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Alur V, Raju V, Vastrad B, Vastrad C, Kavatagimath S, Kotturshetti S. Bioinformatics Analysis of Next Generation Sequencing Data Identifies Molecular Biomarkers Associated With Type 2 Diabetes Mellitus. Clin Med Insights Endocrinol Diabetes 2023; 16:11795514231155635. [PMID: 36844983 PMCID: PMC9944228 DOI: 10.1177/11795514231155635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/19/2023] [Indexed: 02/23/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) is the most common metabolic disorder. The aim of the present investigation was to identify gene signature specific to T2DM. Methods The next generation sequencing (NGS) dataset GSE81608 was retrieved from the gene expression omnibus (GEO) database and analyzed to identify the differentially expressed genes (DEGs) between T2DM and normal controls. Then, Gene Ontology (GO) and pathway enrichment analysis, protein-protein interaction (PPI) network, modules, miRNA (micro RNA)-hub gene regulatory network construction and TF (transcription factor)-hub gene regulatory network construction, and topological analysis were performed. Receiver operating characteristic curve (ROC) analysis was also performed to verify the prognostic value of hub genes. Results A total of 927 DEGs (461 were up regulated and 466 down regulated genes) were identified in T2DM. GO and REACTOME results showed that DEGs mainly enriched in protein metabolic process, establishment of localization, metabolism of proteins, and metabolism. The top centrality hub genes APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1 were screened out as the critical genes. ROC analysis provides prognostic value of hub genes. Conclusion The potential crucial genes, especially APP, MYH9, TCTN2, USP7, SYNPO, GRB2, HSP90AB1, UBC, HSPA5, and SQSTM1, might be linked with risk of T2DM. Our study provided novel insights of T2DM into genetics, molecular pathogenesis, and novel therapeutic targets.
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Affiliation(s)
- Varun Alur
- Department of Endocrinology, J.J.M
Medical College, Davanagere, Karnataka, India
| | - Varshita Raju
- Department of Obstetrics and
Gynecology, J.J.M Medical College, Davanagere, Karnataka, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry,
K.L.E. College of Pharmacy, Gadag, Karnataka, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics,
Chanabasava Nilaya, Dharwad, Karnataka, India,Chanabasayya Vastrad, Biostatistics and
Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka 580001,
India.
| | - Satish Kavatagimath
- Department of Pharmacognosy, K.L.E.
College of Pharmacy, Belagavi, Karnataka, India
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2
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Key role of Rho GTPases in motor disorders associated with neurodevelopmental pathologies. Mol Psychiatry 2023; 28:118-126. [PMID: 35918397 DOI: 10.1038/s41380-022-01702-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/24/2022] [Accepted: 07/02/2022] [Indexed: 01/07/2023]
Abstract
Growing evidence suggests that Rho GTPases and molecules involved in their signaling pathways play a major role in the development of the central nervous system (CNS). Whole exome sequencing (WES) and de novo examination of mutations, including SNP (Single Nucleotide Polymorphism) in genes coding for the molecules of their signaling cascade, has allowed the recent discovery of dominant autosomic mutations and duplication or deletion of candidates in the field of neurodevelopmental diseases (NDD). Epidemiological studies show that the co-occurrence of several of these neurological pathologies may indeed be the rule. The regulators of Rho GTPases have often been considered for cognitive diseases such as intellectual disability (ID) and autism. But, in a remarkable way, mild to severe motor symptoms are now reported in autism and other cognitive NDD. Although a more abundant litterature reports the involvement of Rho GTPases and signaling partners in cognitive development, molecular investigations on their roles in central nervous system (CNS) development or degenerative CNS pathologies also reveal their role in embryonic and perinatal motor wiring through axon guidance and later in synaptic plasticity. Thus, Rho family small GTPases have been revealed to play a key role in brain functions including learning and memory but their precise role in motor development and associated symptoms in NDD has been poorly scoped so far, despite increasing clinical data highlighting the links between cognition and motor development. Indeed, early impairements in fine or gross motor performance is often an associated feature of NDDs, which then impact social communication, cognition, emotion, and behavior. We review here recent insights derived from clinical developmental neurobiology in the field of Rho GTPases and NDD (autism spectrum related disorder (ASD), ID, schizophrenia, hypotonia, spastic paraplegia, bipolar disorder and dyslexia), with a specific focus on genetic alterations affecting Rho GTPases that are involved in motor circuit development.
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3
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Dobrigna M, Poëa-Guyon S, Rousseau V, Vincent A, Toutain A, Barnier JV. The molecular basis of p21-activated kinase-associated neurodevelopmental disorders: From genotype to phenotype. Front Neurosci 2023; 17:1123784. [PMID: 36937657 PMCID: PMC10017488 DOI: 10.3389/fnins.2023.1123784] [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: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Although the identification of numerous genes involved in neurodevelopmental disorders (NDDs) has reshaped our understanding of their etiology, there are still major obstacles in the way of developing therapeutic solutions for intellectual disability (ID) and other NDDs. These include extensive clinical and genetic heterogeneity, rarity of recurrent pathogenic variants, and comorbidity with other psychiatric traits. Moreover, a large intragenic mutational landscape is at play in some NDDs, leading to a broad range of clinical symptoms. Such diversity of symptoms is due to the different effects DNA variations have on protein functions and their impacts on downstream biological processes. The type of functional alterations, such as loss or gain of function, and interference with signaling pathways, has yet to be correlated with clinical symptoms for most genes. This review aims at discussing our current understanding of how the molecular changes of group I p21-activated kinases (PAK1, 2 and 3), which are essential actors of brain development and function; contribute to a broad clinical spectrum of NDDs. Identifying differences in PAK structure, regulation and spatio-temporal expression may help understanding the specific functions of each group I PAK. Deciphering how each variation type affects these parameters will help uncover the mechanisms underlying mutation pathogenicity. This is a prerequisite for the development of personalized therapeutic approaches.
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Affiliation(s)
- Manon Dobrigna
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Sandrine Poëa-Guyon
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Véronique Rousseau
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Aline Vincent
- Department of Genetics, EA7450 BioTARGen, University Hospital of Caen, Caen, France
| | - Annick Toutain
- Department of Genetics, University Hospital of Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
- *Correspondence: Jean-Vianney Barnier,
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Ahammad RU, Nishioka T, Yoshimoto J, Kannon T, Amano M, Funahashi Y, Tsuboi D, Faruk MO, Yamahashi Y, Yamada K, Nagai T, Kaibuchi K. KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. Cells 2021; 11:47. [PMID: 35011609 PMCID: PMC8750479 DOI: 10.3390/cells11010047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Protein phosphorylation plays critical roles in a variety of intracellular signaling pathways and physiological functions that are controlled by neurotransmitters and neuromodulators in the brain. Dysregulation of these signaling pathways has been implicated in neurodevelopmental disorders, including autism spectrum disorder, attention deficit hyperactivity disorder and schizophrenia. While recent advances in mass spectrometry-based proteomics have allowed us to identify approximately 280,000 phosphorylation sites, it remains largely unknown which sites are phosphorylated by which kinases. To overcome this issue, previously, we developed methods for comprehensive screening of the target substrates of given kinases, such as PKA and Rho-kinase, upon stimulation by extracellular signals and identified many candidate substrates for specific kinases and their phosphorylation sites. Here, we developed a novel online database to provide information about the phosphorylation signals identified by our methods, as well as those previously reported in the literature. The "KANPHOS" (Kinase-Associated Neural Phospho-Signaling) database and its web portal were built based on a next-generation XooNIps neuroinformatics tool. To explore the functionality of the KANPHOS database, we obtained phosphoproteomics data for adenosine-A2A-receptor signaling and its downstream MAPK-mediated signaling in the striatum/nucleus accumbens, registered them in KANPHOS, and analyzed the related pathways.
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Grants
- JP18dm0207005, JP21dm0207075, JP21wm0425017 and JP21wm0425008 Japan Agency for Medical Research and Development
- JP16K18393, JP17H01380, JP17K07383, JP17H02220, JP17K19483, JP18K14849, JP19K16370, JP21K06428 and JP21K06427 Japan Society for the Promotion of Science
- JP17H05561, JP19H05209 and JP21H00196 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Rijwan Uddin Ahammad
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, 65 Tsurumai, Nagoya 466-8550, Japan
| | - Tomoki Nishioka
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Junichiro Yoshimoto
- Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
| | - Mutsuki Amano
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, 65 Tsurumai, Nagoya 466-8550, Japan
| | - Yasuhiro Funahashi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Daisuke Tsuboi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Md Omar Faruk
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, 65 Tsurumai, Nagoya 466-8550, Japan
| | - Yukie Yamahashi
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Kiyofumi Yamada
- Department of Neuropsychopharmacology and Hospital Pharmacy, Graduate School of Medicine, Nagoya University, 65 Tsurumai, Nagoya 466-8550, Japan
| | - Taku Nagai
- Division of Behavioral Neuropharmacology, International Center for Brain Science (ICBS), Fujita Health University, Toyoake 470-1192, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, 65 Tsurumai, Nagoya 466-8550, Japan
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
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Disruption of PAK3 Signaling in Social Interaction Induced cFos Positive Cells Impairs Social Recognition Memory. Cells 2021; 10:cells10113010. [PMID: 34831234 PMCID: PMC8616103 DOI: 10.3390/cells10113010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/02/2022] Open
Abstract
P21-activated kinase 3 (PAK3) gene mutations are linked to several neurodevelopmental disorders, but the underlying mechanisms remain unclear. In this study, we used a tetracycline-inducible system to control the expression of a mutant PAK3 (mPAK3) protein in immediate early gene, namely cFos, positive cells to disrupt PAK signaling, specifically in cells activated by social interaction in transgenic mice. We show that the expression of mPAK3-GFP proteins was in cFos-expressing excitatory and inhibitory neurons in various brain regions, such as the cortex and hippocampus, commonly activated during learning and memory. Basal expression of mPAK3-GFP proteins in cFos-positive cells resulted in social recognition memory deficits in the three-chamber social interaction test, without affecting locomotor activity or other forms of memory. The social memory deficit was rescued by doxycycline to halt the mPAK3-GFP transgene expression. In addition, we show that the expression of mPAK3-GFP proteins in a subset of cFos-positive cells, induced by an antecedent short social interaction, termed social pairing, was sufficient to impair social recognition memory. These results indicate that normal PAK signaling in cFos-positive cells activated during social interaction is critical for social memory.
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Liaci C, Camera M, Caslini G, Rando S, Contino S, Romano V, Merlo GR. Neuronal Cytoskeleton in Intellectual Disability: From Systems Biology and Modeling to Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22116167. [PMID: 34200511 PMCID: PMC8201358 DOI: 10.3390/ijms22116167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Intellectual disability (ID) is a pathological condition characterized by limited intellectual functioning and adaptive behaviors. It affects 1–3% of the worldwide population, and no pharmacological therapies are currently available. More than 1000 genes have been found mutated in ID patients pointing out that, despite the common phenotype, the genetic bases are highly heterogeneous and apparently unrelated. Bibliomic analysis reveals that ID genes converge onto a few biological modules, including cytoskeleton dynamics, whose regulation depends on Rho GTPases transduction. Genetic variants exert their effects at different levels in a hierarchical arrangement, starting from the molecular level and moving toward higher levels of organization, i.e., cell compartment and functions, circuits, cognition, and behavior. Thus, cytoskeleton alterations that have an impact on cell processes such as neuronal migration, neuritogenesis, and synaptic plasticity rebound on the overall establishment of an effective network and consequently on the cognitive phenotype. Systems biology (SB) approaches are more focused on the overall interconnected network rather than on individual genes, thus encouraging the design of therapies that aim to correct common dysregulated biological processes. This review summarizes current knowledge about cytoskeleton control in neurons and its relevance for the ID pathogenesis, exploiting in silico modeling and translating the implications of those findings into biomedical research.
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Affiliation(s)
- Carla Liaci
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy; (C.L.); (M.C.); (G.C.); (S.R.)
| | - Mattia Camera
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy; (C.L.); (M.C.); (G.C.); (S.R.)
| | - Giovanni Caslini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy; (C.L.); (M.C.); (G.C.); (S.R.)
| | - Simona Rando
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy; (C.L.); (M.C.); (G.C.); (S.R.)
| | - Salvatore Contino
- Department of Engineering, University of Palermo, Viale delle Scienze Ed. 8, 90128 Palermo, Italy;
| | - Valentino Romano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Ed. 16, 90128 Palermo, Italy;
| | - Giorgio R. Merlo
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy; (C.L.); (M.C.); (G.C.); (S.R.)
- Correspondence: ; Tel.: +39-0116706449; Fax: +39-0116706432
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Serrano C, Dos Santos M, Kereselidze D, Beugnies L, Lestaevel P, Poirier R, Durand C. Targeted Dorsal Dentate Gyrus or Whole Brain Irradiation in Juvenile Mice Differently Affects Spatial Memory and Adult Hippocampal Neurogenesis. BIOLOGY 2021; 10:biology10030192. [PMID: 33806303 PMCID: PMC8002088 DOI: 10.3390/biology10030192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/26/2021] [Indexed: 12/11/2022]
Abstract
The cognitive consequences of postnatal brain exposure to ionizing radiation (IR) at low to moderate doses in the adult are not fully established. Because of the advent of pediatric computed tomography scans used for head exploration, improving our knowledge of these effects represents a major scientific challenge. To evaluate how IR may affect the developing brain, models of either whole brain (WB) or targeted dorsal dentate gyrus (DDG) irradiation in C57Bl/6J ten-day-old male mice were previously developed. Here, using these models, we assessed and compared the effect of IR (doses range: 0.25-2 Gy) on long-term spatial memory in adulthood using a spatial water maze task. We then evaluated the effects of IR exposure on adult hippocampal neurogenesis, a form of plasticity involved in spatial memory. Three months after WB exposure, none of the doses resulted in spatial memory impairment. In contrast, a deficit in memory retrieval was identified after DDG exposure for the dose of 1 Gy only, highlighting a non-monotonic dose-effect relationship in this model. At this dose, a brain irradiated volume effect was also observed when studying adult hippocampal neurogenesis in the two models. In particular, only DDG exposure caused alteration in cell differentiation. The most deleterious effect observed in adult hippocampal neurogenesis after targeted DDG exposure at 1 Gy may contribute to the memory retrieval deficit in this model. Altogether these results highlight the complexity of IR mechanisms in the brain that can lead or not to cognitive disorders and provide new knowledge of interest for the radiation protection of children.
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Affiliation(s)
- Céline Serrano
- Laboratory of Experimental Radiotoxicology and Radiobiology (LRTOX), Research Department on the Biological and Health Effects of Ionizing Radiation (SESANE), Institute for Radiological Protection and Nuclear Safety (IRSN), 92260 Fontenay-aux-Roses, France; (C.S.); (D.K.); (L.B.); (P.L.)
| | - Morgane Dos Santos
- Laboratory of Radiobiology of Accidental Exposure (LRAcc), Research Department in Radiobiology and Regenerative Medicine (SERAMED), Institute for Radiological Protection and Nuclear Safety (IRSN), 92260 Fontenay-aux-Roses, France;
| | - Dimitri Kereselidze
- Laboratory of Experimental Radiotoxicology and Radiobiology (LRTOX), Research Department on the Biological and Health Effects of Ionizing Radiation (SESANE), Institute for Radiological Protection and Nuclear Safety (IRSN), 92260 Fontenay-aux-Roses, France; (C.S.); (D.K.); (L.B.); (P.L.)
| | - Louison Beugnies
- Laboratory of Experimental Radiotoxicology and Radiobiology (LRTOX), Research Department on the Biological and Health Effects of Ionizing Radiation (SESANE), Institute for Radiological Protection and Nuclear Safety (IRSN), 92260 Fontenay-aux-Roses, France; (C.S.); (D.K.); (L.B.); (P.L.)
| | - Philippe Lestaevel
- Laboratory of Experimental Radiotoxicology and Radiobiology (LRTOX), Research Department on the Biological and Health Effects of Ionizing Radiation (SESANE), Institute for Radiological Protection and Nuclear Safety (IRSN), 92260 Fontenay-aux-Roses, France; (C.S.); (D.K.); (L.B.); (P.L.)
| | - Roseline Poirier
- Paris-Saclay Neuroscience Institute (Neuro-PSI), University Paris-Saclay, UMR 9197 CNRS, F-91405 Orsay, France
- Correspondence: (R.P.); (C.D.)
| | - Christelle Durand
- Laboratory of Experimental Radiotoxicology and Radiobiology (LRTOX), Research Department on the Biological and Health Effects of Ionizing Radiation (SESANE), Institute for Radiological Protection and Nuclear Safety (IRSN), 92260 Fontenay-aux-Roses, France; (C.S.); (D.K.); (L.B.); (P.L.)
- Correspondence: (R.P.); (C.D.)
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