the two domains, which is expected to open up a new field for future exploration of cell homeostasis, as well as the regulation of endogenous danger signals. This would provide a new target for the study of diseases in various systems.
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Affiliation(s)
- Hao Chen
- Department of Neurovascular Surgery, First Hospital of Jilin University, 1 Xinmin Avenue Changchun 130021, Jilin Province, China
| | - Zhuyuan Yu
- Department of Neurovascular Surgery, First Hospital of Jilin University, 1 Xinmin Avenue Changchun 130021, Jilin Province, China
| | - Ye Niu
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, Jilin Province, China
| | - Litian Wang
- Department of Neurovascular Surgery, First Hospital of Jilin University, 1 Xinmin Avenue Changchun 130021, Jilin Province, China
| | - Kan Xu
- Department of Neurovascular Surgery, First Hospital of Jilin University, 1 Xinmin Avenue Changchun 130021, Jilin Province, China
| | - Jinyu Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun 130021, Jilin Province, China
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23
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Prakash N. Developmental pathways linked to the vulnerability of adult midbrain dopaminergic neurons to neurodegeneration. Front Mol Neurosci 2022; 15:1071731. [PMID: 36618829 PMCID: PMC9815185 DOI: 10.3389/fnmol.2022.1071731] [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: 10/16/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The degeneration of dopaminergic and other neurons in the aging brain is considered a process starting well beyond the infantile and juvenile period. In contrast to other dopamine-associated neuropsychiatric disorders, such as schizophrenia and drug addiction, typically diagnosed during adolescence or young adulthood and, thus, thought to be rooted in the developing brain, Parkinson's Disease (PD) is rarely viewed as such. However, evidences have accumulated suggesting that several factors might contribute to an increased vulnerability to death of the dopaminergic neurons at an already very early (developmental) phase in life. Despite the remarkable ability of the brain to compensate such dopamine deficits, the early loss or dysfunction of these neurons might predispose an individual to suffer from PD because the critical threshold of dopamine function will be reached much earlier in life, even if the time-course and strength of naturally occurring and age-dependent dopaminergic cell death is not markedly altered in this individual. Several signaling and transcriptional pathways required for the proper embryonic development of the midbrain dopaminergic neurons, which are the most affected in PD, either continue to be active in the adult mammalian midbrain or are reactivated at the transition to adulthood and under neurotoxic conditions. The persistent activity of these pathways often has neuroprotective functions in adult midbrain dopaminergic neurons, whereas the reactivation of silenced pathways under pathological conditions can promote the survival and even regeneration of these neurons in the lesioned or aging brain. This article summarizes our current knowledge about signaling and transcription factors involved in midbrain dopaminergic neuron development, whose reduced gene dosage or signaling activity are implicated in a lower survival rate of these neurons in the postnatal or aging brain. It also discusses the evidences supporting the neuroprotection of the midbrain dopaminergic system after the external supply or ectopic expression of some of these secreted and nuclear factors in the adult and aging brain. Altogether, the timely monitoring and/or correction of these signaling and transcriptional pathways might be a promising approach to a much earlier diagnosis and/or prevention of PD.
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24
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Nishimura K, Yang S, Lee KW, Ásgrímsdóttir ES, Nikouei K, Paslawski W, Gnodde S, Lyu G, Hu L, Saltó C, Svenningsson P, Hjerling-Leffler J, Linnarsson S, Arenas E. Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation. Stem Cell Reports 2022; 18:337-353. [PMID: 36400027 PMCID: PMC9860082 DOI: 10.1016/j.stemcr.2022.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
Stem cell technologies provide new opportunities for modeling cells in health and disease and for regenerative medicine. In both cases, developmental knowledge and defining the molecular properties and quality of the cell types is essential. In this study, we identify developmental factors important for the differentiation of human embryonic stem cells (hESCs) into functional midbrain dopaminergic (mDA) neurons. We found that laminin-511, and dual canonical and non-canonical WNT activation followed by GSK3β inhibition plus FGF8b, improved midbrain patterning. In addition, neurogenesis and differentiation were enhanced by activation of liver X receptors and inhibition of fibroblast growth factor signaling. Moreover, single-cell RNA-sequencing analysis revealed a developmental dynamics similar to that of the endogenous human ventral midbrain and the emergence of high-quality molecularly defined midbrain cell types, including mDA neurons. Our study identifies novel factors important for human midbrain development and opens the door for a future application of molecularly defined hESC-derived cell types in Parkinson disease.
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Affiliation(s)
- Kaneyasu Nishimura
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Shanzheng Yang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ka Wai Lee
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Emilía Sif Ásgrímsdóttir
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kasra Nikouei
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Wojciech Paslawski
- Department of Clinical Neuroscience, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Sabine Gnodde
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Guochang Lyu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Lijuan Hu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Carmen Saltó
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ernest Arenas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.
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25
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Wang L, Tian Y, Cao Y, Ma Q, Zhao S. PBX1 attenuates H 2O 2-induced oxidant stress in human trabecular meshwork cells via promoting NANOG-mediated PI3K/AKT signaling pathway. Cell Stress Chaperones 2022; 27:673-684. [PMID: 36253638 PMCID: PMC9672266 DOI: 10.1007/s12192-022-01304-x] [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: 04/18/2022] [Accepted: 10/04/2022] [Indexed: 01/25/2023] Open
Abstract
Oxidative stress-induced excessive extracellular matrix (ECM) deposition in trabecular meshwork (TM) tissue is considered the major pathological procedure of glaucoma. This study aimed to explore the role and regulatory mechanism of pre-B-cell leukemia transcription factor 1 (PBX1) in H2O2-induced human trabecular meshwork cells (HTMCs). Expressions of PBX1, NANOG, ECM, and pathway-related factors were detected by qRT-PCR and western blot. Cell viability and apoptosis of HTMCs were measured using CCK-8 and flow cytometry assays. Reactive oxygen species (ROS), superoxide dismutase (SOD), and L-glutathione (GSH) levels were detected to evaluate oxidative stress. Through luciferase reporter assay, the association between PBX1 and NANOG was verified. Results presented that PBX1 was significantly upregulated in H2O2-induced HTMCs. Functionally, PBX1 and NANOG promoted cell viability, inhibited cell apoptosis and ECM deposition, suppressed ROS accumulation, and enhanced the productions of SOD and GSH in H2O2-stimulated HTMCs, while PBX1 inhibition showed the opposite effects. In addition, PBX1 promoted the transcription of NANOG by upregulating the promoter activity of NANOG which activated the PI3K-AKT signaling pathway. What's more, the inhibitions of PI3K-AKT signaling pathway or NANOG reversed the protective effect of PBX1 on H2O2-stimulated HTMCs. In summary, our study firstly revealed that PBX1 attenuated the oxidative damage in HTMCs via regulating NANOG-mediated PI3K/AKT signaling, suggesting that PBX1 might be a potential treatment target for glaucoma patients.
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Affiliation(s)
- Liang Wang
- Department of Ophthalmology, Xi'an No. 1 Hospital, No. 30 Powder Lane South Street, Xi'an, 710002, China
| | - Ying Tian
- Department of Ophthalmology, Xi'an No. 1 Hospital, No. 30 Powder Lane South Street, Xi'an, 710002, China
| | - Yan Cao
- Department of Ophthalmology, Xi'an No. 1 Hospital, No. 30 Powder Lane South Street, Xi'an, 710002, China
| | - Qiang Ma
- Department of Ophthalmology, Xi'an No. 1 Hospital, No. 30 Powder Lane South Street, Xi'an, 710002, China
| | - Shuai Zhao
- Department of Ophthalmology, Xi'an No. 1 Hospital, No. 30 Powder Lane South Street, Xi'an, 710002, China.
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26
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Babina M, Franke K, Bal G. How "Neuronal" Are Human Skin Mast Cells? Int J Mol Sci 2022; 23:ijms231810871. [PMID: 36142795 PMCID: PMC9505265 DOI: 10.3390/ijms231810871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Mast cells are evolutionarily old cells and the principal effectors in allergic responses and inflammation. They are seeded from the yolk sac during embryogenesis or are derived from hematopoietic progenitors and are therefore related to other leukocyte subsets, even though they form a separate clade in the hematopoietic system. Herein, we systematically bundle information from several recent high-throughput endeavors, especially those comparing MCs with other cell types, and combine such information with knowledge on the genes’ functions to reveal groups of neuronal markers specifically expressed by MCs. We focus on recent advances made regarding human tissue MCs, but also refer to studies in mice. In broad terms, genes hyper-expressed in MCs, but largely inactive in other myelocytes, can be classified into subcategories such as traffic/lysosomes (MLPH and RAB27B), the dopamine system (MAOB, DRD2, SLC6A3, and SLC18A2), Ca2+-related entities (CALB2), adhesion molecules (L1CAM and NTM) and, as an overall principle, the transcription factors and modulators of transcriptional activity (LMO4, PBX1, MEIS2, and EHMT2). Their function in MCs is generally unknown but may tentatively be deduced by comparison with other systems. MCs share functions with the nervous system, as they express typical neurotransmitters (histamine and serotonin) and a degranulation machinery that shares features with the neuronal apparatus at the synapse. Therefore, selective overlaps are plausible, and they further highlight the uniqueness of MCs within the myeloid system, as well as when compared with basophils. Apart from investigating their functional implications in MCs, a key question is whether their expression in the lineage is due to the specific reactivation of genes normally silenced in leukocytes or whether the genes are not switched off during mastocytic development from early progenitors.
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Affiliation(s)
- Magda Babina
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
- Correspondence:
| | - Kristin Franke
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Gürkan Bal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
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27
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Mary L, Leclerc D, Gilot D, Belaud-Rotureau MA, Jaillard S. The TALE never ends: A comprehensive overview of the role of PBX1, a TALE transcription factor, in human developmental defects. Hum Mutat 2022; 43:1125-1148. [PMID: 35451537 DOI: 10.1002/humu.24388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 11/07/2022]
Abstract
PBX1 is a highly conserved atypical homeodomain transcription factor (TF) belonging to the TALE (three amino acid loop extension) family. Dimerized with other TALE proteins, it can interact with numerous partners and reach dozens of regulating sequences, suggesting its role as a pioneer factor. PBX1 is expressed throughout the embryonic stages (as early as the blastula stage) in vertebrates. In human, PBX1 germline variations are linked to syndromic renal anomalies (CAKUTHED). In this review, we summarized available data on PBX1 functions, PBX1-deficient animal models, and PBX1 germline variations in humans. Two types of genetic alterations were identified in PBX1 gene. PBX1 missense variations generate a severe phenotype including lung hypoplasia, cardiac malformations, and sexual development defects (DSDs). Conversely, truncating variants generate milder phenotypes (mainly cryptorchidism and deafness). We suggest that defects in PBX1 interactions with various partners, including proteins from the HOX (HOXA7, HOXA10, etc.), WNT (WNT9B, WNT3), and Polycomb (BMI1, EED) families are responsible for abnormal proliferation and differentiation of the embryonic mesenchyme. These alterations could explain most of the defects observed in humans. However, some phenotype variability (especially DSDs) remains poorly understood. Further studies are needed to explore the TALE family in greater depth.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Delphine Leclerc
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - David Gilot
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
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28
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Yadav A, Verhaegen S, Filis P, Domanska D, Lyle R, Sundaram AYM, Leithaug M, Østby GC, Aleksandersen M, Berntsen HF, Zimmer KE, Fowler PA, Paulsen RE, Ropstad E. Exposure to a human relevant mixture of persistent organic pollutants or to perfluorooctane sulfonic acid alone dysregulates the developing cerebellum of chicken embryo. ENVIRONMENT INTERNATIONAL 2022; 166:107379. [PMID: 35792514 DOI: 10.1016/j.envint.2022.107379] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/07/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Prenatal exposure to persistent organic pollutants (POPs) is associated with neurodevelopmental disorders. In the present study, we explored whether a human-relevant POP mixture affects the development of chicken embryo cerebellum. We used a defined mixture of 29 POPs, with chemical composition and concentrations based on blood levels in the Scandinavian population. We also evaluated exposure to a prominent compound in the mixture, perfluorooctane sulfonic acid (PFOS), alone. Embryos (n = 7-9 per exposure group) were exposed by injection directly into the allantois at embryonic day 13 (E13). Cerebella were isolated at E17 and subjected to morphological, RNA-seq and shot-gun proteomics analyses. There was a reduction in thickness of the molecular layer of cerebellar cortex in both exposure scenarios. Exposure to the POP mixture significantly affected expression of 65 of 13,800 transcripts, and 43 of 2,568 proteins, when compared to solvent control. PFOS alone affected expression of 80 of 13,859 transcripts, and 69 of 2,555 proteins. Twenty-five genes and 15 proteins were common for both exposure groups. These findings point to alterations in molecular events linked to retinoid X receptor (RXR) signalling, neuronal cell proliferation and migration, cellular stress responses including unfolded protein response, lipid metabolism, and myelination. Exposure to the POP mixture increased methionine oxidation, whereas PFOS decreased oxidation. Several of the altered genes and proteins are involved in a wide variety of neurological disorders. We conclude that POP exposure can interfere with fundamental aspects of neurodevelopment, altering molecular pathways that are associated with adverse neurocognitive and behavioural outcomes.
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Affiliation(s)
- Ajay Yadav
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, NO-0316 Oslo, Norway.
| | - Steven Verhaegen
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Panagiotis Filis
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Diana Domanska
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway; Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
| | - Arvind Y M Sundaram
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Gunn Charlotte Østby
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Mona Aleksandersen
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Hanne Friis Berntsen
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway; National Institute of Occupational Health, P.O. Box 5330 Majorstuen, NO-0304, Oslo, Norway.
| | - Karin Elisabeth Zimmer
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
| | - Paul A Fowler
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Ragnhild Elisabeth Paulsen
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, P.O. Box 1068, Blindern, NO-0316 Oslo, Norway.
| | - Erik Ropstad
- Department of Production Animal Clinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
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29
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Kamath T, Abdulraouf A, Burris SJ, Langlieb J, Gazestani V, Nadaf NM, Balderrama K, Vanderburg C, Macosko EZ. Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease. Nat Neurosci 2022; 25:588-595. [PMID: 35513515 PMCID: PMC9076534 DOI: 10.1038/s41593-022-01061-1] [Citation(s) in RCA: 158] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/24/2022] [Indexed: 12/14/2022]
Abstract
The loss of dopamine (DA) neurons within the substantia nigra pars compacta (SNpc) is a defining pathological hallmark of Parkinson's disease (PD). Nevertheless, the molecular features associated with DA neuron vulnerability have not yet been fully identified. Here, we developed a protocol to enrich and transcriptionally profile DA neurons from patients with PD and matched controls, sampling a total of 387,483 nuclei, including 22,048 DA neuron profiles. We identified ten populations and spatially localized each within the SNpc using Slide-seq. A single subtype, marked by the expression of the gene AGTR1 and spatially confined to the ventral tier of SNpc, was highly susceptible to loss in PD and showed the strongest upregulation of targets of TP53 and NR2F2, nominating molecular processes associated with degeneration. This same vulnerable population was specifically enriched for the heritable risk associated with PD, highlighting the importance of cell-intrinsic processes in determining the differential vulnerability of DA neurons to PD-associated degeneration.
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Affiliation(s)
- Tushar Kamath
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Abdulraouf Abdulraouf
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - S J Burris
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Jonah Langlieb
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Vahid Gazestani
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Karol Balderrama
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Charles Vanderburg
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, Cambridge, MA, USA.
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA.
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30
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Xie S, Yang J, Huang S, Fan Y, Xu T, He J, Guo J, Ji X, Wang Z, Li P, Chen J, Zhang Y. Disrupted myelination network in the cingulate cortex of Parkinson's disease. IET Syst Biol 2022; 16:98-119. [PMID: 35394697 PMCID: PMC9290774 DOI: 10.1049/syb2.12043] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
The cingulate cortex is part of the conserved limbic system, which is considered as a hub of emotional and cognitive control. Accumulating evidence suggested that involvement of the cingulate cortex is significant for cognitive impairment of Parkinson's disease (PD). However, mechanistic studies of the cingulate cortex in PD pathogenesis are limited. Here, transcriptomic and regulatory network analyses were conducted for the cingulate cortex in PD. Enrichment and clustering analyses showed that genes involved in regulation of membrane potential and glutamate receptor signalling pathway were upregulated. Importantly, myelin genes and the oligodendrocyte development pathways were markedly downregulated, indicating disrupted myelination in PD cingulate cortex. Cell‐type‐specific signatures revealed that myelinating oligodendrocytes were the major cell type damaged in the PD cingulate cortex. Furthermore, downregulation of myelination pathways in the cingulate cortex were shared and validated in another independent RNAseq cohort of dementia with Lewy bodies (DLB). In combination with ATACseq data, gene regulatory networks (GRNs) were further constructed for 32 transcription factors (TFs) and 466 target genes among differentially expressed genes (DEGs) using a tree‐based machine learning algorithm. Several transcription factors, including Olig2, Sox8, Sox10, E2F1, and NKX6‐2, were highlighted as key nodes in a sub‐network, which control many overlapping downstream targets associated with myelin formation and gliogenesis. In addition, the authors have validated a subset of DEGs by qPCRs in two PD mouse models. Notably, seven of these genes,TOX3, NECAB2 NOS1, CAPN3, NR4A2, E2F1 and FOXP2, have been implicated previously in PD or neurodegeneration and are worthy of further studies as novel candidate genes. Together, our findings provide new insights into the role of remyelination as a promising new approach to treat PD after demyelination.
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Affiliation(s)
- Song Xie
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiajun Yang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shenghui Huang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yuanlan Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tao Xu
- Molecular Neuropharmacology Lab, School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,The Eye-Brain Research Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang Province, China
| | - Jiangshuang He
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiahao Guo
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, Louisiana, USA
| | - Zhibo Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Peijun Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiangfan Chen
- Molecular Neuropharmacology Lab, School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,The Eye-Brain Research Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang Province, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.,The Eye-Brain Research Center, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang Province, China.,Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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31
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PBX1 attenuates 6-OHDA-induced oxidative stress and apoptosis and affects PINK1/PARKIN expression in dopaminergic neurons via FOXA1. Cytotechnology 2022; 74:217-229. [PMID: 35464170 PMCID: PMC8975925 DOI: 10.1007/s10616-021-00518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/31/2021] [Indexed: 11/03/2022] Open
Abstract
PBX1 expression has been found to be significantly reduced in nigrostriatal neurons of PD patients, but the effect of PBX1 on ROS and apoptosis in nigrostriatal dopamine neurons is not yet known. This paper aimed to explore whether PBX1 could be involved in the development of PD. The construction of the in vitro PD model was followed by the determination of PBX1 expression. Then, PBX1 was overexpressed to observe the changes in the cell viability, TH expression, oxidative stress and apoptosis of the model. The mitochondrial membrane potential analysis and detection of PINK1/parkin expression were also conducted. To observe whether FOXA1 was involved in the mechanism, its expression was measured, and its association with PBX1 was determined. Subsequently, FOXA1 was silenced to observe whether PBX1 did effects on dopaminergic neuron via FOXA1. PBX1 attenuates 6-OHDA-induced dopaminergic neuronal cell injury and oxidative stress, and apoptosis. Its overexpression ameliorates mitochondrial dysfunction in dopaminergic neurons and upregulates the expression of PINK1/parkin. PBX1 could combine with FOXA1 and affects 6-OHDA-induced dopaminergic neuronal damage and regulates PINK1/PARKIN expression via FOXA1. To conclude, PBX1 attenuates 6-OHDA-induced oxidative stress and apoptosis in dopaminergic neurons, and affected PINK1/PARKIN expression via FOXA1, which indicates the great potential of the PBX1 in prevention against PD.
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32
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Ali M, Ribeiro MM, Del Sol A. Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research. Methods Mol Biol 2022; 2471:83-109. [PMID: 35175592 DOI: 10.1007/978-1-0716-2193-6_4] [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: 06/14/2023]
Abstract
The large-scale development of high-throughput sequencing technologies has not only allowed the generation of reliable omics data related to various regulatory layers but also the development of novel computational models in the field of stem cell research. These computational approaches have enabled the disentangling of a complex interplay between these interrelated layers of regulation by interpreting large quantities of biomedical data in a systematic way. In the context of stem cell research, network modeling of complex gene-gene interactions has been successfully used for understanding the mechanisms underlying stem cell differentiation and cellular conversion. Notably, it has proven helpful for predicting cell-fate determinants and signaling molecules controlling such processes. This chapter will provide an overview of various computational approaches that rely on single-cell and/or bulk RNA sequencing data for elucidating the molecular underpinnings of cell subpopulation identities, lineage specification, and the process of cell-fate decisions. Furthermore, we discuss how these computational methods provide the right framework for computational modeling of biological systems in order to address long-standing challenges in the stem cell field by guiding experimental efforts in stem cell research and regenerative medicine.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Mariana Messias Ribeiro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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33
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Wang Y, Sui Y, Lian A, Han X, Liu F, Zuo K, Liu M, Sun W, Wang Z, Liu Z, Zou F, Lu R, Jin M, Du H, Xu K, Liu X, Liu J. PBX1 Attenuates Hair Follicle-Derived Mesenchymal Stem Cell Senescence and Apoptosis by Alleviating Reactive Oxygen Species-Mediated DNA Damage Instead of Enhancing DNA Damage Repair. Front Cell Dev Biol 2021; 9:739868. [PMID: 34869323 PMCID: PMC8634257 DOI: 10.3389/fcell.2021.739868] [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] [Received: 07/28/2021] [Accepted: 10/25/2021] [Indexed: 12/11/2022] Open
Abstract
Tissues and organs undergo structural deterioration and functional decline during aging. DNA damage is considered a major cause of stem cell senescence. Although stem cells develop sophisticated DNA repair systems, when the intrinsic and extrinsic insults exceed the DNA repair capacity, cellular senescence, and age-related diseases inevitably occur. Therefore, the prevention and alleviation of DNA damage is an alternative to DNA repair in attenuating stem cell senescence and preventing age-related diseases. Pre-B-cell leukaemia homeobox 1 (PBX1) participates in maintaining the pluripotency of human embryonic and haematopoietic stem cells. Our recent studies showed that PBX1 promotes hair follicle-derived mesenchymal stem cell (HF-MSC) proliferation, decreases cellular senescence and apoptosis, and enhances induced pluripotent stem cell generation. Whether PBX1 attenuates HF-MSC senescence and apoptosis by alleviating DNA damage or by enhancing DNA repair remains unknown. In this study, we aimed to determine the effects of PBX1 on the intrinsic ROS or extrinsic H2O2-induced cellular senescence of HF-MSCs. To this end, we generated HF-MSCs overexpressing either PBX1, or poly (ADP-ribose) polymerase 1, or both. Our results showed that PBX1 overexpression attenuates HF-MSC senescence and apoptosis by alleviating reactive oxygen species (ROS)-mediated DNA damage instead of enhancing DNA repair. This is the first study to report that PBX1 attenuates stem cell senescence and apoptosis by alleviating DNA damage. It provides new insight into the mechanism of stem cell senescence and lays the foundation for the development of strategies for age-related disease prevention and treatment, and in particular, hair follicle repair and regeneration.
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Affiliation(s)
- Yuan Wang
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Yutong Sui
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Aobo Lian
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Xing Han
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Feilin Liu
- Eye Center, The Second Hospital of Jilin University, Changchun, China.,Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Kuiyang Zuo
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Mingsheng Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Wei Sun
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Ziyu Wang
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Zinan Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Fei Zou
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Rifeng Lu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Minghua Jin
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Haiying Du
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Kan Xu
- Department of Neurovascular Surgery, First Hospital of Jilin University, Changchun, China
| | - Xiaomei Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Jinyu Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
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34
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Veiga RN, de Oliveira JC, Gradia DF. PBX1: a key character of the hallmarks of cancer. J Mol Med (Berl) 2021; 99:1667-1680. [PMID: 34529123 DOI: 10.1007/s00109-021-02139-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022]
Abstract
Pre-B-cell leukemia homeobox transcription factor 1 (PBX1) was first identified as part of a fusion protein resulting from the chromosomal translocation t(1;19) in pre-B cell acute lymphoblastic leukemias. Since then, PBX1 has been associated with important developmental programs, and its expression dysregulation has been related to multifactorial disorders, including cancer. As PBX1 overexpression in many cancers is correlated to poor prognosis, we sought to understand how this transcription factor contributes to carcinogenesis, and to organize PBX1's roles in the hallmarks of cancer. There is enough evidence to associate PBX1 with at least five hallmarks: sustaining proliferative signaling, activating invasion and metastasis, inducing angiogenesis, resisting cell death, and deregulating cellular energetics. The lack of studies investigating a possible role for PBX1 on the remaining hallmarks made it impossible to defend or refute its contribution on them. However, the functions of some of the PBX1's transcription targets indicate a potential engagement of PBX1 in the avoidance of immune destruction and in the tumor-promoting inflammation hallmarks. Interestingly, PBX1 might be a player in tumor suppression by activating the transcription of some DNA damage response genes. This is the first review organizing PBX1 roles into the hallmarks of cancer. Thus, we encourage future studies to uncover the PBX1's underlying mechanisms to promote carcinogenesis, for it is a promising diagnostic and prognostic biomarker, as well as a potential target in cancer treatment.
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Affiliation(s)
- Rafaela Nasser Veiga
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Postgraduate Program in Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Jaqueline Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Postgraduate Program in Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Postgraduate Program in Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil.
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35
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Nfe2l1 deficiency mitigates streptozotocin-induced pancreatic β-cell destruction and development of diabetes in male mice. Food Chem Toxicol 2021; 158:112633. [PMID: 34699923 DOI: 10.1016/j.fct.2021.112633] [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: 06/17/2021] [Revised: 10/07/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022]
Abstract
Streptozotocin (STZ) is a pancreatic β cell-specific toxicant that is widely used to generate models of diabetes in rodents as well as in the treatment of tumors derived from pancreatic β cells. DNA alkylation, oxidative stress and mitochondrial toxicity have been recognized as the mechanisms for STZ-induced pancreatic β cell damage. Here, we found that pancreatic β cell-specific deficiency of nuclear factor erythroid-derived factor 2-related factor 1 (NFE2L1), a master regulator of the cellular adaptive response to a variety of stresses, in mice led to a dramatic resistance to STZ-induced hyperglycemia. Indeed, fifteen days subsequent to last dosage of STZ, the pancreatic β cell specific Nfe2l1 knockout [Nfe2l1(β)-KO] mice showed reduced hyperglycemia, improved glucose tolerance, higher plasma insulin and more intact islets surrounded by exocrine acini compared to the Nfe2l1-Flox control mice with the same treatment. Immunohistochemistry staining revealed a greater amount of insulin-positive cells in the pancreas of Nfe2l1(β)-KO mice than those in Nfe2l1-Flox mice 15 days after the last STZ injection. In line with this observation, both isolated Nfe2l1(β)-KO islets and Nfe2l1-deficient MIN6 (Nfe2l1-KD) cells were resistant to STZ-induced toxicity and apoptosis. Furthermore, pretreatment of the MIN6 cells with glycolysis inhibitor 2-Deoxyglucose sensitized Nfe2l1-KD cells to STZ-induced toxicity. These findings demonstrated that loss of Nfe2l1 attenuates pancreatic β cells damage and dysfunction caused by STZ exposure, partially due to Nfe2l1 deficiency-induced metabolic switch to enhanced glycolysis.
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36
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Fernandes HJR, Patikas N, Foskolou S, Field SF, Park JE, Byrne ML, Bassett AR, Metzakopian E. Single-Cell Transcriptomics of Parkinson's Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses. Cell Rep 2021; 33:108263. [PMID: 33053338 DOI: 10.1016/j.celrep.2020.108263] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
The advent of induced pluripotent stem cell (iPSC)-derived neurons has revolutionized Parkinson's disease (PD) research, but single-cell transcriptomic analysis suggests unresolved cellular heterogeneity within these models. Here, we perform the largest single-cell transcriptomic study of human iPSC-derived dopaminergic neurons to elucidate gene expression dynamics in response to cytotoxic and genetic stressors. We identify multiple neuronal subtypes with transcriptionally distinct profiles and differential sensitivity to stress, highlighting cellular heterogeneity in dopamine in vitro models. We validate this disease model by showing robust expression of PD GWAS genes and overlap with postmortem adult substantia nigra neurons. Importantly, stress signatures are ameliorated using felodipine, an FDA-approved drug. Using isogenic SNCA-A53T mutants, we find perturbations in glycolysis, cholesterol metabolism, synaptic signaling, and ubiquitin-proteasomal degradation. Overall, our study reveals cell type-specific perturbations in human dopamine neurons, which will further our understanding of PD and have implications for cell replacement therapies.
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Affiliation(s)
- Hugo J R Fernandes
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK; Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nikolaos Patikas
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Stefanie Foskolou
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK; Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sarah F Field
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Meg L Byrne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AH, UK.
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37
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Gley K, Hadlich F, Trakooljul N, Haack F, Murani E, Gimsa U, Wimmers K, Ponsuksili S. Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic System. Front Genet 2021; 12:635794. [PMID: 34490028 PMCID: PMC8417057 DOI: 10.3389/fgene.2021.635794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
The molecular basis of porcine coping behavior (CB) relies on a sophisticated interplay of genetic and epigenetic features. Deep sequencing technologies allowed the identification of a plethora of new regulatory small non-coding RNA (sncRNA). We characterized mRNA and sncRNA profiles of central parts of the physiological stress response system including amygdala, hippocampus, hypothalamus and adrenal gland using systems biology for integration. Therefore, ten each of high- (HR) and low- (LR) reactive pigs (n = 20) carrying a CB associated haplotype in a prominent QTL-region on SSC12 were selected for mRNA and sncRNA expression profiling. The molecular markers related to the LR group included ATP1B2, MPDU1, miR-19b-5p, let-7g-5p, and 5′-tiRNALeu in the adrenal gland, miR-194a-5p, miR-125a-5p, miR-7-1-5p, and miR-107-5p in the hippocampus and CBL and PVRL1 in the hypothalamus. Interestingly, amygdalae of the LR group showed 5′-tiRNA and 5′-tRF (5′-tRFLys, 5′-tiRNALys, 5′-tiRNACys, and 5′-tiRNAGln) enrichment. Contrarily, molecular markers associated with the HR group encompassed miR-26b-5p, tRNAArg, tRNAGlyiF in the adrenal gland, IGF1 and APOD in the amygdala and PBX1, TOB1, and C18orf1 in the hippocampus and miR-24 in the hypothalamus. In addition, hypothalami of the HR group were characterized by 3′-tiRNA enrichment (3′-tiRNAGln, 3′-tiRNAAsn, 3′-tiRNAVal, 3′-tRFPro, 3′-tiRNACys, and 3′-tiRNAAla) and 3′-tRFs enrichment (3′-tRFAsn, 3′-tRFGlu, and 3′-tRFVal). These evidence suggest that tRNA-derived fragments and their cleavage activity are a specific marker for coping behavior. Data integration revealed new bio-signatures of important molecular interactions on a multi-transcript level in HPA axis and limbic system of pigs carrying a CB-associated haplotype.
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Affiliation(s)
- Kevin Gley
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Fiete Haack
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Ulrike Gimsa
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Behavioral Physiology, Dummerstorf, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
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38
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Toledo EM, Yang S, Gyllborg D, van Wijk KE, Sinha I, Varas-Godoy M, Grigsby CL, Lönnerberg P, Islam S, Steffensen KR, Linnarsson S, Arenas E. Srebf1 Controls Midbrain Dopaminergic Neurogenesis. Cell Rep 2021; 31:107601. [PMID: 32375051 DOI: 10.1016/j.celrep.2020.107601] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/17/2020] [Accepted: 04/10/2020] [Indexed: 12/20/2022] Open
Abstract
Liver X receptors (LXRs) and their ligands are potent regulators of midbrain dopaminergic (mDA) neurogenesis and differentiation. However, the molecular mechanisms by which LXRs control these functions remain to be elucidated. Here, we perform a combined transcriptome and chromatin immunoprecipitation sequencing (ChIP-seq) analysis of midbrain cells after LXR activation, followed by bioinformatic analysis to elucidate the transcriptional networks controlling mDA neurogenesis. Our results identify the basic helix-loop-helix transcription factor sterol regulatory element binding protein 1 (SREBP1) as part of a cluster of proneural transcription factors in radial glia and as a regulator of transcription factors controlling mDA neurogenesis, such as Foxa2. Moreover, loss- and gain-of-function experiments in vitro and in vivo demonstrate that Srebf1 is both required and sufficient for mDA neurogenesis. Our data, thus, identify Srebf1 as a central player in mDA neurogenesis.
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Affiliation(s)
- Enrique M Toledo
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Shanzheng Yang
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Daniel Gyllborg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Kim E van Wijk
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Manuel Varas-Godoy
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christopher L Grigsby
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden; Division of Biomaterials, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Peter Lönnerberg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Saiful Islam
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Knut R Steffensen
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden
| | - Ernest Arenas
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solnavägen 9, 17177 Stockholm, Sweden.
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39
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Almeida N, Chung MWH, Drudi EM, Engquist EN, Hamrud E, Isaacson A, Tsang VSK, Watt FM, Spagnoli FM. Employing core regulatory circuits to define cell identity. EMBO J 2021; 40:e106785. [PMID: 33934382 PMCID: PMC8126924 DOI: 10.15252/embj.2020106785] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between extrinsic signaling and downstream gene networks controls the establishment of cell identity during development and its maintenance in adult life. Advances in next-generation sequencing and single-cell technologies have revealed additional layers of complexity in cell identity. Here, we review our current understanding of transcription factor (TF) networks as key determinants of cell identity. We discuss the concept of the core regulatory circuit as a set of TFs and interacting factors that together define the gene expression profile of the cell. We propose the core regulatory circuit as a comprehensive conceptual framework for defining cellular identity and discuss its connections to cell function in different contexts.
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Affiliation(s)
- Nathalia Almeida
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Matthew W H Chung
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Elena M Drudi
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Elise N Engquist
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Eva Hamrud
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Abigail Isaacson
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Victoria S K Tsang
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Francesca M Spagnoli
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
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40
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Monteiro FA, Miranda RM, Samina MC, Dias AF, Raposo AASF, Oliveira P, Reguenga C, Castro DS, Lima D. Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord. Front Cell Dev Biol 2021; 9:642697. [PMID: 33996801 PMCID: PMC8117147 DOI: 10.3389/fcell.2021.642697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/30/2021] [Indexed: 11/28/2022] Open
Abstract
The spinal cord dorsal horn is a major station for integration and relay of somatosensory information and comprises both excitatory and inhibitory neuronal populations. The homeobox gene Tlx3 acts as a selector gene to control the development of late-born excitatory (dILB) neurons by specifying glutamatergic transmitter fate in dorsal spinal cord. However, since Tlx3 direct transcriptional targets remain largely unknown, it remains to be uncovered how Tlx3 functions to promote excitatory cell fate. Here we combined a genomics approach based on chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) and expression profiling, with validation experiments in Tlx3 null embryos, to characterize the transcriptional program of Tlx3 in mouse embryonic dorsal spinal cord. We found most dILB neuron specific genes previously identified to be directly activated by Tlx3. Surprisingly, we found Tlx3 also directly represses many genes associated with the alternative inhibitory dILA neuronal fate. In both cases, direct targets include transcription factors and terminal differentiation genes, showing that Tlx3 directly controls cell identity at distinct levels. Our findings provide a molecular frame for the master regulatory role of Tlx3 in developing glutamatergic dILB neurons. In addition, they suggest a novel function for Tlx3 as direct repressor of GABAergic dILA identity, pointing to how generation of the two alternative cell fates being tightly coupled.
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Affiliation(s)
- Filipe A Monteiro
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Rafael M Miranda
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Marta C Samina
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana F Dias
- Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Alexandre A S F Raposo
- Molecular Neurobiology Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Diagnostics, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Carlos Reguenga
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Diogo S Castro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Molecular Neurobiology Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Stem Cells & Neurogenesis Group, Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Deolinda Lima
- Unidade de Biologia Experimental, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Pain Research Group, Instituto de Biologia Molecular e Celular, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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41
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Single-cell brain atlas of Parkinson's disease mouse model. J Genet Genomics 2021; 48:277-288. [PMID: 34052184 DOI: 10.1016/j.jgg.2021.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/26/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease, leading to the impairment of movement execution. PD pathogenesis has been largely investigated, either limited to bulk transcriptomic levels or at certain cell types, which failed to capture the cellular heterogeneity and intrinsic interplays among distinct cell types. Here, we report the application of single-nucleus RNA-seq on midbrain, striatum, and cerebellum of the α-syn-A53T mouse, a well-established PD mouse model, and matched controls, generating the first single cell transcriptomic atlas for the PD model mouse brain composed of 46,174 individual cells. Additionally, we comprehensively depicte the dysfunctions in PD pathology, covering the elevation of NF-κB activity, the alteration of ion channel components, the perturbation of protein homeostasis network, and the dysregulation of glutamatergic signaling. Notably, we identify a variety of cell types closely associated with PD risk genes. Taken together, our study provides valuable resources to systematically dissect the molecular mechanism of PD pathogenesis at the single-cell resolution, which facilitates the development of novel approaches for diagnosis and therapies against PD.
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42
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Parkinson's Disease Master Regulators on Substantia Nigra and Frontal Cortex and Their Use for Drug Repositioning. Mol Neurobiol 2020; 58:1517-1534. [PMID: 33211252 DOI: 10.1007/s12035-020-02203-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
Parkinson's disease (PD) is among the most prevalent neurodegenerative diseases. Available evidences support the view of PD as a complex disease, being the outcome of interactions between genetic and environmental factors. In face of diagnosis and therapy challenges, and the elusive PD etiology, the use of alternative methodological approaches for the elucidation of the disease pathophysiological mechanisms and proposal of novel potential therapeutic interventions has become increasingly necessary. In the present study, we first reconstructed the transcriptional regulatory networks (TN), centered on transcription factors (TF), of two brain regions affected in PD, the substantia nigra pars compacta (SNc) and the frontal cortex (FCtx). Then, we used case-control studies data from these regions to identify TFs working as master regulators (MR) of the disease, based on region-specific TNs. Twenty-nine regulatory units enriched with differentially expressed genes were identified for the SNc, and twenty for the FCtx, all of which were considered MR candidates for PD. Three consensus MR candidates were found for SNc and FCtx, namely ATF2, SLC30A9, and ZFP69B. In order to search for novel potential therapeutic interventions, we used these consensus MR candidate signatures as input to the Connectivity Map (CMap), a computational drug repositioning webtool. This analysis resulted in the identification of four drugs that reverse the expression pattern of all three MR consensus simultaneously, benperidol, harmaline, tubocurarine chloride, and vorinostat, thus suggested as novel potential PD therapeutic interventions.
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43
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Nouri P, Götz S, Rauser B, Irmler M, Peng C, Trümbach D, Kempny C, Lechermeier CG, Bryniok A, Dlugos A, Euchner E, Beckers J, Brodski C, Klümper C, Wurst W, Prakash N. Dose-Dependent and Subset-Specific Regulation of Midbrain Dopaminergic Neuron Differentiation by LEF1-Mediated WNT1/b-Catenin Signaling. Front Cell Dev Biol 2020; 8:587778. [PMID: 33195246 PMCID: PMC7649324 DOI: 10.3389/fcell.2020.587778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/01/2020] [Indexed: 01/07/2023] Open
Abstract
The mesodiencephalic dopaminergic (mdDA) neurons, including the nigrostriatal subset that preferentially degenerates in Parkinson’s Disease (PD), strongly depend on an accurately balanced Wingless-type MMTV integration site family member 1 (WNT1)/beta-catenin signaling pathway during their development. Loss of this pathway abolishes the generation of these neurons, whereas excessive WNT1/b-catenin signaling prevents their correct differentiation. The identity of the cells responding to this pathway in the developing mammalian ventral midbrain (VM) as well as the precise progression of WNT/b-catenin action in these cells are still unknown. We show that strong WNT/b-catenin signaling inhibits the differentiation of WNT/b-catenin-responding mdDA progenitors into PITX3+ and TH+ mdDA neurons by repressing the Pitx3 gene in mice. This effect is mediated by RSPO2, a WNT/b-catenin agonist, and lymphoid enhancer binding factor 1 (LEF1), an essential nuclear effector of the WNT/b-catenin pathway, via conserved LEF1/T-cell factor binding sites in the Pitx3 promoter. LEF1 expression is restricted to a caudolateral mdDA progenitor subset that preferentially responds to WNT/b-catenin signaling and gives rise to a fraction of all mdDA neurons. Our data indicate that an attenuation of WNT/b-catenin signaling in mdDA progenitors is essential for their correct differentiation into specific mdDA neuron subsets. This is an important consideration for stem cell-based regenerative therapies and in vitro models of neuropsychiatric diseases.
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Affiliation(s)
- Parivash Nouri
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Sebastian Götz
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Benedict Rauser
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Changgeng Peng
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Advanced Institute of Translational Medicine, The First Rehabilitation Hospital of Shanghai, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Dietrich Trümbach
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Kempny
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Carina G Lechermeier
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Agnes Bryniok
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Andrea Dlugos
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Ellen Euchner
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, Technical University of Munich, Munich, Germany.,German Center for Diabetes Research, Neuherberg, Germany
| | - Claude Brodski
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Claudia Klümper
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Developmental Genetics, Helmholtz Zentrum München, Technical University of Munich/Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Neurodegenerative Diseases, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Nilima Prakash
- Laboratory of Applied Genetics and Stem Cell Biology, Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
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44
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Ásgrímsdóttir ES, Arenas E. Midbrain Dopaminergic Neuron Development at the Single Cell Level: In vivo and in Stem Cells. Front Cell Dev Biol 2020; 8:463. [PMID: 32733875 PMCID: PMC7357704 DOI: 10.3389/fcell.2020.00463] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder that predominantly affects dopaminergic (DA) neurons of the substantia nigra. Current treatment options for PD are symptomatic and typically involve the replacement of DA neurotransmission by DA drugs, which relieve the patients of some of their motor symptoms. However, by the time of diagnosis, patients have already lost about 70% of their substantia nigra DA neurons and these drugs offer only temporary relief. Therefore, cell replacement therapy has garnered much interest as a potential treatment option for PD. Early studies using human fetal tissue for transplantation in PD patients provided proof of principle for cell replacement therapy, but they also highlighted the ethical and practical difficulties associated with using human fetal tissue as a cell source. In recent years, advancements in stem cell research have made human pluripotent stem cells (hPSCs) an attractive source of material for cell replacement therapy. Studies on how DA neurons are specified and differentiated in the developing mouse midbrain have allowed us to recapitulate many of the positional and temporal cues needed to generate DA neurons in vitro. However, little is known about the developmental programs that govern human DA neuron development. With the advent of single-cell RNA sequencing (scRNA-seq) and bioinformatics, it has become possible to analyze precious human samples with unprecedented detail and extract valuable high-quality information from large data sets. This technology has allowed the systematic classification of cell types present in the human developing midbrain along with their gene expression patterns. By studying human development in such an unbiased manner, we can begin to elucidate human DA neuron development and determine how much it differs from our knowledge of the rodent brain. Importantly, this molecular description of the function of human cells has become and will increasingly be a reference to define, evaluate, and engineer cell types for PD cell replacement therapy and disease modeling.
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Affiliation(s)
| | - Ernest Arenas
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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45
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Flitsch LJ, Laupman KE, Brüstle O. Transcription Factor-Based Fate Specification and Forward Programming for Neural Regeneration. Front Cell Neurosci 2020; 14:121. [PMID: 32508594 PMCID: PMC7251072 DOI: 10.3389/fncel.2020.00121] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
Traditionally, in vitro generation of donor cells for brain repair has been dominated by the application of extrinsic growth factors and morphogens. Recent advances in cell engineering strategies such as reprogramming of somatic cells into induced pluripotent stem cells and direct cell fate conversion have impressively demonstrated the feasibility to manipulate cell identities by the overexpression of cell fate-determining transcription factors. These strategies are now increasingly implemented for transcription factor-guided differentiation of neural precursors and forward programming of pluripotent stem cells toward specific neural subtypes. This review covers major achievements, pros and cons, as well as future prospects of transcription factor-based cell fate specification and the applicability of these approaches for the generation of donor cells for brain repair.
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Affiliation(s)
- Lea J Flitsch
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Karen E Laupman
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany
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46
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Ao X, Ding W, Ge H, Zhang Y, Ding D, Liu Y. PBX1 is a valuable prognostic biomarker for patients with breast cancer. Exp Ther Med 2020; 20:385-394. [PMID: 32565927 PMCID: PMC7286203 DOI: 10.3892/etm.2020.8705] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pre-B-cell leukemia transcription factor (PBX) proteins have important roles in the development of numerous organs. To date, four members of the PBX family have been identified to be involved in human cancer but little is known about their expression patterns and precise functions in breast cancer (BC) progression. The aim of the present study was to determine whether they have the potential to be prognostic biomarkers in patients with BC. The expression patterns of PBXs were evaluated using Oncomine, Cancer Cell Line Encyclopedia and Gene expression-based Outcome for Breast cancer Online algorithm analyses. The prognostic value of PBX1 was determined by Kaplan-Meier plotter analysis. It was observed that, among all PBX family members, only PBX1 was significantly upregulated in BC vs. normal tissues. Meta-analysis in the Oncomine database revealed that PBX1 was significantly upregulated in invasive breast carcinoma stroma, ductal breast carcinoma, invasive lobular breast carcinoma, invasive mixed breast carcinoma and male breast carcinoma compared with normal tissues. In addition, PBX1 was significantly correlated with forkhead box protein A1. Subtype analysis indicated that PBX1 overexpression was associated with luminal-like and hormone receptor-sensitive subtypes. In the survival analysis, a high expression level of PBX1 was associated with poor prognosis of patients with estrogen receptor (ER)-positive, luminal A and luminal B subtypes of BC. The results of the present study indicate that PBX1 may serve as a specific biomarker and essential prognostic factor for ER-positive, luminal A and luminal B subtypes of BC.
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Affiliation(s)
- Xiang Ao
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Wei Ding
- Department of Comprehensive Internal Medicine, Affiliated Hospital, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Hu Ge
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China.,Department of Molecular Informatics, Hengrui Pharmaceutical Co., Ltd., Shanghai 200245, P.R. China
| | - Yuan Zhang
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Dan Ding
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Ying Liu
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
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47
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Remesal L, Roger-Baynat I, Chirivella L, Maicas M, Brocal-Ruiz R, Pérez-Villalba A, Cucarella C, Casado M, Flames N. PBX1 acts as terminal selector for olfactory bulb dopaminergic neurons. Development 2020; 147:dev.186841. [PMID: 32156753 DOI: 10.1242/dev.186841] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/24/2020] [Indexed: 02/03/2023]
Abstract
Neuronal specification is a protracted process that begins with the commitment of progenitor cells and culminates with the generation of mature neurons. Many transcription factors are continuously expressed during this process but it is presently unclear how these factors modify their targets as cells transition through different stages of specification. In olfactory bulb adult neurogenesis, the transcription factor PBX1 controls neurogenesis in progenitor cells and the survival of migrating neuroblasts. Here, we show that, at later differentiation stages, PBX1 also acts as a terminal selector for the dopaminergic neuron fate. PBX1 is also required for the morphological maturation of dopaminergic neurons and to repress alternative interneuron fates, findings that expand the known repertoire of terminal-selector actions. Finally, we reveal that the temporal diversification of PBX1 functions in neuronal specification is achieved, at least in part, through the dynamic regulation of alternative splicing. In Caenorhabditis elegans, PBX/CEH-20 also acts as a dopaminergic neuron terminal selector, which suggests an ancient role for PBX factors in the regulation of terminal differentiation of dopaminergic neurons.
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Affiliation(s)
- Laura Remesal
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Isabel Roger-Baynat
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Laura Chirivella
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Ana Pérez-Villalba
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), and Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Carme Cucarella
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Metabolic Experimental Pathology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Marta Casado
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Metabolic Experimental Pathology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
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Soerensen M, Hozakowska-Roszkowska DM, Nygaard M, Larsen MJ, Schwämmle V, Christensen K, Christiansen L, Tan Q. A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins. Front Neurosci 2020; 14:233. [PMID: 32327964 PMCID: PMC7160301 DOI: 10.3389/fnins.2020.00233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/02/2020] [Indexed: 12/02/2022] Open
Abstract
Monozygotic twins are genetically identical but rarely phenotypically identical. Epigenetic and transcriptional variation could influence this phenotypic discordance. Investigation of intra-pair differences in molecular markers and a given phenotype in monozygotic twins controls most of the genetic contribution, enabling studies of the molecular features of the phenotype. This study aimed to identify genes associated with cognition in later life using integrated enrichment analyses of the results of blood-derived intra-pair epigenome-wide and transcriptome-wide association analyses of cognition in 452 middle-aged and old-aged monozygotic twins (56–80 years). Integrated analyses were performed with an unsupervised approach using KeyPathwayMiner, and a supervised approach using the KEGG and Reactome databases. The supervised approach identified several enriched gene sets, including “neuroactive ligand receptor interaction” (p-value = 1.62∗10-2), “Neurotrophin signaling” (p-value = 2.52∗10-3), “Alzheimer’s disease” (p-value = 1.20∗10-2), and “long-term depression” (p-value = 1.62∗10-2). The unsupervised approach resulted in a 238 gene network, including the Alzheimer’s disease gene APP (Amyloid Beta Precursor Protein) as an exception node, and several novel candidate genes. The strength of the unsupervised method is that it can reveal previously uncharacterized sub-pathways and detect interplay between biological processes, which remain undetected by the current supervised methods. In conclusion, this study identified several previously reported cognition genes and pathways and, additionally, puts forward novel candidates for further verification and validation.
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Affiliation(s)
- Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Center for Individualized Medicine in Arterial Diseases, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Dominika Marzena Hozakowska-Roszkowska
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.,Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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49
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Proteasome Composition in Cytokine-Treated Neurons and Astrocytes is Determined Mainly by Subunit Displacement. Neurochem Res 2020; 45:860-871. [PMID: 31939090 DOI: 10.1007/s11064-020-02958-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/11/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022]
Abstract
In this study, we investigated if subunit displacement and/or alterations in proteasome biosynthesis are responsible for the changes in the levels of constitutive proteasomes (c-20S), immunoproteasomes (i-20S) and the activators PA28 and PA700 in neurons and astrocytes cultured with a cytokine mixture (IFN-γ/TNF-α/IL-1β). Exposure of both cell types to cytokines for 24 h increases mRNA and protein expression of the i-20S-specific subunit β5i and PA28α/β, and leads to a decline in the amount of the c-20S-specific subunit β5. Since β5 mRNA levels are unchanged by the cytokine treatment, it is fair to conclude that displacement of constitutive β-subunits with inducible β5i subunits is likely the mechanism underlying the decrease in c-20S. As expected, the increase in the amount of the IFN-γ-inducible subunits coincides with elevated expression of phospho-STAT-1 and interferon regulatory factor-1 (IRF-1). However, inhibition of NF-κB signaling in cytokine-treated astrocytes reduces IRF-1 expression without affecting that of i-20S, c-20S and PA28. This suggests that STAT-1 is capable of increasing the transcription of i20S-specific subunits and PA28α/β by itself. The lack of a decrease in proteasome β5 mRNA expression is consistent with the fact that Nrf1 (Nfe2l1) and Nrf2 (Nfe2l2) levels are not reduced by pro-inflammatory cytokines. In contrast, we previously found that there is a significant Nrf1 dysregulation and reduced β5 mRNA expression in the spinal cords of mice with experimental autoimmune encephalomyelitis (EAE). Thus, there are stressors in EAE, other than a pro-inflammatory environment, that are not present in cytokine-treated cells.
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50
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Zhu Z, Yichen W, Ziheng Z, Dinghao G, Ming L, Wei L, Enfang S, Gang H, Honda H, Jian Y. The loss of dopaminergic neurons in DEC1 deficient mice potentially involves the decrease of PI3K/Akt/GSK3β signaling. Aging (Albany NY) 2019; 11:12733-12753. [PMID: 31884423 PMCID: PMC6949058 DOI: 10.18632/aging.102599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022]
Abstract
Here we study the effects of differentiated embryonic chondrocyte gene 1(DEC1) deficiency on midbrain dopaminergic(DA) neurons in the substantia nigra pars compacta(SNpc) through behavioral, histological and molecular analysis. We have found that compared to the age-matched WT mice, DEC1 deficient mice show a decrease in locomotor activity and motor coordination, which shows the main features of Parkinson's disease(PD). But there is no significant difference in spatial learning and memory skills between WT and DEC1 KO mice. Compared to the age-matched WT mice, DEC1 deficient mice exhibit the loss of DA neurons in the SNpc and reduction of dopamine and its metabolites in the striatum. The activated caspase-3 and TH/TUNEL+ cells increase in the SNpc of 6- and 12-month-old DEC1 KO mice compared to those of the age-matched WT mice. But we haven't found any NeuN/TUNEL+ cell increase in the hippocampus of the above two types of mice at the age of 6 months. Furthermore, DEC1 deficiency leads to a significant inhibition of PI3K/Akt/GSK3β signaling pathway. Additionally, LiCl could rescue the DA neuron loss of midbrain in the 6-month-old DEC1 KO mice. Taken together, the loss of DA neurons in the DEC1 deficient mice potentially involves the downregulation of PI3K/Akt/GSK3β signaling.
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Affiliation(s)
- Zhu Zhu
- Department of Pharmacology, Nanjing Medical University, Nanjing, China.,, Department of Pharmacology Sciences, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wu Yichen
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Zhang Ziheng
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Ge Dinghao
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Lu Ming
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Liu Wei
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Shan Enfang
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Hu Gang
- Department of Pharmacology, Nanjing Medical University, Nanjing, China.,, Department of Pharmacology Sciences, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hiroaki Honda
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yang Jian
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
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