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Gagnon J, Caron V, Tremblay A. SUMOylation of nuclear receptor Nor1/NR4A3 coordinates microtubule cytoskeletal dynamics and stability in neuronal cells. Cell Biosci 2024; 14:91. [PMID: 38997783 PMCID: PMC11245793 DOI: 10.1186/s13578-024-01273-x] [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: 10/25/2023] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Nor1/NR4A3 is a member of the NR4A subfamily of nuclear receptors that play essential roles in regulating gene expression related to development, cell homeostasis and neurological functions. However, Nor1 is still considered an orphan receptor, as its natural ligand remains unclear for mediating transcriptional activation. Yet other activation signals may modulate Nor1 activity, although their precise role in the development and maintenance of the nervous system remains elusive. METHODS We used transcriptional reporter assays, gene expression profiling, protein turnover measurement, and cell growth assays to assess the functional relevance of Nor1 and SUMO-defective variants in neuronal cells. SUMO1 and SUMO2 conjugation to Nor1 were assessed by immunoprecipitation. Tubulin stability was determined by acetylation and polymerization assays, and live-cell fluorescent microscopy. RESULTS Here, we demonstrate that Nor1 undergoes SUMO1 conjugation at Lys-89 within a canonical ψKxE SUMOylation motif, contributing to the complex pattern of Nor1 SUMOylation, which also includes Lys-137. Disruption of Lys-89, thereby preventing SUMO1 conjugation, led to reduced Nor1 transcriptional competence and protein stability, as well as the downregulation of genes involved in cell growth and metabolism, such as ENO3, EN1, and CFLAR, and in microtubule cytoskeleton dynamics, including MAP2 and MAPT, which resulted in reduced survival of neuronal cells. Interestingly, Lys-89 SUMOylation was potentiated in response to nocodazole, a microtubule depolymerizing drug, although this was insufficient to rescue cells from microtubule disruption despite enhanced Nor1 gene expression. Instead, Lys-89 deSUMOylation reduced the expression of microtubule-severing genes like KATNA1, SPAST, and FIGN, and enhanced α-tubulin cellular levels, acetylation, and microfilament organization, promoting microtubule stability and resistance to nocodazole. These effects contrasted with Lys-137 SUMOylation, suggesting distinct regulatory mechanisms based on specific Nor1 input SUMOylation signals. CONCLUSIONS Our study provides novel insights into Nor1 transcriptional signaling competence and identifies a hierarchical mechanism whereby selective Nor1 SUMOylation may govern neuronal cytoskeleton network dynamics and resistance against microtubule disturbances, a condition strongly associated with neurodegenerative diseases.
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Affiliation(s)
- Jonathan Gagnon
- Research Center, CHU Sainte-Justine, 3175 Côte Ste-Catherine, Montréal, Québec, H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montréal, Québec, H3T 1J4, Canada
| | - Véronique Caron
- Research Center, CHU Sainte-Justine, 3175 Côte Ste-Catherine, Montréal, Québec, H3T 1C5, Canada
| | - André Tremblay
- Research Center, CHU Sainte-Justine, 3175 Côte Ste-Catherine, Montréal, Québec, H3T 1C5, Canada.
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montréal, Québec, H3T 1J4, Canada.
- Centre de Recherche en Reproduction et Fertilité, University of Montreal, Saint-Hyacinthe, Québec, J2S 7C6, Canada.
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Montreal, Montréal, Québec, H3T 1J4, Canada.
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Qian W, Yuan L, Zhuge W, Gu L, Chen Y, Zhuge Q, Ni H, Lv X. Regulating Lars2 in mitochondria: A potential Alzheimer's therapy by inhibiting tau phosphorylation. Neurotherapeutics 2024; 21:e00353. [PMID: 38575503 PMCID: PMC11067343 DOI: 10.1016/j.neurot.2024.e00353] [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: 12/01/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
Driven by the scarcity of effective treatment options in clinical settings, the present study aimed to identify a new potential target for Alzheimer's disease (AD) treatment. We focused on Lars2, an enzyme synthesizing mitochondrial leucyl-tRNA, and its role in maintaining mitochondrial function. Bioinformatics analysis of human brain transcriptome data revealed downregulation of Lars2 in AD patients compared to healthy controls. During in vitro experiments, the knockdown of Lars2 in mouse neuroblastoma cells (neuro-2a cells) and primary cortical neurons led to morphological changes and decreased density in mouse hippocampal neurons. To explore the underlying mechanisms, we investigated how downregulated Lars2 expression could impede the phosphatidylinositol 3-kinase/protein kinase B (PI3K-AKT) pathway, thereby mitigating AKT's inhibitory effect on glycogen synthase kinase 3 beta (GSK3β). This led to the activation of GSK3β, causing excessive phosphorylation of Tau protein and subsequent neuronal degeneration. During in vivo experiments, knockout of lars2 in hippocampal neurons confirmed cognitive impairment through the Barnes maze test, the novel object recognition test, and nest-building experiments. Additionally, immunofluorescence assays indicated an increase in p-tau, atrophy in the hippocampal region, and a decrease in neurons following Lars2 knockout. Taken together, our findings indicate that Lars2 represents a promising therapeutic target for AD.
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Affiliation(s)
- Wenqi Qian
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China; Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Lin Yuan
- Institute of Biomedical Sciences, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Weishan Zhuge
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Liuqing Gu
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China; Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yutian Chen
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Qichuan Zhuge
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China; Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Haoqi Ni
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China; Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Xinhuang Lv
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China; Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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3
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Zhao J, Wei M, Guo M, Wang M, Niu H, Xu T, Zhou Y. GSK3: A potential target and pending issues for treatment of Alzheimer's disease. CNS Neurosci Ther 2024; 30:e14818. [PMID: 38946682 PMCID: PMC11215492 DOI: 10.1111/cns.14818] [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: 04/22/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Glycogen synthase kinase-3 (GSK3), consisting of GSK3α and GSK3β subtypes, is a complex protein kinase that regulates numerous substrates. Research has observed increased GSK3 expression in the brains of Alzheimer's disease (AD) patients and models. AD is a neurodegenerative disorder with diverse pathogenesis and notable cognitive impairments, characterized by Aβ aggregation and excessive tau phosphorylation. This article provides an overview of GSK3's structure and regulation, extensively analyzing its relationship with AD factors. GSK3 overactivation disrupts neural growth, development, and function. It directly promotes tau phosphorylation, regulates amyloid precursor protein (APP) cleavage, leading to Aβ formation, and directly or indirectly triggers neuroinflammation and oxidative damage. We also summarize preclinical research highlighting the inhibition of GSK3 activity as a primary therapeutic approach for AD. Finally, pending issues like the lack of highly specific and affinity-driven GSK3 inhibitors, are raised and expected to be addressed in future research. In conclusion, GSK3 represents a target in AD treatment, filled with hope, challenges, opportunities, and obstacles.
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Affiliation(s)
- Jiahui Zhao
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Mengying Wei
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- Future Health Laboratory, Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxingChina
| | - Minsong Guo
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese MedicineWenzhouChina
| | - Mengyao Wang
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Hongxia Niu
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
- Key Laboratory of Blood‐stasis‐toxin Syndrome of Zhejiang ProvinceHangzhouChina
| | - Tengfei Xu
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
- Cangnan County Qiushi Innovation Research Institute of Traditional Chinese MedicineWenzhouChina
| | - Yuan Zhou
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
- Key Laboratory of Blood‐stasis‐toxin Syndrome of Zhejiang ProvinceHangzhouChina
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4
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Thakur K, Khan H, Grewal AK, Singh TG. Nuclear orphan receptors: A novel therapeutic agent in neuroinflammation. Int Immunopharmacol 2023; 124:110845. [PMID: 37690241 DOI: 10.1016/j.intimp.2023.110845] [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: 03/07/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Orphan receptors constitute a historically varied subsection of a superfamily of nuclear receptors. Nuclear receptors regulate gene expression in response to ligand signals and are particularly alluring therapeutic targets for chronic illnesses. Neuroinflammation and neurodegenerative diseases have been linked to these orphan nuclear receptors. Preclinical and clinical evidence suggests that orphan receptors could serve as future targets in neuroinflammation, such as Parkinson's disease (PD), Alzheimer's Disease (AD), Huntington's Disease (HD), Multiple Sclerosis (MS), and Cerebral Ischemia. Given the therapeutic relevance of certain orphan receptors in a variety of disorders, their potential in neuroinflammation remains unproven. There is substantial evidence that ligand-activated transcription factors have great promise for preventing neurodegenerative and neurological disorders, with certain orphan nuclear receptors i.e., PPARγ, NR4As, and orphan GPCRs holding particularly high potential. Based on previous findings, we attempted to determine the contribution of PPAR, NR4As, and orphan GPCRs-regulated neuroinflammation to the pathogenesis of these disorders and their potential to become novel therapeutic targets.
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Affiliation(s)
- Kiran Thakur
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
| | - Heena Khan
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
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5
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Morello G, La Cognata V, Guarnaccia M, D’Agata V, Cavallaro S. Cracking the Code of Neuronal Cell Fate. Cells 2023; 12:1057. [PMID: 37048129 PMCID: PMC10093029 DOI: 10.3390/cells12071057] [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: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Transcriptional regulation is fundamental to most biological processes and reverse-engineering programs can be used to decipher the underlying programs. In this review, we describe how genomics is offering a systems biology-based perspective of the intricate and temporally coordinated transcriptional programs that control neuronal apoptosis and survival. In addition to providing a new standpoint in human pathology focused on the regulatory program, cracking the code of neuronal cell fate may offer innovative therapeutic approaches focused on downstream targets and regulatory networks. Similar to computers, where faults often arise from a software bug, neuronal fate may critically depend on its transcription program. Thus, cracking the code of neuronal life or death may help finding a patch for neurodegeneration and cancer.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
| | - Velia D’Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), 95126 Catania, Italy
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6
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Dong W, Huang Y. Common Genetic Factors and Pathways in Alzheimer's Disease and Ischemic Stroke: Evidences from GWAS. Genes (Basel) 2023; 14:353. [PMID: 36833280 PMCID: PMC9957001 DOI: 10.3390/genes14020353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide association studies (GWASs) revealed that there were common risk genes between AD and IS, indicating common molecular pathways and their common pathophysiology. In this review, we summarize AD and IS risk single nucleotide polymorphisms (SNPs) and their representative genes from the GWAS Catalog database, and find thirteen common risk genes, but no common risk SNPs. Furthermore, the common molecular pathways associated with these risk gene products are summarized from the GeneCards database and clustered into inflammation and immunity, G protein-coupled receptor, and signal transduction. At least seven of these thirteen genes can be regulated by 23 microRNAs identified from the TargetScan database. Taken together, the imbalance of these molecular pathways may give rise to these two common brain disorders. This review sheds light on the pathogenesis of comorbidity of AD and IS, and provides molecular targets for disease prevention, manipulation, and brain health maintenance.
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Affiliation(s)
- Wei Dong
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yue Huang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Department of Pharmacology, School of Medical Sciences, Faculty of Medicine & Health, UNSW, Sydney, NSW 2052, Australia
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7
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Zhang Q, Zhao H, Luo M, Cheng X, Li Y, Li Q, Wang Z, Niu Q. The Classification and Prediction of Ferroptosis-Related Genes in ALS: A Pilot Study. Front Genet 2022; 13:919188. [PMID: 35873477 PMCID: PMC9305067 DOI: 10.3389/fgene.2022.919188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscle paralysis, which is followed by degeneration of motor neurons in the motor cortex of the brainstem and spinal cord. The etiology of sporadic ALS (sALS) is still unknown, limiting the exploration of potential treatments. Ferroptosis is a new form of cell death and is reported to be closely associated with Alzheimer’s disease (AD), Parkinson’s disease (PD), and ALS. In this study, we used datasets (autopsy data and blood data) from Gene Expression Omnibus (GEO) to explore the role of ferroptosis and ferroptosis-related gene (FRG) alterations in ALS. Gene set enrichment analysis (GSEA) found that the activated ferroptosis pathway displayed a higher enrichment score, and the expression of 26 ferroptosis genes showed obvious group differences between ALS and controls. Using weighted gene correlation network analysis (WGCNA), we identified FRGs associated with ALS, of which the Gene Ontology (GO) analysis displayed that the biological process of oxidative stress was the most to be involved in. KEGG pathway analysis revealed that the FRGs were enriched not only in ferroptosis pathways but also in autophagy, FoxO, and mTOR signaling pathways. Twenty-one FRGs (NR4A1, CYBB, DRD4, SETD1B, LAMP2, ACSL4, MYB, PROM2, CHMP5, ULK1, AKR1C2, TGFBR1, TMBIM4, MLLT1, PSAT1, HIF1A, LINC00336, AMN, SLC38A1, CISD1, and GABARAPL2) in the autopsy data and 16 FRGs (NR4A1, DRD4, SETD1B, MYB, PROM2, CHMP5, ULK1, AKR1C2, TGFBR1, TMBIM4, MLLT1, HIF1A, LINC00336, IL33, SLC38A1, and CISD1) in the blood data were identified as target genes by least absolute shrinkage and selection operator analysis (LASSO), in which gene signature could differentiate ALS patients from controls. Finally, the higher the expression of CHMP5 and SLC38A1 in whole blood, the shorter the lifespan of ALS patients will be. In summary, our study presents potential biomarkers for the diagnosis and prognosis of ALS.
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Affiliation(s)
| | | | | | | | | | | | | | - Qi Niu
- *Correspondence: Qi Niu, ; Zheng Wang,
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8
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Delport A, Hewer R. A superior loading control for the cellular thermal shift assay. Sci Rep 2022; 12:6672. [PMID: 35461337 PMCID: PMC9035151 DOI: 10.1038/s41598-022-10653-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
The cellular thermal shift assay (CETSA), as a method to determine protein-ligand interaction and cellular protein modification, has rapidly become routine laboratory practice. However, current options to determine that (1) sample was loaded in each lane of the analysed western blot and (2) the amount loaded was equal, are suboptimal. Here, we report that the αC-terminal fragment of the amyloid precursor protein (APP-αCTF), detected in several wild-type mammalian cell lines, is a highly stable, soluble protein equally present from 4 to 95 °C. We demonstrate that the level of traditional loading controls (vinculin, GAPDH, β-actin, heat-shock chaperone 70 and superoxide dismutase-1) are all temperature sensitive. Additionally, both APP-CTFs (α and β) behaved similarly upon temperature exposure while APP-βCTF levels were not influenced by the presence of a binding ligand either. This emphasises that these proteins can be used as a loading control in the unlikely event of off-target binding during ligand screening. A working example is also presented for mitogen-activated protein kinase kinase in the presence of two inhibitors, PD184352 and U0126, where APP-αCTF was used to normalise the data across experimental replicates. A reduction in data variance and standard deviations was observed after normalisation. Conclusively, APP-αCTF is a superior CETSA loading control that can be used as a standard for this technique.
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Affiliation(s)
- Alexandré Delport
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa.
| | - Raymond Hewer
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa
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9
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Morello G, Villari A, Spampinato AG, La Cognata V, Guarnaccia M, Gentile G, Ciotti MT, Calissano P, D’Agata V, Severini C, Cavallaro S. Transcriptional Profiles of Cell Fate Transitions Reveal Early Drivers of Neuronal Apoptosis and Survival. Cells 2021; 10:3238. [PMID: 34831459 PMCID: PMC8620386 DOI: 10.3390/cells10113238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Abstract
Neuronal apoptosis and survival are regulated at the transcriptional level. To identify key genes and upstream regulators primarily responsible for these processes, we overlayed the temporal transcriptome of cerebellar granule neurons following induction of apoptosis and their rescue by three different neurotrophic factors. We identified a core set of 175 genes showing opposite expression trends at the intersection of apoptosis and survival. Their functional annotations and expression signatures significantly correlated to neurological, psychiatric and oncological disorders. Transcription regulatory network analysis revealed the action of nine upstream transcription factors, converging pro-apoptosis and pro-survival-inducing signals in a highly interconnected functionally and temporally ordered manner. Five of these transcription factors are potential drug targets. Transcriptome-based computational drug repurposing produced a list of drug candidates that may revert the apoptotic core set signature. Besides elucidating early drivers of neuronal apoptosis and survival, our systems biology-based perspective paves the way to innovative pharmacology focused on upstream targets and regulatory networks.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Ambra Villari
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Antonio Gianmaria Spampinato
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Giulia Gentile
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
| | - Maria Teresa Ciotti
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC-CNR), Via E. Ramarini, 32, Monterotondo Scalo, 00015 Rome, Italy; (M.T.C.); (C.S.)
| | - Pietro Calissano
- European Brain Research Institute (EBRI Foundation), Viale Regina Elena, 295, 00161 Rome, Italy;
| | - Velia D’Agata
- Department of Biomedical and Biotechnological Sciences, Section of Human Anatomy and Histology, University of Catania, Via Santa Sofia, 87, 95123 Catania, Italy;
| | - Cinzia Severini
- Institute of Biochemistry and Cell Biology, National Research Council (IBBC-CNR), Via E. Ramarini, 32, Monterotondo Scalo, 00015 Rome, Italy; (M.T.C.); (C.S.)
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Via Paolo Gaifami, 18, 95125 Catania, Italy; (G.M.); (A.V.); (A.G.S.); (V.L.C.); (M.G.); (G.G.)
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10
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Kuan P, Clouston S, Yang X, Che C, Gandy S, Kotov R, Bromet E, Luft BJ. Single-cell transcriptomics analysis of mild cognitive impairment in World Trade Center disaster responders. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12154. [PMID: 33665344 PMCID: PMC7896635 DOI: 10.1002/dad2.12154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Recent research has found that World Trade Center (WTC) responders in their mid-50s have an elevated prevalence of mild cognitive impairment (MCI) that is associated with neural degeneration and subcortical thinning. This article extends our understanding of the molecular complexity of MCI through gene expression profiling of blood. METHODS The transcriptomics of 40 male WTC responders were profiled across two cohorts (discovery: nine MCI and nine controls; replication: 11 MCI and 11 controls) using CITE-Seq at single-cell resolution in blood. RESULTS Comparing the transcriptomic signatures across seven major cell subpopulations, the largest differences were observed in monocytes in which 226 genes were differentially expressed. Pathway analysis on the genes unique to monocytes identified processes associated with cerebral immune response. DISCUSSION Our findings suggested monocytes may constitute a key cell type to target in blood-based biomarker studies for early detection of risk of MCI and development of new interventions.
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Affiliation(s)
- Pei‐Fen Kuan
- Department of Applied Mathematics and StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Sean Clouston
- Department of Family and Preventive MedicineStony Book UniversityStony BrookNew YorkUSA
| | - Xiaohua Yang
- Department of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Chang Che
- Department of Applied Mathematics and StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Samuel Gandy
- Department of NeurologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Roman Kotov
- Department of PsychiatryStony Book UniversityStony BrookNew YorkUSA
| | - Evelyn Bromet
- Department of PsychiatryStony Book UniversityStony BrookNew YorkUSA
| | - Benjamin J. Luft
- Department of MedicineStony Brook UniversityStony BrookNew YorkUSA
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11
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Pan Q, Liu YJ, Bai XF, Han XL, Jiang Y, Ai B, Shi SS, Wang F, Xu MC, Wang YZ, Zhao J, Chen JX, Zhang J, Li XC, Zhu J, Zhang GR, Wang QY, Li CQ. VARAdb: a comprehensive variation annotation database for human. Nucleic Acids Res 2021; 49:D1431-D1444. [PMID: 33095866 PMCID: PMC7779011 DOI: 10.1093/nar/gkaa922] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/28/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023] Open
Abstract
With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include ‘Variation information’, ‘Regulatory information’, ‘Related genes’, ‘Chromatin accessibility’ and ‘Chromatin interaction’. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.
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Affiliation(s)
- Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yue-Juan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xue-Feng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xiao-Le Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Shan-Shan Shi
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Ming-Cong Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yue-Zhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jia-Xin Chen
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xue-Cang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Guo-Rui Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qiu-Yu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chun-Quan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
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Dmitrzak-Weglarz M, Szczepankiewicz A, Kapelski, Chaberska J, Kwiatkowska K, Duda J, Dziuda S, Skibinska M, Reszka E, Pawlak J. Transcripts of orphan nuclear receptor (NR4A1) & potassium channel (KCNK17) genes as new potential biomarkers for depression. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
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Knutson KA, Deng Y, Pan W. Implicating causal brain imaging endophenotypes in Alzheimer's disease using multivariable IWAS and GWAS summary data. Neuroimage 2020; 223:117347. [PMID: 32898681 PMCID: PMC7778364 DOI: 10.1016/j.neuroimage.2020.117347] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Recent evidence suggests the existence of many undiscovered heritable brain phenotypes involved in Alzheimer's Disease (AD) pathogenesis. This finding necessitates methods for the discovery of causal brain changes in AD that integrate Magnetic Resonance Imaging measures and genotypic data. However, existing approaches for causal inference in this setting, such as the univariate Imaging Wide Association Study (UV-IWAS), suffer from inconsistent effect estimation and inflated Type I errors in the presence of genetic pleiotropy, the phenomenon in which a variant affects multiple causal intermediate risk phenotypes. In this study, we implement a multivariate extension to the IWAS model, namely MV-IWAS, to consistently estimate and test for the causal effects of multiple brain imaging endophenotypes from the Alzheimer's Disease Neuroimaging Initiative (ADNI) in the presence of pleiotropic and possibly correlated SNPs. We further extend MV-IWAS to incorporate variant-specific direct effects on AD, analogous to the existing Egger regression Mendelian Randomization approach, which allows for testing of remaining pleiotropy after adjusting for multiple intermediate pathways. We propose a convenient approach for implementing MV-IWAS that solely relies on publicly available GWAS summary data and a reference panel. Through simulations with either individual-level or summary data, we demonstrate the well controlled Type I errors and superior power of MV-IWAS over UV-IWAS in the presence of pleiotropic SNPs. We apply the summary statistic based tests to 1578 heritable imaging derived phenotypes (IDPs) from the UK Biobank. MV-IWAS detected numerous IDPs as possible false positives by UV-IWAS while uncovering many additional causal neuroimaging phenotypes in AD which are strongly supported by the existing literature.
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Affiliation(s)
- Katherine A Knutson
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota United States
| | - Yangqing Deng
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota United States
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota United States.
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