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Lee S, Woo WS, Kim J, Jin Y, Lee JW, Seo JS, Kwon MG, Lee JH, Park CI, Shim SH. The residue of salinomycin in the muscles of olive flounder (Paralichthys olivaceus) and black rockfish (Sebastes Schlegeli) after oral administration analyzed by LC-Tandem-MS. BMC Vet Res 2024; 20:24. [PMID: 38216988 PMCID: PMC10785415 DOI: 10.1186/s12917-023-03867-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/24/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Salinomycin, an antibiotic, have potential as a veterinary drug for fish due to its anti-parasitic activity against several fish parasites. Thus the residual levels of salinomycin in muscles of two significant aquaculture species in Korea, olive flounder and black rockfish, were analyzed using HPLC-MS-MS. RESULTS The proper method to analyze the residual salinomycin in fish muscles using LC-MS-MS was settled and the method was validated according to CODEX guidelines. The residues in three distinct groups for two fish species were analyzed using the matrix match calibration curves at points of five different times following oral administration. After oral administration, salinomycin rapidly breaks down in both olive flounder and black rockfish. After 7th days, the average residue in all groups of two fish spp. decreased below limit of quantitation (LOQ). CONCLUSION Due to low residue levels in fish muscles, salinomycin may therefore be a treatment that is safe for both fish and humans. This result could contribute to establishment of MRL (minimal residual limit) for approval of salinomycin for use in aquaculture.
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Affiliation(s)
- Seungjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won-Sik Woo
- Department of Marine Biology & Aquaculture, Institute of Marine Industry, College of Marine Science, Gyeongsang National University, Tongyeong, 53064, Republic of Korea
| | - Jaekyeong Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeongwoon Jin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin Woo Lee
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea
| | - Jung-Soo Seo
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, 337 Haeyang-ro, Yeongdo-gu, Busan, 49111, Republic of Korea
| | - Mun-Gyeong Kwon
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, 337 Haeyang-ro, Yeongdo-gu, Busan, 49111, Republic of Korea
| | - Ji-Hoon Lee
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, 337 Haeyang-ro, Yeongdo-gu, Busan, 49111, Republic of Korea.
| | - Chan-Il Park
- Department of Marine Biology & Aquaculture, Institute of Marine Industry, College of Marine Science, Gyeongsang National University, Tongyeong, 53064, Republic of Korea.
| | - Sang Hee Shim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Leiner J, Pellissier V, König S, Hohenstein S, Ueberham L, Nachtigall I, Meier-Hellmann A, Kuhlen R, Hindricks G, Bollmann A. Machine learning-derived prediction of in-hospital mortality in patients with severe acute respiratory infection: analysis of claims data from the German-wide Helios hospital network. Respir Res 2022; 23:264. [PMID: 36151525 PMCID: PMC9502925 DOI: 10.1186/s12931-022-02180-w] [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: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Severe acute respiratory infections (SARI) are the most common infectious causes of death. Previous work regarding mortality prediction models for SARI using machine learning (ML) algorithms that can be useful for both individual risk stratification and quality of care assessment is scarce. We aimed to develop reliable models for mortality prediction in SARI patients utilizing ML algorithms and compare its performances with a classic regression analysis approach. METHODS Administrative data (dataset randomly split 75%/25% for model training/testing) from years 2016-2019 of 86 German Helios hospitals was retrospectively analyzed. Inpatient SARI cases were defined by ICD-codes J09-J22. Three ML algorithms were evaluated and its performance compared to generalized linear models (GLM) by computing receiver operating characteristic area under the curve (AUC) and area under the precision-recall curve (AUPRC). RESULTS The dataset contained 241,988 inpatient SARI cases (75 years or older: 49%; male 56.2%). In-hospital mortality was 11.6%. AUC and AUPRC in the testing dataset were 0.83 and 0.372 for GLM, 0.831 and 0.384 for random forest (RF), 0.834 and 0.382 for single layer neural network (NNET) and 0.834 and 0.389 for extreme gradient boosting (XGBoost). Statistical comparison of ROC AUCs revealed a better performance of NNET and XGBoost as compared to GLM. CONCLUSION ML algorithms for predicting in-hospital mortality were trained and tested on a large real-world administrative dataset of SARI patients and showed good discriminatory performances. Broad application of our models in clinical routine practice can contribute to patients' risk assessment and quality management.
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Affiliation(s)
- Johannes Leiner
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany. .,Real World Evidence and Health Technology Assessment, Helios Health Institute, Berlin, Germany.
| | - Vincent Pellissier
- Real World Evidence and Health Technology Assessment, Helios Health Institute, Berlin, Germany
| | - Sebastian König
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany.,Real World Evidence and Health Technology Assessment, Helios Health Institute, Berlin, Germany
| | - Sven Hohenstein
- Real World Evidence and Health Technology Assessment, Helios Health Institute, Berlin, Germany
| | - Laura Ueberham
- Clinic for Cardiology, University Hospital Leipzig, Leipzig, Germany
| | - Irit Nachtigall
- Department of Infectious Diseases and Infection Prevention, Helios Hospital Emil-von-Behring, Berlin, Germany.,Institute of Hygiene and Environmental Medicine, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | | | | | - Gerhard Hindricks
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany
| | - Andreas Bollmann
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany.,Real World Evidence and Health Technology Assessment, Helios Health Institute, Berlin, Germany
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The Isolation and Full-Length Transcriptome Sequencing of a Novel Nidovirus and Response of Its Infection in Japanese Flounder (Paralichthys olivaceus). Viruses 2022; 14:v14061216. [PMID: 35746687 PMCID: PMC9230003 DOI: 10.3390/v14061216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023] Open
Abstract
A novel nidovirus, CSBV Bces-Po19, was isolated from the marine fish, Japanese flounder (Paralichthys olivaceus). The viral genome was 26,597 nucleotides long and shared 98.62% nucleotide identity with CSBV WHQSR4345. PacBio Sequel and Illumina sequencing were used to perform full-length transcriptome sequencing on CSBV Bces-Po19-sensitive (S) and -resistant (R) Japanese flounder. The results of negative staining revealed bacilliform and spherical virions. There were in total 1444 different genes between CSBV Bces-Po19 S and R groups, with 935 being up-regulated and 513 being down-regulated. Metabolism-, immune-, and RNA-related pathways were significantly enriched. Furthermore, CSBV Bces-Po19 infection induced alternative splicing (AS) events in Japanese flounder; the S group had a higher numbers of AS events (12,352) than the R group (11,452). The number of long non-coding RNA (lncRNA) in the S group, on the other hand, was significantly lower than in the R group. In addition to providing valuable information that sheds more light on CSBV Bces-Po19 infection, these research findings provide further clues for CSBV Bces-Po19 prevention and treatment.
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4
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Wang R, Huang Y, Shi Y, Zhao Z. Transcriptome Analysis of the Kidney of Obscure Puffer, Takifugu obscurus, Challenged with Poly(I:C). Zoolog Sci 2022; 39:198-205. [DOI: 10.2108/zs210070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/12/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Ruixia Wang
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu 210098, China
| | - Ying Huang
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu 210098, China
| | - Yan Shi
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu 210098, China
| | - Zhe Zhao
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu 210098, China
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5
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Sharma KB, Chhabra S, Aggarwal S, Tripathi A, Banerjee A, Yadav AK, Vrati S, Kalia M. Proteomic landscape of Japanese encephalitis virus-infected fibroblasts. J Gen Virol 2021; 102. [PMID: 34546869 DOI: 10.1099/jgv.0.001657] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Advances in proteomics have enabled a comprehensive understanding of host-pathogen interactions. Here we have characterized Japanese encephalitis virus (JEV) infection-driven changes in the mouse embryonic fibroblast (MEF) proteome. Through tandem mass tagging (TMT)-based mass spectrometry, we describe changes in 7.85 % of the identified proteome due to JEV infection. Pathway enrichment analysis showed that proteins involved in innate immune sensing, interferon responses and inflammation were the major upregulated group, along with the immunoproteasome and poly ADP-ribosylation proteins. Functional validation of several upregulated anti-viral innate immune proteins, including an active cGAS-STING axis, was performed. Through siRNA depletion, we describe a crucial role of the DNA sensor cGAS in restricting JEV replication. Further, many interferon-stimulated genes (ISGs) were observed to be induced in infected cells. We also observed activation of TLR2 and inhibition of TLR2 signalling using TLR1/2 inhibitor CU-CPT22-blocked production of inflammatory cytokines IL6 and TNF-α from virus-infected N9 microglial cells. The major proteins that were downregulated by infection were involved in cell adhesion (collagens), transport (solute carrier and ATP-binding cassette transporters), sterol and lipid biosynthesis. Several collagens were found to be transcriptionally downregulated in infected MEFs and mouse brain. Collectively, our data provide a bird's-eye view into how fibroblast protein composition is rewired following JEV infection.
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Affiliation(s)
- Kiran Bala Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.,Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Simran Chhabra
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Suruchi Aggarwal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Aarti Tripathi
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Arup Banerjee
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.,Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Amit Kumar Yadav
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.,Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Manjula Kalia
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.,Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
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6
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Salem AZ, Medhat D, Fathy SA, Mohamed MR, El-Khayat Z, El-Daly SM. Indole glucosinolates exhibit anti-inflammatory effects on Ehrlich ascites carcinoma cells through modulation of inflammatory markers and miRNAs. Mol Biol Rep 2021; 48:6845-6855. [PMID: 34476740 DOI: 10.1007/s11033-021-06683-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Nuclear factor-κB (NF-κB) has been identified as the major link between inflammation and cancer. Natural agents that inhibit this pathway are essential in attenuating inflammation induced by cancer or chemotherapeutic drugs. High intake of Brassicaceae vegetables has been determined to modulate essential pathways related to chronic diseases. In this study, we investigated the anti-proliferative and anti-inflammatory effects of the indole glucosinolates; indole-3-carbinol (I3C) and its metabolite 3,3-diindolylmethane (DIM) on the inflammatory biomarkers and miRNAs controlling the NF-κB pathway. METHODS AND RESULTS In our study, we inoculated Ehrlich ascites carcinoma (EAC) cells in female albino mice, which increased their packed cell volume and induced a significant increase in the levels of several cytokines and inflammatory biomarkers (NF-κB IL-6, IL-1b, TNF-α, and NO). A significant elevation in inflammatory-medicated miRNAs (miR-31 and miR-21) was also noted. Treatment with 5-fluorouracil (5-FU) significantly reduced packed cell volume and viable cell count. However, it was accompanied by a significant increase in the levels of inflammatory markers and expression of miR-31 and miR-21. Nevertheless, although treatment with indoles (I3C and DIM) significantly reduced the packed cell volume and viable cell count, their prominent effect was the marked reduction of all inflammatory biomarkers compared to both the EAC untreated group and the EAC group treated with 5-FU. Moreover, the anti-inflammatory effect of I3C or DIM was accompanied by a significant decrease in the expression of miR-31 and miR-21. CONCLUSION Our findings have; therefore, revealed that I3C and DIM have strong anti-inflammatory effects, implying that their use as a co-treatment with chemotherapeutic drugs can effectively improve the anti-tumor effect of chemotherapeutic drugs.
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Affiliation(s)
- Ayah Z Salem
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Dalia Medhat
- Medical Biochemistry Department, Medical Research Division, National Research Centre, 33 El Buhouth St. Dokki, Cairo, 12622, Egypt
| | - Shadia A Fathy
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed R Mohamed
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Zakaria El-Khayat
- Medical Biochemistry Department, Medical Research Division, National Research Centre, 33 El Buhouth St. Dokki, Cairo, 12622, Egypt
| | - Sherien M El-Daly
- Medical Biochemistry Department, Medical Research Division, National Research Centre, 33 El Buhouth St. Dokki, Cairo, 12622, Egypt. .,Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt.
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7
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Temporal dynamics of eye movements and attentional modulation in perceptual judgments of structure-from-motion (SFM). ACTA PSYCHOLOGICA SINICA 2021. [DOI: 10.3724/sp.j.1041.2021.00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Esmaeili A, Hosseini S, Baghaban Eslaminejad M. Engineered-extracellular vesicles as an optimistic tool for microRNA delivery for osteoarthritis treatment. Cell Mol Life Sci 2021; 78:79-91. [PMID: 32601714 PMCID: PMC11072722 DOI: 10.1007/s00018-020-03585-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 06/13/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
Worldwide, osteoarthritis (OA) is one of the most common chronic diseases. In OA, profiling gene expression changes occur and cartilage tissue homeostasis is lost. Suggestions for OA treatment include regulation of gene expressions via the use of microRNAs (miRNAs). However, problems exist with the use of miRNAs, the most important of which is the delivery of sufficient amounts of effective miRNAs to save cartilage tissue. The engineering of extracellular vesicles (EVs) with the use of advanced techniques would be an efficient OA treatment. Therefore, we discuss the importance of miRNAs in terms of cartilage tissue regeneration and review recent advances in production of enriched EVs and miRNA delivery by EVs for future clinical applications.
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Affiliation(s)
- Abazar Esmaeili
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Samaneh Hosseini
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Cell Engineering, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mohamadreza Baghaban Eslaminejad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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9
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Liyanage TD, Nikapitiya C, Lee J, De Zoysa M. Molecular insight into regulation of miRNAs in the spleen of zebrafish (Danio rerio) upon pathogenic Streptococcus parauberis infection. FISH & SHELLFISH IMMUNOLOGY 2020; 106:898-909. [PMID: 32889099 DOI: 10.1016/j.fsi.2020.08.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) constitute a group of small non-coding RNAs (~22 nucleotides) and one of their main functions is to regulate the immune responses. Gram-positive bacterium, Streptococcus parauberis is the main causative agent of "Streptococcosis" in wide range of fish species. In this study, we performed high throughput sequencing analysis to identify the miRNA profile against S. parauberis infection in the spleen of zebrafish (Danio rerio). Overall, 349 known and 151 novel miRNAs were discovered. Among them, 12 known miRNAs (dre-miR-34b, dre-miR-135a, dre-miR-200b-5p, dre-miR-146b, dre-miR-31, dre-miR-17a-3p, dre-miR-222a-3p, dre-miR-731, dre-miR-301b-3p and dre-miR-30a-3p) and 9 novel miRNAs were differentially expressed (DE) in the spleen of S. parauberis challenged zebrafish. The identified 12 DE miRNAs were predicted to regulate 721 target genes. We confirmed the miRNA expression results by validating selected known and novel DE miRNAs using qRT-PCR. Gene Ontology (GO), Kyoto Encyclopedia of Genes (KEGG) pathway analysis and miRNA-mRNA interactions implies that specific target genes of DE miRNAs are associated with immune responses. The enriched pathways included Toll-like receptor (TLR), C-type lectin, NOD-like receptor, and RIG-I-like receptor signaling pathways, etc. Especially, dre-miR-200b-5p, dre-miR-146b, dre-miR-731, dre-miR-222a-3p, and dre-miR-34b were able to target potential immune-related genes such as il10, irak1, traf6, hspa8 and ikbke upon S. parauberis challenge. Thus, overall results could lay a foundation to understand the underlying immune regulatory role of miRNAs in response to pathogenic S. parauberis infection in teleosts.
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Affiliation(s)
- T D Liyanage
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu Daejeon, 34134, Republic of Korea
| | - Chamilani Nikapitiya
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu Daejeon, 34134, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province 63243, Republic of Korea
| | - Mahanama De Zoysa
- College of Veterinary Medicine, Chungnam National University, Yuseong-gu Daejeon, 34134, Republic of Korea.
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10
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Fulzele S, Sahay B, Yusufu I, Lee TJ, Sharma A, Kolhe R, Isales CM. COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile. Aging Dis 2020; 11:509-522. [PMID: 32489698 PMCID: PMC7220294 DOI: 10.14336/ad.2020.0428] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023] Open
Abstract
The World health organization (WHO) declared Coronavirus disease 2019 (COVID-19) a global pandemic and a severe public health crisis. Drastic measures to combat COVID-19 are warranted due to its contagiousness and higher mortality rates, specifically in the aged patient population. At the current stage, due to the lack of effective treatment strategies for COVID-19 innovative approaches need to be considered. It is well known that host cellular miRNAs can directly target both viral 3'UTR and coding region of the viral genome to induce the antiviral effect. In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. We found 848 common miRNAs targeting the SARS genome and 873 common microRNAs targeting the COVID-19 genome. Out of a total of 848 miRNAs from SARS, only 558 commonly present in all COVID-19 isolates. Interestingly, 315 miRNAs are unique for COVID-19 isolates and 290 miRNAs unique to SARS. We also noted that out of 29 COVID-19 isolates, 19 isolates have identical miRNA targets. The COVID-19 isolates, Netherland (EPI_ISL_422601), Australia (EPI_ISL_413214), and Wuhan (EPI_ISL_403931) showed six, four, and four unique miRNAs targets, respectively. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Recent studies also suggested that some of the human miRNAs targeting COVID-19 decreased with aging and underlying conditions. GO and KEGG identified impaired signaling pathway may be due to low abundance miRNA which might be one of the contributing factors for the increasing severity and mortality in aged individuals and with other underlying conditions. Further, in vitro and in vivo studies are needed to validate some of these targets and identify potential therapeutic targets.
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Affiliation(s)
- Sadanand Fulzele
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
| | - Bikash Sahay
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA.
| | - Ibrahim Yusufu
- Department of Medicine, Augusta University, Augusta, GA, USA.
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Ravindra Kolhe
- Departments of Pathology, Augusta University, Augusta, GA 30912, USA
| | - Carlos M Isales
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
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Ning X, Sun L. Gene network analysis reveals a core set of genes involved in the immune response of Japanese flounder (Paralichthys olivaceus) against Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2020; 98:800-809. [PMID: 31743762 DOI: 10.1016/j.fsi.2019.11.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/30/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine fish cultured in north Asia. Vibrio anguillarum is a severe bacterial pathogen to Japanese flounder and many other aquaculture species. In order to understand the immune response of flounder during bacterial infection, we systematically examined the transcriptome profiles of flounder spleen at three time points after V. anguillarum challenge. More than one billion high quality reads were obtained, approximately 80.70% of which were successfully mapped to the reference genome of flounder. A total of 6060, 4688 and 4235 differentially expressed genes (DEGs) were captured at 6, 12 and 24-h post-infection, respectively. The DEGs exhibited dynamic changes in expression and were assigned into four different profiles based on expression trend. GO and KEGG analysis showed that the DEGs were enriched in various immune-related terms, including response to stimulation, immune system and pathways of cytokine-cytokine receptor interaction, Jak-STAT signaling and Toll-like receptor signaling. Furthermore, a network of highly interactive DEGs involved in 11 immune-related pathways was detected by utilizing the weighted co-expressing network analysis (WGCNA). Accordingly, 26 hub genes were discovered that constituted an elaborate immune regulatory network and functioned mainly in pathogen recognition, antigen processing, and molecular signaling. The results of this study provided the first systematical transcriptome profile of flounder in association with V. anguillarum infection and can serve as a valuable resource of target genes for future studies on the molecular mechanisms underlying the immune defense of flounder against bacterial infection.
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Affiliation(s)
- Xianhui Ning
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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