1
|
Li C, Wei A, Qin Y. Expression of GADD45B in Renal Tissue of Children with IgA Nephropathy and Correlation with Mesangial Hypercellularity. Fetal Pediatr Pathol 2023; 42:785-795. [PMID: 37534585 DOI: 10.1080/15513815.2023.2239904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/05/2023] [Indexed: 08/04/2023]
Abstract
Background: We correlated the expression of growth arrest and DNA damage-inducible protein beta (GADD45B) in renal tissue with IgA nephropathy (IgAN) with clinical characteristics and mesangial hypercellularity. Materials and methods: Biopsies from IgAN children were divided into M0 and M1 groups based on the Oxford classification, and biopsies with minimal change disease (MCD) were selected as controls. The mesangial cell proliferation area was evaluated on PAS-stained tissues, and the relative level of GADD45B in renal tissue was assessed by immunohistochemical staining (IHC). Results: Compared with the MCD group, levels of GADD45B in the M0 and M1 groups were significantly higher (p < 0.05). Levels of GADD45B positively correlated with mesangial cell proliferation, proteinuria, and total cholesterol, negatively correlated with Alb levels. Conclusions: It is suggested that high expression of GADD45B may play a regulatory role in mesangial hypercellularity.
Collapse
Affiliation(s)
- Chong Li
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ailing Wei
- Department of Rehabilitation, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yuanhan Qin
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| |
Collapse
|
2
|
Fritz BG, Kirkegaard JB, Nielsen CH, Kirketerp-Møller K, Malone M, Bjarnsholt T. Transcriptomic fingerprint of bacterial infection in lower extremity ulcers. APMIS 2022; 130:524-534. [PMID: 35567538 PMCID: PMC9545044 DOI: 10.1111/apm.13234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/11/2022] [Indexed: 12/22/2022]
Abstract
Clinicians and researchers utilize subjective, clinical classification systems to stratify lower extremity ulcer infections for treatment and research. The purpose of this study was to examine whether these clinical classifications are reflected in the ulcer's transcriptome. RNA sequencing (RNA‐seq) was performed on biopsies from clinically infected lower extremity ulcers (n = 44). Resulting sequences were aligned to the host reference genome to create a transcriptome profile. Differential gene expression analysis and gene ontology (GO) enrichment analysis were performed between ulcer severities as well as between sample groups identified by k‐means clustering. Lastly, a support vector classifier was trained to estimate clinical infection score or k‐means cluster based on a subset of genes. Clinical infection severity did not explain the major sources of variability among the samples and samples with the same clinical classification demonstrated high inter‐sample variability. High proportions of bacterial RNA were identified in some samples, which resulted in a strong effect on transcription and increased expression of genes associated with immune response and inflammation. K‐means clustering identified two clusters of samples, one of which contained all of the samples with high levels of bacterial RNA. A support vector classifier identified a fingerprint of 20 genes, including immune‐associated genes such as CXCL8, GADD45B, and HILPDA, which accurately identified samples with signs of infection via cross‐validation. This study identified a unique, host‐transcriptome signature in the presence of infecting bacteria, often incongruent with clinical infection‐severity classifications. This suggests that stratification of infection status based on a transcriptomic fingerprint may be useful as an objective classification method to classify infection severity, as well as a tool for studying host–pathogen interactions.
Collapse
Affiliation(s)
- Blaine G Fritz
- Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Claus Henrik Nielsen
- Department of Rheumatology and Spine Diseases, Institute for Inflammation Research, Rigshospitalet, Copenhagen, Denmark
| | | | - Matthew Malone
- South West Sydney Limb Preservation and Wound Research, Liverpool Hospital, Sydney, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
3
|
Deng K, Fan Y, Liang Y, Cai Y, Zhang G, Deng M, Wang Z, Lu J, Shi J, Wang F, Zhang Y. FTO-mediated demethylation of GADD45B promotes myogenesis through the activation of p38 MAPK pathway. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:34-48. [PMID: 34513292 PMCID: PMC8408560 DOI: 10.1016/j.omtn.2021.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/14/2021] [Indexed: 12/14/2022]
Abstract
N6-methyladenosine (m6A) modification plays a critical role in mammalian development. However, the role of m6A in the skeletal muscle development remains largely unknown. Here, we report a global m6A modification pattern of goat skeletal muscle at two key development stages and identified that the m6A modification regulated the expression of the growth arrest and DNA damage-inducible 45B (GADD45B) gene, which is involved in myogenic differentiation. We showed that GADD45B expression increased during myoblast differentiation, whereas the downregulation of GADD45B inhibits myogenic differentiation and mitochondrial biogenesis. Moreover, the expression of GADD45B regulates the expression of myogenic regulatory factors and peroxisome proliferator-activated receptor gamma coactivator 1 alpha by activating the p38 mitogen-activated protein kinase (MAPK) pathway. Conversely, the inactivation of p38 MAPK abolished the GADD45B-mediated myogenic differentiation. Furthermore, we found that the knockdown of fat mass and obesity-associated protein (FTO) increases GADD45B m6A modification and decreases the stability of GADD45B mRNA, which impairs myogenic differentiation. Our results indicate that the FTO-mediated m6A modification in GADD45B mRNA drives skeletal muscle differentiation by activating the p38 MAPK pathway, which provides a molecular mechanism for the regulation of myogenesis via RNA methylation.
Collapse
Affiliation(s)
- Kaiping Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yixuan Fan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yaxu Liang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Cai
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Guomin Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingtian Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhibo Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiawei Lu
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianfei Shi
- Haimen Goat Breeding Farm, Nantong 226100, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China.,Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
4
|
Cambra JM, Martinez EA, Rodriguez-Martinez H, Gil MA, Cuello C. Transcriptional Profiling of Porcine Blastocysts Produced In Vitro in a Chemically Defined Culture Medium. Animals (Basel) 2021; 11:ani11051414. [PMID: 34069238 PMCID: PMC8156047 DOI: 10.3390/ani11051414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
The development of chemically defined media is a growing trend in in vitro embryo production (IVP). Recently, traditional undefined culture medium with bovine serum albumin (BSA) has been successfully replaced by a chemically defined medium using substances with embryotrophic properties such as platelet factor 4 (PF4). Although the use of this medium sustains IVP, the impact of defined media on the embryonic transcriptome has not been fully elucidated. This study analyzed the transcriptome of porcine IVP blastocysts, cultured in defined (PF4 group) and undefined media (BSA group) by microarrays. In vivo-derived blastocysts (IVV group) were used as a standard of maximum embryo quality. The results showed no differentially expressed genes (DEG) between the PF4 and BSA groups. However, a total of 2780 and 2577 DEGs were detected when comparing the PF4 or the BSA group with the IVV group, respectively. Most of these genes were common in both in vitro groups (2132) and present in some enriched pathways, such as cell cycle, lysosome and/or metabolic pathways. These results show that IVP conditions strongly affect embryo transcriptome and that the defined culture medium with PF4 is a guaranteed replacement for traditional culture with BSA.
Collapse
Affiliation(s)
- Josep M. Cambra
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Excellence Campus for Higher Education and Research, University of Murcia, 30100 Murcia, Spain; (J.M.C.); (E.A.M.); (C.C.)
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Campus de Ciencias de la Salud, Carretera Buenavista s/n, El Palmar, 30120 Murcia, Spain
| | - Emilio A. Martinez
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Excellence Campus for Higher Education and Research, University of Murcia, 30100 Murcia, Spain; (J.M.C.); (E.A.M.); (C.C.)
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Campus de Ciencias de la Salud, Carretera Buenavista s/n, El Palmar, 30120 Murcia, Spain
| | - Heriberto Rodriguez-Martinez
- Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden;
| | - Maria A. Gil
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Excellence Campus for Higher Education and Research, University of Murcia, 30100 Murcia, Spain; (J.M.C.); (E.A.M.); (C.C.)
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Campus de Ciencias de la Salud, Carretera Buenavista s/n, El Palmar, 30120 Murcia, Spain
- Correspondence:
| | - Cristina Cuello
- Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Excellence Campus for Higher Education and Research, University of Murcia, 30100 Murcia, Spain; (J.M.C.); (E.A.M.); (C.C.)
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Campus de Ciencias de la Salud, Carretera Buenavista s/n, El Palmar, 30120 Murcia, Spain
| |
Collapse
|
5
|
Zipperly ME, Sultan FA, Graham GE, Brane AC, Simpkins NA, Carullo NVN, Ianov L, Day JJ. Regulation of dopamine-dependent transcription and cocaine action by Gadd45b. Neuropsychopharmacology 2021; 46:709-720. [PMID: 32927466 PMCID: PMC8027017 DOI: 10.1038/s41386-020-00828-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022]
Abstract
Exposure to drugs of abuse produces robust transcriptional and epigenetic reorganization within brain reward circuits that outlives the direct effects of the drug and may contribute to addiction. DNA methylation is a covalent epigenetic modification that is altered following stimulant exposure and is critical for behavioral and physiological adaptations to drugs of abuse. Although activity-related loss of DNA methylation requires the Gadd45 (Growth arrest and DNA-damage-inducible) gene family, very little is known about how this family regulates activity within the nucleus accumbens or behavioral responses to drugs of abuse. Here, we combined genome-wide transcriptional profiling, pharmacological manipulations, electrophysiological measurements, and CRISPR tools with traditional knockout and behavioral approaches in rodent model systems to dissect the role of Gadd45b in dopamine-dependent epigenetic regulation and cocaine reward. We show that acute cocaine administration induces rapid upregulation of Gadd45b mRNA in the rat nucleus accumbens, and that knockout or site-specific CRISPR/Cas9 gene knockdown of Gadd45b blocks cocaine conditioned place preference. In vitro, dopamine treatment in primary striatal neurons increases Gadd45b mRNA expression through a dopamine receptor type 1 (DRD1)-dependent mechanism. Moreover, shRNA-induced Gadd45b knockdown decreases expression of genes involved in psychostimulant addiction, blocks induction of immediate early genes by DRD1 stimulation, and prevents DRD1-mediated changes in DNA methylation. Finally, we demonstrate that Gadd45b knockdown decreases striatal neuron action potential burst duration in vitro, without altering other electrophysiological characteristics. These results suggest that striatal Gadd45b functions as a dopamine-induced gene that is necessary for cocaine reward memory and DRD1-mediated transcriptional activity.
Collapse
Affiliation(s)
- Morgan E. Zipperly
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Faraz A. Sultan
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Guan-En Graham
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Andrew C. Brane
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Natalie A. Simpkins
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Nancy V. N. Carullo
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Lara Ianov
- grid.265892.20000000106344187Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Jeremy J. Day
- grid.265892.20000000106344187Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA ,grid.265892.20000000106344187Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| |
Collapse
|
6
|
Pepin ME, Schiano C, Miceli M, Benincasa G, Mansueto G, Grimaldi V, Soricelli A, Wende AR, Napoli C. The human aortic endothelium undergoes dose-dependent DNA methylation in response to transient hyperglycemia. Exp Cell Res 2021; 400:112485. [PMID: 33515594 DOI: 10.1016/j.yexcr.2021.112485] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/28/2020] [Accepted: 01/09/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Glycemic control is a strong predictor of long-term cardiovascular risk in patients with diabetes mellitus, and poor glycemic control influences long-term risk of cardiovascular disease even decades after optimal medical management. This phenomenon, termed glycemic memory, has been proposed to occur due to stable programs of cardiac and endothelial cell gene expression. This transcriptional remodeling has been shown to occur in the vascular endothelium through a yet undefined mechanism of cellular reprogramming. METHODS In the current study, we quantified genome-wide DNA methylation of cultured human endothelial aortic cells (HAECs) via reduced-representation bisulfite sequencing (RRBS) following exposure to diabetic (250 mg/dL), pre-diabetic (125 mg/dL), or euglycemic (100 mg/dL) glucose concentrations for 72 h (n = 2). RESULTS We discovered glucose-dependent methylation of genomic regions (DMRs) encompassing 2199 genes, with a disproportionate number found among genes associated with angiogenesis and nitric oxide (NO) signaling-related pathways. Multi-omics analysis revealed differential methylation and gene expression of VEGF (↑5.6% DMR, ↑3.6-fold expression), and NOS3 (↓20.3% DMR, ↓1.6-fold expression), nodal regulators of angiogenesis and NO signaling, respectively. CONCLUSION In the current exploratory study, we examine glucose-dependent and dose-responsive alterations in endothelial DNA methylation to examine a putative epigenetic mechanism underlying diabetic vasculopathy. Specifically, we uncover the disproportionate glucose-dependent methylation and gene expression of VEGF and NO signaling cascades, a physiologic imbalance known to cause endothelial dysfunction in diabetes. We therefore hypothesize that epigenetic mechanisms encode a glycemic memory within endothelial cells.
Collapse
Affiliation(s)
- Mark E Pepin
- Dept. of Pathology, Division of Molecular & Cellular Pathology, University of Alabama at Birmingham, Birmingham, USA; Dept. of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, USA; Institüt für Experimentelle Kardiologie, Universitätsklinikum Heidelberg, Heidelberg, Germany.
| | - Concetta Schiano
- Dept. of Advanced Medical and Surgical Sciences (DAMSS), Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy.
| | - Marco Miceli
- IRCCS SDN, Via E. Gianturco, 113 - 80143, Naples, Italy.
| | - Giuditta Benincasa
- Dept. of Advanced Medical and Surgical Sciences (DAMSS), Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy.
| | - Gelsomina Mansueto
- Dept. of Advanced Medical and Surgical Sciences (DAMSS), Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy; Clinical Dept. of Internal Medicine and Specialistic Units, Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy.
| | - Vincenzo Grimaldi
- Dept. of Advanced Medical and Surgical Sciences (DAMSS), Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy; IRCCS SDN, Via E. Gianturco, 113 - 80143, Naples, Italy.
| | - Andrea Soricelli
- IRCCS SDN, Via E. Gianturco, 113 - 80143, Naples, Italy; Dept of Exercise and Wellness Sciences, University of Naples Parthenope, Via Ammiraglio Ferdinando Acton, 38 - 80133 Naples, Italy.
| | - Adam R Wende
- Dept. of Pathology, Division of Molecular & Cellular Pathology, University of Alabama at Birmingham, Birmingham, USA; Dept. of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, USA.
| | - Claudio Napoli
- Dept. of Advanced Medical and Surgical Sciences (DAMSS), Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy; IRCCS SDN, Via E. Gianturco, 113 - 80143, Naples, Italy; Clinical Dept. of Internal Medicine and Specialistic Units, Università Della Campania "Luigi Vanvitelli", P.za Miraglia, 2 - 80138, Naples, Italy.
| |
Collapse
|
7
|
Zhao Y, Song Y, Zhao R, Zhao M, Huang Q. Gene Panel of Persister Cells as a Prognostic Indicator for Tumor Repopulation After Radiation. Front Oncol 2020; 10:607727. [PMID: 33330109 PMCID: PMC7714959 DOI: 10.3389/fonc.2020.607727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Tumor repopulation during cycles of radiotherapy limits the radio-response in ensuing cycles and causes failure of treatment. It is thus of vital importance to unveil the mechanisms underlying tumor repopulating cells. Increasing evidence suggests that a subpopulation of drug-tolerant persister cancer cells (DTPs) could survive the cytotoxic treatment and resume to propagate. Whether these persister cells contribute to development of radio-resistance remains elusive. Based on the genetic profiling of DTPs by integrating datasets from Gene Expression Omnibus database, this study aimed to provide novel insights into tumor-repopulation mediated radio-resistance and identify predictive biomarkers for radio-response in clinic. A prognostic risk index, grounded on four persister genes (LYNX1, SYNPO, GADD45B, and PDLIM1), was constructed in non-small-cell lung cancer patients from The Cancer Genome Atlas Program (TCGA) using stepwise Cox regression analysis. Weighted gene co-expression network analysis further confirmed the interaction among persister-gene based risk score, radio-response and overall survival time. In addition, the predictive role of risk index was validated in vitro and in other types of TCGA patients. Gene set enrichment analysis was performed to decipher the possible biological signaling, which indicated that two forces behind persister cells, stress response and survival adaptation, might fuel the tumor repopulation after radiation. Targeting these persister cells may represent a new prognostic and therapeutic approach to enhance radio-response and prevent radio-resistance induced by tumor repopulation.
Collapse
Affiliation(s)
- Yucui Zhao
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanwei Song
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruyi Zhao
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minghui Zhao
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Huang
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
8
|
Chen T, Yan J, Li Z. Expression of miR-34a is a sensitive biomarker for exposure to genotoxic agents in human lymphoblastoid TK6 cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 856-857:503232. [PMID: 32928372 DOI: 10.1016/j.mrgentox.2020.503232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 07/11/2020] [Indexed: 01/07/2023]
Abstract
miR-34a has been identified as a tumor suppressor microRNA (miRNA) involved in the P53 network. Its expression levels correlate to carcinogenesis, which are generally lower in tumor tissue and higher in response to DNA damage. In this study, the response of miR-34a from exposure to genotoxic agents in human lymphoblastoid TK6 cells was evaluated to assess whether the expression of this miRNA could be used as an early indicator for genotoxic damage in mammalian cells. TK6 cells were treated with seven genotoxic agents with different mode-of-actions (cisplatin, N-ethyl-N-nitrosourea, etoposide, mitomycin C, methyl methanesulphonate, taxol, and X-ray radiation) and a non-genetic toxin (usnic acid) at different concentrations for four hours (except for X-rays) and the expression levels of miR-34a were measured 24 h after the beginning of the treatments. The expression levels of miR-34a were significantly increased by these genetic toxins in a dose-dependent manner, while no significant change in miRNA expression was found in the usnic acid-treated cells. These results suggest that miR-34a can respond to genotoxic insults sensitively; thus, miR-34a expression has the potential to be used to evaluate genotoxicity of agents.
Collapse
Affiliation(s)
- Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, United States.
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, United States
| | - Zhiguang Li
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079, United States
| |
Collapse
|
9
|
GADD45γ Activated Early in the Course of Herpes Simplex Virus 1 Infection Suppresses the Activation of a Network of Innate Immunity Genes. J Virol 2019; 93:JVI.02201-18. [PMID: 30700604 DOI: 10.1128/jvi.02201-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 12/18/2022] Open
Abstract
The stress response genes encoding GADD45γ, and to a lesser extent GADD45β, are activated early in infection with herpes simplex virus 1 (HSV-1). Cells that had been depleted of GADD45γ by transfection of short hairpin RNA (shRNA) or in which the gene had been knocked out (ΔGADD45γ) yielded significantly less virus than untreated infected cells. Consistent with lower virus yields, the ΔGADD45γ cells (either uninfected or infected with HSV-1) exhibited significantly higher levels of transcripts of a cluster of innate immunity genes, including those encoding IFI16, IFIT1, MDA5, and RIG-I. Members of this cluster of genes were reported by this laboratory to be activated concurrently with significantly reduced virus yields in cells depleted of LGP2 or HDAC4. We conclude that innate immunity to HSV-1 is normally repressed in unstressed cells and repression appears to be determined by two mechanisms. The first, illustrated here, is through activation by HSV-1 infection of the gene encoding GADD45γ. The second mechanism requires constitutively active expression of LGP2 and HDAC4.IMPORTANCE Previous studies from our laboratory reported that knockout of some innate immunity genes was associated with increases in the expression of overlapping networks of genes and significant loss of the ability to support the replication of HSV-1; knockout of other genes was associated with decreases in the expression of overlapping networks of genes and had no effect on virus replication. In this report, we document that depletion of GADD45γ reduced virus yields concurrently with significant upregulation of the expression of a cluster of innate immunity genes comprising IFI16, IFIT1, MDA5, and RIG-I. This report differs from the preceding study in an important respect; i.e., the preceding study found no evidence to support the hypothesis that HSV-1 maintained adequate levels of LGP2 or HDAC4 to block upregulation of the cluster of innate immunity genes. We show that HSV-1 causes upregulation of the GADD45γ gene to prevent the upregulation of innate immunity genes.
Collapse
|
10
|
Park W, Srikanth K, Lim D, Park M, Hur T, Kemp S, Dessie T, Kim MS, Lee SR, te Pas MFW, Kim JM, Park JE. Comparative transcriptome analysis of Ethiopian indigenous chickens from low and high altitudes under heat stress condition reveals differential immune response. Anim Genet 2018; 50:42-53. [DOI: 10.1111/age.12740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2018] [Indexed: 01/22/2023]
Affiliation(s)
- W. Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - K. Srikanth
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - D. Lim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - M. Park
- Animal Breeding and Genomics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - T. Hur
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - S. Kemp
- Animal Biosciences; International Livestock Research Institute (ILRI); P.O. Box 30709 Nairobi 00100 Kenya
| | - T. Dessie
- Animal Biosciences; International Livestock Research Institute (ILRI); P.O. Box 5689 Addis Ababa Ethiopia
| | - M. S. Kim
- Department of Animal Science; College of Agriculture and Life Sciences; Chonnam National University; Republic of Korea Gwangju 61186 Korea
| | - S.-R. Lee
- Department of Agro-biotechnology Convergence; Jeonju University; Republic of Korea 55069 Jeonju Korea
| | - M. F. W. te Pas
- Animal Breeding and Genomics; Wageningen UR Livestock Research; 6700AH Wageningen The Netherlands
| | - J.-M. Kim
- Department of Animal Science and Technology; Chung-Ang University; Anseong Gyeonggi-do 17546 Korea
| | - J.-E. Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| |
Collapse
|
11
|
Myint KZ, Kongpracha P, Rattanasinganchan P, Leelawat K, Moolthiya P, Chaiyabutr K, Tohtong R. Gadd45β silencing impaired viability and metastatic phenotypes in cholangiocarcinoma cells by modulating the EMT pathway. Oncol Lett 2017; 15:3031-3041. [PMID: 29435034 PMCID: PMC5778851 DOI: 10.3892/ol.2017.7706] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 11/10/2017] [Indexed: 12/16/2022] Open
Abstract
Growth arrest and DNA damage-inducible-β (Gadd45β) is a stress-response protein involved in a number of processes, including cell cycle control, DNA repair, survival and death control, and stress signaling, depending on its interactions. Gadd45β expression is dysregulated in numerous types of cancer, functioning as either a tumor promoter or a tumor suppressor. However, the functions of Gadd45β in cholangiocarcinoma (CCA), particularly in metastasis, has not been studied. The immunohistochemical analysis of Gadd45β expression revealed that 75% of histological specimens from patients with CCA expressed high levels of Gadd45β, and that high Gadd45β expression was associated with metastasis. The role of Gadd45β in CCA was examined using siRNA-mediated gene knockdown in HuCCA-1, a human CCA cell line established from a Thai patient. The effects of Gadd45β downregulation upon cell viability and death, invasion, migration, matrix metalloproteinase (MMP) activity and epithelial-mesenchymal transition (EMT) marker expression were investigated. Gadd45β knockdown impaired cell viability, which was associated with the induction of apoptosis. In addition, there was a marked reduction in invasion and migration, although MMP activity was unaffected. Impairment of these metastatic properties was accompanied by the decreased expression of EMT markers, including Slug, vimentin, claudin-1 and zona occludens protein 1, whereas E-cadherin expression was increased. The present study suggests that Gadd45β is involved in regulating the viability and the metastatic potential of CCA cells, which may be mediated by the modulation of the EMT pathway.
Collapse
Affiliation(s)
- Kyaw Zwar Myint
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pornparn Kongpracha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Panthip Rattanasinganchan
- Department of Clinical Chemistry, Faculty of Medical Technology, Huachiew Chalermprakiet University, Bangkok 10400, Thailand
| | - Kawin Leelawat
- Department of Surgery, Rajavithi Hospital, Bangkok 10400, Thailand
| | - Penpak Moolthiya
- Department of Clinical Chemistry, Faculty of Medical Technology, Huachiew Chalermprakiet University, Bangkok 10400, Thailand
| | | | - Rutaiwan Tohtong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| |
Collapse
|
12
|
Ueda T, Kohama Y, Kuge A, Kido E, Sakurai H. GADD45 family proteins suppress JNK signaling by targeting MKK7. Arch Biochem Biophys 2017; 635:1-7. [PMID: 29037961 DOI: 10.1016/j.abb.2017.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/01/2017] [Accepted: 10/11/2017] [Indexed: 01/22/2023]
Abstract
Growth arrest and DNA damage-inducible 45 (GADD45) family genes encode related proteins, including GADD45α, GADD45β, and GADD45γ. In HeLa cells, expression of GADD45 members is differentially regulated under a variety of environmental conditions, but thermal and genotoxic stresses induce the expression of all genes. The heat shock response of GADD45β is mediated by the heat shock transcription factor 1 (HSF1), and GADD45β is necessary for heat stress survival. Heat and genotoxic stress-induced activation of c-Jun N-terminal kinase (JNK) is suppressed by the expression of GADD45 proteins. GADD45 proteins bind the JNK kinase mitogen-activated protein kinase kinase 7 (MKK7) and inhibit its activity, even under normal physiological conditions. Our findings indicate that GADD45 essentially suppresses the MKK7-JNK pathway and suggest that differentially expressed GADD45 family members fine-tune stress-inducible JNK activity.
Collapse
Affiliation(s)
- Takumi Ueda
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Yuri Kohama
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Ayana Kuge
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Eriko Kido
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Hiroshi Sakurai
- Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan.
| |
Collapse
|
13
|
Dynamic microtubule association of Doublecortin X (DCX) is regulated by its C-terminus. Sci Rep 2017; 7:5245. [PMID: 28701724 PMCID: PMC5507856 DOI: 10.1038/s41598-017-05340-x] [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: 03/10/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Doublecortin X (DCX), known to be essential for neuronal migration and cortical layering in the developing brain, is a 40 kDa microtubule (MT)-associated protein. DCX directly interacts with MTs via its two structured doublecortin (DC) domains, but the dynamics of this association and the possible regulatory roles played by the flanking unstructured regions remain poorly defined. Here, we employ quantitative fluorescence recovery after photobleaching (FRAP) protocols in living cells to reveal that DCX shows remarkably rapid and complete exchange within the MT network but that the removal of the C-terminal region significantly slows this exchange. We further probed how MT organization or external stimuli could additionally modulate DCX exchange dynamics. MT depolymerisation (nocodazole treatment) or stabilization (taxol treatment) further enhanced DCX exchange rates, however the exchange rates for the C-terminal truncated DCX protein were resistant to the impact of taxol-induced stabilization. Furthermore, in response to a hyperosmotic stress stimulus, DCX exchange dynamics were slowed, and again the C-terminal truncated DCX protein was resistant to the stimulus. Thus, the DCX dynamically associates with MTs in living cells and its C-terminal region plays important roles in the MT-DCX association.
Collapse
|
14
|
Wu SH, Hsiao YT, Chen JC, Lin JH, Hsu SC, Hsia TC, Yang ST, Hsu WH, Chung JG. Bufalin alters gene expressions associated DNA damage, cell cycle, and apoptosis in human lung cancer NCI-H460 cells in vitro. Molecules 2014; 19:6047-57. [PMID: 24828377 PMCID: PMC6271037 DOI: 10.3390/molecules19056047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/02/2014] [Accepted: 05/08/2014] [Indexed: 12/22/2022] Open
Abstract
Lung cancer is the leading cause of cancer related death and there is no effective treatment to date. Bufalin has been shown effective in inducing apoptosis and DNA damage in lung cancer cells. However, the genetic mechanisms underlying these actions have not been elucidated yet. Cultured NCI-H460 cells were treated with or without 2 μM of bufalin for 24 h. The total RNA was extracted from each treatment for cDNA synthesis and labeling, microarray hybridization, and then followed by flour-labeled cDNA hybridized on chip. The localized concentrations of fluorescent molecules were detected and quantitated and analyzed by Expression Console software (Affymetrix) with default RMA parameters. The key genes involved and their possible interaction pathways were mapped by GeneGo software. About 165 apoptosis-related genes were affected. CASP9 was up-regulated by 5.51 fold and THAP1 by 2.75-fold while CCAR1 was down-regulated by 2.24 fold. 107 genes related to DNA damage/repair were affected. MDC1 was down-regulated by 2.22-fold, DDIT4 by 2.52 fold while GADD45B up-regulated by 3.72 fold. 201 genes related to cell cycles were affected. CCPG1 was down-regulated by 2.11 fold and CDCA7L by 2.71 fold. Many genes about apoptosis, cell cycle regulation and DNA repair are changed significantly following bufalin treatment in NCI-H460 cells. These changes provide an in depth understanding of cytotoxic mechanism of bufalin in genetic level and also offer many potentially useful biomarkers for diagnosis and treatment of lung cancer in future.
Collapse
Affiliation(s)
- Shin-Hwar Wu
- Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan
| | - Yung-Ting Hsiao
- Department of Biological Science and Technology, China Medical University, Taichung 40402, Taiwan
| | - Jaw-Chyum Chen
- Department of Medicinal Botany and Health Applications, Da-Yeh University, Changhua 51591, Taiwan
| | - Ju-Hwa Lin
- Department of Biological Science and Technology, China Medical University, Taichung 40402, Taiwan
| | - Shu-Chun Hsu
- Department of Biological Science and Technology, China Medical University, Taichung 40402, Taiwan
| | - Te-Chun Hsia
- Gradualted Institute of Chinese Medical Science, China Medical University, Taichung 40402, Taiwan
| | - Su-Tso Yang
- Department of Radiology, China Medical University Hospital, Taichung 40447, Taiwan
| | - Wu-Huei Hsu
- Department of Internal Medicine, China Medical University Hospital, Taichung 40447, Taiwan.
| | - Jing-Gung Chung
- Department of Biological Science and Technology, China Medical University, Taichung 40402, Taiwan.
| |
Collapse
|
15
|
Chen H, Lu S, Zhou J, Bai Z, Fu H, Xu X, Yang S, Jiao B, Sun Y. An integrated approach for the identification of USF1-centered transcriptional regulatory networks during liver regeneration. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:415-23. [PMID: 24686121 DOI: 10.1016/j.bbagrm.2014.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/08/2014] [Accepted: 03/19/2014] [Indexed: 01/20/2023]
Abstract
Liver regeneration after partial hepatectomy (PH) is a synchronized process that is precisely controlled by system-wide transcriptional regulatory networks. To clarify the transcriptional changes and regulatory networks that involve transcription factors (TFs) and their target genes during the priming phase, an advanced mouse oligonucleotide array-based transcription factor assay (MOUSE OATFA), mRNA microarray analysis, bioinformatic analysis and ChIP-on-chip experiments were used. A total of 774 genes were upregulated or downregulated in PH liver samples compared with the sham operation (SH) group. Seventeen TFs showed significant changes in activity in the regenerating livers, some of which have not been extensively studied in previous reports, including upstream stimulatory transcription factor 1 (USF1). The TF signatures from MOUSE OATFA were combined with mRNA expression profiles and ChIP-on-chip analyses to construct experimental transcriptional regulatory networks in regenerating livers. USF1-centered regulatory networks were further confirmed by ChIP assays, revealing some of its target genes and novel coregulatory networks. The combination of MOUSE OATFA with transcriptome profiling and bioinformatic analysis represents a novel paradigm for the comprehensive prediction of transcriptional coregulatory networks during the early phase of liver regeneration.
Collapse
Affiliation(s)
- Huan Chen
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Shan Lu
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Jiansheng Zhou
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Zihe Bai
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Hailong Fu
- Department of Anesthesiology, Changzheng Hospital, Second Military Medical University, Shanghai 200433, China
| | - Xiaoping Xu
- School of Pharm. Sichuan University, 3-17 Ren-min-nan Road, Chengdu, Sichuan 610041, China
| | - Shengsheng Yang
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China.
| | - Yimin Sun
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, China; National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Beijing 102206, China.
| |
Collapse
|
16
|
Hensen SMM, Heldens L, van Genesen ST, Pruijn GJM, Lubsen NH. A delayed antioxidant response in heat-stressed cells expressing a non-DNA binding HSF1 mutant. Cell Stress Chaperones 2013; 18:455-73. [PMID: 23321918 PMCID: PMC3682012 DOI: 10.1007/s12192-012-0400-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 12/30/2022] Open
Abstract
To assess the consequences of inactivation of heat shock factor 1 (HSF1) during aging, we analyzed the effect of HSF1 K80Q, a mutant unable to bind DNA, and of dnHSF1, a mutant lacking the activation domain, on the transcriptome of cells 6 and 24 h after heat shock. The primary response to heat shock (6 h recovery), of which 30 % was HSF1-dependent, had decayed 24 h after heat shock in control cells but was extended in HSF1 K80Q and dnHSF1 cells. Comparison with literature data showed that even the HSF1 dependent primary stress response is largely cell specific. HSF1 K80Q, but not HSF1 siRNA-treated, cells showed a delayed stress response: an increase in transcript levels of HSF1 target genes 24 h after heat stress. Knockdown of NRF2, but not of ATF4, c-Fos or FosB, inhibited this delayed stress response. EEF1D_L siRNA inhibited both the delayed and the extended primary stress responses, but had off target effects. In control cells an antioxidant response (ARE binding, HMOX1 mRNA levels) was detected 6 h after heat shock; in HSF1 K80Q cells this response was delayed to 24 h and the ARE complex had a different mobility. Inactivation of HSF1 thus affects the timing and nature of the antioxidant response and NRF2 can activate at least some HSF1 target genes in the absence of HSF1 activity.
Collapse
Affiliation(s)
- Sanne M. M. Hensen
- 271 Department of Biomolecular Chemistry, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Lonneke Heldens
- 271 Department of Biomolecular Chemistry, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Siebe T. van Genesen
- 271 Department of Biomolecular Chemistry, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- 271 Department of Biomolecular Chemistry, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Nicolette H. Lubsen
- 271 Department of Biomolecular Chemistry, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| |
Collapse
|
17
|
Human renal stem/progenitor cells repair tubular epithelial cell injury through TLR2-driven inhibin-A and microvesicle-shuttled decorin. Kidney Int 2013; 83:392-403. [PMID: 23325086 DOI: 10.1038/ki.2012.413] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Acute kidney injury (AKI) is emerging as a worldwide public health problem. Recent studies have focused on the possibility of using human adult renal stem/progenitor cells (ARPCs) to improve the repair of AKI. Here we studied the influence of ARPCs on the healing of cisplatin-injured renal proximal tubular epithelial cells. Tubular, but not glomerular, ARPCs provided a protective effect promoting proliferation of surviving tubular cells and inhibiting cisplatin-induced apoptosis. The recovery effect was specific to tubular ARPCs, occurred only after damage sensing, and was completely cancelled by TLR2 blockade on tubular ARPCs. Moreover, tubular, but not glomerular, ARPCs were resistant to the apoptotic effect of cisplatin. Tubular ARPCs operate mainly through the engagement of TLR2, the secretion of inhibin-A protein, and microvesicle-shuttled decorin, inhibin-A, and cyclin D1 mRNAs. These factors worked synergistically and were essential to the repair process. The involvement of tubular ARPC-secreted inhibin-A and decorin mRNA in the pathophysiology of AKI was also confirmed in transplant patients affected by delayed graft function. Hence, identification of this TLR2-driven recovery mechanism may shed light on new therapeutic strategies to promote the recovery capacity of the kidney in acute tubular damage. Use of these components, derived from ARPCs, avoids injecting stem cells.
Collapse
|
18
|
Yoshioka W, Endo N, Kurashige A, Haijima A, Endo T, Shibata T, Nishiyama R, Kakeyama M, Tohyama C. Fluorescence laser microdissection reveals a distinct pattern of gene activation in the mouse hippocampal region. Sci Rep 2012; 2:783. [PMID: 23136640 PMCID: PMC3491666 DOI: 10.1038/srep00783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/10/2012] [Indexed: 02/06/2023] Open
Abstract
A histoanatomical context is imperative in an analysis of gene expression in a cell in a tissue to elucidate physiological function of the cell. In this study, we made technical advances in fluorescence laser microdissection (LMD) in combination with the absolute quantification of small amounts of mRNAs from a region of interest (ROI) in fluorescence-labeled tissue sections. We demonstrate that our fluorescence LMD-RTqPCR method has three orders of dynamic range, with the lower limit of ROI-size corresponding to a single cell. The absolute quantification of the expression levels of the immediate early genes in an ROI equivalent to a few hundred neurons in the hippocampus revealed that mice transferred from their home cage to a novel environment have distinct activation profiles in the hippocampal regions (CA1, CA3, and DG) and that the gene expression pattern in CA1, but not in the other regions, follows a power law distribution.
Collapse
Affiliation(s)
- Wataru Yoshioka
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Nozomi Endo
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akie Kurashige
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Asahi Haijima
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Current address: Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Toshihiro Endo
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Toshiyuki Shibata
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryutaro Nishiyama
- Research/Clinical/Industrial Division, Leica Microsystems K.K., Tokyo 108-0072, Japan
| | - Masaki Kakeyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Chiharu Tohyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| |
Collapse
|
19
|
Daniels-Wells TR, Helguera G, Rodríguez JA, Leoh LS, Erb MA, Diamante G, Casero D, Pellegrini M, Martínez-Maza O, Penichet ML. Insights into the mechanism of cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1. Toxicol In Vitro 2012; 27:220-31. [PMID: 23085102 DOI: 10.1016/j.tiv.2012.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/04/2012] [Accepted: 10/08/2012] [Indexed: 02/07/2023]
Abstract
We previously developed an antibody-avidin fusion protein (ch128.1Av) that targets the human transferrin receptor 1 (TfR1) and exhibits direct cytotoxicity against malignant B cells in an iron-dependent manner. ch128.1Av is also a delivery system and its conjugation with biotinylated saporin (b-SO6), a plant ribosome-inactivating toxin, results in a dramatic iron-independent cytotoxicity, both in malignant cells that are sensitive or resistant to ch128.1Av alone, in which the toxin effectively inhibits protein synthesis and triggers caspase activation. We have now found that the ch128.1Av/b-SO6 complex induces a transcriptional response consistent with oxidative stress and DNA damage, a response that is not observed with ch128.1Av alone. Furthermore, we show that the antioxidant N-acetylcysteine partially blocks saporin-induced apoptosis suggesting that oxidative stress contributes to DNA damage and ultimately saporin-induced cell death. Interestingly, the toxin was detected in nuclear extracts by immunoblotting, suggesting the possibility that saporin might induce direct DNA damage. However, confocal microscopy did not show a clear and consistent pattern of intranuclear localization. Finally, using the long-term culture-initiating cell assay we found that ch128.1Av/b-SO6 is not toxic to normal human hematopoietic stem cells suggesting that this critical cell population would be preserved in therapeutic interventions using this immunotoxin.
Collapse
Affiliation(s)
- Tracy R Daniels-Wells
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Tamura RE, de Vasconcellos JF, Sarkar D, Libermann TA, Fisher PB, Zerbini LF. GADD45 proteins: central players in tumorigenesis. Curr Mol Med 2012; 12:634-51. [PMID: 22515981 PMCID: PMC3797964 DOI: 10.2174/156652412800619978] [Citation(s) in RCA: 235] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 11/23/2011] [Accepted: 12/15/2011] [Indexed: 12/18/2022]
Abstract
The Growth Arrest and DNA Damage-inducible 45 (GADD45) proteins have been implicated in regulation of many cellular functions including DNA repair, cell cycle control, senescence and genotoxic stress. However, the pro-apoptotic activities have also positioned GADD45 as an essential player in oncogenesis. Emerging functional evidence implies that GADD45 proteins serve as tumor suppressors in response to diverse stimuli, connecting multiple cell signaling modules. Defects in the GADD45 pathway can be related to the initiation and progression of malignancies. Moreover, induction of GADD45 expression is an essential step for mediating anti-cancer activity of multiple chemotherapeutic drugs and the absence of GADD45 might abrogate their effects in cancer cells. In this review, we present a comprehensive discussion of the functions of GADD45 proteins, linking their regulation to effectors of cell cycle arrest, DNA repair and apoptosis. The ramifications regarding their roles as essential and central players in tumor growth suppression are also examined. We also extensively review recent literature to clarify how different chemotherapeutic drugs induce GADD45 gene expression and how its up-regulation and interaction with different molecular partners may benefit cancer chemotherapy and facilitate novel drug discovery.
Collapse
Affiliation(s)
- Rodrigo Esaki Tamura
- International Centre for Genetic Engineering and Biotechnology, and Medical Biochemistry Division, University of Cape Town, Cape Town, South Africa
| | - Jaíra Ferreira de Vasconcellos
- Centro Infantil Boldrini, Molecular Biology Laboratory, Campinas, Brazil
- State University of Campinas, Faculty of Medical Sciences, Department of Medical Genetics, Campinas, Brazil
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA
| | - Towia A Libermann
- BIDMC Genomics and Proteomics Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Paul B Fisher
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology, and Medical Biochemistry Division, University of Cape Town, Cape Town, South Africa
- BIDMC Genomics and Proteomics Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
21
|
Moskalev AA, Smit-McBride Z, Shaposhnikov MV, Plyusnina EN, Zhavoronkov A, Budovsky A, Tacutu R, Fraifeld VE. Gadd45 proteins: relevance to aging, longevity and age-related pathologies. Ageing Res Rev 2012; 11:51-66. [PMID: 21986581 PMCID: PMC3765067 DOI: 10.1016/j.arr.2011.09.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/25/2011] [Accepted: 09/27/2011] [Indexed: 12/12/2022]
Abstract
The Gadd45 proteins have been intensively studied, in view of their important role in key cellular processes. Indeed, the Gadd45 proteins stand at the crossroad of the cell fates by controlling the balance between cell (DNA) repair, eliminating (apoptosis) or preventing the expansion of potentially dangerous cells (cell cycle arrest, cellular senescence), and maintaining the stem cell pool. However, the biogerontological aspects have not thus far received sufficient attention. Here we analyzed the pathways and modes of action by which Gadd45 members are involved in aging, longevity and age-related diseases. Because of their pleiotropic action, a decreased inducibility of Gadd45 members may have far-reaching consequences including genome instability, accumulation of DNA damage, and disorders in cellular homeostasis - all of which may eventually contribute to the aging process and age-related disorders (promotion of tumorigenesis, immune disorders, insulin resistance and reduced responsiveness to stress). Most recently, the dGadd45 gene has been identified as a longevity regulator in Drosophila. Although further wide-scale research is warranted, it is becoming increasingly clear that Gadd45s are highly relevant to aging, age-related diseases (ARDs) and to the control of life span, suggesting them as potential therapeutic targets in ARDs and pro-longevity interventions.
Collapse
Affiliation(s)
- Alexey A Moskalev
- Group of Molecular Radiobiology and Gerontology, Institute of Biology, Komi Science Center of Russian Academy of Sciences.
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Dolfini D, Gatta R, Mantovani R. NF-Y and the transcriptional activation of CCAAT promoters. Crit Rev Biochem Mol Biol 2011; 47:29-49. [PMID: 22050321 DOI: 10.3109/10409238.2011.628970] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the "innovative" NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y - also termed CBF and CP1 - is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; Hatamochi et al., 1988; Hooft van Huijsduijnen et al, 1987; Kim & Sheffery, 1990). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (Suzuki et al., 2001, 2004; Elkon et al., 2003; Mariño-Ramírez et al., 2004; FitzGerald et al., 2004; Linhart et al., 2005; Zhu et al., 2005; Lee et al., 2007; Abnizova et al., 2007; Grskovic et al., 2007; Halperin et al., 2009; Häkkinen et al., 2011). The same consensus, as determined by mutagenesis and SELEX studies (Bi et al., 1997), was also retrieved in ChIP-on-chip analysis (Testa et al., 2005; Ceribelli et al., 2006; Ceribelli et al., 2008; Reed et al., 2008). Additional structural features of the CCAAT box - position, orientation, presence of multiple Transcriptional Start Sites - were previously reviewed (Dolfini et al., 2009) and will not be considered in detail here.
Collapse
Affiliation(s)
- Diletta Dolfini
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
| | | | | |
Collapse
|
23
|
Ramachandran S, Tran DDH, Klebba-Faerber S, Kardinal C, Whetton AD, Tamura T. An ataxia-telangiectasia-mutated (ATM) kinase mediated response to DNA damage down-regulates the mRNA-binding potential of THOC5. RNA (NEW YORK, N.Y.) 2011; 17:1957-1966. [PMID: 21937706 PMCID: PMC3198589 DOI: 10.1261/rna.2820911] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In response to DNA damage, transcription is blocked by inhibition of RNA polymerase II activity. The regulation of a preexisting pool of mRNAs, therefore, plays a key role in DNA repair, cell cycle arrest, or inhibition of differentiation. THOC5 is a member of the THO complex and plays a role in the export of a subset of mRNA, which plays an important role in hematopoiesis and maintaining primitive cells. Since three serine residues in the PEST domain of THOC5 have been shown to be directly phosphorylated by ataxia-telangiectasia-mutated (ATM) kinase, we examined the THOC5-dependent mRNA export under DNA damage. We show here that DNA damage drastically decreased the cytoplasmic pool of a set of THOC5-dependent mRNAs and impaired the THOC5/mRNA complex formation. The mRNP complex formed with nonphosphorylation mutant (S307/312/314A) THOC5, but not with a C-terminal deletion mutant after DNA damage, suggesting that the C-terminal domain of THOC5, but not its phosphorylation in the PEST domain, is necessary for the regulation of the mRNA-binding potency of THOC5. The cytoplasmic THOC5-dependent mRNAs were recovered by treatment with ATM kinase-specific or p53-specific siRNA, as well as by treatment with ATM kinase inhibitor, KU55933, under DNA damage conditions, suggesting that the ATM-kinase-p53 pathway is involved in this response to the DNA damage. Furthermore, the treatment with KU55933 blocked DNA damage-induced THOC5mRNP complex dissociation, indicating that activation of ATM kinase suppresses the ability of THOC5 to bind to its target mRNAs.
Collapse
Affiliation(s)
- Sheetal Ramachandran
- Institut für Biochemie, OE4310, Medizinische Hochschule Hannover, D-30623 Hannover, Germany
| | | | | | | | | | | |
Collapse
|