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Fei X, Zhu C, Liu P, Liu S, Ren L, Lu R, Hou J, Gao Y, Wang X, Pan Y. PELI1: key players in the oncogenic characteristics of pancreatic Cancer. J Exp Clin Cancer Res 2024; 43:91. [PMID: 38528516 PMCID: PMC10962118 DOI: 10.1186/s13046-024-03008-9] [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: 11/22/2023] [Accepted: 03/09/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is a highly malignant gastrointestinal tumor, which is characterized by difficulties in early diagnosis, early metastasis, limited therapeutic response and a grim prognosis. Therefore, it is imperative to explore potential therapeutic targets for PC. Currently, although the involvement of the Pellino E3 Ubiquitin Protein Ligase 1 (PELI1) in the human growth of some malignant tumors has been demonstrated, its association with PC remains uncertain. METHODS Bioinformatics, qRT-PCR, Western blot and IHC were used to detect the expression of PELI1 in pancreas or PC tissues and cells at mRNA and protein levels. The effects of PELI1 on the proliferation and metastatic ability of pancreatic cancer in vitro and in vivo were investigated using CCK8, cloning formation, EdU, flow cytometry, IHC, Transwell assay, wound healing, nude mice subcutaneous tumorigenesis and intrasplenic injection to construct a liver metastasis model. The interactions of PELI1 with proteins as well as the main functions and pathways were investigated by protein profiling, Co-IP, GST-pull down, Immunofluorescence techniques, immunohistochemical co-localization and enrichment analysis. The rescue experiment verified the above experimental results. RESULTS The mRNA and protein expression levels of PELI1 in PC tissues were upregulated and were associated with poor prognosis of patients, in vitro and in vivo experiments confirmed that PELI1 can affect the proliferation and metastatic ability of PC cells. Co-IP, GST-pull down, and other experiments found that PELI1 interacted with Ribosomal Protein S3 (RPS3) through the FHA structural domain and promoted the polyubiquitination of RPS3 in the K48 chain, thereby activates the PI3K/Akt/GSK3β signaling pathway. Moreover, ubiquitinated degradation of RPS3 further reduces Tumor Protein P53 (p53) protein stability and increases p53 degradation by MDM2 Proto-Oncogene (MDM2). CONCLUSION PELI1 is overexpressed in PC, which increased ubiquitination of RPS3 proteins and activates the PI3K/Akt/GSK3β signaling pathway, as well as reduces the protective effect of RPS3 on p53 and promotes the degradation of the p53 protein, which facilitates the progression of PC and leads to a poor prognosis for patients. Therefore, PELI1 is a potential target for the treatment of PC.
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Affiliation(s)
- Xiaobin Fei
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Changhao Zhu
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Peng Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Songbai Liu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
- Department of Hepatobiliary Surgery, Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Likun Ren
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Rishang Lu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Junyi Hou
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Yongjia Gao
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Xing Wang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China.
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China.
| | - Yaozhen Pan
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou Province, China.
- Department of Hepatobiliary Surgery, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China.
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Jin S, Xiong Y, Zhang W, Qiao H, Wu Y, Jiang S, Fu H. Identification of Candidate Male-Reproduction-Related Genes from the Testis and Androgenic Gland of Macrobrachium nipponense, Regulated by PDHE1, through Transcriptome Profiling Analysis. Int J Mol Sci 2024; 25:1940. [PMID: 38339218 PMCID: PMC10856083 DOI: 10.3390/ijms25031940] [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: 01/05/2024] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The previous publication identified that pyruvate dehydrogenase E1 (PDHE1) positively regulated the process of male reproduction in M. nipponense through affecting the expressions of insulin-like androgenic gland hormone. The present study aimed to identify the potential male-reproduction-related genes that were regulated by PDHE1 through performing the transcriptome profiling analysis in the testis and androgenic gland after the knockdown of the expressions of PDHE1 by the injection of dsPDHE1. Both RNA-Seq and qPCR analysis identified the significant decreases in PDHE1 expressions in the testis and androgenic gland in dsPDHE1-injected prawns compared to those in dsGFP-injected prawns, indicating the efficiency of dsPDHE1 in the present study. Transcriptome profiling analysis identified 56 and 127 differentially expressed genes (DEGs) in the testis and androgenic gland, respectively. KEGG analysis revealed that the energy-metabolism-related pathways represented the main enriched metabolic pathways of DEGs in both the testis and androgenic gland, including pyruvate metabolism, the Citrate cycle (TCA cycle), Glycolysis/Gluconeogenesis, and the Glucagon signaling pathway. Thus, it is predicted that these metabolic pathways and the DEGs from these metabolic pathways regulated by PDHE1 may be involved in the regulation of male reproduction in M. nipponense. Furthermore, four genes were found to be differentially expressed in both the testis and androgenic gland, of which ribosomal protein S3 was down-regulated and uncharacterized protein LOC113829596 was up-regulated in both the testis and androgenic gland in dsPDHE1-injected prawns. The present study provided valuable evidence for the establishment of an artificial technique to regulate the process of male reproduction in M. nipponense.
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Affiliation(s)
- Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Yan Wu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
| | - Hongtuo Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (Y.X.); (W.Z.); (H.Q.); (Y.W.); (S.J.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
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Hao J, Liu Y, Guo F, Fu G, Ning J, Ruan X, Zheng X, Gao M. Lnc-SNHG5 Promoted Hepatocellular Carcinoma Progression Through the RPS3-NFκB Pathway. Int J Gen Med 2023; 16:5651-5664. [PMID: 38059157 PMCID: PMC10697148 DOI: 10.2147/ijgm.s442937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Background We planned to explore the underlying mechanism and clinical significance of lnc-SNHG5 and RPS3 in hepatocellular carcinoma in this current study. Methods The expression of Lnc-SNHG5 and RPS3 in HCC tissues and several cell lines were affirmed, respectively, using UALCAN, TIMER, TCGA and RT-qPCR assay. Cell proliferation ability was detected by colony formation assay and CCK8 assay. Cell apoptosis was monitored by flow cytometry assay. Next, the RPS3 expression levels and the related proteins in NFκB pathway were examined using Western blot analysis. The role of lnc-SNHG5 and RPS3 in vivo was identified by subcutaneous tumor bearing experiment. Results Lnc-SNHG5 was significantly increased in hepatocellular carcinoma tissues and in hepatocellular carcinoma cells. Further investigation showed that up-regulated lnc-SNHG5 promoted cell viability and cell proliferation ability of SMMC-7721 cells by regulating the cell apoptosis, while down-regulation of lnc-SNHG5 revealed opposite results in QGY-7703 cells. In terms of mechanism, we found that lnc-SNHG5 interacted with RPS3. Lnc-SNHG5 regulated the NFκB pathway through RPS3 in vitro and in vivo. Conclusion This study suggested that lnc-SNHG5 expression was signally up-regulated in hepatocellular carcinoma, and lnc-SNHG5 promoted the malignant phenotypes in vitro and in vivo via directly regulating RPS3-NFκB pathway. Lnc-SNHG5 might be a target for molecular targeted therapy, a potential and novel diagnostic marker for HCC patients.
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Affiliation(s)
- Jie Hao
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Department of Breast and Thyroid Surgery, Tianjin Union Medical Center of Nankai University, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center Nankai University, Tianjin, People’s Republic of China
| | - Yu Liu
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
| | - Fengli Guo
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital, Binzhou, People’s Republic of China
| | - Guiming Fu
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Thyroid-Otolaryngology Department, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Junya Ning
- Department of Breast and Thyroid Surgery, Tianjin Union Medical Center of Nankai University, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center Nankai University, Tianjin, People’s Republic of China
| | - Xianhui Ruan
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
| | - Ming Gao
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, People’s Republic of China
- Department of Breast and Thyroid Surgery, Tianjin Union Medical Center of Nankai University, Tianjin, People’s Republic of China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center Nankai University, Tianjin, People’s Republic of China
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Tresse E, Marturia-Navarro J, Sew WQG, Cisquella-Serra M, Jaberi E, Riera-Ponsati L, Fauerby N, Hu E, Kretz O, Aznar S, Issazadeh-Navikas S. Mitochondrial DNA damage triggers spread of Parkinson's disease-like pathology. Mol Psychiatry 2023; 28:4902-4914. [PMID: 37779111 PMCID: PMC10914608 DOI: 10.1038/s41380-023-02251-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
In the field of neurodegenerative diseases, especially sporadic Parkinson's disease (sPD) with dementia (sPDD), the question of how the disease starts and spreads in the brain remains central. While prion-like proteins have been designated as a culprit, recent studies suggest the involvement of additional factors. We found that oxidative stress, damaged DNA binding, cytosolic DNA sensing, and Toll-Like Receptor (TLR)4/9 activation pathways are strongly associated with the sPDD transcriptome, which has dysregulated type I Interferon (IFN) signaling. In sPD patients, we confirmed deletions of mitochondrial (mt)DNA in the medial frontal gyrus, suggesting a potential role of damaged mtDNA in the disease pathophysiology. To explore its contribution to pathology, we used spontaneous models of sPDD caused by deletion of type I IFN signaling (Ifnb-/-/Ifnar-/- mice). We found that the lack of neuronal IFNβ/IFNAR leads to oxidization, mutation, and deletion in mtDNA, which is subsequently released outside the neurons. Injecting damaged mtDNA into mouse brain induced PDD-like behavioral symptoms, including neuropsychiatric, motor, and cognitive impairments. Furthermore, it caused neurodegeneration in brain regions distant from the injection site, suggesting that damaged mtDNA triggers spread of PDD characteristics in an "infectious-like" manner. We also discovered that the mechanism through which damaged mtDNA causes pathology in healthy neurons is independent of Cyclic GMP-AMP synthase and IFNβ/IFNAR, but rather involves the dual activation of TLR9/4 pathways, resulting in increased oxidative stress and neuronal cell death, respectively. Our proteomic analysis of extracellular vesicles containing damaged mtDNA identified the TLR4 activator, Ribosomal Protein S3 as a key protein involved in recognizing and extruding damaged mtDNA. These findings might shed light on new molecular pathways through which damaged mtDNA initiates and spreads PD-like disease, potentially opening new avenues for therapeutic interventions or disease monitoring.
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Affiliation(s)
- Emilie Tresse
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Joana Marturia-Navarro
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Wei Qi Guinevere Sew
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Marina Cisquella-Serra
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Elham Jaberi
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Lluis Riera-Ponsati
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Natasha Fauerby
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Erling Hu
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Oliver Kretz
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susana Aznar
- Centre for Neuroscience and Stereology, University Hospital Bispebjerg-Frederiksberg, 2400, Copenhagen, Denmark
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research & Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Biocentre, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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Shao W, Sun K, Ma T, Jiang H, Hahn M, Ma Z, Jiao C, Yin Y. SUMOylation regulates low-temperature survival and oxidative DNA damage tolerance in Botrytis cinerea. THE NEW PHYTOLOGIST 2023; 238:817-834. [PMID: 36651012 DOI: 10.1111/nph.18748] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
SUMOylation as one of the protein post-translational modifications plays crucial roles in multiple biological processes of eukaryotic organisms. Botrytis cinerea is a devastating fungal pathogen and capable of infecting plant hosts at low temperature. However, the molecular mechanisms of low-temperature adaptation are largely unknown in fungi. Combining with biochemical methods and biological analyses, we report that SUMOylation regulates pathogen survival at low temperature and oxidative DNA damage response during infection in B. cinerea. The heat shock protein (Hsp70) BcSsb and E3 ubiquitin ligase BcRad18 were identified as substrates of SUMOylation; moreover, their SUMOylation both requires a single unique SUMO-interacting motif (SIM). SUMOylated BcSsb regulates β-tubulin accumulation, thereby affecting the stability of microtubules and consequently mycelial growth at low temperature. On the contrary, SUMOylated BcRad18 modulates mono-ubiquitination of the sliding clamp protein proliferating cell nuclear antigen (PCNA), which is involved in response to oxidative DNA damage during infection. Our study uncovers the molecular mechanisms of SUMOylation-mediated low-temperature survival and oxidative DNA damage tolerance during infection in a devastating fungal pathogen, which provides novel insights into low-temperature adaptation and pathogenesis for postharvest pathogens as well as new targets for inhibitor invention in disease control.
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Affiliation(s)
- Wenyong Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kewei Sun
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Tianling Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Huixian Jiang
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, PO Box 3049, 67653, Kaiserslautern, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Chen Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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Filipek K, Deryło K, Michalec-Wawiórka B, Zaciura M, González-Ibarra A, Krokowski D, Latoch P, Starosta AL, Czapiński J, Rivero-Müller A, Wawiórka L, Tchórzewski M. Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194890. [PMID: 36328276 DOI: 10.1016/j.bbagrm.2022.194890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is one of the key mechanisms extending the complexity of genetic information and at the same time adaptability of higher eukaryotes. As a result, the broad spectrum of isoforms produced by alternative splicing allows organisms to fine-tune their proteome; however, the functions of the majority of alternatively spliced protein isoforms are largely unknown. Ribosomal protein isoforms are one of the groups for which data are limited. Here we report characterization of an alternatively spliced isoform of the ribosomal uL10 protein, named uL10β. The uL10 protein constitutes the core element of the ribosomal stalk structure within the GTPase associated center, which represents the landing platform for translational GTPases - trGTPases. The stalk plays an important role in the ribosome-dependent stimulation of GTP by trGTPases, which confer unidirectional trajectory for the ribosome, allosterically contributing to the speed and accuracy of translation. We have shown that the newly identified uL10β protein is stably expressed in mammalian cells and is primarily located within the nuclear compartment with a minor signal within the cytoplasm. Importantly, uL10β is able to bind to the ribosomal particle, but is mainly associated with 60S and 80S particles; additionally, the uL10β undergoes re-localization into the mitochondria upon endoplasmic reticulum stress induction. Our results suggest a specific stress-related dual role of uL10β, supporting the idea of existence of specialized ribosomes with an altered GTPase associated center.
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Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Monika Zaciura
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Alan González-Ibarra
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Latoch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Polish-Japanese Academy of Information Technology, Warsaw 02-008, Poland
| | - Agata L Starosta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
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RpS3 Is Required for Spermatogenesis of Drosophila melanogaster. Cells 2023; 12:cells12040573. [PMID: 36831240 PMCID: PMC9954509 DOI: 10.3390/cells12040573] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Ribosomal proteins (RPs) constitute the ribosome, thus participating in the protein biosynthesis process. Emerging studies have suggested that many RPs exhibit different expression levels across various tissues and function in a context-dependent manner for animal development. Drosophila melanogaster RpS3 encodes the ribosomal protein S3, one component of the 40S subunit of ribosomes. We found that RpS3 is highly expressed in the reproductive organs of adult flies and its depletion in male germline cells led to severe defects in sperm production and male fertility. Immunofluorescence staining showed that RpS3 knockdown had little effect on early germ cell differentiation, but strongly disrupted the spermatid elongation and individualization processes. Furthermore, we observed abnormal morphology and activity of mitochondrial derivatives in the elongating spermatids of RpS3-knockdown testes, which could cause the failure of axoneme elongation. We also found that RpS3 RNAi inhibited the formation of the individualization complex that takes charge of disassociating the spermatid bundle. In addition, excessive apoptotic cells were detected in the RpS3-knockdown testes, possibly to clean the defective spermatids. Together, our data demonstrated that RpS3 plays an important role in regulating spermatid elongation and individualization processes and, therefore, is required for normal Drosophila spermatogenesis.
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Law CTY, Nivesvivat T, Xiong Q, Kulkeaw K, Shi L, Ruenchit P, Suwanpakdee D, Suwanpakdee P, Tongkrajang N, Sarasombath PT, Tsui SKW. Mitochondrial genome diversity of Balamuthia mandrillaris revealed by a fatal case of granulomatous amoebic encephalitis. Front Microbiol 2023; 14:1162963. [PMID: 37213512 PMCID: PMC10196457 DOI: 10.3389/fmicb.2023.1162963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/06/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Balamuthia (B.) mandrillaris is a free-living amoeba that can cause rare yet fatal granulomatous amoebic encephalitis (GAE). However, efficacious treatment for GAE is currently unavailable, especially when genomic studies on B. mandrillaris are limited. Methods In this study, B. mandrillaris strain KM-20 was isolated from the brain tissue of a GAE patient, and its mitochondrial genome was de novo assembled using high-coverage Nanopore long reads and Illumina short reads. Results and Discussion Phylogenetic and comparative analyses revealed a range of diversification in the mitochondrial genome of KM-20 and nine other B. mandrillaris strains. According to the mitochondrial genome alignment, one of the most variable regions was observed in the ribosomal protein S3 (rps3), which was caused by an array of novel protein tandem repeats. The repeating units in the rps3 protein tandem region present significant copy number variations (CNVs) among B. mandrillaris strains and suggest KM-20 as the most divergent strain for its highly variable sequence and highest copy number in rps3. Moreover, mitochondrial heteroplasmy was observed in strain V039, and two genotypes of rps3 are caused by the CNVs in the tandem repeats. Taken together, the copy number and sequence variations of the protein tandem repeats enable rps3 to be a perfect target for clinical genotyping assay for B. mandrillaris. The mitochondrial genome diversity of B. mandrillaris paves the way to investigate the phylogeny and diversification of pathogenic amoebae.
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Affiliation(s)
- Cherie Tsz-Yiu Law
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Thirapa Nivesvivat
- Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kasem Kulkeaw
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ling Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Pichet Ruenchit
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Detchvijitr Suwanpakdee
- Infectious Disease Unit, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Piradee Suwanpakdee
- Neurology Division, Department of Pediatrics, Phramongkutklao Hospital, Bangkok, Thailand
| | - Nongnat Tongkrajang
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patsharaporn T. Sarasombath
- Siriraj Integrative Center for Neglected Parasitic Diseases, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Patsharaporn T. Sarasombath, ;
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Stephen Kwok-Wing Tsui,
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9
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Wang YL, Zhao WW, Bai SM, Ma Y, Yin XK, Feng LL, Zeng GD, Wang F, Feng WX, Zheng J, Wang YN, Zeng B, Liu Q, Hung MC, Wan XB. DNA damage-induced paraspeckle formation enhances DNA repair and tumor radioresistance by recruiting ribosomal protein P0. Cell Death Dis 2022; 13:709. [PMID: 35974014 PMCID: PMC9381602 DOI: 10.1038/s41419-022-05092-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2023]
Abstract
Paraspeckles are mammal-specific membraneless nuclear bodies that participate in various biological processes. NONO, a central paraspeckle component, has been shown to play pivotal roles in DNA double-strand breaks (DSB) repair, whereas its underlying mechanism needs to be further disclosed. Here, using co-immunoprecipitation and mass spectrum, we identified ribosomal protein P0 (RPLP0) as a DSB-induced NONO-binding protein; RPLP0 binds to the RRM1 and RRM2 domains of NONO. Similar to NONO, RPLP0 enhances non-homologous end joining-mediated DSB repair, which was ascribed to a ribosome-independent manner. Interestingly, paraspeckles were induced as early as 15 min after irradiation; it further recruited nuclear RPLP0 to enhance its interaction with NONO. Radiation-induced NONO/RPLP0 complex subsequently anchored at the damaged DNA and increased the autophosphorylation of DNA-PK at Thr2609, thereby enhancing DSB repair. Consistently, in vivo and in vitro experiments showed that depletion of NONO sensitizes tumor cells to radiation. For patients with locally advanced rectal cancer, NONO expression was remarkably increased in tumor tissues and correlated with a poor response to radiochemotherapy. Our findings suggest a pivotal role of radiation-induced paraspeckles in DNA repair and tumor radioresistance, and provide a new insight into the ribosome-independent function of ribosomal proteins.
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Affiliation(s)
- Yun-Long Wang
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Wan-Wen Zhao
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Shao-Mei Bai
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Yan Ma
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Xin-Ke Yin
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Li-Li Feng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Guang-Dong Zeng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Fang Wang
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Wei-Xing Feng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Jian Zheng
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Ying-Nai Wang
- grid.240145.60000 0001 2291 4776Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Bing Zeng
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
| | - Quentin Liu
- grid.411971.b0000 0000 9558 1426Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044 People’s Republic of China ,grid.12981.330000 0001 2360 039XState Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060 People’s Republic of China
| | - Mien-Chie Hung
- grid.240145.60000 0001 2291 4776Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ,grid.254145.30000 0001 0083 6092Graduate Institute of Biomedical Sciences and Research Centers for Cancer Biology and Molecular Medicine, China Medical University, Taichung, 404 Taiwan ,grid.252470.60000 0000 9263 9645Department of Biotechnology, Asia University, Taichung, 413 Taiwan
| | - Xiang-Bo Wan
- grid.12981.330000 0001 2360 039XGuangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655 People’s Republic of China
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10
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Šrajer Gajdošik M, Kovač Peić A, Begić M, Grbčić P, Brilliant KE, Hixson DC, Josić D. Possible Role of Extracellular Vesicles in Hepatotoxicity of Acetaminophen. Int J Mol Sci 2022; 23:8870. [PMID: 36012131 PMCID: PMC9408656 DOI: 10.3390/ijms23168870] [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: 07/18/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
We examined proteomic profiles of rat liver extracellular vesicles (EVs) shed following treatment with a sub-toxic dose (500 mg/kg) of the pain reliever drug, acetaminophen (APAP). EVs representing the entire complement of hepatic cells were isolated after perfusion of the intact liver and analyzed with LC-MS/MS. The investigation was focused on revealing the function and cellular origin of identified EVs proteins shed by different parenchymal and non-parenchymal liver cells and their possible role in an early response of this organ to a toxic environment. Comparison of EV proteomic profiles from control and APAP-treated animals revealed significant differences. Alpha-1-macroglobulin and members of the cytochrome P450 superfamily were highly abundant proteins in EVs shed by the normal liver. In contrast, proteins like aminopeptidase N, metalloreductase STEAP4, different surface antigens like CD14 and CD45, and most members of the annexin family were detected only in EVs that were shed by livers of APAP-treated animals. In EVs from treated livers, there was almost a complete disappearance of members of the cytochrome P450 superfamily and a major decrease in other enzymes involved in the detoxification of xenobiotics. Additionally, there were proteins that predominated in non-parenchymal liver cells and in the extracellular matrix, like fibronectin, receptor-type tyrosine-protein phosphatase C, and endothelial type gp91. These differences indicate that even treatment with a sub-toxic concentration of APAP initiates dramatic perturbation in the function of this vital organ.
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Affiliation(s)
| | | | - Marija Begić
- Faculty of Medicine, University Juraj Dobrila of Pula, 52100 Pula, Croatia
| | - Petra Grbčić
- Faculty of Medicine, University Juraj Dobrila of Pula, 52100 Pula, Croatia
| | - Kate E. Brilliant
- Proteomics Core, COBRE CCRD, Rhode Island Hospital, Providence, RI 02903, USA
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Douglas C. Hixson
- Proteomics Core, COBRE CCRD, Rhode Island Hospital, Providence, RI 02903, USA
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Djuro Josić
- Faculty of Medicine, University Juraj Dobrila of Pula, 52100 Pula, Croatia
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
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11
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Chen L, Gao W, Sha C, Yang M, Lin L, Li T, Wei H, Chen Q, Xing J, Zhang M, Zhao S, Xu W, Li Y, Zhu X. SIAH1-mediated RPS3 ubiquitination contributes to chemosensitivity in epithelial ovarian cancer. Aging (Albany NY) 2022; 14:6202-6226. [PMID: 35951361 PMCID: PMC9417229 DOI: 10.18632/aging.204211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022]
Abstract
The E3 ligase SIAH1 is deregulated in human cancers and correlated with poor prognosis, but its contributions to chemoresistance in epithelial ovarian cancer (EOC) are not evident. Herein we found that SIAH1 was decreased in EOC tumour tissues and cell lines and negatively correlated with the RPS3 levels. SIAH1 overexpression suppressed tumour cell growth, colony formation, invasion, metastasis, and cisplatin resistance in vivo and in vitro. SIAH1 promoted RPS3 ubiquitination and degradation using the RING-finger domain, and these steps were required for RPS3 localization to the cytoplasm, which led to subsequent NF-κB inactivation and thereby conferred chemosensitivity. Moreover, ectopic expression of RPS3 or depletion of RPS3 ubiquitination mediated by SIAH1 via the K214R mutant significantly impaired cisplatin-induced tumour suppression in cells stably expressing SIAH1. Together, our findings reveal a tumour suppressor function of SIAH1 and provide evidence showing that the SIAH1-RPS3-NF-κB axis may act as an appealing strategy for tackling treatment resistance in EOC.
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Affiliation(s)
- Lu Chen
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wujiang Gao
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Chunli Sha
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Meiling Yang
- Obstetrics and Gynecology, The First People's Hospital of Nantong City, Nantong, Jiangsu, China
| | - Li Lin
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Taoqiong Li
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hong Wei
- Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qi Chen
- Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jie Xing
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Mengxue Zhang
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shijie Zhao
- Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wenlin Xu
- Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuefeng Li
- Department of Radiology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaolan Zhu
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Central laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.,International Genome Center of Jiangsu University, Zhenjiang, Jiangsu, China
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12
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Vagiona AC, Mier P, Petrakis S, Andrade-Navarro MA. Analysis of Huntington's Disease Modifiers Using the Hyperbolic Mapping of the Protein Interaction Network. Int J Mol Sci 2022; 23:5853. [PMID: 35628660 PMCID: PMC9144261 DOI: 10.3390/ijms23105853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
Huntington's disease (HD) is caused by the production of a mutant huntingtin (HTT) with an abnormally long poly-glutamine (polyQ) tract, forming aggregates and inclusions in neurons. Previous work by us and others has shown that an increase or decrease in polyQ-triggered aggregates can be passive simply due to the interaction of proteins with the aggregates. To search for proteins with active (functional) effects, which might be more effective in finding therapies and mechanisms of HD, we selected among the proteins that interact with HTT a total of 49 pairs of proteins that, while being paralogous to each other (and thus expected to have similar passive interaction with HTT), are located in different regions of the protein interaction network (suggesting participation in different pathways or complexes). Three of these 49 pairs contained members with opposite effects on HD, according to the literature. The negative members of the three pairs, MID1, IKBKG, and IKBKB, interact with PPP2CA and TUBB, which are known negative factors in HD, as well as with HSP90AA1 and RPS3. The positive members of the three pairs interact with HSPA9. Our results provide potential HD modifiers of functional relevance and reveal the dynamic aspect of paralog evolution within the interaction network.
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Affiliation(s)
- Aimilia-Christina Vagiona
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany; (A.-C.V.); (P.M.)
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany; (A.-C.V.); (P.M.)
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece;
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany; (A.-C.V.); (P.M.)
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13
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Wu Z, Wei W, Fan H, Gu Y, Li L, Wang H. Integrated Analysis of Competitive Endogenous RNA Networks in Acute Ischemic Stroke. Front Genet 2022; 13:833545. [PMID: 35401659 PMCID: PMC8990852 DOI: 10.3389/fgene.2022.833545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/25/2022] [Indexed: 12/28/2022] Open
Abstract
Background: Acute ischemic stroke (AIS) is a severe neurological disease with complex pathophysiology, resulting in the disability and death. The goal of this study is to explore the underlying molecular mechanisms of AIS and search for new potential biomarkers and therapeutic targets. Methods: Integrative analysis of mRNA and miRNA profiles downloaded from Gene Expression Omnibus (GEO) was performed. We explored differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMirs) after AIS. Target mRNAs of DEMirs and target miRNAs of DEGs were predicted with target prediction tools, and the intersections between DEGs and target genes were determined. Subsequently, Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses, Gene set enrichment analysis (GSEA), Gene set variation analysis (GSVA), competitive endogenous RNA (ceRNA) (lncRNA-miRNA-mRNA) network, protein–protein interaction (PPI) network, and gene transcription factors (TFs) network analyses were performed to identify hub genes and associated pathways. Furthermore, we obtained AIS samples with evaluation of immune cell infiltration and used CIBERSORT to determine the relationship between the expression of hub genes and infiltrating immune cells. Finally, we used the Genomics of Drug Sensitivity in Cancer (GDSC) database to predict the effect of the identified targets on drug sensitivity. Result: We identified 293 DEGs and 26 DEMirs associated with AIS. DEGs were found to be mainly enriched in inflammation and immune-related signaling pathways through enrichment analysis. The ceRNA network included nine lncRNAs, 13 miRNAs, and 21 mRNAs. We used the criterion AUC >0.8, to screen a 3-gene signature (FBL, RPS3, and RPS15) and the aberrantly expressed miRNAs (hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-148b-3p, and hsa-miR-143-3p) in AIS, which were verified by a method of quantitative PCR (qPCR) in HT22 cells. T cells CD8, B cells naïve, and activated NK cells had statistical increased in number compared with the acute cerebral infarction group. By predicting the IC50 of the patient to the drug, AZD0530, Z.LLNle.CHO and NSC-87877 with significant differences between the groups were screened out. AIS demonstrated heterogeneity in immune infiltrates that correlated with the occurrence and development of diseases. Conclusion: These findings may contribute to a better understanding of the molecular mechanisms of AIS and provide the basis for the development of novel treatment targets in AIS.
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Affiliation(s)
- Zongkai Wu
- Department of Neurology, Hebei Medical University, Shijiazhuang, China
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Wanyi Wei
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Hongzhen Fan
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Yongsheng Gu
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Litao Li
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Hebo Wang
- Department of Neurology, Hebei Medical University, Shijiazhuang, China
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
- *Correspondence: Hebo Wang, , https://orcid.org/0000-0002-0598-5772
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14
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Grodstein F, Yu L, de Jager PL, Levey A, Seyfried NT, Bennett DA. Exploring Cortical Proteins Underlying the Relation of Neuroticism to Cognitive Resilience. AGING BRAIN 2022; 2:100031. [PMID: 36874358 PMCID: PMC9979250 DOI: 10.1016/j.nbas.2022.100031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Some individuals maintain cognitive health despite neuropathology. Targets impacting "cognitive resilience" may provide interventions for preventing dementia without decreasing neuropathology. Neuroticism represents the tendency to experience negative emotions, and is related to worse cognitive resilience. Exploring proteins associated with cognitive resilience risk factors, such as neuroticism, could yield new protein targets. We used 355 postmortem prefrontal cortex from two cohorts to measure 8356 proteins. We identified (i) proteins associated with both neuroticism and cognitive resilience, and (ii) proteins statistically mediating relations of neuroticism to cognitive resilience. We found two proteins, 40S ribosomal proteinS3 (RPS3) and branched chain keto acid dehydrogenase E1, subunit beta (BCKDHB), ranked in the top 1% of smallest p-values in parallel linear regression models of neuroticism to protein levels, and protein levels to cognitive decline resilience. In mediation models, RPS3 and BCKDHB accounted for 25% (p=0.005) of the relation of neuroticism to cognitive resilience. Our sample size is modest, thus results may be due to chance (p-values did not meet Bonferroni significance) and will require further confirmation; however, investigating biologic mediators of associations of risk factors to cognitive resilience may help discover targets to promote cognitive resilience and reduce dementia.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer's Disease Center, Chicago, IL, 60612, USA.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Lei Yu
- Rush Alzheimer's Disease Center, Chicago, IL, 60612, USA.,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L de Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, NY, NY, 10032, USA
| | - Allan Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Chicago, IL, 60612, USA.,Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA
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15
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Ahn WS, Kim TS, Park YJ, Park YK, Kim HD, Kim J. Production, characterization, and epitope mapping of monoclonal antibodies of ribosomal protein S3 (rpS3). Anim Cells Syst (Seoul) 2021; 25:323-336. [PMID: 34745438 PMCID: PMC8567880 DOI: 10.1080/19768354.2021.1980100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ribosomal protein S3 (rpS3), a member of 40S small ribosomal subunit, is a multifunctional protein with various extra-ribosomal functions including DNA repair endonuclease activity and is secreted from cancer cells. Therefore, antibodies with high specificity against rpS3 protein could be useful cancer biomarkers. In this study, polyclonal antibody (pAb) and monoclonal antibodies (mAbs) were raised against rpS3 protein and epitope mapping was performed for each antibody; the amino acid residues of rpS3 were scanned from amino acid 185 to 243 through peptide scanning to reveal the epitopes of each mAb. Results showed that pAb R2 has an epitope from amino acid 203 to 230, mAb M7 has an epitope from amino acid 213 to 221, and mAb M8 has an epitope from amino acid 197 to 219. Taken together, novel mAbs and pAb against rpS3 were raised and mapped against rpS3 with different specific epitopes.
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Affiliation(s)
- Woo-Sung Ahn
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Tae-Sung Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Yong Jun Park
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Young Kwang Park
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- HAEL Lab, Korea University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, Korea University, Seoul, Republic of Korea
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16
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Gueiderikh A, Maczkowiak-Chartois F, Rosselli F. A new frontier in Fanconi anemia: From DNA repair to ribosome biogenesis. Blood Rev 2021; 52:100904. [PMID: 34750031 DOI: 10.1016/j.blre.2021.100904] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 12/27/2022]
Abstract
Described by Guido Fanconi almost 100 years ago, Fanconi anemia (FA) is a rare genetic disease characterized by developmental abnormalities, bone marrow failure (BMF) and cancer predisposition. The proteins encoded by FA-mutated genes (FANC proteins) and assembled in the so-called FANC/BRCA pathway have key functions in DNA repair and replication safeguarding, which loss leads to chromosome structural aberrancies. Therefore, since the 1980s, FA has been considered a genomic instability and chromosome fragility syndrome. However, recent findings have demonstrated new and unexpected roles of FANC proteins in nucleolar homeostasis and ribosome biogenesis, the alteration of which impacts cellular proteostasis. Here, we review the different cellular, biochemical and molecular anomalies associated with the loss of function of FANC proteins and discuss how these anomalies contribute to BMF by comparing FA to other major inherited BMF syndromes. Our aim is to determine the extent to which alterations in the DNA damage response in FA contribute to BMF compared to the consequences of the loss of function of the FANC/BRCA pathway on the other roles of the pathway.
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Affiliation(s)
- Anna Gueiderikh
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Frédérique Maczkowiak-Chartois
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Filippo Rosselli
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
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17
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Development of Carbazole Derivatives Compounds against Candida albicans: Candidates to Prevent Hyphal Formation via the Ras1-MAPK Pathway. J Fungi (Basel) 2021; 7:jof7090688. [PMID: 34575726 PMCID: PMC8466151 DOI: 10.3390/jof7090688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/03/2022] Open
Abstract
Morphogenesis contributes to the virulence of the opportunistic human fungal pathogen Candida albicans. Ras1-MAPK pathways play a critical role in the virulence of C. albicans by regulating cell growth, morphogenesis, and biofilm formation. Ume6 acts as a transcription factor, and Nrg1 is a transcriptional repressor for the expression of hyphal-specific genes in morphogenesis. Azoles or echinocandin drugs have been extensively prescribed for C. albicans infections, which has led to the development of drug-resistant strains. Therefore, it is necessary to develop new molecules to effectively treat fungal infections. Here, we showed that Molecule B and Molecule C, which contained a carbazole structure, attenuated the pathogenicity of C. albicans through inhibition of the Ras1/MAPK pathway. We found that Molecule B and Molecule C inhibit morphogenesis through repressing protein and RNA levels of Ras/MAPK-related genes, including UME6 and NRG1. Furthermore, we determined the antifungal effects of Molecule B and Molecule C in vivo using a candidiasis murine model. We anticipate our findings are that Molecule B and Molecule C, which inhibits the Ras1/MAPK pathway, are promising compounds for the development of new antifungal agents for the treatment of systemic candidiasis and possibly for other fungal diseases.
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18
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Rosenberg AM, Rausser S, Ren J, Mosharov EV, Sturm G, Ogden RT, Patel P, Kumar Soni R, Lacefield C, Tobin DJ, Paus R, Picard M. Quantitative mapping of human hair greying and reversal in relation to life stress. eLife 2021; 10:67437. [PMID: 34155974 PMCID: PMC8219384 DOI: 10.7554/elife.67437] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Hair greying is a hallmark of aging generally believed to be irreversible and linked to psychological stress. Methods: Here, we develop an approach to profile hair pigmentation patterns (HPPs) along individual human hair shafts, producing quantifiable physical timescales of rapid greying transitions. Results: Using this method, we show white/grey hairs that naturally regain pigmentation across sex, ethnicities, ages, and body regions, thereby quantitatively defining the reversibility of greying in humans. Molecularly, grey hairs upregulate proteins related to energy metabolism, mitochondria, and antioxidant defenses. Combining HPP profiling and proteomics on single hairs, we also report hair greying and reversal that can occur in parallel with psychological stressors. To generalize these observations, we develop a computational simulation, which suggests a threshold-based mechanism for the temporary reversibility of greying. Conclusions: Overall, this new method to quantitatively map recent life history in HPPs provides an opportunity to longitudinally examine the influence of recent life exposures on human biology. Funding: This work was supported by the Wharton Fund and NIH grants GM119793, MH119336, and AG066828 (MP). Hair greying is a visible sign of aging that affects everyone. The loss of hair color is due to the loss of melanin, a pigment found in the skin, eyes and hair. Research in mice suggests stress may accelerate hair greying, but there is no definitive research on this in humans. This is because there are no research tools to precisely map stress and hair color over time. But, just like tree rings hold information about past decades, and rocks hold information about past centuries, hairs hold information about past months and years. Hair growth is an active process that happens under the skin inside hair follicles. It demands lots of energy, supplied by structures inside cells called mitochondria. While hairs are growing, cells receive chemical and electrical signals from inside the body, including stress hormones. It is possible that these exposures change proteins and other molecules laid down in the growing hair shaft. As the hair grows out of the scalp, it hardens, preserving these molecules into a stable form. This preservation is visible as patterns of pigmentation. Examining single-hairs and matching the patterns to life events could allow researchers to look back in time through a person’s biological history. Rosenberg et al. report a new way to digitize and measure small changes in color along single human hairs. This method revealed that some white hairs naturally regain their color, something that had not been reported in a cohort of healthy individuals before. Aligning the hair pigmentation patterns with recent reports of stress in the hair donors’ lives showed striking associations. When one donor reported an increase in stress, a hair lost its pigment. When the donor reported a reduction in stress, the same hair regained its pigment. Rosenberg et al. mapped hundreds of proteins inside the hairs to show that white hairs contained more proteins linked to mitochondria and energy use. This suggests that metabolism and mitochondria may play a role in hair greying. To explore these observations in more detail Rosenberg et al. developed a mathematical model that simulates the greying of a whole head of hair over a lifetime, an experiment impossible to do with living people. The model suggested that there might be a threshold for temporary greying; if hairs are about to go grey anyway, a stressful event might trigger that change earlier. And when the stressful event ends, if a hair is just above the threshold, then it could revert back to dark. The new method for measuring small changes in hair coloring opens up the possibility of using hair pigmentation patterns like tree rings. This could track the influence of past life events on human biology. In the future, monitoring hair pigmentation patterns could provide a way to trace the effectiveness of treatments aimed at reducing stress or slowing the aging process. Understanding how ‘old’ white hairs regain their ‘young’ pigmented state could also reveal new information about the malleability of human aging more generally.
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Affiliation(s)
- Ayelet M Rosenberg
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, United States
| | - Shannon Rausser
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, United States
| | - Junting Ren
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, United States
| | - Eugene V Mosharov
- Department of Psychiatry, Division of Molecular Therapeutics, Columbia University Irving Medical Center, New York, United States.,New York State Psychiatric Institute, New York, United States
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, United States
| | - R Todd Ogden
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, United States
| | - Purvi Patel
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University Irving Medical Center, New York, United States
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University Irving Medical Center, New York, United States
| | - Clay Lacefield
- New York State Psychiatric Institute, New York, United States
| | - Desmond J Tobin
- UCD Charles Institute of Dermatology & UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Ralf Paus
- Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, United States.,Centre for Dermatology Research, University of Manchester, Manchester, United Kingdom.,Monasterium Laboratory, Münster, Germany
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, United States.,New York State Psychiatric Institute, New York, United States.,Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, United States
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19
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Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3. Cells 2021; 10:cells10061310. [PMID: 34070332 PMCID: PMC8228307 DOI: 10.3390/cells10061310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Dysregulated fucosylation has been characterized as an underlying cause or a contributor to the pathogenesis of several disease states. However, to date, there is not a clear understanding of how and what proteins, signaling pathways, and cellular processes are impacted by fucosylation. Here, we characterized the proteins recognized by a fucose-binding lectin and unexpectedly discovered that many intracellular proteins are putatively subject to posttranslational fucosylation. We further found that fucosylation on intracellular ribosomal protein S3 responds to stimulus, and that it appears to be independent of the currently characterized fucosylation pathway. This work suggests a to-date-underappreciated role for fucosylation on intracellular proteins and supports the existence of fucosylation capabilities within cells that is not fully known. Abstract Alterations in genes encoding for proteins that control fucosylation are known to play causative roles in several developmental disorders, such as Dowling-Degos disease 2 and congenital disorder of glycosylation type IIc (CDGIIc). Recent studies have provided evidence that changes in fucosylation can contribute to the development and progression of several different types of cancers. It is therefore important to gain a detailed understanding of how fucosylation is altered in disease states so that interventions may be developed for therapeutic purposes. In this report, we find that fucosylation occurs on many intracellular proteins. This is an interesting finding, as the fucosylation machinery is restricted to the secretory pathway and is thought to predominately affect cell-membrane-bound and secreted proteins. We find that Ribosomal protein S3 (RPS3) is fucosylated in normal tissues and in cancer cells, and that the extent of its fucosylation appears to respond to stress, including MAPK inhibitors, suggesting a new role in posttranslational protein function. Our data identify a new ribosome-independent species of fucosylated RPS3 that interacts with proteins involved in posttranscriptional regulation of RNA, such as Heterogeneous nuclear ribonucleoprotein U (HNRNPU), as well as with a predominance of non-coding RNAs. These data highlight a novel role for RPS3, which, given previously reported oncogenic roles for RPS3, might represent functions that are perturbed in pathologies such as cancer. Together, our findings suggest a previously unrecognized role for fucosylation in directly influencing intracellular protein functions.
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20
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Park YJ, Kim SH, Kim TS, Lee SM, Cho BS, Seo CI, Kim HD, Kim J. Ribosomal protein S3 associates with the TFIIH complex and positively regulates nucleotide excision repair. Cell Mol Life Sci 2021; 78:3591-3606. [PMID: 33464383 PMCID: PMC11072392 DOI: 10.1007/s00018-020-03754-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
In mammalian cells, the bulky DNA adducts caused by ultraviolet radiation are mainly repaired via the nucleotide excision repair (NER) pathway; some defects in this pathway lead to a genetic disorder known as xeroderma pigmentosum (XP). Ribosomal protein S3 (rpS3), a constituent of the 40S ribosomal subunit, is a multi-functional protein with various extra-ribosomal functions, including a role in the cellular stress response and DNA repair-related activities. We report that rpS3 associates with transcription factor IIH (TFIIH) via an interaction with the xeroderma pigmentosum complementation group D (XPD) protein and complements its function in the NER pathway. For optimal repair of UV-induced duplex DNA lesions, the strong helicase activity of the TFIIH complex is required for unwinding damaged DNA around the lesion. Here, we show that XP-D cells overexpressing rpS3 showed markedly increased resistance to UV radiation through XPD and rpS3 interaction. Additionally, the knockdown of rpS3 caused reduced NER efficiency in HeLa cells and the overexpression of rpS3 partially restored helicase activity of the TFIIH complex of XP-D cells in vitro. We also present data suggesting that rpS3 is involved in post-excision processing in NER, assisting TFIIH in expediting the repair process by increasing its turnover rate when DNA is damaged. We propose that rpS3 is an accessory protein of the NER pathway and its recruitment to the repair machinery augments repair efficiency upon UV damage by enhancing XPD helicase function and increasing its turnover rate.
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Affiliation(s)
- Y J Park
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - S H Kim
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - T S Kim
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - S M Lee
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - B S Cho
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - C I Seo
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - H D Kim
- TechnoComplex Building, HAEL Lab, Korea University, Seoul, 02841, Korea
| | - J Kim
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea.
- TechnoComplex Building, HAEL Lab, Korea University, Seoul, 02841, Korea.
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21
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Zhu Y, Ren C, Jiang D, Yang L, Chen Y, Li F, Wang B, Zhang Y. RPL34-AS1-induced RPL34 inhibits cervical cancer cell tumorigenesis via the MDM2-P53 pathway. Cancer Sci 2021; 112:1811-1821. [PMID: 33675124 PMCID: PMC8088949 DOI: 10.1111/cas.14874] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Ribosomal proteins (RPs) are important components of ribosomes and related to the occurrence and development of tumors. However, little is known about the effects of the RP network on cervical cancer (CC). In this study, we screened differentially expressed RPL34 in CC by high‐throughput quantitative proteome assay. We found that RPL34 acted as a tumor suppressor and was downregulated in CC and inhibited the proliferation, migration, and invasion abilities of CC cells. Next, we verified that RPL34 regulated the CC through the MDM2‐P53 pathway by using Act D medicine, MDM2 inhibitor, and a series of western blotting(WB)assays. Moreover, an antisense lncRNA, RPL34‐AS1, regulated the expression of RPL34 and participated in the tumorigenesis of CC. RPL34 can reverse the effect of RPL34‐AS1 in CC cells. Finally, by RNA‐binding protein immunoprecipitation (RIP) assay we found that eukaryotic initiation factor 4A3 (EIF4A3), which binds to RPL34‐AS1, regulated RPL34‐AS1 expression in CC. Therefore, our findings indicate that RPL34‐AS1–induced RPL34 inhibits CC cell proliferation, invasion, and metastasis through modulation of the MDM2‐P53 signaling pathway, which provides a meaningful target for the early diagnosis and treatment of CC.
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Affiliation(s)
- Yuanhang Zhu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Chenchen Ren
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Dongyuan Jiang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Li Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Yannan Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Feiyan Li
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Baojin Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Yali Zhang
- Department of pathology, Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, P.R. China
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22
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Cai M, Li H, Chen R, Zhou X. MRPL13 Promotes Tumor Cell Proliferation, Migration and EMT Process in Breast Cancer Through the PI3K-AKT-mTOR Pathway. Cancer Manag Res 2021; 13:2009-2024. [PMID: 33658859 PMCID: PMC7920513 DOI: 10.2147/cmar.s296038] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose Breast cancer (BC), with varying histopathology, biology and response to systemic treatment, is the second leading cause of cancer-related mortality. Previous studies have inferred that the expression of mitochondrial ribosomal proteins (MRPs) is possibly related to the occurrence/progression of BC. MRPL13 might be one of the potential MRP candidates that are involved in BC tumorigenesis, but its role in BC has rarely been reported. The purpose of the current study was to evaluate the prognostic significance of MRPL13, as well as to explore its potential biological functions in BC. Materials and Methods A series of bioinformatic and statistical methods were adopted to assess the MRPL13 expression profile, its relationship with clinicopathological characteristics, copy number variation (CNV), impact on clinical outcomes and relevant functions. All the results are analysed by 1097 BC patients collected from The Cancer Genome Atlas (TCGA) dataset and 52 clinical samples for immunohistochemistry (IHC) assay. Results The results demonstrated that the expression of MRPL13 in BC tissues was remarkably elevated than that in normal breast tissues. In addition, the Kaplan-Meier curves and Cox model indicated that patients with high MRPL13 expression were connected to a worse prognosis, heralding the independent prognostic value of this protein in BC. Moreover, an enrichment analysis showed that MRPL13 was mainly involved in cell cycle/division-related, RNA processing (degradation/splicing), MYC targets and the MTORC1 pathways. In addition, RNA interference (RNAi)-mediated MRPL13 silencing remarkedly inhibited proliferation and migration as well as the expression of EMT-related genes of BC cells in vitro. Mechanistically, attenuation of MRPL13 significantly suppressed the phosphorylation of AKT and mTOR, which could be partially abolished by 740Y-P (a PI3K agonist). Conclusion Our results provide evidence for the first time that increased MRPL13 expression correlates with adverse clinicopathological variables and unfavorable clinical outcomes of BC patients. Knockdown of MRPL13 restrains the proliferation and migration potential and EMT process of BC through inhibiting PI3K/AKT/mTOR signaling pathway.
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Affiliation(s)
- Miaomiao Cai
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Hanning Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, People's Republic of China
| | - Runfa Chen
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Xiang Zhou
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
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23
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Sun MY, Xu B, Wu QX, Chen WL, Cai S, Zhang H, Tang QF. Cisplatin-Resistant Gastric Cancer Cells Promote the Chemoresistance of Cisplatin-Sensitive Cells via the Exosomal RPS3-Mediated PI3K-Akt-Cofilin-1 Signaling Axis. Front Cell Dev Biol 2021; 9:618899. [PMID: 33644057 PMCID: PMC7905060 DOI: 10.3389/fcell.2021.618899] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Cisplatin is an important agent in first-line chemotherapy against gastric cancer (GC). However, consequential drug resistance limits its effectiveness for the treatment of GC. In this study, a cisplatin resistant gastric cancer cell line SGC7901R was determined by LC-MS/MS with increased exosomal levels of RPS3 protein. SGC7901R cell-derived exosomes were readily taken up by cisplatin-sensitive SGC7901S cells, thus triggering off a phenotype of chemoresistance in the receptor cells. Subsequently, it was demonstrated that exosomal RPS3 was essential for inducing chemoresistance of receptor cells as shown by the acquisition of this phenotype in SGC7901S cells with enforced expression of RPS3. Further mechanism study demonstrated that cisplatin-resistant gastric cancer cell-derived exosomal RPS3 enhanced the chemoresistance of cisplatin-sensitive gastric cancer cells through the PI3K-Akt-cofilin-1 signaling pathway. All these findings demonstrated that cisplatin-resistant gastric cancer cells communicate with sensitive cells through the intercellular delivery of exosomal RPS3 and activation of the PI3K-Akt-cofilin-1 signaling pathway. Targeting exosomal RPS3 protein in cisplatin-resistant gastric cancer cells may thus be a promising strategy to overcome cisplatin resistance in gastric cancer.
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Affiliation(s)
- Meng-Yao Sun
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bo Xu
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qiu-Xue Wu
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wen-Lian Chen
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Si Cai
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hui Zhang
- Research Center for Traditional Chinese Medicine Complexity System, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing-Feng Tang
- Department of Clinical Laboratory and Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Clinical Laboratory, Jiading Branch of Shanghai General Hospital, Shanghai, China
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Zubaer A, Wai A, Patel N, Perillo J, Hausner G. The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales. Front Microbiol 2021; 12:618649. [PMID: 33643245 PMCID: PMC7902536 DOI: 10.3389/fmicb.2021.618649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
Fungi assigned to the Ophiostomatales are of economic concern as many are blue-stain fungi and some are plant pathogens. The mitogenomes of two blue-stain fungi, Ophiostoma minus and Ophiostoma piliferum, were sequenced and compared with currently available mitogenomes for other members of the Ophiostomatales. Species representing various genera within the Ophiostomatales have been examined for gene content, gene order, phylogenetic relationships, and the distribution of mobile elements. Gene synteny is conserved among the Ophiostomatales but some members were missing the atp9 gene. A genome wide intron landscape has been prepared to demonstrate the distribution of the mobile genetic elements (group I and II introns and homing endonucleases) and to provide insight into the evolutionary dynamics of introns among members of this group of fungi. Examples of complex introns or nested introns composed of two or three intron modules have been observed in some species. The size variation among the mitogenomes (from 23.7 kb to about 150 kb) is mostly due to the presence and absence of introns. Members of the genus Sporothrix sensu stricto appear to have the smallest mitogenomes due to loss of introns. The taxonomy of the Ophiostomatales has recently undergone considerable revisions; however, some lineages remain unresolved. The data showed that genera such as Raffaelea appear to be polyphyletic and the separation of Sporothrix sensu stricto from Ophiostoma is justified.
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Affiliation(s)
- Abdullah Zubaer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Nikita Patel
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Jordan Perillo
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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25
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Pereira HABS, Araújo TT, Dionizio A, Trevizol JS, Pereira FS, Iano FG, Faria Ximenes V, Buzalaf MAR. Increase of complex I and reduction of complex II mitochondrial activity are possible adaptive effects provoked by fluoride exposure. Heliyon 2021; 7:e06028. [PMID: 33532647 PMCID: PMC7829207 DOI: 10.1016/j.heliyon.2021.e06028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/30/2020] [Accepted: 01/14/2021] [Indexed: 12/19/2022] Open
Abstract
Fluoride (F) can induce changes in the expression of several liver proteins, most of them localized in the mitochondria and its effect is dose- and time-dependent. This study analyzed the effect of distinct F concentrations and exposure periods on the mitochondrial activity of complex I-III and II-III in the liver. Thirty-six 21-day-old male Wistar rats were divided into 2 groups (n = 18) according to the duration of the treatment (20 or 60 days). They were subdivided into 3 subgroups (n = 6) according to the concentration of F (0 mg/L, 15 mg/L or 50 mg/L). After the experimental periods, the animals were anesthetized, liver mitochondria were isolated and stored for activity analyses. The determination of complexes II-III and I-III was based on the reduction of cytochrome c3+ to cytochrome c2+ performed spectrophotometrically. Bioinformatics analyses were performed using data from a previous study (Pereira et al., 2018). The mitochondrial complex I-III was significantly activated in the groups treated with 50 mgF/L for 20 days and 15 mgF/L for 60 days. The complex II-III was significantly reduced in the group treated with the higher F dose for 60 days. The networks indicated more changes in mitochondrial proteins in the group treated with the higher dose for 20 days; the reduction is probably linked to the activation of the complex I-III. The reduction in the complex II-III upon exposure to the higher F dose in the long term might be part of an adaptative mechanism of the body to counteract the deleterious effects of this ion on the energy metabolism.
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Affiliation(s)
| | - Tamara Teodoro Araújo
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901, Bauru, São Paulo, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901, Bauru, São Paulo, Brazil
| | - Juliana Sanches Trevizol
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901, Bauru, São Paulo, Brazil
| | - Fabrício Soares Pereira
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901, Bauru, São Paulo, Brazil
| | - Flávia Godoy Iano
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901, Bauru, São Paulo, Brazil
| | - Valdecir Faria Ximenes
- Department of Chemistry, Faculty of Sciences, São Paulo State University (UNESP), P. O. Box 473, 17033-36, Bauru, São Paulo, Brazil
| | - Marília Afonso Rabelo Buzalaf
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901, Bauru, São Paulo, Brazil
- Corresponding author.
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26
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Interactions between tumor-derived proteins and Toll-like receptors. Exp Mol Med 2020; 52:1926-1935. [PMID: 33299138 PMCID: PMC8080774 DOI: 10.1038/s12276-020-00540-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/20/2020] [Accepted: 11/02/2020] [Indexed: 12/23/2022] Open
Abstract
Damage-associated molecular patterns (DAMPs) are danger signals (or alarmins) alerting immune cells through pattern recognition receptors (PRRs) to begin defense activity. Moreover, DAMPs are host biomolecules that can initiate a noninflammatory response to infection, and pathogen-associated molecular pattern (PAMPs) perpetuate the inflammatory response to infection. Many DAMPs are proteins that have defined intracellular functions and are released from dying cells after tissue injury or chemo-/radiotherapy. In the tumor microenvironment, DAMPs can be ligands for Toll-like receptors (TLRs) expressed on immune cells and induce cytokine production and T-cell activation. Moreover, DAMPs released from tumor cells can directly activate tumor-expressed TLRs that induce chemoresistance, migration, invasion, and metastasis. Furthermore, DAMP-induced chronic inflammation in the tumor microenvironment causes an increase in immunosuppressive populations, such as M2 macrophages, myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs). Therefore, regulation of DAMP proteins can reduce excessive inflammation to create an immunogenic tumor microenvironment. Here, we review tumor-derived DAMP proteins as ligands of TLRs and discuss their association with immune cells, tumors, and the composition of the tumor microenvironment. Tumor cells killed by radiotherapy or chemotherapy release signaling molecules that stimulate both immune response and tumor aggressiveness; regulating these molecules could improve treatment efficacy. Tae Heung Kang, Yeong-Min Park, and co-workers at Konkuk University, Seoul, South Korea, have reviewed the role of damage-associated molecular patterns (DAMPs) in immunity and cancer. These signaling molecules act as danger signals, activating immune cells by binding to specific receptors. However, tumor cells have the same receptors, and DAMPs binding triggers chemoresistance and increases invasiveness. The researchers report that although DAMPs can trigger a helpful immune response, they can also cause chronic inflammation, which in turn promotes an immune suppression response, allowing tumors to escape immune detection. Improving our understanding of the functions of different DAMPs could improve our ability to boost the immune response and decrease tumor aggressiveness.
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Rius-Pérez S, Pérez S, Martí-Andrés P, Monsalve M, Sastre J. Nuclear Factor Kappa B Signaling Complexes in Acute Inflammation. Antioxid Redox Signal 2020; 33:145-165. [PMID: 31856585 DOI: 10.1089/ars.2019.7975] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Significance: Nuclear factor kappa B (NF-κB) is a master regulator of the inflammatory response and represents a key regulatory node in the complex inflammatory signaling network. In addition, selective NF-κB transcriptional activity on specific target genes occurs through the control of redox-sensitive NF-κB interactions. Recent Advances: The selective NF-κB response is mediated by redox-modulated NF-κB complexes with ribosomal protein S3 (RPS3), Pirin (PIR). cAMP response element-binding (CREB)-binding protein (CBP)/p300, peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), activator protein-1 (AP-1), signal transducer and activator of transcription 3 (STAT3), early growth response protein 1 (EGR-1), and SP-1. NF-κB is cooperatively coactivated with AP-1, STAT3, EGR-1, and SP-1 during the inflammatory process, whereas NF-κB complexes with CBP/p300 and PGC-1α regulate the expression of antioxidant genes. PGC-1α may act as selective repressor of phospho-p65 toward interleukin-6 (IL-6) in acute inflammation. p65 and nuclear factor erythroid 2-related factor 2 (NRF2) compete for binding to coactivator CBP/p300 playing opposite roles in the regulation of inflammatory genes. S-nitrosylation or tyrosine nitration favors the recruitment of specific NF-κB subunits to κB sites. Critical Issues: NF-κB is a redox-sensitive transcription factor that forms specific signaling complexes to regulate selectively the expression of target genes in acute inflammation. Protein-protein interactions with coregulatory proteins, other transcription factors, and chromatin-remodeling proteins provide transcriptional specificity to NF-κB. Furthermore, different NF-κB subunits may form distinct redox-sensitive homo- and heterodimers with distinct affinities for κB sites. Future Directions: Further research is required to elucidate the whole NF-κB interactome to fully characterize the complex NF-κB signaling network in redox signaling, inflammation, and cancer.
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Affiliation(s)
- Sergio Rius-Pérez
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Valencia, Spain
| | - Salvador Pérez
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Valencia, Spain
| | - Pablo Martí-Andrés
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Valencia, Spain
| | - María Monsalve
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Juan Sastre
- Department of Physiology, Faculty of Pharmacy, University of Valencia, Valencia, Spain
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina.,Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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Park YJ, Kim TS, Kim EH, Kim HD, Kim J. Ribosomal protein S3 is a novel negative regulator of non-homologous end joining repair of DNA double-strand breaks. FASEB J 2020; 34:8102-8113. [PMID: 32297663 DOI: 10.1096/fj.201903245r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/16/2020] [Accepted: 03/31/2020] [Indexed: 11/11/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the most serious types of DNA damage. However, multiple repair pathways are present in cells to ensure rapid and appropriate repair of DSBs. Pathway selection depends on several factors including cell type, cell cycle phase, and damage severity. Ribosomal protein S3 (rpS3), a component of the 40S small ribosomal subunit, is a multi-functional protein primarily involved in protein synthesis. rpS3 is also involved in the mediation of various extra-ribosomal pathways, including DNA damage processing and the stress response. Here, we report that rpS3 is a novel negative regulator of non-homologous end joining (NHEJ)-mediated repair of DSBs. We found that rpS3 interacts with the Ku heterodimers of the DNA-dependent protein kinase (DNA-PK) complex and slows down NHEJ ligation reactions, ultimately triggering p53-dependent cell death following treatment with high-dose ionizing radiation. After DSB formation, DNA-PK phosphorylates rpS3, which consequently reduces the binding of rpS3 to the Ku complex. We hypothesized that rpS3 may play a role in DSB repair by repressing NHEJ, while inducing other repair pathways, and by initiating DSB-induced cell death in response to severe DNA damage.
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Affiliation(s)
- Yong Jun Park
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Tae-Sung Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Eun-Ho Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | | | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, Korea University, Seoul, Korea
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Zhang Y, Yang G, Fang M, Deng C, Zhang KQ, Yu Z, Xu J. Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi. Front Microbiol 2020; 11:617. [PMID: 32351475 PMCID: PMC7174627 DOI: 10.3389/fmicb.2020.00617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/19/2020] [Indexed: 01/10/2023] Open
Abstract
Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Guangzhu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Meiling Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Chu Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Kampen KR, Sulima SO, Vereecke S, De Keersmaecker K. Hallmarks of ribosomopathies. Nucleic Acids Res 2020; 48:1013-1028. [PMID: 31350888 PMCID: PMC7026650 DOI: 10.1093/nar/gkz637] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Ribosomopathies are diseases caused by defects in ribosomal constituents or in factors with a role in ribosome assembly. Intriguingly, congenital ribosomopathies display a paradoxical transition from early symptoms due to cellular hypo-proliferation to an elevated cancer risk later in life. Another association between ribosome defects and cancer came into view after the recent discovery of somatic mutations in ribosomal proteins and rDNA copy number changes in a variety of tumor types, giving rise to somatic ribosomopathies. Despite these clear connections between ribosome defects and cancer, the molecular mechanisms by which defects in this essential cellular machinery are oncogenic only start to emerge. In this review, the impact of ribosomal defects on the cellular function and their mechanisms of promoting oncogenesis are described. In particular, we discuss the emerging hallmarks of ribosomopathies such as the appearance of ‘onco-ribosomes’ that are specialized in translating oncoproteins, dysregulation of translation-independent extra-ribosomal functions of ribosomal proteins, rewired cellular protein and energy metabolism, and extensive oxidative stress leading to DNA damage. We end by integrating these findings in a model that can provide an explanation how ribosomopathies could lead to the transition from hypo- to hyper-proliferation in bone marrow failure syndromes with elevated cancer risk.
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Affiliation(s)
- Kim R Kampen
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Sergey O Sulima
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Stijn Vereecke
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
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Wang G, Lin J, Shi Y, Chang X, Wang Y, Guo L, Wang W, Dou M, Deng Y, Ming R, Zhang J. Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya. BMC Genomics 2019; 20:765. [PMID: 31640544 PMCID: PMC6805638 DOI: 10.1186/s12864-019-6133-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells. RESULTS In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene. CONCLUSIONS Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.
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Affiliation(s)
- Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jingxian Lin
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yang Shi
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoguang Chang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuanyuan Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lin Guo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wenhui Wang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Meijie Dou
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Sahu PK, Salim S, Pp M, Chauhan S, Tomar RS. Reverse genetic analysis of yeast YPR099C/MRPL51 reveals a critical role of both overlapping ORFs in respiratory growth and MRPL51 in mitochondrial DNA maintenance. FEMS Yeast Res 2019; 19:5543219. [PMID: 31374566 DOI: 10.1093/femsyr/foz056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/01/2019] [Indexed: 11/14/2022] Open
Abstract
The Saccharomyces cerevisiae genome contains 6572 ORFs, of which 680 ORFs are classified as dubious ORFs. A dubious ORF is a small, noncoding, nonconserved ORF that overlaps with another ORF of the complementary strand. Our study characterizes a dubious/nondubious ORF pair, YPR099C/MRPL51, and shows the transcript and protein level expression of YPR099C. Its subcellular localization was observed in the mitochondria. The overlapping ORF, MRPL51, encodes a mitochondrial ribosomal protein of large subunit. Deletion of any ORF from YPR099C/MRPL51 pair induces common phenotypes, i.e. loss of mtDNA, lack of mitochondrial fusion and lack of respiratory growth, due to the double deletion (ypr099cΔ/Δmrpl51Δ/Δ) caused by sequence overlap. Hence, we created the single deletions of each ORF of the YPR099C/MRPL51 pair by an alternative approach to distinguish their phenotypes and identify the specific functions. Both the ORFs were found essential for the functional mitochondria and respiratory growth, but MRPL51 showed its specific requirement in mtDNA stability. The mechanism of mtDNA maintenance by Mrpl51 is probably Mhr1 dependent that physically interacts with Mrpl51 and also regulates mtDNA repair. Overall, our study provides strong evidence for the protein level expression of a dubious ORF YPR099C and the bifunctional role of Mrpl51 in mtDNA maintenance.
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Affiliation(s)
- Pushpendra Kumar Sahu
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Sagar Salim
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Mubthasima Pp
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Sakshi Chauhan
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, Madhya Pradesh, India
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Zhao L, Cao J, Hu K, Wang P, Li G, He X, Tong T, Han L. RNA-binding protein RPS3 contributes to hepatocarcinogenesis by post-transcriptionally up-regulating SIRT1. Nucleic Acids Res 2019; 47:2011-2028. [PMID: 30517713 PMCID: PMC6393244 DOI: 10.1093/nar/gky1209] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 11/19/2018] [Accepted: 12/01/2018] [Indexed: 12/19/2022] Open
Abstract
Although several studies indicate that RNA-binding proteins (RBPs) contribute to key steps in a variety of physiological processes and cancer, the detailed biological functions and mechanisms remain to be determined. By performing bioinformatics analysis using well-established hepatocellular carcinoma (HCC) datasets, we identified a set of HCC progression-associated RBPs (HPARBPs) and found that the global expression of HPARBPs was significantly correlated with patient prognosis. Among the 42 HPARBPs, human ribosomal protein S3 (RPS3) was one of the most abundant genes whose role remains uncharacterized in HCC. Gain- and loss-of-function analyses demonstrated that RPS3 promoted HCC tumorigenesis both in vitro and in vivo. Mechanistically, we revealed that silent information regulator 1 (SIRT1) was a critical target of RPS3 and was essential for sustaining the RPS3-induced malignant phenotypes of HCC cells. RPS3 stabilized SIRT1 mRNA by binding to AUUUA motifs in the 3448–3530 region of the 3′ untranslated region (UTR) of SIRT1 mRNA. In addition, we found that (5-formylfuran-2-yl) methyl 4-hydroxy-2-methylenebutanoate (FMHM) inhibited HCC progression by repressing the RPS3/SIRT1 pathway. Our study unveils a novel extra-ribosomal role of RPS3 in facilitating hepatocarcinogenesis via the post-transcriptional regulation of SIRT1 expression and proposes that the RPS3/SIRT1 pathway serves as a potential therapeutic target in HCC.
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Affiliation(s)
- Lijun Zhao
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Beijing 100191, P.R. China
| | - Jianzhong Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Kexin Hu
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Beijing 100191, P.R. China
| | - Penghui Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Guodong Li
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Beijing 100191, P.R. China
| | - Xiaodong He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
| | - Tanjun Tong
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Beijing 100191, P.R. China
| | - Limin Han
- Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Beijing 100191, P.R. China
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Protective Effects of Euthyroidism Restoration on Mitochondria Function and Quality Control in Cardiac Pathophysiology. Int J Mol Sci 2019; 20:ijms20143377. [PMID: 31295805 PMCID: PMC6678270 DOI: 10.3390/ijms20143377] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunctions are major contributors to heart disease onset and progression. Under ischemic injuries or cardiac overload, mitochondrial-derived oxidative stress, Ca2+ dis-homeostasis, and inflammation initiate cross-talking vicious cycles leading to defects of mitochondrial DNA, lipids, and proteins, concurrently resulting in fatal energy crisis and cell loss. Blunting such noxious stimuli and preserving mitochondrial homeostasis are essential to cell survival. In this context, mitochondrial quality control (MQC) represents an expanding research topic and therapeutic target in the field of cardiac physiology. MQC is a multi-tier surveillance system operating at the protein, organelle, and cell level to repair or eliminate damaged mitochondrial components and replace them by biogenesis. Novel evidence highlights the critical role of thyroid hormones (TH) in regulating multiple aspects of MQC, resulting in increased organelle turnover, improved mitochondrial bioenergetics, and the retention of cell function. In the present review, these emerging protective effects are discussed in the context of cardiac ischemia-reperfusion (IR) and heart failure, focusing on MQC as a strategy to blunt the propagation of connected dangerous signaling cascades and limit adverse remodeling. A better understanding of such TH-dependent signaling could provide insights into the development of mitochondria-targeted treatments in patients with cardiac disease.
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Cheng X, Li Y, Guo Q, Tian Q, Zhang Y, Fang H, Zhang S, Guo Y. A planarian RPS3 homolog is critical to the modulation of planarian regeneration. Gene 2019; 691:153-159. [PMID: 30615916 DOI: 10.1016/j.gene.2018.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/24/2018] [Accepted: 12/10/2018] [Indexed: 11/13/2022]
Abstract
Planarians are an important model for stem cell and regeneration biology, because they can regenerate any missing body structure in a short time. As an important component of ribosomes, ribosomal proteins can synthesize proteins and play a central role in cell cycle checkpoint, cell survival/senescence/apoptosis, and organismal growth and development. In this study, we identified and amplified the homologous gene of RPS3 in Dugesia japonica. Double-stranded RNA mediated RNAi revealed that when the Dj-RPS3 function was lost by planarians; they did not form blastemas and died 100%. Further investigation, confirmed that Dj-RPS3 was involved in regulating the proliferative and early differentiation of neoblasts.
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Affiliation(s)
- Xina Cheng
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China
| | - Yingzhao Li
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China
| | - Qi Guo
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China
| | - Qingnan Tian
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China
| | - Yizhe Zhang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China
| | - Huimin Fang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China; Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou, Henan, China.
| | - Yanan Guo
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, Henan 450001, China; Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou, Henan, China.
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Nerva L, Vigani G, Di Silvestre D, Ciuffo M, Forgia M, Chitarra W, Turina M. Biological and Molecular Characterization of Chenopodium quinoa Mitovirus 1 Reveals a Distinct Small RNA Response Compared to Those of Cytoplasmic RNA Viruses. J Virol 2019; 93:e01998-18. [PMID: 30651361 PMCID: PMC6430534 DOI: 10.1128/jvi.01998-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023] Open
Abstract
Indirect evidence of mitochondrial viruses in plants comes from discovery of genomic fragments integrated into the nuclear and mitochondrial DNA of a number of plant species. Here, we report the existence of replicating mitochondrial virus in plants: from transcriptome sequencing (RNA-seq) data of infected Chenopodium quinoa, a plant species commonly used as a test plant in virus host range experiments, among other virus contigs, we could assemble a 2.7-kb contig that had highest similarity to mitoviruses found in plant genomes. Northern blot analyses confirmed the existence of plus- and minus-strand RNA corresponding to the mitovirus genome. No DNA corresponding to the genomic RNA was detected, excluding the endogenization of such virus. We have tested a number of C. quinoa accessions, and the virus was present in a number of commercial varieties but absent from a large collection of Bolivian and Peruvian accessions. The virus could not be transmitted mechanically or by grafting, but it is transmitted vertically through seeds at a 100% rate. Small RNA analysis of a C. quinoa line carrying the mitovirus and infected by alfalfa mosaic virus showed that the typical antiviral silencing response active against cytoplasmic viruses (21- to 22-nucleotide [nt] vsRNA peaks) is not active against CqMV1, since in this specific case the longest accumulating vsRNA length is 16 nt, which is the same as that corresponding to RNA from mitochondrial genes. This is evidence of a distinct viral RNA degradation mechanism active inside mitochondria that also may have an antiviral effect.IMPORTANCE This paper reports the first biological characterization of a bona fide plant mitovirus in an important crop, Chenopodium quinoa, providing data supporting that mitoviruses have the typical features of cryptic (persistent) plant viruses. We, for the first time, demonstrate that plant mitoviruses are associated with mitochondria in plants. In contrast to fungal mitoviruses, plant mitoviruses are not substantially affected by the antiviral silencing pathway, and the most abundant mitovirus small RNA length is 16 nt.
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Affiliation(s)
- L Nerva
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - G Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - D Di Silvestre
- Institute for Biomedical Technology, CNR, Segrate, Milan, Italy
| | - M Ciuffo
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
| | - M Forgia
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - W Chitarra
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
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Sulima SO, Kampen KR, De Keersmaecker K. Cancer Biogenesis in Ribosomopathies. Cells 2019; 8:E229. [PMID: 30862070 PMCID: PMC6468915 DOI: 10.3390/cells8030229] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/23/2022] Open
Abstract
Ribosomopathies are congenital diseases with defects in ribosome assembly and are characterized by elevated cancer risks. Additionally, somatic mutations in ribosomal proteins have recently been linked to a variety of cancers. Despite a clear correlation between ribosome defects and cancer, the molecular mechanisms by which these defects promote tumorigenesis are unclear. In this review, we focus on the emerging mechanisms that link ribosomal defects in ribosomopathies to cancer progression. This includes functional "onco-specialization" of mutant ribosomes, extra-ribosomal consequences of mutations in ribosomal proteins and ribosome assembly factors, and effects of ribosomal mutations on cellular stress and metabolism. We integrate some of these recent findings in a single model that can partially explain the paradoxical transition from hypo- to hyperproliferation phenotypes, as observed in ribosomopathies. Finally, we discuss the current and potential strategies, and the associated challenges for therapeutic intervention in ribosome-mutant diseases.
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Affiliation(s)
- Sergey O Sulima
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
| | - Kim R Kampen
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, LKI⁻Leuven Cancer Institute, 3000 Leuven, Belgium.
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Park HJ, Jang GY, Kim YS, Park JH, Lee SE, Vo MC, Lee JJ, Han HD, Jung ID, Kang TH, Park YM. A novel TLR4 binding protein, 40S ribosomal protein S3, has potential utility as an adjuvant in a dendritic cell-based vaccine. J Immunother Cancer 2019; 7:60. [PMID: 30819254 PMCID: PMC6394096 DOI: 10.1186/s40425-019-0539-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/20/2019] [Indexed: 02/06/2023] Open
Abstract
Background Dendritic cells (DCs) are professional antigen presenting cells (APCs), which can activate antigen-specific CD8+ T cell immunity, resulting in tumor clearance. Immature DCs are usually stimulated by various adjuvants through their immune receptors. Among them, Toll-like receptor 4 (TLR4) has an important role in activating DCs to cause their maturation. In fact, TLR4 is well-known to induce innate and adaptive immune responses against various external microbial or internal damage associated molecular patterns (DAMP). LPS is widely regarded as a strong stimulator of TLR4 signaling. However, LPS is inappropriate for use in humans since it is an endotoxin. Unfortunately, other TLR4 ligands such as HMGB1 or heat shock proteins have weak adjuvant effects. Therefore, there is a need to identify novel, biocompatible, strong, TLR4 ligands. Methods 40S ribosomal protein S3 (RPS3) was screened through pull-down assay using TLR4. BMDCs from wild type (WT) and TLR4 knock-out mice were treated by RPS3 to identify the activation and maturation of DCs. T cell generation including memory T cells, tumor prevention, and treatment experiments were performed with BMDCs based vaccination. Also, human DCs originated from patients were treated by RPS3 to confirm the activation and maturation of DCs. Results In this study, we identified 40S ribosomal protein S3 (RPS3) through a pull-down assay using a variety of human cancer cell-derived proteins that could bind to TLR4. RPS3 was released from tumor cells following treatment with an anticancer drug, and it was shown that the released RPS3 binds to TLR4. Recombinant RPS3 induced maturation and activation of DCs, and following pulsing with tumor specific antigens, these DCs could be used as a vaccine to significantly increase tumor specific CD8+IFN-γ+ T cells, and provide both tumor prevention and tumor treatment effects. The effect of RPS3 on DC maturation and its utility as a vaccine were shown to be dependent on TLR4 using TLR4 knockout mice. Conclusions This study therefore proved that human cancer cell-derived RPS3, a novel TLR4 ligand, has great potential as an adjuvant in tumor-specific antigen DC-based vaccines. Electronic supplementary material The online version of this article (10.1186/s40425-019-0539-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyun Jin Park
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - Gun-Young Jang
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - Young Seob Kim
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - Jung Hwa Park
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - Sung Eun Lee
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - Manh-Cuong Vo
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Hwasun-gun, Jeollanam-do, 58128, South Korea
| | - Je-Jung Lee
- Hematology-Oncology, Chonnam National University Hwasun Hospital, Hwasun-gun, Jeollanam-do, 58128, South Korea
| | - Hee Dong Han
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - In Duk Jung
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea
| | - Tae Heung Kang
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea.
| | - Yeong-Min Park
- Department of Immunology, KU Open Innovation Center, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju, 274798, South Korea.
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Peng H, Zhao Y, Chen J, Huo J, Zhang Y, Xiao T. Knockdown of ribosomal protein S3 causes preimplantation developmental arrest in mice. Theriogenology 2019; 129:77-81. [PMID: 30826720 DOI: 10.1016/j.theriogenology.2019.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/09/2019] [Accepted: 02/22/2019] [Indexed: 01/05/2023]
Abstract
Ribosomal protein S3 (RpS3), a member of the ribosome 40S subunit, has conventional ribosomal function and additional extraribosomal functions. The aim of the present study was to analyze the expression and localization of RpS3 and its function in early embryogenesis in mice. RpS3 mRNA and protein were expressed in multiple mouse tissues. In the ovary, RpS3 protein was ubiquitously and highly expressed in oocytes and granulosa cells. After ovulation and fertilization, RpS3 mRNA and protein were detected in oocytes and preimplantation embryos. Furthermore, RpS3 protein was localized in the cytoplasm of oocytes and preimplantation embryos. Moreover, knockdown of RpS3 in zygotes led to a significantly decreased rate of blastocyst formation. These results provide the first evidence for a novel function of RpS3 in regulating early embryonic development in mice.
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Affiliation(s)
- Hui Peng
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China; University Key Lab for Integrated Chinese Traditional and Western Veterinary Medicine and Animal Healthcare in Fujian Province, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Yifan Zhao
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Jing Chen
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Jianchao Huo
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Yanyan Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China
| | - Tianfang Xiao
- College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, 350002, PR China.
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Li Q, Yin W, Li W, Zhang Z, Zhang X, Zhang XE, Cui Z. Encapsulating Quantum Dots within HIV-1 Virions through Site-Specific Decoration of the Matrix Protein Enables Single Virus Tracking in Live Primary Macrophages. NANO LETTERS 2018; 18:7457-7468. [PMID: 30398057 DOI: 10.1021/acs.nanolett.8b02800] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Labeling and imaging with quantum dots (QDs) provides powerful tools to visualize viral infection in living cells. Encapsulating QDs within virions represents a novel strategy for virus labeling. Here, we developed infectious HIV-1 virions encapsulating QDs through site-specific decoration of the viral matrix protein (MA) and used them to visualize early infection events in human primary macrophages by single-particle imaging. The MA protein was fused to a biotin acceptor peptide (BAP) tag, biotinylated, complexed with streptavidin-conjugated QDs in live cells, and incorporated into virions during virus assembly. The QD-encapsulated virions were tracked during infection of macrophages at a single particle level. The dynamic dissociation of MA and Vpr was also tracked in real time, and the results demonstrated that MA has multiple dynamic behaviors and functions during virus entry. More importantly, we tracked the dynamic interplay of QD-encapsulated virions with cellular mitochondria in live primary macrophages. We also found that HIV-1 can induce fission of mitochondria during the early phases of infection. In summary, we have constructed a type of QD-encapsulated virus particle and used this technology to further our understanding of the early events of HIV-1 infection.
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Affiliation(s)
- Qin Li
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan , People's Republic of China
- Engineering Research Center of Industrial Microbiology, Ministry of Education, College of Life Sciences , Fujian Normal University , Fujian 350007 , People's Republic of China
| | - Wen Yin
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Wei Li
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Zhiping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan , People's Republic of China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology , Chinese Academy of Sciences , Wuhan , People's Republic of China
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Molavi G, Samadi N, Hosseingholi EZ. The roles of moonlight ribosomal proteins in the development of human cancers. J Cell Physiol 2018; 234:8327-8341. [PMID: 30417503 DOI: 10.1002/jcp.27722] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
"Moonlighting protein" is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.
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Affiliation(s)
- Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Knockout of Mpv17-Like Protein (M-LPH) Gene in Human Hepatoma Cells Results in Impairment of mtDNA Integrity through Reduction of TFAM, OGG1, and LIG3 at the Protein Levels. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6956414. [PMID: 30310528 PMCID: PMC6166373 DOI: 10.1155/2018/6956414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/18/2018] [Accepted: 08/05/2018] [Indexed: 12/05/2022]
Abstract
Human Mpv17-like protein (M-LPH) has been suggested to participate in prevention of mitochondrial dysfunction caused by mitochondrial DNA (mtDNA) damage. To clarify the molecular mechanism of M-LPH function, we knocked out M-LPH in human hepatoma HepG2 using CRISPR-Cas9 technology. An increase in mtDNA damage in M-LPH-KO HepG2 cells was demonstrated by PCR-based quantitation and 8-hydroxy-2′-deoxyguanosine (8-OHdG) measurement. Furthermore, confocal immunofluorescence analysis and Western blot analysis of mitochondrial extracts demonstrated that M-LPH-KO caused reductions in the protein levels of mitochondrial transcription factor A (TFAM), an essential factor for transcription and maintenance of mtDNA, and two DNA repair enzymes, 8-oxoguanine DNA glycosylase (OGG1) and DNA ligase 3 (LIG3), both involved in mitochondrial base excision repair (BER). Accordingly, it was suggested that the increase in mtDNA damage was due to a cumulative effect of mtDNA instability resulting from deficiencies of TFAM and diminished ability for BER arising from deficiencies in BER-related enzymes. These findings suggest that M-LPH could be involved in the maintenance of mtDNA, and therefore mitochondrial function, by protecting proteins essential for mtDNA stability and maintenance, in an integrated manner.
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Pereira HABDS, Dionizio AS, Araujo TT, Fernandes MDS, Iano FG, Buzalaf MAR. Proposed mechanism for understanding the dose- and time-dependency of the effects of fluoride in the liver. Toxicol Appl Pharmacol 2018; 358:68-75. [PMID: 30217653 DOI: 10.1016/j.taap.2018.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/22/2018] [Accepted: 09/08/2018] [Indexed: 12/25/2022]
Abstract
Fluoride (F) can induce changes in the expression of several liver proteins. It is suggested that these changes are dose- and time-dependent. The objective of this study was to analyze the effect of different F concentrations and exposure times to this ion on the pattern of protein expression in the liver of rats. Thirt-six 21-day-old male Wistar rats were divided into 2 groups (n = 18) according to the treatment duration (20 or 60 days). Each of these groups was then divided into 3 subgroups (n = 6) according to the concentration of F administered in drinking water, as follows: 0 mg/L (control), 15 mg/L or 50 mg/L. After the experiment periods, the animals were anesthetized and the liver and blood were collected. F was analyzed in plasma and liver. Part of the liver was fixed for histological analysis. Liver proteins were extracted and prepared for quantitative label-free mass spectrometry analysis. F concentrations in plasma and liver were significantly higher in the group treated with 50 mg /L in comparison with control, regardless the time of exposure. Histological alterations in the liver were more evident in the subgroups treated for 20 days. The proteomic analysis revealed changes in proteins related to endoplasmic reticulum and mitochondrial oxidative stress, mitochondrial alteration, apoptosis and cellular respiration upon exposure to F. The results reinforce previous findings showing that the effects of F in the liver are dose- and time-dependent and provide the molecular basis for understanding the evolution of these effects.
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Affiliation(s)
- Heloisa Aparecida Barbosa da Silva Pereira
- Department of Genetics and Evolution, Center of Biological Sciences and the Health, Federal University of São Carlos, Washington Luis, km 235, 13560-970 São Carlos, São Paulo, Brazil
| | - Aline Salgado Dionizio
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Tamara Teodoro Araujo
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Mileni da Silva Fernandes
- Department of Genetics and Evolution, Center of Biological Sciences and the Health, Federal University of São Carlos, Washington Luis, km 235, 13560-970 São Carlos, São Paulo, Brazil
| | - Flávia Godoy Iano
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil
| | - Marília Afonso Rabelo Buzalaf
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Al. Octávio Pinheiro Brisolla, 9-75, 17012-901 Bauru, São Paulo, Brazil.
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RPS3A positively regulates the mitochondrial function of human periaortic adipose tissue and is associated with coronary artery diseases. Cell Discov 2018; 4:52. [PMID: 30131868 PMCID: PMC6102269 DOI: 10.1038/s41421-018-0041-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/27/2018] [Accepted: 05/29/2018] [Indexed: 02/07/2023] Open
Abstract
Pericardial adipose tissue, which comprises both epicardial adipose tissue (EAT) and paracardial adipose tissue (PAT), has recently been recognized as a novel factor in the pathophysiology of cardiovascular diseases, especially coronary artery disease (CAD). The goal of this study was to evaluate differences in the brown-like characteristic and proteome among human EAT, PAT, and subcutaneous adipose tissue (SAT) to identify candidate molecules causing CAD. Uncoupling protein 1 (UCP-1) and other brown-related proteins were highly expressed in pericardial adipose tissue but was weakly expressed in SAT from the same non-CAD patient. Moreover, pericardial adipose tissues displayed a higher thermogenesis than SAT. However, brown-related genes were lower in CAD pericardial fat. Remarkably, there were lower levels of metabolic enzymes involved in glycolysis, tricarboxylic acid cycle, and fatty acid metabolism in pericardial adipose tissues of CAD. EAT is an organ adjacent to aortic root without anatomy barriers, which differs from PAT. We found that the expression of ribosomal protein S3A (RPS3A) was decreased in human EAT as well as in mouse perivascular adipose tissue (PVAT). Knockdown of RPS3A significantly inhibited adipocyte differentiation in preadipocytes and impaired the function of mitochondria in mature adipocytes. Moreover, RPS3A knockdown in mouse periaortic adipose tissue impaired browning of PVAT, accelerated vascular inflammation, and atherosclerosis progression. Mechanistically, RPS3A can migrate to the mitochondria to maintain the function of brown adipocytes. These findings provide compelling evidence that RPS3A was a key factor for modulating the brown fat-specific gene UCP-1 and carbon metabolic enzymes in EAT for preventing CAD.
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Abstract
PURPOSE OF REVIEW Hematopoietic stem cells (HSCs) produce mature blood cells throughout lifetime. Natural genetic diversity offers an important yet largely untapped reservoir for deciphering regulatory mechanisms of HSCs and hematopoiesis. In this review, we explore the role of latexin, identified by natural variation, in regulating homeostatic and stress hematopoiesis, unravel the underlying signaling pathways, and propose its therapeutic implication. RECENT FINDINGS Latexin acts endogenously in HSCs to negatively regulate their population size by enhancing apoptosis and by decreasing self-renewal. Deletion of latexin in vivo increases HSC repopulation capacity and survival, expands the entire hematopoietic system, and mitigates myelosuppression. Latexin inactivation downregulates thrombospondin 1 (Thbs1). It inhibits nuclear translocation of ribosomal protein subunit 3 (Rps3), a novel latexin-binding protein, and sensitizes hematopoietic cells to radiation-induced cell death. However, how latexin-Rps3 pathway regulates Thbs1 transcription is unclear. Latexin is downregulated in cancer cells because of promoter hypermethylation, but latexin-depleted mice do not inherently develop hematologic malignancies even with aging. The mechanism of action of latexin in tumorigenesis remains largely unknown. SUMMARY Understanding how latexin regulates HSC survival, self-renewal, and stress response will advance our knowledge of HSC biology. It will facilitate the development of a novel therapeutic strategy for hematopoietic regeneration and cancer treatment.
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Chen L, Chen L, Zhang X, Liu T, Niu S, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Identification of miRNAs that regulate silique development in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:106-117. [PMID: 29606207 DOI: 10.1016/j.plantsci.2018.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/05/2018] [Accepted: 01/22/2018] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate these roles. Four small RNA libraries from siliques in an early stage of development were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known and 394 novel miRNAs. Expression analyses revealed that 17 miRNAs were differentially expressed in LS and SS lines. Furthermore, through degradome sequencing, we identified 522 cleavage events. Correlation analysis of the differentially expressed miRNAs and their targets suggested that miR159 and miR319 represses cell proliferation and miR160 regulates auxin signal transduction to control silique length. Additionally, the upregulation of miR2111, miR399, miR827, and miR408 reflected restricted silique development due to inorganic phosphate/copper deficiency. More significantly, high expression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length might be regulated via an auxin-response pathway.
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Affiliation(s)
- Li Chen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lei Chen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Xiangxiang Zhang
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingting Liu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Sailun Niu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, PR China.
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Scott DD, Oeffinger M. Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol 2016; 94:419-432. [PMID: 27673355 DOI: 10.1139/bcb-2016-0068] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle, and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations. Numerous nucleolar proteins have been identified that, upon sensing nucleolar stress, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and (or) NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis, and therapeutic targeting of NPM1 and NCL.
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Affiliation(s)
- Daniel D Scott
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
| | - Marlene Oeffinger
- a Laboratory of RNP Biochemistry, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- b Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, QC H3A 2A3, Canada
- c Département de biochimie et médecine moléculaire, Faculté de Médecine, Université de Montréal, QC H3T 1J4, Canada
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Xing Y, Zhang J, Lu L, Li D, Wang Y, Huang S, Li C, Zhang Z, Li J, Meng A. Identification of hub genes of pneumocyte senescence induced by thoracic irradiation using weighted gene co‑expression network analysis. Mol Med Rep 2015; 13:107-16. [PMID: 26572216 PMCID: PMC4686054 DOI: 10.3892/mmr.2015.4566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 10/14/2015] [Indexed: 01/03/2023] Open
Abstract
Irradiation commonly causes pneumocyte senescence, which may lead to severe fatal lung injury characterized by pulmonary dysfunction and respiratory failure. However, the molecular mechanism underlying the induction of pneumocyte senescence by irradiation remains to be elucidated. In the present study, weighted gene co-expression network analysis (WGCNA) was used to screen for differentially expressed genes, and to identify the hub genes and gene modules, which may be critical for senescence. A total of 2,916 differentially expressed genes were identified between the senescence and non-senescence groups following thoracic irradiation. In total, 10 gene modules associated with cell senescence were detected, and six hub genes were identified, including B-cell scaffold protein with ankyrin repeats 1, translocase of outer mitochondrial membrane 70 homolog A, actin filament-associated protein 1, Cd84, Nuf2 and nuclear factor erythroid 2. These genes were markedly associated with cell proliferation, cell division and cell cycle arrest. The results of the present study demonstrated that WGCNA of microarray data may provide further insight into the molecular mechanism underlying pneumocyte senescence.
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Affiliation(s)
- Yonghua Xing
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Junling Zhang
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Lu Lu
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Deguan Li
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Yueying Wang
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Song Huang
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Chengcheng Li
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Zhubo Zhang
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Jianguo Li
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
| | - Aimin Meng
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science and Peking Union Medical College, Nankai, Tianjin 300192, P.R. China
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Low T3 State Is Correlated with Cardiac Mitochondrial Impairments after Ischemia Reperfusion Injury: Evidence from a Proteomic Approach. Int J Mol Sci 2015; 16:26687-705. [PMID: 26561807 PMCID: PMC4661832 DOI: 10.3390/ijms161125973] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/13/2015] [Accepted: 10/26/2015] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are major determinants of cell fate in ischemia/reperfusion injury (IR) and common effectors of cardio-protective strategies in cardiac ischemic disease. Thyroid hormone homeostasis critically affects mitochondrial function and energy production. Since a low T3 state (LT3S) is frequently observed in the post infarction setting, the study was aimed to investigate the relationship between 72 h post IR T3 levels and both the cardiac function and the mitochondrial proteome in a rat model of IR. The low T3 group exhibits the most compromised cardiac performance along with the worst mitochondrial activity. Accordingly, our results show a different remodeling of the mitochondrial proteome in the presence or absence of a LT3S, with alterations in groups of proteins that play a key role in energy metabolism, quality control and regulation of cell death pathways. Overall, our findings highlight a relationship between LT3S in the early post IR and poor cardiac and mitochondrial outcomes, and suggest a potential implication of thyroid hormone in the cardio-protection and tissue remodeling in ischemic disease.
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