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Zhou X, Zhao M, Fan Y, Xu Y. Identification of a necroptosis-related gene signature for making clinical predictions of the survival of patients with lung adenocarcinoma. PeerJ 2024; 12:e16616. [PMID: 38213773 PMCID: PMC10782958 DOI: 10.7717/peerj.16616] [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: 06/08/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a major pathological subtype of malignant lung cancer with a poor prognosis. Necroptosis is a caspase-independent programmed cell death mode that plays a pivotal role in cancer oncogenesis and metastasis. Here, we explore the prognostic values of different necroptosis-related genes (NRGs) in LUAD. Methods mRNA expression data and related clinical information for LUAD samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. NRGs were identified using the GeneCards database. Least absolute shrinkage and selection operator Cox regression and multivariate Cox analysis were used to construct a prognostic risk model. Time-dependent receiver-operating characteristic curves and a nomogram were constructed to validate the predictive values of the prognostic signatures. A necroptosis-related protein-protein interaction network was visualised using the STRING database and Cytoscape software. Functional analyses, including Gene Ontology, Kyoto Encyclopaedia of Genes and Genomes pathway enrichment, gene set enrichment, and gene set variation analyses, were conducted to explore the underlying molecular mechanisms. Finally, the mRNA expression of the prognostic signatures in LUAD cell lines was assessed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. Results A prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort. Patients with low-risk scores had better survival outcomes than those with high-risk scores (p = 0.00013). The nomogram was used to predict the prognosis of patients with LUAD. The prediction curves for 1-, 3-, and 5-year OS showed good predictive performance and the accuracy of the nomograms increased over time. RT-qPCR results demonstrated that these eight genes, especially CALM1, PRDX1, and PGLYRP1, were differentially expressed in LUAD cells. Conclusion We constructed a reliable eight-NRG signature that provides new insights for guiding clinical practice in the prognosis and treatment of LUAD.
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Affiliation(s)
- Xiaoping Zhou
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ming Zhao
- Department of Gastroenterology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Yingzi Fan
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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2
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Aygün N, Krupa O, Mory J, Le B, Valone J, Liang D, Love MI, Stein JL. Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555019. [PMID: 37693528 PMCID: PMC10491258 DOI: 10.1101/2023.08.30.555019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA-editing and alternative polyadenylation (APA), within a cell-type-specific population of human neural progenitors and neurons. More RNA-editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting genetically mediated post-transcriptional regulation during brain development lead to differences in brain function.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Mory
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brandon Le
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan Valone
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lead contact
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3
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Li Z, Wang D, Guo W, Zhang S, Chen L, Zhang YH, Lu L, Pan X, Huang T, Cai YD. Identification of cortical interneuron cell markers in mouse embryos based on machine learning analysis of single-cell transcriptomics. Front Neurosci 2022; 16:841145. [PMID: 35911980 PMCID: PMC9337837 DOI: 10.3389/fnins.2022.841145] [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: 12/24/2021] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Mammalian cortical interneurons (CINs) could be classified into more than two dozen cell types that possess diverse electrophysiological and molecular characteristics, and participate in various essential biological processes in the human neural system. However, the mechanism to generate diversity in CINs remains controversial. This study aims to predict CIN diversity in mouse embryo by using single-cell transcriptomics and the machine learning methods. Data of 2,669 single-cell transcriptome sequencing results are employed. The 2,669 cells are classified into three categories, caudal ganglionic eminence (CGE) cells, dorsal medial ganglionic eminence (dMGE) cells, and ventral medial ganglionic eminence (vMGE) cells, corresponding to the three regions in the mouse subpallium where the cells are collected. Such transcriptomic profiles were first analyzed by the minimum redundancy and maximum relevance method. A feature list was obtained, which was further fed into the incremental feature selection, incorporating two classification algorithms (random forest and repeated incremental pruning to produce error reduction), to extract key genes and construct powerful classifiers and classification rules. The optimal classifier could achieve an MCC of 0.725, and category-specified prediction accuracies of 0.958, 0.760, and 0.737 for the CGE, dMGE, and vMGE cells, respectively. The related genes and rules may provide helpful information for deepening the understanding of CIN diversity.
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Affiliation(s)
- Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- State Key Laboratory of Oncology in South China, Department of Radiology, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shiqi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - Lin Lu
- Department of Radiology, Columbia University Irving Medical Center, New York, NY, United States
| | - XiaoYong Pan
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- Yu-Dong Cai,
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4
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Yang Y, Paul A, Bach TN, Huang ZJ, Zhang MQ. Single-cell alternative polyadenylation analysis delineates GABAergic neuron types. BMC Biol 2021; 19:144. [PMID: 34301239 PMCID: PMC8299648 DOI: 10.1186/s12915-021-01076-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/17/2021] [Indexed: 01/10/2023] Open
Abstract
Background Alternative polyadenylation (APA) is emerging as an important mechanism in the post-transcriptional regulation of gene expression across eukaryotic species. Recent studies have shown that APA plays key roles in biological processes, such as cell proliferation and differentiation. Single-cell RNA-seq technologies are widely used in gene expression heterogeneity studies; however, systematic studies of APA at the single-cell level are still lacking. Results Here, we described a novel computational framework, SAPAS, that utilizes 3′-tag-based scRNA-seq data to identify novel poly(A) sites and quantify APA at the single-cell level. Applying SAPAS to the scRNA-seq data of phenotype characterized GABAergic interneurons, we identified cell type-specific APA events for different GABAergic neuron types. Genes with cell type-specific APA events are enriched for synaptic architecture and communications. In further, we observed a strong enrichment of heritability for several psychiatric disorders and brain traits in altered 3′ UTRs and coding sequences of cell type-specific APA events. Finally, by exploring the modalities of APA, we discovered that the bimodal APA pattern of Pak3 could classify chandelier cells into different subpopulations that are from different laminar positions. Conclusions We established a method to characterize APA at the single-cell level. When applied to a scRNA-seq dataset of GABAergic interneurons, the single-cell APA analysis not only identified cell type-specific APA events but also revealed that the modality of APA could classify cell subpopulations. Thus, SAPAS will expand our understanding of cellular heterogeneity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01076-3.
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Affiliation(s)
- Yang Yang
- Present Address: Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.,Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Harbor, Cold Spring, NY, 11724, USA.,Deparment of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Thao Nguyen Bach
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Harbor, Cold Spring, NY, 11724, USA.,Deparment of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75080, USA.
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5
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Liu T, Han X, Zheng S, Liu Q, Tuerxun A, Zhang Q, Yang L, Lu X. CALM1 promotes progression and dampens chemosensitivity to EGFR inhibitor in esophageal squamous cell carcinoma. Cancer Cell Int 2021; 21:121. [PMID: 33602237 PMCID: PMC7890995 DOI: 10.1186/s12935-021-01801-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Background Calmodulin1 (CALM1) has been identified as one of the overexpression genes in a variety of cancers and EGFR inhibitor have been widely used in clinical treatment but it is unknown whether CALM1 and epidermal growth factor receptor (EGFR) have a synergistic effect in esophageal squamous cell carcinoma (ESCC). The aim of the present study was to explore the synergistic effects of knock-out CALM1 combined with EGFR inhibitor (Afatinib) and to elucidate the role of CALM1 in sensitizing the resistance to Afatinib in ESCC. Method Immunohistochemistry (IHC) and qRT-PCR were used to examine the expression of CALM1 and EGFR in ESCC tissues. Kaplan–Meier survival analysis was used to analyze the clinical and prognostic significance of CALM1 and EGFR expression in ESCC. Furthermore, to evaluate the biological function of CALM1 in ESCC, the latest gene editing technique CRISPR/Cas9(Clustered regularly interspaced short palindromic repeats)was applied to knockout CALM1 in ESCC cell lines KYSE150, Eca109 and TE-1. MTT, flow cytometry, Transwell migration, scratch wound-healing and colony formation assays were performed to assay the combined effect of knock-out CALM1 and EGFR inhibitor on ESCC cell proliferation and migration. In addition, nude mice xenograft model was used to observe the synergistic inhibition of knock-out CALM1 and Afatinib. Results Both CALM1 and EGFR were found to be significantly over-expressed in ESCC compared with paired normal control. Over-expressed CALM1 and EGFR were significantly associated with clinical stage, T classification and poor overall prognosis, respectively. In vitro, the combined effect of knock-out CALM1 mediated by the lentivirus and EGFR inhibitor was shown to be capable of inhibiting the proliferation, inducing cell cycle arrest at G1/S stage and increasing apoptosis of KYSE-150 and Eca109 cells; invasion and migration were also suppressed. In vivo, the results of tumor weight and total fluorescence were markedly reduced compared with the sgCtrl-infected group and sgCAML1 group. Conclusion Our data demonstrated that knock-out of CALM1 could sensitize ESCC cells to EGFR inhibitor, and it may exert oncogenic role via promotion of EMT. Taken together, CALM1 may be a tempting target to overcome Afatinib resistance.
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Affiliation(s)
- Tao Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China.,Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Xiujuan Han
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Shutao Zheng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Aerziguli Tuerxun
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Qiqi Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Lifei Yang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China
| | - Xiaomei Lu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Disease in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, PR China.
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6
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Xiang W, Long Z, Zeng J, Zhu X, Yuan M, Wu J, Wu Y, Liu L. Mechanism of Radix Rhei Et Rhizome Intervention in Cerebral Infarction: A Research Based on Chemoinformatics and Systematic Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:6789835. [PMID: 34531920 PMCID: PMC8440083 DOI: 10.1155/2021/6789835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/13/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To explore the therapeutic targets, network modules, and coexpressed genes of Radix Rhei Et Rhizome intervention in cerebral infarction (CI), and to predict significant biological processes and pathways through network pharmacology. To explore the differential proteins of Radix Rhei Et Rhizome intervention in CI, conduct bioinformatics verification, and initially explain the possible therapeutic mechanism of Radix Rhei Et Rhizome intervention in CI through proteomics. METHODS The TCM database was used to predict the potential compounds of Radix Rhei Et Rhizome, and the PharmMapper was used to predict its potential targets. GeneCards and OMIM were used to search for CI-related genes. Cytoscape was used to construct a protein-protein interaction (PPI) network and to screen out core genes and detection network modules. Then, DAVID and Metascape were used for enrichment analysis. After that, in-depth analysis of the proteomics data was carried out to further explore the mechanism of Radix Rhei Et Rhizome intervention in CI. RESULTS (1) A total of 14 Radix Rhei Et Rhizome potential components and 425 potential targets were obtained. The core components include sennoside A, palmidin A, emodin, toralactone, and so on. The potential targets were combined with 297 CI genes to construct a PPI network. The targets shared by Radix Rhei Et Rhizome and CI include ALB, AKT1, MMP9, IGF1, CASP3, etc. The biological processes that Radix Rhei Et Rhizome may treat CI include platelet degranulation, cell migration, fibrinolysis, platelet activation, hypoxia, angiogenesis, endothelial cell apoptosis, coagulation, and neuronal apoptosis. The signaling pathways include Ras, PI3K-Akt, TNF, FoxO, HIF-1, and Rap1 signaling pathways. (2) Proteomics shows that the top 20 proteins in the differential protein PPI network were Syp, Syn1, Mbp, Gap43, Aif1, Camk2a, Syt1, Calm1, Calb1, Nsf, Nefl, Hspa5, Nefh, Ncam1, Dcx, Unc13a, Mapk1, Syt2, Dnm1, and Cltc. Differential protein enrichment results show that these proteins may be related to synaptic vesicle cycle, vesicle-mediated transport in synapse, presynaptic endocytosis, synaptic vesicle endocytosis, axon guidance, calcium signaling pathway, and so on. CONCLUSION This study combined network pharmacology and proteomics to explore the main material basis of Radix Rhei Et Rhizome for the treatment of CI such as sennoside A, palmidin A, emodin, and toralactone. The mechanism may be related to the regulation of biological processes (such as synaptic vesicle cycle, vesicle-mediated transport in synapse, presynaptic endocytosis, and synaptic vesicle endocytosis) and signaling pathways (such as Ras, PI3K-Akt, TNF, FoxO, HIF-1, Rap1, and axon guidance).
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Affiliation(s)
- Wang Xiang
- The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Province, China
| | - Zhiyong Long
- Shantou University Medical College, Shantou University, Shantou, Guangdong, China
| | - Jinsong Zeng
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, Hunan Province, China
- Hunan University of Chinese Medicine, Changsha, Hunan Province, China
| | - Xiaofei Zhu
- Hunan University of Chinese Medicine, Changsha, Hunan Province, China
| | - Mengxia Yuan
- Shantou University Medical College, Shantou University, Shantou, Guangdong, China
| | - Jiamin Wu
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yonghe Wu
- Hunan University of Chinese Medicine, Changsha, Hunan Province, China
| | - Liang Liu
- Hunan University of Chinese Medicine, Changsha, Hunan Province, China
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7
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Bae B, Gruner HN, Lynch M, Feng T, So K, Oliver D, Mastick GS, Yan W, Pieraut S, Miura P. Elimination of Calm1 long 3'-UTR mRNA isoform by CRISPR-Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice. RNA (NEW YORK, N.Y.) 2020; 26:1414-1430. [PMID: 32522888 PMCID: PMC7491327 DOI: 10.1261/rna.076430.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 05/04/2023]
Abstract
The majority of mouse and human genes are subject to alternative cleavage and polyadenylation (APA), which most often leads to the expression of two or more alternative length 3' untranslated region (3'-UTR) mRNA isoforms. In neural tissues, there is enhanced expression of APA isoforms with longer 3'-UTRs on a global scale, but the physiological relevance of these alternative 3'-UTR isoforms is poorly understood. Calmodulin 1 (Calm1) is a key integrator of calcium signaling that generates short (Calm1-S) and long (Calm1-L) 3'-UTR mRNA isoforms via APA. We found Calm1-L expression to be largely restricted to neural tissues in mice including the dorsal root ganglion (DRG) and hippocampus, whereas Calm1-S was more broadly expressed. smFISH revealed that both Calm1-S and Calm1-L were subcellularly localized to neural processes of primary hippocampal neurons. In contrast, cultured DRG showed restriction of Calm1-L to soma. To investigate the in vivo functions of Calm1-L, we implemented a CRISPR-Cas9 gene editing strategy to delete a small region encompassing the Calm1 distal poly(A) site. This eliminated Calm1-L expression while maintaining expression of Calm1-S Mice lacking Calm1-L (Calm1ΔL/ΔL ) exhibited disorganized DRG migration in embryos, and reduced experience-induced neuronal activation in the adult hippocampus. These data indicate that Calm1-L plays functional roles in the central and peripheral nervous systems.
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Affiliation(s)
- Bongmin Bae
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Hannah N Gruner
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Maebh Lynch
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Ting Feng
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Kevin So
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Grant S Mastick
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Wei Yan
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Simon Pieraut
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Nevada 89557, USA
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8
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Comprehensive Analysis of a circRNA-miRNA-mRNA Network to Reveal Potential Inflammation-Related Targets for Gastric Adenocarcinoma. Mediators Inflamm 2020; 2020:9435608. [PMID: 32801999 PMCID: PMC7416288 DOI: 10.1155/2020/9435608] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC) is the most common malignancy of the stomach. This study was aimed at elucidating the regulatory network of circRNA-miRNA-mRNA and identifying the precise inflammation-related targets in GC. The expression profiles of GSE83521, GSE78091, and GSE33651 were obtained from the GEO database. Interactions between miRNAs and circRNAs were investigated by the Circular RNA Interactome, and targets of miRNAs were predicted with miRTarBase. Then, a circRNA/miRNA/mRNA regulatory network was constructed. Also, functional enrichment analysis of selected differentially expressed genes (DEGs) was performed. The inflammation-/GC-related targets were collected in the GeneCards and GenLiP3 database, respectively. And a protein-protein interaction (PPI) network of DE mRNAs was constructed with STRING and Cytoscape to identify hub genes. The genetic alterations, neighboring gene networks, expression levels, and the poor prognosis of hub genes were investigated in cBioPortal, Oncomine, and Human Protein Atlas databases and Kaplan-Meier plotter, respectively. A total of 10 DE miRNAs and 33 DEGs were identified. The regulatory network contained 26 circRNAs, 10 miRNAs, and 1459 mRNAs. Functional enrichment analysis revealed that the selected 33 DEGs were involved in negative regulation of fat cell differentiation, response to wounding, extracellular matrix- (ECM-) receptor interaction, and regulation of cell growth pathways. THBS1, FN1, CALM1, COL4A1, CTGF, and IGFBP5 were selected as inflammation-related hub genes of GC in the PPI network. The genetic alterations in these hub genes were related to amplification and missense mutations. Furthermore, the genes RYR2, ERBB2, PI3KCA, and HELZ2 were connected to hub genes in this study. The hub gene levels in clinical specimens were markedly upregulated in GC tissues and correlated with poor overall survival (OS). Our results suggest that THBS1, FN1, CALM1, COL4A1, CTGF, and IGFBP5 were associated with the pathogenesis of gastric carcinogenesis and may serve as biomarkers and inflammation-related targets for GC.
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9
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Chemokine receptor CXCR7 non-cell-autonomously controls pontine neuronal migration and nucleus formation. Sci Rep 2020; 10:11830. [PMID: 32678266 PMCID: PMC7367352 DOI: 10.1038/s41598-020-68852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/30/2020] [Indexed: 11/28/2022] Open
Abstract
Long distance tangential migration transports neurons from their birth places to distant destinations to be incorporated into neuronal circuits. How neuronal migration is guided during these long journeys is still not fully understood. We address this issue by studying the migration of pontine nucleus (PN) neurons in the mouse hindbrain. PN neurons migrate from the lower rhombic lip first anteriorly and then turn ventrally near the trigeminal ganglion root towards the anterior ventral hindbrain. Previously we showed that in mouse depleted of chemokine receptor CXCR4 or its ligand CXCL12, PN neurons make their anterior-to-ventral turn at posteriorized positions. However, the mechanism that spatiotemporally controls the anterior-to-ventral turning is still unclear. Furthermore, the role of CXCR7, the atypical receptor of CXCL12, in pontine migration has yet to be examined. Here, we find that the PN is elongated in Cxcr7 knockout due to a broadened anterior-to-ventral turning positions. Cxcr7 is not expressed in migrating PN neurons en route to their destinations, but is strongly expressed in the pial meninges. Neuroepithelium-specific knockout of Cxcr7 does not recapitulate the PN phenotype in Cxcr7 knockout, suggesting that CXCR7 acts non-cell-autonomously possibly from the pial meninges. We show further that CXCR7 regulates pontine migration by modulating CXCL12 protein levels.
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10
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Villalobo A, Berchtold MW. The Role of Calmodulin in Tumor Cell Migration, Invasiveness, and Metastasis. Int J Mol Sci 2020; 21:ijms21030765. [PMID: 31991573 PMCID: PMC7037201 DOI: 10.3390/ijms21030765] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Calmodulin (CaM) is the principal Ca2+ sensor protein in all eukaryotic cells, that upon binding to target proteins transduces signals encoded by global or subcellular-specific changes of Ca2+ concentration within the cell. The Ca2+/CaM complex as well as Ca2+-free CaM modulate the activity of a vast number of enzymes, channels, signaling, adaptor and structural proteins, and hence the functionality of implicated signaling pathways, which control multiple cellular functions. A basic and important cellular function controlled by CaM in various ways is cell motility. Here we discuss the role of CaM-dependent systems involved in cell migration, tumor cell invasiveness, and metastasis development. Emphasis is given to phosphorylation/dephosphorylation events catalyzed by myosin light-chain kinase, CaM-dependent kinase-II, as well as other CaM-dependent kinases, and the CaM-dependent phosphatase calcineurin. In addition, the role of the CaM-regulated small GTPases Rac1 and Cdc42 (cell division cycle protein 42) as well as CaM-binding adaptor/scaffold proteins such as Grb7 (growth factor receptor bound protein 7), IQGAP (IQ motif containing GTPase activating protein) and AKAP12 (A kinase anchoring protein 12) will be reviewed. CaM-regulated mechanisms in cancer cells responsible for their greater migratory capacity compared to non-malignant cells, invasion of adjacent normal tissues and their systemic dissemination will be discussed, including closely linked processes such as the epithelial–mesenchymal transition and the activation of metalloproteases. This review covers as well the role of CaM in establishing metastatic foci in distant organs. Finally, the use of CaM antagonists and other blocking techniques to downregulate CaM-dependent systems aimed at preventing cancer cell invasiveness and metastasis development will be outlined.
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Affiliation(s)
- Antonio Villalobo
- Cancer and Human Molecular Genetics Area—Oto-Neurosurgery Research Group, University Hospital La Paz Research Institute (IdiPAZ), Paseo de la Castellana 261, E-28046 Madrid, Spain
- Correspondence: (A.V.); (M.W.B.)
| | - Martin W. Berchtold
- Department of Biology, University of Copenhagen, 13 Universitetsparken, DK-2100 Copenhagen, Denmark
- Correspondence: (A.V.); (M.W.B.)
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11
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Abstract
In utero electroporation is a rapid and powerful technique to study the development of many brain regions. This approach presents several advantages over other methods to study specific steps of brain development in vivo, from proliferation to synaptic integration. Here, we describe in detail the individual steps necessary to carry out the technique. We also highlight the variations that can be implemented to target different cerebral structures and to study specific steps of development.
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12
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Jiménez-González V, Ogalla-García E, García-Quintanilla M, García-Quintanilla A. Deciphering GRINA/Lifeguard1: Nuclear Location, Ca 2+ Homeostasis and Vesicle Transport. Int J Mol Sci 2019; 20:ijms20164005. [PMID: 31426446 PMCID: PMC6719933 DOI: 10.3390/ijms20164005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 01/31/2023] Open
Abstract
The Glutamate Receptor Ionotropic NMDA-Associated Protein 1 (GRINA) belongs to the Lifeguard family and is involved in calcium homeostasis, which governs key processes, such as cell survival or the release of neurotransmitters. GRINA is mainly associated with membranes of the endoplasmic reticulum, Golgi, endosome, and the cell surface, but its presence in the nucleus has not been explained yet. Here we dissect, with the help of different software tools, the potential roles of GRINA in the cell and how they may be altered in diseases, such as schizophrenia or celiac disease. We describe for the first time that the cytoplasmic N-terminal half of GRINA (which spans a Proline-rich domain) contains a potential DNA-binding sequence, in addition to cleavage target sites and probable PY-nuclear localization sequences, that may enable it to be released from the rest of the protein and enter the nucleus under suitable conditions, where it could participate in the transcription, alternative splicing, and mRNA export of a subset of genes likely involved in lipid and sterol synthesis, ribosome biogenesis, or cell cycle progression. To support these findings, we include additional evidence based on an exhaustive review of the literature and our preliminary data of the protein–protein interaction network of GRINA.
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Affiliation(s)
| | - Elena Ogalla-García
- Department of Pharmacology, School of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Meritxell García-Quintanilla
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Albert García-Quintanilla
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, 41012 Seville, Spain.
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13
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Horigane SI, Ozawa Y, Yamada H, Takemoto-Kimura S. Calcium signalling: a key regulator of neuronal migration. J Biochem 2019; 165:401-409. [PMID: 30753600 DOI: 10.1093/jb/mvz012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 02/10/2019] [Indexed: 12/12/2022] Open
Abstract
Neuronal migration is a crucial event in neuronal development for the construction of brain architecture and neuronal networks. Newborn neurons proliferate in the germinal zone and start migration toward their final destination. Migrating neurons adopt different routes, cell shapes and migratory modes depending on extracellular factors and outer physical substrates. Intracellular Ca2+ is an essential second messenger that regulates diverse cellular functions by activating Ca2+-dependent signalling molecules that underlie Ca2+-responsive cellular functions. Neuronal migration during brain architecture construction is no exception. Spontaneous Ca2+ transients are observed in several types of migrating neurons, and a series of Ca2+-dependent signalling molecules governing neuronal migration has been identified. In this review, we first summarize the molecular mechanisms that trigger intracellular Ca2+ elevation in migrating neurons. In the latter half of this review, we provide an overview of the literature on Ca2+-dependent signalling molecules underlying neuronal migration.
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Affiliation(s)
- Shin-Ichiro Horigane
- Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihiro Ozawa
- Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Pathology and Laboratory Medicine, Nagoya University Hospital, Nagoya, Japan
| | - Hirokazu Yamada
- Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sayaka Takemoto-Kimura
- Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan
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14
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Kan J, Zhao C, Lu S, Shen G, Yang J, Tong P, Xi L, Zhang R, Liang X, Su D, Li D, Liu Y. S100A16, a novel lipogenesis promoting factor in livers of mice and hepatocytes in vitro. J Cell Physiol 2019; 234:21395-21406. [PMID: 31069793 DOI: 10.1002/jcp.28748] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Jingbao Kan
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Cuiping Zhao
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Shan Lu
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Geqian Shen
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Jie Yang
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Pei Tong
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Ling Xi
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Rihua Zhang
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
| | - Xiubin Liang
- The Center of Metabolic Disease Research Nanjing Medical University Nanjing China
| | - Dongming Su
- The Center of Metabolic Disease Research Nanjing Medical University Nanjing China
| | - Dong Li
- Department of Orthopedics Jiangsu Province Hospital of TCM Affiliated Hospital of Nanjing University of TCM Nanjing Jiangsu China
| | - Yun Liu
- Department of Geriatrics The First Affiliated Hospital of Nanjing Medical University Nanjing China
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15
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Calvo AC, Cibreiro GA, Merino PT, Roy JF, Galiana A, Rufián AJ, Cano JM, Martín MA, Moreno L, Larrodé P, Vázquez PC, Galán L, Mora J, Muñoz-Blanco JL, Muñoz MJ, Zaragoza P, Pegoraro E, Sorarù G, Mora M, Lunetta C, Penco S, Tarlarini C, Esteban J, Osta R, Redondo AG. Collagen XIX Alpha 1 Improves Prognosis in Amyotrophic Lateral Sclerosis. Aging Dis 2019; 10:278-292. [PMID: 31011479 PMCID: PMC6457048 DOI: 10.14336/ad.2018.0917] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
The identification of more reliable diagnostic or prognostic biomarkers in age-related neurodegenerative diseases, such as Amyotrophic Lateral Sclerosis (ALS), is urgently needed. The objective in this study was to identify more reliable prognostic biomarkers of ALS mirroring neurodegeneration that could be of help in clinical trials. A total of 268 participants from three cohorts were included in this study. The muscle and blood cohorts were analyzed in two cross-sectional studies, while the serial blood cohort was analyzed in a longitudinal study at 6-monthly intervals. Fifteen target genes and fourteen proteins involved in muscle physiology and differentiation, metabolic processes and neuromuscular junction dismantlement were studied in the three cohorts. In the muscle biopsy cohort, the risk for a higher mortality in an ALS patient that showed high Collagen type XIX, alpha 1 (COL19A1) protein levels and a fast progression of the disease was 70.5% (P < 0.05), while in the blood cohort, this risk was 20% (P < 0.01). In the serial blood cohort, the linear mixed model analysis showed a significant association between increasing COL19A1 gene levels along disease progression and a faster progression during the follow-up period of 24 months (P < 0.05). Additionally, higher COL19A1 levels and a faster progression increased 17.9% the mortality risk (P < 0.01). We provide new evidence that COL19A1 can be considered a prognostic biomarker that could help the selection of homogeneous groups of patients for upcoming clinical trial and may be pointed out as a promising therapeutic target in ALS.
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Affiliation(s)
- Ana C Calvo
- 1LAGENBIO (Laboratory of Genetics and Biochemistry), Faculty of Veterinary-IIS, IA2-CITA, University of Zaragoza, Zaragoza, Spain
| | - Gabriela Atencia Cibreiro
- 2Neurology Department, ALS Unit, CIBERER U-723, Health Research Institute, October 12th Hospital "IIS I+12", Madrid, Spain
| | - Paz Torre Merino
- 2Neurology Department, ALS Unit, CIBERER U-723, Health Research Institute, October 12th Hospital "IIS I+12", Madrid, Spain
| | - Juan F Roy
- 3Ferkauf Graduate School of Psychology, Yeshiva University, NY 10461, USA
| | - Adrián Galiana
- 4Servicio de Reumatología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | - Alexandra Juárez Rufián
- 2Neurology Department, ALS Unit, CIBERER U-723, Health Research Institute, October 12th Hospital "IIS I+12", Madrid, Spain
| | - Juan M Cano
- 5Orthopaedic Surgery Department, October 12th Hospital, Madrid, Spain
| | - Miguel A Martín
- 6Grupo Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), U723-CIBERER, Madrid, España
| | - Laura Moreno
- 1LAGENBIO (Laboratory of Genetics and Biochemistry), Faculty of Veterinary-IIS, IA2-CITA, University of Zaragoza, Zaragoza, Spain
| | - Pilar Larrodé
- 1LAGENBIO (Laboratory of Genetics and Biochemistry), Faculty of Veterinary-IIS, IA2-CITA, University of Zaragoza, Zaragoza, Spain
| | - Pilar Cordero Vázquez
- 2Neurology Department, ALS Unit, CIBERER U-723, Health Research Institute, October 12th Hospital "IIS I+12", Madrid, Spain
| | - Lucía Galán
- 7Neurology Department, ALS Unit, Clínico Universitario San Carlos Hospital, Madrid, Spain
| | - Jesús Mora
- 8Neurology Department, ALS Unit, Carlos III Hospital, Madrid, Spain
| | - José L Muñoz-Blanco
- 9Neurology Department, ALS Unit, Health Research Institute, Gregorio Marañón Hospital "IISGM", Madrid, Spain
| | - María J Muñoz
- 1LAGENBIO (Laboratory of Genetics and Biochemistry), Faculty of Veterinary-IIS, IA2-CITA, University of Zaragoza, Zaragoza, Spain
| | - Pilar Zaragoza
- 1LAGENBIO (Laboratory of Genetics and Biochemistry), Faculty of Veterinary-IIS, IA2-CITA, University of Zaragoza, Zaragoza, Spain
| | - Elena Pegoraro
- 10Neurological Clinic, Department of Neurosciences, University of Padova, Padova, Italy
| | - Gianni Sorarù
- 10Neurological Clinic, Department of Neurosciences, University of Padova, Padova, Italy
| | - Marina Mora
- 11Muscle Cell Biology Laboratory, Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Christian Lunetta
- 12NEMO (NEuroMuscular Omnicentre) Clinical Center, Fondazione Serena Onlus, Milan, Italy
| | - Silvana Penco
- 13Medical Genetics Unit, Department of Laboratory Medicine, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Claudia Tarlarini
- 13Medical Genetics Unit, Department of Laboratory Medicine, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Jesús Esteban
- 2Neurology Department, ALS Unit, CIBERER U-723, Health Research Institute, October 12th Hospital "IIS I+12", Madrid, Spain
| | - Rosario Osta
- 1LAGENBIO (Laboratory of Genetics and Biochemistry), Faculty of Veterinary-IIS, IA2-CITA, University of Zaragoza, Zaragoza, Spain
| | - Alberto García Redondo
- 2Neurology Department, ALS Unit, CIBERER U-723, Health Research Institute, October 12th Hospital "IIS I+12", Madrid, Spain
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16
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Srikanth P, Lagomarsino VN, Pearse RV, Liao M, Ghosh S, Nehme R, Seyfried N, Eggan K, Young-Pearse TL. Convergence of independent DISC1 mutations on impaired neurite growth via decreased UNC5D expression. Transl Psychiatry 2018; 8:245. [PMID: 30410030 PMCID: PMC6224395 DOI: 10.1038/s41398-018-0281-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022] Open
Abstract
The identification of convergent phenotypes in different models of psychiatric illness highlights robust phenotypes that are more likely to be implicated in disease pathophysiology. Here, we utilize human iPSCs harboring distinct mutations in DISC1 that have been found in families with major mental illness. One mutation was engineered to mimic the consequences on DISC1 protein of a balanced translocation linked to mental illness in a Scottish pedigree; the other mutation was identified in an American pedigree with a high incidence of mental illness. Directed differentiation of these iPSCs using NGN2 expression shows rapid conversion to a homogenous population of mature excitatory neurons. Both DISC1 mutations result in reduced DISC1 protein expression, and show subtle effects on certain presynaptic proteins. In addition, RNA sequencing and qPCR showed decreased expression of UNC5D, DPP10, PCDHA6, and ZNF506 in neurons with both DISC1 mutations. Longitudinal analysis of neurite outgrowth revealed decreased neurite outgrowth in neurons with each DISC1 mutation, which was mimicked by UNC5D knockdown and rescued by transient upregulation of endogenous UNC5D. This study shows a narrow range of convergent phenotypes of two mutations found in families with major mental illness, and implicates dysregulated netrin signaling in DISC1 biology.
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Affiliation(s)
- Priya Srikanth
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Valentina N. Lagomarsino
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Richard V. Pearse
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Meichen Liao
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
| | - Sulagna Ghosh
- 000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Ralda Nehme
- 000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Nicholas Seyfried
- 0000 0001 0941 6502grid.189967.8Department of Biochemistry, Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Kevin Eggan
- 000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Tracy L. Young-Pearse
- 0000 0004 0378 8294grid.62560.37Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA USA
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17
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Recabarren-Leiva D, Alarcón M. New insights into the gene expression associated to amyotrophic lateral sclerosis. Life Sci 2018; 193:110-123. [DOI: 10.1016/j.lfs.2017.12.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/01/2017] [Accepted: 12/10/2017] [Indexed: 12/11/2022]
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18
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Yang J, Cai W, Lu X, Liu S, Zhao S. RNA-Sequencing Analyses Demonstrate the Involvement of Canonical Transient Receptor Potential Channels in Rat Tooth Germ Development. Front Physiol 2017; 8:455. [PMID: 28706494 PMCID: PMC5489664 DOI: 10.3389/fphys.2017.00455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/14/2017] [Indexed: 02/03/2023] Open
Abstract
Tooth development depends on multiple molecular interactions between the dental epithelium and mesenchyme, which are derived from ectodermal and ectomesenchymal cells, respectively. We report on a systematic RNA sequencing analysis of transcriptional expression levels from the bud to hard tissue formation stages of rat tooth germ development. We found that GNAO1, ENO1, EFNB1, CALM1, SIAH2, ATP6V0A1, KDELR2, GTPBP1, POLR2C, SORT1, and members of the canonical transient receptor potential (TRPC) channel family are involved in tooth germ development. Furthermore, Cell Counting Kit 8 (CCK8) and Transwell migration assays were performed to explore the effects of these differentially expressed genes (DEGs) on the proliferation and migration of dental pulp stem cells. Immunostaining revealed that TRPC channels are expressed at varying levels during odontogenesis. The identified genes represent novel candidates that are likely to be vital for rat tooth germ development. Together, the results provide a valuable resource to elucidate the gene regulatory mechanisms underlying mammalian tooth germ development.
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Affiliation(s)
- Jun Yang
- Department of Stomatology, Huashan Hospital, Fudan UniversityShanghai, China
| | - Wenping Cai
- Department of Stomatology, Huashan Hospital, Fudan UniversityShanghai, China
| | - Xi Lu
- Department of Stomatology, Huashan Hospital, Fudan UniversityShanghai, China
| | - Shangfeng Liu
- Department of Stomatology, Huashan Hospital, Fudan UniversityShanghai, China
| | - Shouliang Zhao
- Department of Stomatology, Huashan Hospital, Fudan UniversityShanghai, China
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19
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Abstract
Three neurodegenerative diseases [Amyotrophic Lateral Sclerosis (ALS), Parkinson's disease (PD) and Alzheimer's disease (AD)] have many characteristics like pathological mechanisms and genes. In this sense some researchers postulate that these diseases share the same alterations and that one alteration in a specific protein triggers one of these diseases. Analyses of gene expression may shed more light on how to discover pathways, pathologic mechanisms associated with the disease, biomarkers and potential therapeutic targets. In this review, we analyze four microarrays related to three neurodegenerative diseases. We will systematically examine seven genes (CHN1, MDH1, PCP4, RTN1, SLC14A1, SNAP25 and VSNL1) that are altered in the three neurodegenerative diseases. A network was built and used to identify pathways, miRNA and drugs associated with ALS, AD and PD using Cytoscape software an interaction network based on the protein interactions of these genes. The most important affected pathway is PI3K-Akt signalling. Thirteen microRNAs (miRNA-19B1, miRNA-107, miRNA-124-1, miRNA-124-2, miRNA-9-2, miRNA-29A, miRNA-9-3, miRNA-328, miRNA-19B2, miRNA-29B2, miRNA-124-3, miRNA-15A and miRNA-9-1) and four drugs (Estradiol, Acetaminophen, Resveratrol and Progesterone) for new possible treatments were identified.
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Affiliation(s)
| | - Marcelo Alarcón
- Department of Clinical Biochemistry and Immunohematology, Faculty of Health Sciences, Universidad de Talca, Talca 3460000, Chile; Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca, Talca 3460000, Chile.
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20
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Kratochwil CF, Maheshwari U, Rijli FM. The Long Journey of Pontine Nuclei Neurons: From Rhombic Lip to Cortico-Ponto-Cerebellar Circuitry. Front Neural Circuits 2017; 11:33. [PMID: 28567005 PMCID: PMC5434118 DOI: 10.3389/fncir.2017.00033] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/28/2017] [Indexed: 01/26/2023] Open
Abstract
The pontine nuclei (PN) are the largest of the precerebellar nuclei, neuronal assemblies in the hindbrain providing principal input to the cerebellum. The PN are predominantly innervated by the cerebral cortex and project as mossy fibers to the cerebellar hemispheres. Here, we comprehensively review the development of the PN from specification to migration, nucleogenesis and circuit formation. PN neurons originate at the posterior rhombic lip and migrate tangentially crossing several rhombomere derived territories to reach their final position in ventral part of the pons. The developing PN provide a classical example of tangential neuronal migration and a study system for understanding its molecular underpinnings. We anticipate that understanding the mechanisms of PN migration and assembly will also permit a deeper understanding of the molecular and cellular basis of cortico-cerebellar circuit formation and function.
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Affiliation(s)
- Claudius F Kratochwil
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of KonstanzKonstanz, Germany.,Zukunftskolleg, University of KonstanzKonstanz, Germany
| | - Upasana Maheshwari
- Friedrich Miescher Institute for Biomedical ResearchBasel, Switzerland.,University of BaselBasel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical ResearchBasel, Switzerland.,University of BaselBasel, Switzerland
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21
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Sahu SU, Visetsouk MR, Garde RJ, Hennes L, Kwas C, Gutzman JH. Calcium signals drive cell shape changes during zebrafish midbrain-hindbrain boundary formation. Mol Biol Cell 2017; 28:875-882. [PMID: 28148652 PMCID: PMC5385936 DOI: 10.1091/mbc.e16-08-0561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/27/2016] [Accepted: 01/25/2017] [Indexed: 01/19/2023] Open
Abstract
Calcium signals via calmodulin, myosin light chain kinase, and nonmuscle myosin II to mediate neuroepithelial apical-basal cell length during zebrafish brain morphogenesis. One of the first morphogenetic events in the vertebrate brain is the formation of the highly conserved midbrain–hindbrain boundary (MHB). Specific cell shape changes occur at the point of deepest constriction of the MHB, the midbrain–hindbrain boundary constriction (MHBC), and are critical for proper MHB formation. These cell shape changes are controlled by nonmuscle myosin II (NMII) motor proteins, which are tightly regulated via the phosphorylation of their associated myosin regulatory light chains (MRLCs). However, the upstream signaling pathways that initiate the regulation of NMII to mediate cell shape changes during MHB morphogenesis are not known. We show that intracellular calcium signals are critical for the regulation of cell shortening during initial MHB formation. We demonstrate that the MHB region is poised to respond to calcium transients that occur in the MHB at the onset of MHB morphogenesis and that calcium mediates phosphorylation of MRLC specifically in MHB tissue. Our results indicate that calmodulin 1a (calm1a), expressed specifically in the MHB, and myosin light chain kinase together mediate MHBC cell length. Our data suggest that modulation of NMII activity by calcium is critical for proper regulation of cell length to determine embryonic brain shape during development.
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Affiliation(s)
- Srishti U Sahu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
| | - Mike R Visetsouk
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
| | - Ryan J Garde
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
| | - Leah Hennes
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
| | - Constance Kwas
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
| | - Jennifer H Gutzman
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201
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22
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Kobayashi H, Saragai S, Naito A, Ichio K, Kawauchi D, Murakami F. Calm1 signaling pathway is essential for the migration of mouse precerebellar neurons. J Cell Sci 2015. [DOI: 10.1242/jcs.168658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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