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McVey DG, Andreadi C, Gong P, Stanczyk PJ, Solomon CU, Turner L, Yan L, Chen R, Cao J, Nelson CP, Thompson JR, Yu H, Webb TR, Samani NJ, Ye S. Genetic influence on vascular smooth muscle cell apoptosis. Cell Death Dis 2024; 15:402. [PMID: 38851795 PMCID: PMC11162461 DOI: 10.1038/s41419-024-06799-z] [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: 10/02/2023] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Vascular smooth muscle cell (VSMC) proliferation, migration, and apoptosis play important roles in many physiological processes and pathological conditions. To identify genetic influences on VSMC behavior, we measured these traits and undertook genome-wide association studies in primary umbilical artery-derived VSMCs from >2000 individuals. Although there were no genome-wide significant associations for VSMC proliferation or migration, genetic variants at two genomic loci (7p15.3 and 7q32.3) showed highly significant associations with VSMC apoptosis (P = 1.95 × 10-13 and P = 7.47 × 10-9, respectively). The lead variant at the 7p51.3 locus was associated with increased expression of the GSDME and PALS2 genes in VSMCs. Knockdown of GSDME or PALS2 in VSMCs attenuated apoptotic cell death. A protein co-immunoprecipitation assay indicated that GSDME complexed with PALS2. PALS2 knockdown attenuated activated caspase-3 and GSDME fragmentation, whilst GSDME knockdown also reduced activated caspase-3. These findings provide new insights into the genetic regulation of VSMC apoptosis, with potential utility for therapeutic development.
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Affiliation(s)
- David G McVey
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Catherine Andreadi
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Peng Gong
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Paulina J Stanczyk
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Charles U Solomon
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Lenka Turner
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Liu Yan
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore
| | - Runji Chen
- Shantou University Medical College, Shantou, China
| | - Junjun Cao
- Shantou University Medical College, Shantou, China
| | - Christopher P Nelson
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - John R Thompson
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Haojie Yu
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore
| | - Tom R Webb
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Shu Ye
- Department of Cardiovascular Sciences and National Institute for Health Research Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
- Cardiovascular-Metabolic Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of, Singapore, Singapore.
- Shantou University Medical College, Shantou, China.
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Janakiraman V, Sudhan M, Alzahrani KJ, Alshammeri S, Ahmed SSSJ, Patil S. Dynamics of TUBB protein with five majorly occurring natural variants: a risk of cortical dysplasia. J Mol Model 2023; 29:100. [PMID: 36928665 DOI: 10.1007/s00894-023-05506-7] [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: 09/23/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
Beta-tubulin (TUBB) protein is one of the components of the microtubule cytoskeleton that plays a critical role in the central nervous system. Genetic variants of TUBB cause cortical dysplasia, a developmental brain defect implicated in axonal guidance and the neuron migration. In this study, we assess pathogenic variants (Q15K, Y222F, M299V, V353I, and E401K) of TUBB protein and compared with non-pathogenic variant G235S to determine their impact on protein dynamic to cause cortical dysplasia. Among the analyzed variants, Q15K, Y222F, M299V, and E401K were noticed to have deleterious effect. Then, variant structures were modeled and their affinity with their known cofactor Guanosine-5'-triphosphate (GTP) was assessed which showed diverse binding energies ranged between (-7.436 to -6.950 kcal/mol) for the variants compared to wild-type (-7.428 kcal/mol). Finally, the molecular dynamics simulation of each variant was investigated which showed difference in trajectory between the pathogenic and non-pathogenic variant. Our analysis suggests change in amino acid residue of TUBB structure has notably affects the protein flexibility and their interactions with known cofactor. Overall, our findings provide insight on the relationship between TUBB variants and their structural dynamics that may cause diverse effects leading to cortical dysplasia.
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Affiliation(s)
- V Janakiraman
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India
| | - M Sudhan
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Saleh Alshammeri
- Department of Optometry, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, USA
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Changes on proteomic and metabolomic profiling of cryopreserved sperm effected by melatonin. J Proteomics 2023; 273:104791. [PMID: 36538967 DOI: 10.1016/j.jprot.2022.104791] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
Cryopreservation may reduce sperm fertility due to cryodamage including physical-chemical and oxidative stress damages. As a powerful antioxidant, melatonin has been reported to improve cryoprotective effect of sperm. However, the molecular mechanism of melatonin on cryopreserved ram sperm hasn't been fully understand. Give this, this study aimed to investigate the postthaw motility parameters, antioxidative enzyme activities and lipid peroxidation, as well as proteomic, metabolomic changes of Huang-huai ram spermatozoa with freezing medium supplemented with melatonin. Melatonin was firstly replenished to the medium to yield five different final concentrations: 0.1, 0.5, 1.0, 1.5, and 2.0 mM. A control (NC) group without melatonin replenishment was included. Protective effects of melatonin as evidenced by postthaw motility, activities of T-AOC, T-SOD, GSH-Px, CAT, contents of MDA, 4-HNE, as well as acrosome integrity, plasma membrane integrity, with 0.5 mM being the most effective concentration (MC group). Furthermore, 29 differentially abundant proteins involving in sperm functions were screened among Fresh, NC and MC groups of samples (n = 5) based on the 4D-LFQ, with 7 of them upregulated in Fresh and MC groups. 26 differentially abundant metabolites were obtained involving in sperm metabolism among the three groups of samples (n = 8) based on the UHPLC-QE-MS, with 18 of them upregulated in Fresh and MC groups. According to the bioinformatic analysis, melatonin may have positive effects on frozen ram spermatozoa by regulating the abundance changes of vital proteins and metabolites related to sperm function. Particularly, several proteins such as PRCP, NDUFB8, NDUFB9, SDHC, DCTN1, TUBB6, TUBA3E, SSNA1, as well as metabolites like L-histidine, L-targinine, ursolic acid, xanthine may be potential novel biomarkers for evaluating the postthaw quality of ram spermatozoa. In conclusion, a dose-dependent replenishment of melatonin to freezing medium protected ram spermatozoa during cryopreservation, which can improve motility, antioxidant enzyme activities, reduce levels of lipid peroxidation products, modify the proteomic and metabolomic profiling of cryopreserved ram spermatozoa through reduction of oxidative stress, maintenance of OXPHOS and microtubule structure. SIGNIFICANCE: Melatonin, a powerful antioxidant protects ram spermatozoa from cryopreservation injuries in a dose-dependent manner, with 0.5 mM being the most effective concentration. Furthermore, sequencing results based on the 4D-LFQ combined with the UHPLC-QE-MS indicated that melatonin modifies proteomic and metabolomic profiling of ram sperm during cryopreservation. According to the bioinformatic analysis, melatonin may have positive effects on frozen ram spermatozoa by regulating the expression changes of vital proteins and metabolites related to sperm metabolism and function. Particularly, several potential novel biomarkers for evaluating the postthaw quality of ram spermatozoa were acquired, proteins such as PRCP, NDUFB8, NDUFB9, SDHC, DCTN1, TUBB6, TUBA3E, SSNA1, as well as metabolites like L-histidine, L-targinine, ursolic acid, xanthine.
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4
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Davis MA, Gale M. Assessing Cytoskeletal Destruction During Pyroptosis. Methods Mol Biol 2023; 2641:179-188. [PMID: 37074651 DOI: 10.1007/978-1-0716-3040-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Pyroptosis is an inflammatory form of cell death driven by the activation of caspase-1 and/or caspase-11 which cleaves and activates the pore-forming and cell-permeabilizing protein gasdermin-D. Pyroptosis is characterized by cell swelling and release of inflammatory cytosolic content, which were thought to be driven by colloid-osmotic lysis. Instead, we previously demonstrated that in vitro, pyroptotic cells do not in fact lyse. We also demonstrated that calpain cleaves vimentin, leading to loss of intermediate filaments, which in turn makes cells fragile and susceptible to rupture by extrinsic pressure. However, if, as our observations suggest, cells do not swell due to osmotic forces, what then causes cell rupture? Interestingly, in addition to intermediate filament loss, we demonstrated that other cytoskeletal networks, such as microtubules, actin, and nuclear lamina, are similarly lost during pyroptosis; however, the mechanisms driving these cytoskeletal disruptions as well as their functional significance are unclear. To facilitate the study of these processes, we present here the immunocytochemical methods by which we detected and assayed cytoskeletal destruction during pyroptosis.
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Affiliation(s)
- Michael A Davis
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA
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5
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. CELL GENOMICS 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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6
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Han Y, Tan L, Zhou T, Yang L, Carrau L, Lacko LA, Saeed M, Zhu J, Zhao Z, Nilsson-Payant BE, Lira Neto FT, Cahir C, Giani AM, Chai JC, Li Y, Dong X, Moroziewicz D, Paull D, Zhang T, Koo S, Tan C, Danziger R, Ba Q, Feng L, Chen Z, Zhong A, Wise GJ, Xiang JZ, Wang H, Schwartz RE, tenOever BR, Noggle SA, Rice CM, Qi Q, Evans T, Chen S. A human iPSC-array-based GWAS identifies a virus susceptibility locus in the NDUFA4 gene and functional variants. Cell Stem Cell 2022; 29:1475-1490.e6. [PMID: 36206731 PMCID: PMC9550219 DOI: 10.1016/j.stem.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 06/09/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022]
Abstract
Population-based studies to identify disease-associated risk alleles typically require samples from a large number of individuals. Here, we report a human-induced pluripotent stem cell (hiPSC)-based screening strategy to link human genetics with viral infectivity. A genome-wide association study (GWAS) identified a cluster of single-nucleotide polymorphisms (SNPs) in a cis-regulatory region of the NDUFA4 gene, which was associated with susceptibility to Zika virus (ZIKV) infection. Loss of NDUFA4 led to decreased sensitivity to ZIKV, dengue virus, and SARS-CoV-2 infection. Isogenic hiPSC lines carrying non-risk alleles of SNPs or deletion of the cis-regulatory region lower sensitivity to viral infection. Mechanistic studies indicated that loss/reduction of NDUFA4 causes mitochondrial stress, which leads to the leakage of mtDNA and thereby upregulation of type I interferon signaling. This study provides proof-of-principle for the application of iPSC arrays in GWAS and identifies NDUFA4 as a previously unknown susceptibility locus for viral infection.
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Affiliation(s)
- Yuling Han
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lei Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ting Zhou
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Liuliu Yang
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lucia Carrau
- Department of Microbiology, New York University, 430 E 29th Street, New York, NY 10016, USA
| | - Lauretta A Lacko
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Zeping Zhao
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | | | | | - Clare Cahir
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; The Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Alice Maria Giani
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Jin Chou Chai
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yang Li
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Xue Dong
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Dorota Moroziewicz
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Tuo Zhang
- Genomic Resource Core Facility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Soyeon Koo
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Christina Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Ron Danziger
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Qian Ba
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingling Feng
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, China
| | - Zhengming Chen
- Department of Population Health Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Gilbert J Wise
- Department of Urology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Jenny Z Xiang
- Genomic Resource Core Facility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Benjamin R tenOever
- Department of Microbiology, New York University, 430 E 29th Street, New York, NY 10016, USA
| | - Scott A Noggle
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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7
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Guan SH, Wang XY, Shang P, Du QC, Li MZ, Xing X, Yan B. Pyroptosis-related genes play a significant role in the prognosis of gastric cancer. World J Clin Cases 2022; 10:8490-8505. [PMID: 36157810 PMCID: PMC9453351 DOI: 10.12998/wjcc.v10.i24.8490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/14/2022] [Accepted: 07/17/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Pyroptosis is an inflammatory form of programmed cell death, which has been shown to be related to the prognosis of many tumors. However, its role in gastric cancer (GC) is not fully understood.
AIM To evaluate the expression of pyroptosis-related genes in GC and its correlation with prognosis.
METHODS We constructed prognostic multigene markers of differentially expressed genes associated with pyroptosis by least absolute contraction and selection operator Cox regression. The risk model was analyzed by Kaplan-Meier curve, two-sided log-rank test and functional enrichment analysis.
RESULTS Sixty-three pyroptosis-related genes were differentially expressed in tumor tissues and adjacent nontumor tissues. Based on these differentially expressed genes, 5 gene signature were constructed and all GC patients were classified into two risk groups. Kaplan-Meier survival curve showed that the overall survival (OS) of patients in the high-risk group was significantly lower than that of the low-risk group. Multivariate Cox regression analyses showed that the risk score was an independent risk factor for OS. Receiver operating characteristic curve analysis confirmed the predictive ability of the model. External validation indicated increased OS in the low-risk group. The immune function and immune cell scores of the high-risk group were generally higher than those of the low-risk group.
CONCLUSION Pyroptosis-related genes play a significant role in tumor immune microenvironment. This novel model, which contains 5 pyroptosis-related genes, is an independent predicting factor for OS in GC patients, and may help to evaluate the prognosis of GC.
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Affiliation(s)
- Shi-Hao Guan
- Department of General Surgery, The Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai 201700, China
| | - Xin-Yu Wang
- Department of General Surgery, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai 200434, China
| | - Ping Shang
- Department of General Surgery, The Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai 201700, China
| | - Qian-Cheng Du
- Department of General Surgery, Zhongshan-xuhui Hospital, Fudan University, Shanghai 200030, China
| | - Ming-Zhi Li
- Department of General Surgery, The Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai 201700, China
| | - Xiao Xing
- Department of General Surgery, The Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai 201700, China
| | - Bin Yan
- Department of General Surgery, The Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai 201700, China
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8
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Ludueña RF. Possible Roles of Specific Amino Acids in β-Tubulin Isotypes in the Growth and Maintenance of Neurons: Novel Insights From Cephalopod Mollusks. Front Mol Neurosci 2022; 15:838393. [PMID: 35493322 PMCID: PMC9048481 DOI: 10.3389/fnmol.2022.838393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/17/2022] [Indexed: 11/18/2022] Open
Abstract
Microtubules, are formed of the protein tubulin, which is a heterodimer of α- and β-tubulin subunits. Both α- and β-tubulin exist as numerous isotypes, differing in amino acid sequence and tissue distribution. Among the vertebrate β isotypes, βIII has a very narrow distribution, being found primarily in neurons and in advanced cancers. The places in the amino acid sequence where βIII differs from the other β isotypes are highly conserved in evolution. βIII appears to be highly resistant to reactive oxygen species and it forms highly dynamic microtubules. The first property would be very useful in neurons, which have high concentrations of free radicals, and the high dynamicity would aid neurite outgrowth. The same properties make βIII useful in cancers. Examination of the amino acid sequences indicates a cysteine cluster at positions 124–129 in βIII (CXXCXC). This occurs in all βIII isotypes but not in βI, βII, or βIV. βIII also lacks the easily oxidized C239. Both features could play roles in free radical resistance. Many aggressive tumors over-express βIII. However, a recent study of breast cancer patients showed that many of them mutated their βI, βII, and βIV at particular places to change the residues to those found at the corresponding sites in βIII; these are all sites that are highly conserved in vertebrate βIII. It is possible that these residues are important, not only in the resistance to free radicals, but also in the high dynamicity of βIII. The cephalopod mollusks are well known to be highly intelligent and can remodel their own brains. Interestingly, several cephalopods contain the cysteine cluster as well as up to 7 of the 17 residues that are highly conserved in vertebrate βIII, but are not found in βI, βII, or βIV. In short, it is possible that we are looking at a case of convergent evolution, that a βIII-like isotype may be required for neuronal growth and function and that a structure-function study of the particular residues conserved between vertebrate βIII and cephalopod tubulin isotypes could greatly increase our understanding of the role of the various tubulin isotypes in neuronal growth and function and could aid in the development of novel anti-tumor drugs.
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Sheng C, Guo Y, Ma J, Hong EK, Zhang B, Yang Y, Zhang X, Zhang D. Metabolomic Profiling Reveals Protective Effects and Mechanisms of Sea Buckthorn Sterol against Carbon Tetrachloride-Induced Acute Liver Injury in Rats. Molecules 2022; 27:molecules27072224. [PMID: 35408620 PMCID: PMC9000363 DOI: 10.3390/molecules27072224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/18/2022] [Accepted: 03/26/2022] [Indexed: 12/26/2022] Open
Abstract
The present study was designed to examine the efficacy and protection mechanisms of sea buckthorn sterol (SBS) against acute liver injury induced by carbon tetrachloride (CCl4) in rats. Five-week-old male Sprague-Dawley (SD) rats were divided into six groups and fed with saline (Group BG), 50% CCl4 (Group MG), or bifendate 200 mg/kg (Group DDB), or treated with low-dose (Group LD), medium-dose (Group MD), or high-dose (Group HD) SBS. This study, for the first time, observed the protection of SBS against CCl4-induced liver injury in rats and its underlying mechanisms. Investigation of enzyme activities showed that SBS-fed rats exhibited a significant alleviation of inflammatory lesions, as evidenced by the decrease in cyclooxygenase-2 (COX-2), prostaglandin E2 (PGE2), and gamma-glutamyl transpeptidase (γ-GT). In addition, compared to the MG group, the increased indices (superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), total antioxidant capacity (T-AOC), and total protein (TP)) of lipid peroxidation and decreased malondialdehyde (MDA) in liver tissues of SBS-treated groups showed the anti-lipid peroxidation effects of SBS. Using the wide range of targeted technologies and a combination of means (UPLC-MS/MS detection platform, self-built database, and multivariate statistical analysis), the addition of SBS was found to restore the expression of metabolic pathways (e.g., L-malic acid, N-acetyl-aspartic acid, N-acetyl-l-alanine, etc.) in rats, which means that the metabolic damage induced by CCl4 was alleviated. Furthermore, transcriptomics was employed to analyze and compare gene expression levels of different groups. It showed that the expressions of genes (Cyp1a1, Noct, and TUBB6) related to liver injury were regulated by SBS. In conclusion, SBS exhibited protective effects against CCl4-induced liver injury in rats. The liver protection mechanism of SBS is probably related to the regulation of metabolic disorders, anti-lipid peroxidation, and inhibition of the inflammatory response.
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Affiliation(s)
- Changting Sheng
- College of Medicine, Qinghai University, Xining 810016, China; (C.S.); (Y.G.)
| | - Yang Guo
- College of Medicine, Qinghai University, Xining 810016, China; (C.S.); (Y.G.)
| | - Jing Ma
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (J.M.); (B.Z.); (Y.Y.); (X.Z.)
| | - Eun-Kyung Hong
- Medvill Co., Ltd., Medvill Research Institute, Seoul 100744, Korea;
| | - Benyin Zhang
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (J.M.); (B.Z.); (Y.Y.); (X.Z.)
| | - Yongjing Yang
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (J.M.); (B.Z.); (Y.Y.); (X.Z.)
| | - Xiaofeng Zhang
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (J.M.); (B.Z.); (Y.Y.); (X.Z.)
| | - Dejun Zhang
- College of Ecological and Environmental Engineering, Qinghai University, Xining 810016, China; (J.M.); (B.Z.); (Y.Y.); (X.Z.)
- Correspondence:
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A Novel Pyroptosis-Related Prognostic Signature for Risk Stratification and Clinical Prognosis in Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2022; 2022:8093837. [PMID: 35308143 PMCID: PMC8927973 DOI: 10.1155/2022/8093837] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 01/12/2023]
Abstract
Emerging research has substantiated that pyroptosis-related biomarkers were mightily related to the clinical outcome of patients with clear cell renal cell carcinoma (ccRCC). However, a single-gene biomarker's moderate predictive power is insufficient, and more accurate prognostic models are urgently needed. We conducted this investigation in order to develop a robust pyroptosis-related gene signature for use in risk stratification and survival prognosis in colorectal cancer. We downloaded transcriptomic data and survival information of ccRCC patients from TCGA. Bioinformatic methods were used to generate a pyroptosis-related gene signature based on data from TCGA training cohort. ROC curve, uni- and multivariate regression analyses were used for the prognostic assays. What is more, we explored the relationship between model-based risk score and the tumor microenvironment. Herein, 11 pyroptosis-related hub genes (CASP9, TUBB6, NFKB1, BNIP3, CAPN1, CD14, PRDM1, BST2, SDHB, TFAM, and GSDMB) were determined as risk signature for risk stratification and prognosis prediction for ccRCC. Kaplan-Meier curves, ROC curves, and risk plots were employed to analyze and verify its performance in all groups. Multivariate assays exhibited that risk score could be an independent prognostic factor for patients' OS. ESTIMATE algorithm showed a higher immune score in the group of high-risk. Overall, a novel pyroptosis-related gene signature generated can be employed for prognosis prediction of ccRCC patients. This may assist in individual treatment of clinical decision-making.
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Yalçin M, Malhan D, Basti A, Peralta AR, Ferreira JJ, Relógio A. A Computational Analysis in a Cohort of Parkinson's Disease Patients and Clock-Modified Colorectal Cancer Cells Reveals Common Expression Alterations in Clock-Regulated Genes. Cancers (Basel) 2021; 13:cancers13235978. [PMID: 34885088 PMCID: PMC8657387 DOI: 10.3390/cancers13235978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Cancer and neurodegenerative diseases are two aging-related pathologies with differential developmental characteristics, but they share altered cellular pathways. Interestingly, dysregulations in the biological clock are reported in both diseases, though the extent and potential consequences of such disruption have not been fully elucidated. In this study, we aimed at characterizing global changes on common cellular pathways associated with Parkinson’s disease (PD) and colorectal cancer (CRC). We used gene expression data retrieved from an idiopathic PD (IPD) patient cohort and from CRC cells with unmodified versus genetically altered clocks. Our results highlight common differentially expressed genes between IPD patients and cells with disrupted clocks, suggesting a role for the circadian clock in the regulation of pathways altered in both pathologies. Interestingly, several of these genes are related to cancer hallmarks and may have an impact on the overall survival of colon cancer patients, as suggested by our analysis. Abstract Increasing evidence suggests a role for circadian dysregulation in prompting disease-related phenotypes in mammals. Cancer and neurodegenerative disorders are two aging related diseases reported to be associated with circadian disruption. In this study, we investigated a possible effect of circadian disruption in Parkinson’s disease (PD) and colorectal cancer (CRC). We used high-throughput data sets retrieved from whole blood of idiopathic PD (IPD) patients and time course data sets derived from an in vitro model of CRC including the wildtype and three core-clock knockout (KO) cell lines. Several gene expression alterations in IPD patients resembled the expression profiles in the core-clock KO cells. These include expression changes in DBP, GBA, TEF, SNCA, SERPINA1 and TGFB1. Notably, our results pointed to alterations in the core-clock network in IPD patients when compared to healthy controls and revealed variations in the expression profile of PD-associated genes (e.g., HRAS and GBA) upon disruption of the core-clock genes. Our study characterizes changes at the transcriptomic level following circadian clock disruption on common cellular pathways associated with cancer and neurodegeneration (e.g., immune system, energy metabolism and RNA processing), and it points to a significant influence on the overall survival of colon cancer patients for several genes resulting from our analysis (e.g., TUBB6, PAK6, SLC11A1).
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Affiliation(s)
- Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
| | - Ana Rita Peralta
- EEG/Sleep Laboratory, Department Neurosciences and Mental Health, Hospital de Santa Maria—CHULN, 1649-035 Lisbon, Portugal;
- Department of Neurology, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- CNS-Campus Neurológico Senior, 2560-280 Torres Vedras, Portugal;
| | - Joaquim J. Ferreira
- CNS-Campus Neurológico Senior, 2560-280 Torres Vedras, Portugal;
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Laboratory of Clinical Pharmacology and Therapeutics, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
- Correspondence: or
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Zheng Z, Wang T, Chen J, Qiu H, Zhang C, Liu W, Qin S, Tian J, Guo J. Inflammasome-Induced Osmotic Pressure and the Mechanical Mechanisms Underlying Astrocytic Swelling and Membrane Blebbing in Pyroptosis. Front Immunol 2021; 12:688674. [PMID: 34305921 PMCID: PMC8293990 DOI: 10.3389/fimmu.2021.688674] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/25/2021] [Indexed: 01/26/2023] Open
Abstract
Cell swelling and membrane blebbing are characteristic of pyroptosis. In the present study, we explored the role of intracellular tension activity in the deformation of pyroptotic astrocytes. Protein nanoparticle-induced osmotic pressure (PN-OP) was found to be involved in cell swelling and membrane blebbing in pyroptotic astrocytes, and was associated closely with inflammasome production and cytoskeleton depolymerization. However, accumulation of protein nanoparticles seemed not to be absolutely required for pyroptotic permeabilization in response to cytoskeleton depolymerization. Gasdermin D activation was observed to be involved in modification of typical pyroptotic features through inflammasome-induced OP upregulation and calcium increment. Blockage of nonselective ion pores can inhibit permeabilization, but not inflammasome production and ion influx in pyroptotic astrocytes. The results suggested that the inflammasomes, as protein nanoparticles, are involved in PN-OP upregulation and control the typical features of pyroptotic astrocytes.
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Affiliation(s)
- Zihui Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingting Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiahui Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huimin Qiu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chencheng Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Weizhen Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Simiao Qin
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jilai Tian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Guo
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, China
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13
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Dixit AB, Srivastava A, Sharma D, Tripathi M, Paul D, Lalwani S, Doddamani R, Sharma MC, Banerjee J, Chandra PS. Integrated Genome-Wide DNA Methylation and RNAseq Analysis of Hippocampal Specimens Identifies Potential Candidate Genes and Aberrant Signalling Pathways in Patients with Hippocampal Sclerosis. Neurol India 2021; 68:307-313. [PMID: 32189710 DOI: 10.4103/0028-3886.280649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background and Aims DNA methylation and demethylation play a crucial role in the regulation of gene expression, though their interplay during pathogenesis of hippocampal scelerosis (HS) remains elusive. The present study was designed to investigate the DNA methylation regulated changes in expression of HS patients. Methods We performed integrative analysis of genome-wide CpG-DNA methylation profiling and RNA sequencing to profile global changes in promoter methylation and gene expression in HS patients. Real time PCR was performed to validate the findings of methylation and RNA sequencing. Results A total of 16040 sites showed altered DNA methylation in all the CpG islands. Of these, 3185 sites were in the promoter regions, of which 66 genes showed an inverse correlation between methylation and expression. These genes are largely related to pathways predicted to participate in axon guidance by semaphorins, MAPK, ionotropic glutamate receptor pathway, notch signaling, regulatory activities related to TFAP2A and immune response, with the most distinct ones included TFAP2A, NRP1, SEMA3B, CACNG2, MAP3K11, and ADAM17. Conclusion We performed integrated analysis of genomic methylation signature and differential gene expression patterns of hippocampal tissues resected from patients with HS for the first time. Collectively, our findings implicate DNA methylation as a critical regulator of the pathogenic mechanisms of epileptogenesis associated with HS.
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Affiliation(s)
- Aparna Banerjee Dixit
- Dr B R Ambedkar Centre for Biomedical Sciences, University of Delhi, Delhi; Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration, New Delhi, India
| | - Arpna Srivastava
- Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration; Department of Neurosurgery, AIIMS, New Delhi, India
| | | | - Manjari Tripathi
- Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration; Department of Neurology, AIIMS, New Delhi, India
| | | | - Sanjeev Lalwani
- Department of Forensic Medicine and Toxicology, AIIMS, New Delhi, India
| | | | - M C Sharma
- Department of Pathology, AIIMS, New Delhi, India
| | | | - P Sarat Chandra
- Center of Excellence for Epilepsy, A Joint NBRC-AIIMS Collaboration; Department of Neurosurgery, AIIMS, New Delhi, India
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14
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Schott BH, Antonia AL, Wang L, Pittman KJ, Sixt BS, Barnes AB, Valdivia RH, Ko DC. Modeling of variables in cellular infection reveals CXCL10 levels are regulated by human genetic variation and the Chlamydia-encoded CPAF protease. Sci Rep 2020; 10:18269. [PMID: 33106516 PMCID: PMC7588472 DOI: 10.1038/s41598-020-75129-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
Susceptibility to infectious diseases is determined by a complex interaction between host and pathogen. For infections with the obligate intracellular bacterium Chlamydia trachomatis, variation in immune activation and disease presentation are regulated by both host genetic diversity and pathogen immune evasion. Previously, we discovered a single nucleotide polymorphism (rs2869462) associated with absolute abundance of CXCL10, a pro-inflammatory T-cell chemokine. Here, we report that levels of CXCL10 change during C. trachomatis infection of cultured cells in a manner dependent on both host and pathogen. Linear modeling of cellular traits associated with CXCL10 levels identified a strong, negative correlation with bacterial burden, suggesting that C. trachomatis actively suppresses CXCL10. We identified the pathogen-encoded factor responsible for this suppression as the chlamydial protease- or proteasome-like activity factor, CPAF. Further, we applied our modeling approach to other host cytokines in response to C. trachomatis and found evidence that RANTES, another T-cell chemoattractant, is actively suppressed by Chlamydia. However, this observed suppression of RANTES is not mediated by CPAF. Overall, our results demonstrate that CPAF suppresses CXCL10 to evade the host cytokine response and that modeling of cellular infection parameters can reveal previously unrecognized facets of host-pathogen interactions.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC, 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Barbara S Sixt
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Alyson B Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA.
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC, 27710, USA.
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.
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15
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Nichterwitz S, Nijssen J, Storvall H, Schweingruber C, Comley LH, Allodi I, Lee MVD, Deng Q, Sandberg R, Hedlund E. LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy. Genome Res 2020; 30:1083-1096. [PMID: 32820007 PMCID: PMC7462070 DOI: 10.1101/gr.265017.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/10/2020] [Indexed: 11/25/2022]
Abstract
Somatic motor neurons are selectively vulnerable in spinal muscular atrophy (SMA), which is caused by a deficiency of the ubiquitously expressed survival of motor neuron protein. However, some motor neuron groups, including oculomotor and trochlear (ocular), which innervate eye muscles, are for unknown reasons spared. To reveal mechanisms of vulnerability and resistance in SMA, we investigate the transcriptional dynamics in discrete neuronal populations using laser capture microdissection coupled with RNA sequencing (LCM-seq). Using gene correlation network analysis, we reveal a TRP53-mediated stress response that is intrinsic to all somatic motor neurons independent of their vulnerability, but absent in relatively resistant red nucleus and visceral motor neurons. However, the temporal and spatial expression analysis across neuron types shows that the majority of SMA-induced modulations are cell type-specific. Using Gene Ontology and protein network analyses, we show that ocular motor neurons present unique disease-adaptation mechanisms that could explain their resilience. Specifically, ocular motor neurons up-regulate (1) Syt1, Syt5, and Cplx2, which modulate neurotransmitter release; (2) the neuronal survival factors Gdf15, Chl1, and Lif; (3) Aldh4, that protects cells from oxidative stress; and (4) the caspase inhibitor Pak4. Finally, we show that GDF15 can rescue vulnerable human spinal motor neurons from degeneration. This confirms that adaptation mechanisms identified in resilient neurons can be used to reduce susceptibility of vulnerable neurons. In conclusion, this in-depth longitudinal transcriptomics analysis in SMA reveals novel cell type-specific changes that, alone and combined, present compelling targets, including Gdf15, for future gene therapy studies aimed toward preserving vulnerable motor neurons.
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Affiliation(s)
| | - Jik Nijssen
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Helena Storvall
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Ludwig Institute for Cancer Research, Karolinska Institutet, 171 77 Stockholm, Sweden
| | | | - Laura Helen Comley
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ilary Allodi
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mirjam van der Lee
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Qiaolin Deng
- Ludwig Institute for Cancer Research, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Ludwig Institute for Cancer Research, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
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16
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Roll-Mecak A. The Tubulin Code in Microtubule Dynamics and Information Encoding. Dev Cell 2020; 54:7-20. [PMID: 32634400 PMCID: PMC11042690 DOI: 10.1016/j.devcel.2020.06.008] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 05/08/2020] [Accepted: 06/03/2020] [Indexed: 01/05/2023]
Abstract
Microtubules are non-covalent mesoscale polymers central to the eukaryotic cytoskeleton. Microtubule structure, dynamics, and mechanics are modulated by a cell's choice of tubulin isoforms and post-translational modifications, a "tubulin code," which is thought to support the diverse morphology and dynamics of microtubule arrays across various cell types, cell cycle, and developmental stages. We give a brief historical overview of research into tubulin diversity and highlight recent progress toward uncovering the mechanistic underpinnings of the tubulin code. As a large number of essential pathways converge upon the microtubule cytoskeleton, understanding how cells utilize tubulin diversity is crucial to understanding cellular physiology and disease.
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Affiliation(s)
- Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA; Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, Bethesda, MD 20892, USA.
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17
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Guérit D, Marie P, Morel A, Maurin J, Verollet C, Raynaud-Messina B, Urbach S, Blangy A. Primary myeloid cell proteomics and transcriptomics: importance of β-tubulin isotypes for osteoclast function. J Cell Sci 2020; 133:jcs239772. [PMID: 32265273 DOI: 10.1242/jcs.239772] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/19/2020] [Indexed: 08/31/2023] Open
Abstract
Among hematopoietic cells, osteoclasts (OCs) and immature dendritic cells (DCs) are closely related myeloid cells with distinct functions: OCs participate skeleton maintenance while DCs sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during OC and DC differentiation. We provide global proteomic and transcriptomic analyses of primary mouse OCs and DCs, based on original stable isotope labeling with amino acids in cell culture (SILAC) and RNAseq data. We established specific signatures for OCs and DCs, including genes and proteins of unknown functions. In particular, we showed that OCs and DCs have the same α- and β-tubulin isotype repertoire but that OCs express much more of the β tubulin isotype Tubb6 (also known as TBB6). In both mouse and human OCs, we demonstrate that elevated expression of Tubb6 in OCs is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hinders OC resorption activity. Overall, we highlight here potential new regulators of OC and DC biology, and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.
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Affiliation(s)
- David Guérit
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), Montpellier Univ., CNRS, 34000 Montpellier, France
| | - Pauline Marie
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), Montpellier Univ., CNRS, 34000 Montpellier, France
| | - Anne Morel
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), Montpellier Univ., CNRS, 34000 Montpellier, France
| | - Justine Maurin
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), Montpellier Univ., CNRS, 34000 Montpellier, France
| | - Christel Verollet
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
- International associated laboratory (LIA) CNRS 'IM-TB/HIV' (1167), 31077 Toulouse Cedex 04, France
- International associated laboratory (LIA) CNRS 'IM-TB/HIV' (1167), Buenos Aires C1425AUM, Argentina
| | - Brigitte Raynaud-Messina
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
- International associated laboratory (LIA) CNRS 'IM-TB/HIV' (1167), 31077 Toulouse Cedex 04, France
- International associated laboratory (LIA) CNRS 'IM-TB/HIV' (1167), Buenos Aires C1425AUM, Argentina
| | - Serge Urbach
- Functional Proteomics Facility, Institute of Functional Genomics, Montpellier Univ., CNRS, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Anne Blangy
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), Montpellier Univ., CNRS, 34000 Montpellier, France
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Čermák V, Dostál V, Jelínek M, Libusová L, Kovář J, Rösel D, Brábek J. Microtubule-targeting agents and their impact on cancer treatment. Eur J Cell Biol 2020; 99:151075. [PMID: 32414588 DOI: 10.1016/j.ejcb.2020.151075] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/25/2020] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
Microtubule-targeting agents (MTAs) constitute a diverse group of chemical compounds that bind to microtubules and affect their properties and function. Disruption of microtubules induces various cellular responses often leading to cell cycle arrest or cell death, the most common effect of MTAs. MTAs have found a plethora of practical applications in weed control, as fungicides and antiparasitics, and particularly in cancer treatment. Here we summarize the current knowledge of MTAs, the mechanisms of action and their role in cancer treatment. We further outline the potential use of MTAs in anti-metastatic therapy based on inhibition of cancer cell migration and invasiveness. The two main problems associated with cancer therapy by MTAs are high systemic toxicity and development of resistance. Toxic side effects of MTAs can be, at least partly, eliminated by conjugation of the drugs with various carriers. Moreover, some of the novel MTAs overcome the resistance mediated by both multidrug resistance transporters as well as overexpression of specific β-tubulin types. In anti-metastatic therapy, MTAs should be combined with other drugs to target all modes of cancer cell invasion.
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Affiliation(s)
- Vladimír Čermák
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242 Vestec u Prahy, Czech Republic
| | - Vojtěch Dostál
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic
| | - Michael Jelínek
- Department of Biochemistry, Cell and Molecular Biology & Center for Research of Diabetes, Metabolism, and Nutrition, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Libusová
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic
| | - Jan Kovář
- Department of Biochemistry, Cell and Molecular Biology & Center for Research of Diabetes, Metabolism, and Nutrition, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Daniel Rösel
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242 Vestec u Prahy, Czech Republic
| | - Jan Brábek
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242 Vestec u Prahy, Czech Republic.
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19
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Randazzo D, Khalique U, Belanto JJ, Kenea A, Talsness DM, Olthoff JT, Tran MD, Zaal KJ, Pak K, Pinal-Fernandez I, Mammen AL, Sackett D, Ervasti JM, Ralston E. Persistent upregulation of the β-tubulin tubb6, linked to muscle regeneration, is a source of microtubule disorganization in dystrophic muscle. Hum Mol Genet 2019; 28:1117-1135. [PMID: 30535187 DOI: 10.1093/hmg/ddy418] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 12/20/2022] Open
Abstract
In healthy adult skeletal muscle fibers microtubules form a three-dimensional grid-like network. In the mdx mouse, a model of Duchenne muscular dystrophy (DMD), microtubules are mostly disordered, without periodicity. These microtubule defects have been linked to the mdx mouse pathology. We now report that increased expression of the beta 6 class V β-tubulin (tubb6) contributes to the microtubule changes of mdx muscles. Wild-type muscle fibers overexpressing green fluorescent protein (GFP)-tubb6 (but not GFP-tubb5) have disorganized microtubules whereas mdx muscle fibers depleted of tubb6 (but not of tubb5) normalize their microtubules, suggesting that increasing tubb6 is toxic. However, tubb6 increases spontaneously during differentiation of mouse and human muscle cultures. Furthermore, endogenous tubb6 is not uniformly expressed in mdx muscles but is selectively increased in fiber clusters, which we identify as regenerating. Similarly, mdx-based rescued transgenic mice that retain a higher than expected tubb6 level show focal expression of tubb6 in subsets of fibers. Tubb6 is also upregulated in cardiotoxin-induced mouse muscle regeneration, in human myositis and DMD biopsies, and the tubb6 level correlates with that of embryonic myosin heavy chain, a regeneration marker. In conclusion, modulation of a β-tubulin isotype plays a role in muscle differentiation and regeneration. Increased tubb6 expression and microtubule reorganization are not pathological per se but reflect a return to an earlier developmental stage. However, chronic elevation of tubb6, as occurs in the mdx mouse, may contribute to the repeated cycles of regeneration and to the pathology of the disease.
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Affiliation(s)
- Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Umara Khalique
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joseph J Belanto
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Aster Kenea
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dana M Talsness
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - John T Olthoff
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Michelle D Tran
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kristien J Zaal
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Katherine Pak
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA
| | - Iago Pinal-Fernandez
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew L Mammen
- Laboratory of Muscle Stem Cells and Gene Regulation, Muscle Disease Unit, NIAMS, NIH, Bethesda, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - James M Ervasti
- Department of Biochemistry, Molecular Biology, and Biophysics, and Program in Molecular, Cellular, Developmental Biology, and Genetics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Evelyn Ralston
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
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20
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Abstract
ABSTRACT
The rapid development of genomics and other “-omics” approaches has significantly impacted how we have investigated host-pathogen interactions since the turn of the millennium. Technologies such as next-generation sequencing, stem cell biology, and high-throughput proteomics have transformed the scale and sensitivity with which we interrogate biological samples. These approaches are impacting experimental design in the laboratory and transforming clinical management in health care systems. Here, we review this area from the perspective of research on bacterial pathogens.
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21
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Calpain drives pyroptotic vimentin cleavage, intermediate filament loss, and cell rupture that mediates immunostimulation. Proc Natl Acad Sci U S A 2019; 116:5061-5070. [PMID: 30796192 DOI: 10.1073/pnas.1818598116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Pyroptosis is an inflammatory form of programmed cell death following cellular damage or infection. It is a lytic process driven by gasdermin D-mediated cellular permeabilization and presumed osmotic forces thought to induce swelling and rupture. We found that pyroptotic cells do not spontaneously rupture in culture but lose mechanical resilience. As a result, cells were susceptible to rupture by extrinsic forces, such as shear stress or compression. Cell analyses revealed that all major cytoskeleton components were disrupted during pyroptosis and that sensitivity to rupture was calpain-dependent and linked with cleavage of vimentin and loss of intermediate filaments. Moreover, while release of lactate dehydrogenase (LDH), HMGB1, and IL-1β occurred without rupture, rupture was required for release of large inflammatory stimuli-ASC specks, mitochondria, nuclei, and bacteria. Importantly, supernatants from ruptured cells were more immunostimulatory than those from nonruptured cells. These observations reveal undiscovered cellular events occurring during pyroptosis, define the mechanisms driving pyroptotic rupture, and highlight the immunologic importance of this event.
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22
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Beggs AD, James J, Caldwell G, Prout T, Dilworth MP, Taniere P, Iqbal T, Morton DG, Matthews G. Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia. Inflamm Bowel Dis 2018; 24:1503-1509. [PMID: 29762666 PMCID: PMC6176894 DOI: 10.1093/ibd/izy119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Indexed: 12/11/2022]
Abstract
Background and aims Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers. Methods Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array. Markers were validated by bisulphite pyrosequencing on a secondary validation cohort and accuracy calculated using logistic regression and receiver-operator curves. Results Twelve samples from 4 patients underwent methylation array analysis and 6 markers (GNG7, VAV3, KIF5C, PIK3R5, TUBB6, and ZNF583) were taken forward for secondary validation on a cohort of 71 colonic biopsy samples consisting of normal uninflamed mucosa from control patients, acute and chronic colitis, "field" mucosa in patients with dysplasia/neoplasia, dysplasia, and neoplasia. Methylation in the beta-tubulin TUBB6 correlated with the presence of dysplasia (P < 0.0001) and accurately discriminated between dysplasia and nondysplastic tissue, even in the apparently normal field mucosa downstream from dysplastic lesions (AUC 0.84, 95% CI 0.81-0.87). Conclusions Methylation in TUBB6 is a potential biomarker for UC- associated dysplasia. Further validation is needed and is ongoing as part of the ENDCAP-C study.
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Affiliation(s)
- Andrew D Beggs
- Institute of Cancer and Genomic Science, University of Birmingham
| | - Jonathan James
- Institute of Cancer and Genomic Science, University of Birmingham
| | | | - Toby Prout
- Institute of Cancer and Genomic Science, University of Birmingham
| | - Mark P Dilworth
- Institute of Cancer and Genomic Science, University of Birmingham
| | - Phillipe Taniere
- Institute of Cancer and Genomic Science, University of Birmingham
| | - Tariq Iqbal
- Institute of Cancer and Genomic Science, University of Birmingham
| | - Dion G Morton
- Institute of Cancer and Genomic Science, University of Birmingham
| | - Glenn Matthews
- Institute of Cancer and Genomic Science, University of Birmingham
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23
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Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol. Proc Natl Acad Sci U S A 2017; 114:E7746-E7755. [PMID: 28827342 DOI: 10.1073/pnas.1706070114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Risk, severity, and outcome of infection depend on the interplay of pathogen virulence and host susceptibility. Systematic identification of genetic susceptibility to infection is being undertaken through genome-wide association studies, but how to expeditiously move from genetic differences to functional mechanisms is unclear. Here, we use genetic association of molecular, cellular, and human disease traits and experimental validation to demonstrate that genetic variation affects expression of VAC14, a phosphoinositide-regulating protein, to influence susceptibility to Salmonella enterica serovar Typhi (S Typhi) infection. Decreased VAC14 expression increased plasma membrane cholesterol, facilitating Salmonella docking and invasion. This increased susceptibility at the cellular level manifests as increased susceptibility to typhoid fever in a Vietnamese population. Furthermore, treating zebrafish with a cholesterol-lowering agent, ezetimibe, reduced susceptibility to S Typhi. Thus, coupling multiple genetic association studies with mechanistic dissection revealed how VAC14 regulates Salmonella invasion and typhoid fever susceptibility and may open doors to new prophylactic/therapeutic approaches.
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24
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Fazeli W, Herkenrath P, Stiller B, Neugebauer A, Fricke J, Lang-Roth R, Nürnberg G, Thoenes M, Becker J, Altmüller J, Volk AE, Kubisch C, Heller R. A TUBB6 mutation is associated with autosomal dominant non-progressive congenital facial palsy, bilateral ptosis and velopharyngeal dysfunction. Hum Mol Genet 2017; 26:4055-4066. [DOI: 10.1093/hmg/ddx296] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/23/2017] [Indexed: 01/06/2023] Open
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25
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Sánchez-Elordi E, Baluška F, Echevarría C, Vicente C, Legaz ME. Defence sugarcane glycoproteins disorganize microtubules and prevent nuclear polarization and germination of Sporisorium scitamineum teliospores. JOURNAL OF PLANT PHYSIOLOGY 2016; 200:111-123. [PMID: 27372179 DOI: 10.1016/j.jplph.2016.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Microtubules (MTs) are involved in the germination of Sporisorium scitamineum teliospores. Resistant varieties of sugar cane plants produce defence glycoproteins that prevent the infection of the plants by the filamentous fungi Sporisorium scitamineum. Here, we show that a fraction of these glycoproteins prevents the correct arrangement of MTs and causes nuclear fragmentation defects. As a result, nuclei cannot correctly migrate through the growing hyphae, causing germinative failure. Arginase activity contained in defence glycoproteins is already described for preventing fungal germination. Now, its enzymatically active form is presented as a link between the defensive capacity of glycoproteins and the MT disorganization in fungal cells. Active arginase is produced in healthy and resistant plants; conversely, it is not detected in the juice from susceptible varieties, which explains why MT depolarization, nuclear disorganization as well as germination of teliospores are not significantly affected by glycoproteins from non-resistant plants. Our results also suggest that susceptible plants try to increase their levels of arginase after detecting the presence of the pathogen. However, this signal comes "too late" and such defensive mechanism fails.
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Affiliation(s)
- Elena Sánchez-Elordi
- Team of Intercellular Communication in Plant Symbiosis, Faculty of Biology, Complutense University. 12 José Antonio Novais Av., 28040 Madrid, Spain
| | - František Baluška
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany (IZMB), University Bonn. 1 Kirschallee St., D-53115 Bonn, Germany
| | - Clara Echevarría
- Team of Intercellular Communication in Plant Symbiosis, Faculty of Biology, Complutense University. 12 José Antonio Novais Av., 28040 Madrid, Spain
| | - Carlos Vicente
- Team of Intercellular Communication in Plant Symbiosis, Faculty of Biology, Complutense University. 12 José Antonio Novais Av., 28040 Madrid, Spain.
| | - M Estrella Legaz
- Team of Intercellular Communication in Plant Symbiosis, Faculty of Biology, Complutense University. 12 José Antonio Novais Av., 28040 Madrid, Spain
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Miller SI, Chaudhary A. A Cellular GWAS Approach to Define Human Variation in Cellular Pathways Important to Inflammation. Pathogens 2016; 5:pathogens5020039. [PMID: 27128945 PMCID: PMC4931390 DOI: 10.3390/pathogens5020039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 04/07/2016] [Accepted: 04/21/2016] [Indexed: 12/17/2022] Open
Abstract
An understanding of common human diversity in innate immune pathways should be beneficial in understanding autoimmune diseases, susceptibility to infection, and choices of anti-inflammatory treatment. Such understanding could also result in definition of currently unknown components of human inflammation pathways. A cellular genome-wide association studies (GWAS) platform, termed Hi-HOST (High-throughput human in vitro susceptibility testing), was developed to assay in vitro cellular phenotypes of infection in genotyped lymphoblastoid cells from genetically diverse human populations. Hi-HOST allows for measurement of multiple host and pathogen parameters of infection/inflammation including: bacterial invasion and intracellular replication, host cell death, and cytokine production. Hi-HOST has been used to successfully define a significant portion of the heritable human diversity in inflammatory cell death in response to Salmonella typhimurium. It also led to the discovery of genetic variants important to protection against systemic inflammatory response syndrome (SIRS) and protection against death and bacteremia in individuals with SIRS. Our laboratory is currently using this platform to define human diversity in autophagy and the NLPR3 inflammasome pathways, and to define new components that can impact the expression of phenotypes related to these pathways.
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Affiliation(s)
- Samuel I Miller
- Department of Microbiology, Department of Immunology, Department of Medicine, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Anu Chaudhary
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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27
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Cellular visualization of macrophage pyroptosis and interleukin-1β release in a viral hemorrhagic infection in zebrafish larvae. J Virol 2014; 88:12026-40. [PMID: 25100833 DOI: 10.1128/jvi.02056-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Hemorrhagic viral diseases are distributed worldwide with important pathogens, such as dengue virus or hantaviruses. The lack of adequate in vivo infection models has limited the research on viral pathogenesis and the current understanding of the underlying infection mechanisms. Although hemorrhages have been associated with the infection of endothelial cells, other cellular types could be the main targets for hemorrhagic viruses. Our objective was to take advantage of the use of zebrafish larvae in the study of viral hemorrhagic diseases, focusing on the interaction between viruses and host cells. Cellular processes, such as transendothelial migration of leukocytes, virus-induced pyroptosis of macrophages. and interleukin-1β (Il-1β) release, could be observed in individual cells, providing a deeper knowledge of the immune mechanisms implicated in the disease. Furthermore, the application of these techniques to other pathogens will improve the current knowledge of host-pathogen interactions and increase the potential for the discovery of new therapeutic targets. Importance: Pathogenic mechanisms of hemorrhagic viruses are diverse, and most of the research regarding interactions between viruses and host cells has been performed in cell lines that might not be major targets during natural infections. Thus, viral pathogenesis research has been limited because of the lack of adequate in vivo infection models. The understanding of the relative pathogenic roles of the viral agent and the host response to the infection is crucial. This will be facilitated by the establishment of in vivo infection models using organisms such as zebrafish, which allows the study of the diseases in the context of a complete individual. The use of this animal model with other pathogens could improve the current knowledge on host-pathogen interactions and increase the potential for the discovery of new therapeutic targets against diverse viral diseases.
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Ko DC, Jaslow SL. The marriage of quantitative genetics and cell biology: a novel screening approach reveals people have genetically encoded variation in microtubule stability. BIOARCHITECTURE 2014; 4:58-61. [PMID: 24618686 DOI: 10.4161/bioa.28481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microtubules play a central role in many essential cellular processes, including chromosome segregation, intracellular transport, and cell polarity. As these dynamic polymers are crucial components of eukaryotic cellular architecture, we were surprised by our recent discovery that a common human genetic difference leads to variation in microtubule stability in cells from different people. A single nucleotide polymorphism (SNP) near the TUBB6 gene, encoding class V β-tubulin, is associated with the expression level of this protein, which reduces microtubule stability at higher levels of expression. We discuss the novel cellular GWAS (genome-wide association study) platform that led to this discovery of natural, common variation in microtubule stability and the implications this finding may have for human health and disease, including cancer and neurological disorders. Furthermore, our generalizable approach provides a gateway for cell biologists to help interpret the functional consequences of human genetic variation.
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Affiliation(s)
- Dennis C Ko
- Department of Molecular Genetics and Microbiology; School of Medicine; Duke University; Durham, NC USA; Department of Medicine and the Center for Human Genome Variation; School of Medicine; Duke University; Durham, NC USA
| | - Sarah L Jaslow
- Department of Molecular Genetics and Microbiology; School of Medicine; Duke University; Durham, NC USA
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