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Szydełko J, Czop M, Petniak A, Lenart-Lipińska M, Kocki J, Zapolski T, Matyjaszek-Matuszek B. Identification of plasma miR-4505, miR-4743-5p and miR-4750-3p as novel diagnostic biomarkers for coronary artery disease in patients with type 2 diabetes mellitus: a case-control study. Cardiovasc Diabetol 2024; 23:278. [PMID: 39080630 PMCID: PMC11287982 DOI: 10.1186/s12933-024-02374-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/23/2024] [Indexed: 08/03/2024] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) and coronary artery disease (CAD) are commonly coexisting clinical entities with still growing incidence worldwide. Recently, circulating microRNAs (miRNAs) have emerged as novel molecular players in cardiometabolic diseases. This study aimed to identify a specific miRNA signature as a candidate biomarker for CAD in T2DM and to delineate potential miRNA-dependent mechanisms contributing to diabetic atherosclerosis. METHODS A total of 38 plasma samples from T2DM patients with and without CAD, CAD patients and healthy controls were collected for expression profiling of 2,578 miRNAs using microarrays. To investigate the regulatory role of differentially expressed (DE)-miRNA target genes, functional annotation and pathway enrichment analyses were performed utilizing multiple bioinformatics tools. Then, protein-protein interaction networks were established leveraging the STRING database in Cytoscape software, followed by cluster analysis and hub gene identification. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was carried out for microarray data validation in the larger replication cohort of 94 participants. Receiver operating characteristic analysis was applied to evaluate the diagnostic values of miRNAs. Multivariate logistic regression analysis was used to develop miRNA-based diagnostic models. RESULTS In the discovery stage, overexpression of hsa-miR-4505, hsa-miR-4743-5p, hsa-miR-6846-5p, and down-regulation of hsa-miR-3613-3p, hsa-miR-4668-5p, hsa-miR-4706, hsa-miR-6511b-5p, hsa-miR-6750-5p, hsa-miR-4750-3p, hsa-miR-320e, hsa-miR-4717-3p, hsa-miR-7850-5p were detected in T2DM-CAD patients. The DE-miRNA target genes were significantly enriched in calcium ion binding, regulation of actin cytoskeleton, and gene expression. hsa-miR-4505, hsa-miR-4743-5p, and hsa-miR-4750-3p were found to be involved in fatty acid metabolism, leukocyte transendothelial migration, and neurotrophin signaling pathway. Dysregulation of hsa-miR-4505, hsa-miR-4743-5p, and hsa-miR-4750-3p in T2DM-CAD patients compared with T2DM subjects and controls (all p < 0.001) was further confirmed by RT-qPCR. All validated miRNAs demonstrated good discriminatory values for T2DM-CAD (AUC = 0.833-0.876). The best performance in detecting CAD in T2DM was achieved for a combination of three miRNAs (AUC = 0.959, 100% sensitivity, 86.67% specificity). CONCLUSIONS Our study revealed a unique profile of plasma-derived miRNAs in T2DM patients with CAD. Potential miRNA-regulated pathways were also identified, exploring the underlying pathogenesis of CAD in T2DM. We developed a specific three-miRNA panel of hsa-miR-4505, hsa-miR-4743-5p and hsa-miR-4750-3p, that could serve as a novel non-invasive biomarker for CAD in patients with T2DM.
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Affiliation(s)
- Joanna Szydełko
- Department of Endocrinology, Diabetology and Metabolic Diseases, Medical University of Lublin, Jaczewskiego 8, 20-090, Lublin, Poland.
| | - Marcin Czop
- Department of Clinical Genetics, Medical University of Lublin, Radziwillowska 11, 20-080, Lublin, Poland
| | - Alicja Petniak
- Department of Clinical Genetics, Medical University of Lublin, Radziwillowska 11, 20-080, Lublin, Poland
| | - Monika Lenart-Lipińska
- Department of Endocrinology, Diabetology and Metabolic Diseases, Medical University of Lublin, Jaczewskiego 8, 20-090, Lublin, Poland
| | - Janusz Kocki
- Department of Clinical Genetics, Medical University of Lublin, Radziwillowska 11, 20-080, Lublin, Poland
| | - Tomasz Zapolski
- Department of Cardiology, Medical University of Lublin, Jaczewskiego 8, 20-090, Lublin, Poland
| | - Beata Matyjaszek-Matuszek
- Department of Endocrinology, Diabetology and Metabolic Diseases, Medical University of Lublin, Jaczewskiego 8, 20-090, Lublin, Poland
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Nguyen CM, Sallam M, Islam MS, Clack K, Soda N, Nguyen NT, Shiddiky MJA. Placental Exosomes as Biomarkers for Maternal Diseases: Current Advances in Isolation, Characterization, and Detection. ACS Sens 2023. [PMID: 37449399 DOI: 10.1021/acssensors.3c00689] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Serving as the interface between fetal and maternal circulation, the placenta plays a critical role in fetal growth and development. Placental exosomes are small membrane-bound extracellular vesicles released by the placenta during pregnancy. They contain a variety of biomolecules, including lipids, proteins, and nucleic acids, which can potentially be biomarkers of maternal diseases. An increasing number of studies have demonstrated the utility of placental exosomes for the diagnosis and monitoring of pathological conditions such as pre-eclampsia and gestational diabetes. This suggests that placental exosomes may serve as new biomarkers in liquid biopsy analysis. This review provides an overview of the current understanding of the biological function of placental exosomes and their potential as biomarkers of maternal diseases. Additionally, this review highlights current barriers and the way forward for standardization and validation of known techniques for exosome isolation, characterization, and detection. Finally, microfluidic devices for exosome research are discussed.
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Affiliation(s)
- Cong Minh Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Mohamed Sallam
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Md Sajedul Islam
- School of Medicine and Dentistry, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Kimberley Clack
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Narshone Soda
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, NSW 2800, Australia
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Ju Y, Choi GE, Lee MW, Jeong M, Kwon H, Kim DH, Kim J, Jin H, Lee KE, Hyun KY, Jang A. Identification of miR-143-3p as a diagnostic biomarker in gastric cancer. BMC Med Genomics 2023; 16:135. [PMID: 37328880 PMCID: PMC10273760 DOI: 10.1186/s12920-023-01554-3] [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: 01/20/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is among the most common types of gastrointestinal cancers and has a high incidence and mortality around the world. To suppress the progression of GC, it is essential to develop diagnostic markers. MicroRNAs regulate GC development, but a clearer insight into their role is needed before they can be applied as a molecular markers and targets. METHODS In this study, we assessed the diagnostic value of differentially expressed microRNAs as potential diagnostic biomarkers for GC using data for 389 tissue samples from the Cancer Genome Atlas (TCGA) and 21 plasma samples from GC patients. RESULTS The expression of hsa-miR-143-3p (also known as hsa-miR-143) was significantly downregulated in GC according to the TCGA data and plasma samples. The 228 potential target genes of hsa-miR-143-3p were analyzed using a bioinformatics tool for miRNA target prediction. The target genes correlated with extracellular matrix organization, the cytoplasm, and identical protein binding. Furthermore, the pathway enrichment analysis of target genes showed that they were involved in pathways in cancer, the phosphoinositide 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway, and proteoglycans in cancer. The hub genes in the protein-protein interaction (PPI) network, were matrix metallopeptidase 2 (MMP2), CD44 molecule (CD44), and SMAD family member 3 (SMAD3). CONCLUSIONS This study suggests that hsa-miR-143-3p may be used as a diagnostic marker for GC, contributing via the pathways involved in the development of GC.
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Affiliation(s)
- Yeongdon Ju
- Medical Science Research Center, Pusan National University, Yangsan, 50612, Republic of Korea
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Go-Eun Choi
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Moon Won Lee
- Division of Gastroenterology, Pusan National University Hospital, Busan, 49241, Republic of Korea
- Department of Internal Medicine, Pusan National University College of Medicine, Busan, 49241, Republic of Korea
| | - Myeongguk Jeong
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Hyeokjin Kwon
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Dong Hyeok Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Jungho Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Hyunwoo Jin
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Kyung Eun Lee
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea
| | - Kyung-Yae Hyun
- Department of Clinical Laboratory Science, Dong-Eui University, Busan, 47340, Republic of Korea.
| | - Aelee Jang
- Department of Nursing, University of Ulsan, Ulsan, 44610, Republic of Korea.
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Karengera A, Bao C, Bovee TFH, Dinkla IJT, Murk AJ. A Multiplex Gene Expression Assay for Direct Measurement of RNA Transcripts in Crude Lysates of the Nematode Caenorhabditis elegans Used as a Bioanalytical Tool. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:130-142. [PMID: 36282018 PMCID: PMC10107722 DOI: 10.1002/etc.5505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/19/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Gene expression profiling in Caenorhabditis elegans has been demonstrated to be a potential bioanalytical tool to detect the toxic potency of environmental contaminants. The RNA transcripts of genes responding to toxic exposure can be used as biomarkers for detecting these toxins. For routine application in environmental quality monitoring, an easy-to-use multiplex assay is required to reliably quantify expression levels of these biomarkers. In the present study, a bead-based assay was developed to fingerprint gene expression in C. elegans by quantitating messenger RNAs (mRNAs) of multiple target genes directly from crude nematode lysates, circumventing RNA extraction and purification steps. The assay uses signal amplification rather than target amplification for direct measurement of toxin-induced RNA transcripts. Using a 50-gene panel, the expression changes of four candidate reference genes and 46 target mRNAs for various contaminants and wastewaters were successfully measured, and the expression profiles indicated the type of toxin present. Moreover, the multiplex assay response was in line with previous results obtained with more time-consuming reverse-transcription quantitative polymerase chain reaction and microarray analyses. In addition, the transcriptomic profiles of nematodes exposed to wastewater samples and extracts prepared from tissues of swimming crabs were evaluated. The profiles indicated the presence of organic pollutants. The present study illustrates the successful development of a multiplex fluorescent bead-based approach using nematode C. elegans crude lysates for gene expression profiling of target RNAs. This method can be used to routinely fingerprint the presence of toxic contaminants in environmental samples and to identify the most biologically active fraction of the contaminant mixture in a toxicity identification and evaluation approach. Environ Toxicol Chem 2023;42:130-142. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Antoine Karengera
- Department of Animal Sciences, Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
- Wetsus, European Centre of Excellence for Sustainable Water TechnologyLeeuwardenThe Netherlands
| | - Cong Bao
- Department of Animal Sciences, Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
- Department of Analysis and Testing CenterYangtze Delta Region Institute of Tsinghua UniversityJiaxingChina
| | - Toine F. H. Bovee
- Wageningen Food Safety Research, Team Bioassays & BiosensorsWageningen University & ResearchWageningenThe Netherlands
| | - Inez J. T. Dinkla
- Wetsus, European Centre of Excellence for Sustainable Water TechnologyLeeuwardenThe Netherlands
| | - Albertinka J. Murk
- Department of Animal Sciences, Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
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Wallace SJ, de Solla SR, Langlois VS. Phenology of the transcriptome coincides with the physiology of double-crested cormorant embryonic development. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101029. [PMID: 36302318 DOI: 10.1016/j.cbd.2022.101029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/19/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022]
Abstract
The rigorous timing of the dynamic transcriptome within the embryo has to be well orchestrated for normal development. Identifying the phenology of the transcriptome along with the physiology of embryonic development in birds may suggest periods of increased sensitivity to contaminant exposure depending on the contaminant's mechanism of action. Double-crested cormorants (Nannopterum auritum, formerly Phalacrocorax auritus) are commonly used in ecotoxicological studies, but relatively little is known about their functional transcriptome profile in early development. In this study, we tracked the phenology of the transcriptome during N. auritum embryogenesis. Fresh eggs were collected from a reference site and artificially incubated from collection until four days prior to hatching. Embryos were periodically sampled throughout incubation for a total of seven time points. A custom microarray was designed for cormorants (over 14,000 probes) and used for transcriptome analysis in whole body (days 5, 8) and liver tissue (days 12, 14, 16, 20, 24). Three main developmental periods (early, mid, and late incubation) were identified with differentially expressed genes, gene sets, and pathways within and between each developmental transition. Overall, the timing of differentially expressed genes and enriched pathways corresponded to previously documented changes in morphology, neurology, or physiology during avian embryonic development. Targeted investigation of a subset of genes involved in endogenous and xenobiotic metabolism (e.g., cytochrome P450 cyp1a, cyp1b1, superoxide dismutase 1 sod1) were expressed in a pattern similar to reported endogenous compound levels. These data can provide insights on normal embryonic development in an ecologically relevant species without any environmental contaminant exposure.
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Affiliation(s)
- Sarah J Wallace
- Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Quebec, QC, Canada. https://twitter.com/@sjwallace06
| | - Shane R de Solla
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Burlington, ON, Canada
| | - Valerie S Langlois
- Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, Quebec, QC, Canada.
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Hidayat AS, Lefebvre KA, MacDonald J, Bammler T, Aluru N. Symptomatic and asymptomatic domoic acid exposure in zebrafish (Danio rerio) revealed distinct non-overlapping gene expression patterns in the brain. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 252:106310. [PMID: 36198224 PMCID: PMC9701550 DOI: 10.1016/j.aquatox.2022.106310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Domoic acid (DA) is a naturally produced neurotoxin synthesized by marine diatoms in the genus Pseudo-nitzschia. DA accumulates in filter-feeders such as shellfish, and can cause severe neurotoxicity when contaminated seafood is ingested, resulting in Amnesic Shellfish Poisoning (ASP) in humans. Overt clinical signs of neurotoxicity include seizures and disorientation. ASP is a significant public health concern, and though seafood regulations have effectively minimized the human risk of severe acute DA poisoning, the effects of exposure at asymptomatic levels are poorly understood. The objective of this study was to determine the effects of exposure to symptomatic and asymptomatic doses of DA on gene expression patterns in the zebrafish brain. We exposed adult zebrafish to either a symptomatic (1.1 ± 0.2 μg DA/g fish) or an asymptomatic (0.31 ± 0.03 µg DA/g fish) dose of DA by intracelomic injection and sampled at 24, 48 and 168 h post-injection. Transcriptional profiling was done using Agilent and Affymetrix microarrays. Our analysis revealed distinct, non-overlapping changes in gene expression between the two doses. We found that the majority of transcriptional changes were observed at 24 h post-injection with both doses. Interestingly, asymptomatic exposure produced more persistent transcriptional effects - in response to symptomatic dose exposure, we observed only one differentially expressed gene one week after exposure, compared to 26 in the asymptomatic dose at the same time (FDR <0.05). GO term analysis revealed that symptomatic DA exposure affected genes associated with peptidyl proline modification and retinoic acid metabolism. Asymptomatic exposure caused differential expression of genes that were associated with GO terms including circadian rhythms and visual system, and also the neuroactive ligand-receptor signaling KEGG pathway. Overall, these results suggest that transcriptional responses are specific to the DA dose and that asymptomatic exposure can cause long-term changes. Further studies are needed to characterize the potential downstream neurobehavioral impacts of DA exposure.
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Affiliation(s)
- Alia S Hidayat
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge and Woods Hole, MA, USA; Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Kathi A Lefebvre
- Environmental and Fisheries Science Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | - James MacDonald
- Department of Environmental and Occupational Health, University of Washington, Seattle, WA, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health, University of Washington, Seattle, WA, USA
| | - Neelakanteswar Aluru
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Aichinger G, Pahlke G, Puntscher H, Groestlinger J, Grabher S, Braun D, Tillmann K, Plasenzotti R, Del Favero G, Warth B, Höger H, Marko D. Markers for DNA damage are induced in the rat colon by the Alternaria toxin altertoxin-II, but not a complex extract of cultured Alternaria alternata. FRONTIERS IN TOXICOLOGY 2022; 4:977147. [PMID: 36353200 PMCID: PMC9638006 DOI: 10.3389/ftox.2022.977147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/12/2022] [Indexed: 01/19/2024] Open
Abstract
Mycotoxins produced by Alternaria spp. act genotoxic in cell-based studies, but data on their toxicity in vivo is scarce and urgently required for risk assessment. Thus, male Sprague-Dawley rats received single doses of a complex Alternaria toxin extract (CE; 50 mg/kg bw), altertoxin II (ATX-II; 0.21 mg/kg bw) or vehicle by gavage, one of the most genotoxic metabolites in vitro and were sacrificed after 3 or 24 h, respectively. Using SDS-PAGE/Western Blot, a significant increase of histone 2a.X phosphorylation and depletion of the native protein was observed for rats that were exposed to ATX-II for 24 h. Applying RT-PCR array technology we identified genes of interest for qRT-PCR testing, which in turn confirmed an induction of Rnf8 transcription in the colon of rats treated with ATX-II for 3 h and CE for 24 h. A decrease of Cdkn1a transcription was observed in rats exposed to ATX-II for 24 h, possibly indicating tissue repair after chemical injury. In contrast to the observed response in the colon, no markers for genotoxicity were induced in the liver of treated animals. We hereby provide the first report of ATX-II as a genotoxicant in vivo. Deviating results for similar concentrations of ATX-II in a natural Alternaria toxin mixture argue for substantial mixture effects.
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Affiliation(s)
- Georg Aichinger
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Laboratory of Toxicology, Department of Health Science and Technology, ETH Zurich, Switzerland
| | - Gudrun Pahlke
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Hannes Puntscher
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Julia Groestlinger
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Stephanie Grabher
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Dominik Braun
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Tillmann
- Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Roberto Plasenzotti
- Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Harald Höger
- Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
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Kramberger K, Barlič-Maganja D, Pražnikar ZJ, Režen T, Rozman D, Pražnikar J, Kenig S. Whole transcriptome expression array analysis of human colon fibroblasts culture treated with Helichrysum italicum supports its use in traditional medicine. JOURNAL OF ETHNOPHARMACOLOGY 2022; 296:115505. [PMID: 35764197 DOI: 10.1016/j.jep.2022.115505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Helichrysum italicum (HI) is a Mediterranean plant with well-reported use in traditional medicine for a wide range of applications, including digestive and liver disorders, intestinal parasitic infections, wound healing, stomach ache and asthma. However, little is known about the global mechanism behind its pleiotropic activity. AIM OF THE STUDY The aim of this study was to explain the mechanism behind the previously demonstrated effects of HI and to justify its use in traditional medicine. MATERIALS AND METHODS A microarray-based transcriptome analysis was used to discover the global transcriptional alterations in primary colon fibroblasts after exposure to HI infusion for 6 h and 24 h. In addition, quantitative real-time PCR was used to verify the microarray results. RESULTS Altogether we identified 217 differentially expressed genes compared to non-treated cells, and only 8 were common to both treatments. Gene ontology analysis revealed that 24 h treatment with HI infusion altered the expression of genes involved in cytoskeletal rearrangement and cell growth, whereas pathway analysis further showed the importance of interleukin signaling and transcriptional regulation by TP53. For the 6 h treatment only the process of hemostasis appeared in the results of both enrichment analyses. In functional assays, HI infusion increased cell migration and decreased blood clotting and prothrombin time. CONCLUSIONS With the careful evaluation of the role of individual genes, especially SERPING1, ARHGAP1, IL33 and CDKN1A, represented in the enriched pathways and processes, we propose the main mode of HI action, which is wound healing. In addition to its indirect prevention of diseases resulting from the impaired barrier integrity, HI also effects inflammation and metabolic processes directly, as it regulates genes such as LRPPRC, LIPA, ABCA12, PRKAR1A and ANXA6.
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Affiliation(s)
- Katja Kramberger
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310, Izola, Slovenia.
| | - Darja Barlič-Maganja
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310, Izola, Slovenia.
| | - Zala Jenko Pražnikar
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310, Izola, Slovenia.
| | - Tadeja Režen
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia.
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia.
| | - Jure Pražnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia.
| | - Saša Kenig
- Faculty of Health Sciences, University of Primorska, Polje 42, 6310, Izola, Slovenia.
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TWEAK and TNFα, Both TNF Ligand Family Members and Multiple Sclerosis-Related Cytokines, Induce Distinct Gene Response in Human Brain Microvascular Endothelial Cells. Genes (Basel) 2022; 13:genes13101714. [PMID: 36292599 PMCID: PMC9601571 DOI: 10.3390/genes13101714] [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: 09/07/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/31/2022] Open
Abstract
Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is a member of the TNF ligand family involved in various diseases including brain inflammatory pathologies such as multiple sclerosis. It has been demonstrated that TWEAK can induce cerebrovascular permeability in an in vitro model of the blood-brain barrier. The molecular mechanisms playing a role in TWEAK versus TNFα signaling on cerebral microvascular endothelial cells are not well defined. Therefore, we aimed to identify gene expression changes in cultures of human brain microvascular endothelial cells (hCMEC/D3) to address changes initiated by TWEAK exposure. Taken together, our studies highlighted that gene involved in leukocyte extravasation, notably claudin-5, were differentially modulated by TWEAK and TNFα. We identified differential gene expression of hCMEC/D3 cells at three timepoints following TWEAK versus TNFα stimulation and also found distinct modulations of several canonical pathways including the actin cytoskeleton, vascular endothelial growth factor (VEGF), Rho family GTPases, and phosphatase and tensin homolog (PTEN) pathways. To our knowledge, this is the first study to interrogate and compare the effects of TWEAK versus TNFα on gene expression in brain microvascular endothelial cells.
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Gillis RF, Palmour RM. mRNA expression analysis of the hippocampus in a vervet monkey model of fetal alcohol spectrum disorder. J Neurodev Disord 2022; 14:21. [PMID: 35305552 PMCID: PMC8934503 DOI: 10.1186/s11689-022-09427-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 02/10/2022] [Indexed: 11/12/2022] Open
Abstract
Background Fetal alcohol spectrum disorders (FASD) are common, yet preventable developmental disorders that stem from prenatal exposure to alcohol. This exposure leads to a wide array of behavioural and physical problems with a complex and poorly defined biological basis. Molecular investigations to date predominantly use rodent animal models, but because of genetic, developmental and social behavioral similarity, primate models are more relevant. We previously reported reduced cortical and hippocampal neuron levels in an Old World monkey (Chlorocebus sabaeus) model with ethanol exposure targeted to the period of rapid synaptogenesis and report here an initial molecular study of this model. The goal of this study was to evaluate mRNA expression of the hippocampus at two different behavioural stages (5 months, 2 years) corresponding to human infancy and early childhood. Methods Offspring of alcohol-preferring or control dams drank a maximum of 3.5 g ethanol per kg body weight or calorically matched sucrose solution 4 days per week during the last 2 months of gestation. Total mRNA expression was measured with the Affymetrix GeneChip Rhesus Macaque Genome Array in a 2 × 2 study design that interrogated two independent variables, age at sacrifice, and alcohol consumption during gestation. Results and discussion Statistical analysis identified a preferential downregulation of expression when interrogating the factor ‘alcohol’ with a balanced effect of upregulation vs. downregulation for the independent variable ‘age’. Functional exploration of both independent variables shows that the alcohol consumption factor generates broad functional annotation clusters that likely implicate a role for epigenetics in the observed differential expression, while the variable age reliably produced functional annotation clusters predominantly related to development. Furthermore, our data reveals a novel connection between EFNB1 and the FASDs; this is highly plausible both due to the role of EFNB1 in neuronal development as well as its central role in craniofrontal nasal syndrome (CFNS). Fold changes for key genes were subsequently confirmed via qRT-PCR. Conclusion Prenatal alcohol exposure leads to global downregulation in mRNA expression. The cellular interference model of EFNB1 provides a potential clue regarding how genetically susceptible individuals may develop the phenotypic triad generally associated with classic fetal alcohol syndrome. Supplementary Information The online version contains supplementary material available at 10.1186/s11689-022-09427-z.
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11
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Valanti EK, Dalakoura-Karagkouni K, Fotakis P, Vafiadaki E, Mantzoros CS, Chroni A, Zannis V, Kardassis D, Sanoudou D. Reconstituted HDL-apoE3 promotes endothelial cell migration through ID1 and its downstream kinases ERK1/2, AKT and p38 MAPK. Metabolism 2022; 127:154954. [PMID: 34875308 DOI: 10.1016/j.metabol.2021.154954] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/15/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Atherosclerotic Coronary Artery Disease (ASCAD) is the leading cause of mortality worldwide. Novel therapeutic approaches aiming to improve the atheroprotective functions of High Density Lipoprotein (HDL) include the use of reconstituted HDL forms containing human apolipoprotein A-I (rHDL-apoA-I). Given the strong atheroprotective properties of apolipoprotein E3 (apoE3), rHDL-apoE3 may represent an attractive yet largely unexplored therapeutic agent. OBJECTIVE To evaluate the atheroprotective potential of rHDL-apoE3 starting with the unbiased assessment of global transcriptome effects and focusing on endothelial cell (EC) migration as a critical process in re-endothelialization and atherosclerosis prevention. The cellular, molecular and functional effects of rHDL-apoE3 on EC migration-associated pathways were assessed, as well as the potential translatability of these findings in vivo. METHODS Human Aortic ECs (HAEC) were treated with rHDL-apoE3 and total RNA was analyzed by whole genome microarrays. Expression and phosphorylation changes of key EC migration-associated molecules were validated by qRT-PCR and Western blot analysis in primary HAEC, Human Coronary Artery ECs (HCAEC) and the human EA.hy926 EC line. The capacity of rHDL-apoE3 to stimulate EC migration was assessed by wound healing and transwell migration assays. The contribution of MEK1/2, PI3K and the transcription factor ID1 in rHDL-apoE3-induced EC migration and activation of EC migration-related effectors was assessed using specific inhibitors (PD98059: MEK1/2, LY294002: PI3K) and siRNA-mediated gene silencing, respectively. The capacity of rHDL-apoE3 to improve vascular permeability and hypercholesterolemia in vivo was tested in a mouse model of hypercholesterolemia (apoE KO mice) using Evans Blue assays and lipid/lipoprotein analysis in the serum, respectively. RESULTS rHDL-apoE3 induced significant expression changes in 198 genes of HAEC mainly involved in re-endothelialization and atherosclerosis-associated functions. The most pronounced effect was observed for EC migration, with 42/198 genes being involved in the following EC migration-related pathways: 1) MEK/ERK, 2) PI3K/AKT/eNOS-MMP2/9, 3) RHO-GTPases, 4) integrin. rHDL-apoE3 induced changes in 24 representative transcripts of these pathways in HAEC, increasing the expression of their key proteins PIK3CG, EFNB2, ID1 and FLT1 in HCAEC and EA.hy926 cells. In addition, rHDL-apoE3 stimulated migration of HCAEC and EA.hy926 cells, and the migration was markedly attenuated in the presence of PD98059 or LY294002. rHDL-apoE3 also increased the phosphorylation of ERK1/2, AKT, eNOS and p38 MAPK in these cells, while PD98059 and LY294002 inhibited rHDL-apoE3-induced phosphorylation of ERK1/2, AKT and p38 MAPK, respectively. LY had no effect on rHDL-apoE3-mediated eNOS phosphorylation. ID1 siRNA markedly decreased EA.hy926 cell migration by inhibiting rHDL-apoE3-triggered ERK1/2 and AKT phosphorylation. Finally, administration of a single dose of rHDL-apoE3 in apoE KO mice markedly improved vascular permeability as demonstrated by the reduced concentration of Evans Blue dye in tissues such as the stomach, the tongue and the urinary bladder and ameliorated hypercholesterolemia. CONCLUSIONS rHDL-apoE3 significantly enhanced EC migration in vitro, predominantly via overexpression of ID1 and subsequent activation of MEK1/2 and PI3K, and their downstream targets ERK1/2, AKT and p38 MAPK, respectively, and improved vascular permeability in vivo. These novel insights into the rHDL-apoE3 functions suggest a potential clinical use to promote re-endothelialization and retard development of atherosclerosis.
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Affiliation(s)
- Eftaxia-Konstantina Valanti
- 4th Department of Internal Medicine, Clinical Genomics and Pharmacogenomics Unit, 'Attikon' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Katerina Dalakoura-Karagkouni
- Laboratory of Biochemistry, University of Crete Medical School, Heraklion, Greece; Division of Gene Regulation and Genomics, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology of Hellas, Heraklion, Greece
| | | | - Elizabeth Vafiadaki
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Angeliki Chroni
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Vassilis Zannis
- Molecular Genetics, Boston University Medical School, Boston, USA
| | - Dimitris Kardassis
- Laboratory of Biochemistry, University of Crete Medical School, Heraklion, Greece; Division of Gene Regulation and Genomics, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology of Hellas, Heraklion, Greece
| | - Despina Sanoudou
- 4th Department of Internal Medicine, Clinical Genomics and Pharmacogenomics Unit, 'Attikon' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Curr Biol 2022; 32:289-303.e6. [PMID: 34793695 PMCID: PMC8792248 DOI: 10.1016/j.cub.2021.10.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/16/2021] [Accepted: 10/28/2021] [Indexed: 01/26/2023]
Abstract
Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Pushpanathan Muthuirulan
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Stanley J Neufeld
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Mai P Tran
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haydee L Gutierrez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kevin D Chen
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joel M Erberich
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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13
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Xicota L, De Toma I, Maffioletti E, Pisanu C, Squassina A, Baune BT, Potier MC, Stacey D, Dierssen M. Recommendations for pharmacotranscriptomic profiling of drug response in CNS disorders. Eur Neuropsychopharmacol 2022; 54:41-53. [PMID: 34743061 DOI: 10.1016/j.euroneuro.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022]
Abstract
Pharmacotranscriptomics is a still very new field of research that has just begun to flourish and promises to enable target discovery, inform biomarker and evaluate drug efficacy beyond pharmacogenomics. The aim of this review is to provide a critical overview of the biological foundations of transcriptomics, methodological approaches to transcriptomic studies, and their advantages and limitations. We present the different RNA species (rRNAs, tRNAs, mtRNAs, snRNAs, scRNAs, mRNAs, ncRNAs, LINE and SINE transcripts, circular RNAs, piRNAs, miRNAs, snoRNAs) and their potential for pharmacotranscriptomic studies as markers to predict treatment response in neurological and psychiatric disorders. We also review the accessible sources of RNA in patients peripheral blood cells (including platelets), plasma, microvesicles, exosomes, apoptotic bodies, and how those affect the integrity and relative abundances of RNAs and reflect the situation in the Central Nervous System (CNS). Finally, we discuss the suitability and indications of different techniques, such as microarrays and RNA-sequencing (RNA-Seq) techniques to understand gene expression differences or to reveal variation in expression levels of coding and non-coding genes. We conclude with some recommendations for future directions, e.g., gaps of knowledge and particular RNAs/tissues that have been overlooked.
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Affiliation(s)
- Laura Xicota
- Paris Brain Institute, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Ilario De Toma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elisabetta Maffioletti
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy; Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Bernhard T Baune
- Department of Psychiatry, University of Muenster, Muenster, Germany; Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Marie Claude Potier
- Paris Brain Institute, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David Stacey
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland United Kingdom
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.
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Stute P, Ehrentraut S, Henneicke-von Zepelin HH, Nicken P. Gene expression analyses on multi-target mode of action of black cohosh in menopausal complaints - a pilot study in rodents. Arch Gynecol Obstet 2022; 305:275-286. [PMID: 34259940 PMCID: PMC8782806 DOI: 10.1007/s00404-021-06105-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/22/2021] [Indexed: 10/26/2022]
Abstract
PURPOSE This study aimed at assessing gene expression profiles in hippocampus and hypothalamus of ovariectomized (OVX) rats with or without treatment with an isopropanolic extract of Cimicifuga racemosa rhizomes (iCR) in comparison to intact rats. METHODS Exploration of hippocampal (Hi) and hypothalamic (Hy) tissue from Sprague Dawley rats: without OVX (NHi = NHy = 4), tissues 3 months after OVX (NHi = 4, NHy = 3), or tissues of rats after their treatment with iCR for 3 months after OVX (NHi = NHy = 2). Gene expression profiles in these tissues were investigated by RNA-microarray-analysis and subsequent verification by qPCR. RESULTS 4812 genes were differentially regulated when comparing the three groups in hippocampus and hypothalamus. iCR compensated the effects of OVX in 518 genes. This compensatory effect was most prominent in hippocampal signalling pathways, thereof genes (GAL, CALCA, HCRT, AVPR1A, PNOC, etc.) involved in thermoregulation, regulation of sleep and arousal, blood pressure regulation, metabolism, nociception, hormonal regulation, homeostasis, learning and cognition, mood regulation, neuroendocrine modulation, etc.. In the hypothalamus, iCR compensated OVX-effects at TAC3 and OPRM1 but not at KISS1. These genes are involved in the pathophysiology of hot flashes. CONCLUSIONS Our pilot study findings support a multifaceted mode of action of iCR in menopausal complaints on a tissue-specific brain gene expression level.
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Affiliation(s)
- Petra Stute
- Department of Obstetrics, Gynaecologic Endocrinology and Reproductive Medicine, University Women's Hospital, University Clinic of Bern, Friedbuehlstrasse 19, 3010, Bern, Switzerland.
| | | | | | - Petra Nicken
- Department of Regulatory Affairs, Schaper and Brümmer GmbH and Co. KG, Salzgitter, Germany
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15
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Islam B, Stephenson J, Young B, Manca M, Buckley DA, Radford H, Zis P, Johnson MI, Finn DP, McHugh PC. The Identification of Blood Biomarkers of Chronic Neuropathic Pain by Comparative Transcriptomics. Neuromolecular Med 2021; 24:320-338. [PMID: 34741226 PMCID: PMC9402512 DOI: 10.1007/s12017-021-08694-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022]
Abstract
In this study, we recruited 50 chronic pain (neuropathic and nociceptive) and 43 pain-free controls to identify specific blood biomarkers of chronic neuropathic pain (CNP). Affymetrix microarray was carried out on a subset of samples selected 10 CNP and 10 pain-free control participants. The most significant genes were cross-validated using the entire dataset by quantitative real-time PCR (qRT-PCR). In comparative analysis of controls and CNP patients, WLS (P = 4.80 × 10–7), CHPT1 (P = 7.74 × 10–7) and CASP5 (P = 2.30 × 10–5) were highly significant, whilst FGFBP2 (P = 0.00162), STAT1 (P = 0.00223), FCRL6 (P = 0.00335), MYC (P = 0.00335), XCL2 (P = 0.0144) and GZMA (P = 0.0168) were significant in all CNP patients. A three-arm comparative analysis was also carried out with control as the reference group and CNP samples differentiated into two groups of high and low S-LANSS score using a cut-off of 12. STAT1, XCL2 and GZMA were not significant but KIR3DL2 (P = 0.00838), SH2D1B (P = 0.00295) and CXCR31 (P = 0.0136) were significant in CNP high S-LANSS group (S-LANSS score > 12), along with WLS (P = 8.40 × 10–5), CHPT1 (P = 7.89 × 10–4), CASP5 (P = 0.00393), FGFBP2 (P = 8.70 × 10–4) and FCRL6 (P = 0.00199), suggesting involvement of immune pathways in CNP mechanisms. None of the genes was significant in CNP samples with low (< 12) S-LANSS score. The area under the receiver operating characteristic (AUROC) analysis showed that combination of MYC, STAT1, TLR4, CASP5 and WLS gene expression could be potentially used as a biomarker signature of CNP (AUROC − 0.852, (0.773, 0.931 95% CI)).
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Affiliation(s)
- Barira Islam
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, HD1 3DH, UK.,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - John Stephenson
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, HD1 3DH, UK.,School of Human and Health Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - Bethan Young
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, HD1 3DH, UK.,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - Maurizio Manca
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, HD1 3DH, UK.,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - David A Buckley
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, HD1 3DH, UK.,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | | | | | - Mark I Johnson
- Centre for Pain Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - David P Finn
- Pharmacology & Therapeutics, School of Medicine, Galway, Neuroscience Centre and Centre for Pain Research, National University of Ireland Galway, University Road, Galway, Ireland
| | - Patrick C McHugh
- Centre for Biomarker Research, University of Huddersfield, Huddersfield, HD1 3DH, UK. .,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK.
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16
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Effects of cyclic tensile strain and microgravity on the distribution of actin fiber and Fat1 cadherin in murine articular chondrocytes. J Biomech 2021; 129:110774. [PMID: 34627073 DOI: 10.1016/j.jbiomech.2021.110774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022]
Abstract
Chondrocytes as mechano-sensitive cells can sense and respond to mechanical stress throughout life. In chondrocytes, changes of structure and morphology in the cytoskeleton have been potentially involved in various mechano-transductions such as stretch-activated ion channels, integrins, and intracellular organelles. However, the mechanism of cytoskeleton rearrangement in response to mechanical loading and unloading remains unclear. In this study, we exposed chondrocytes to a physiological range of cyclic tensile strain as mechanical loading or to simulated microgravity by 3D-clinostat that produces an unloading environment. Based on microarray profiling, we focused on Fat1 that implicated in the formation and rearrangement of actin fibers. Next, we examined the relationship between the distribution of Fat1 proteins and actin fibers after cyclic tensile strain and microgravity. As a result, Fat1 proteins did not colocalize with actin stress fibers after cyclic tensile strain, but accumulated near the cell membrane and colocalized with cortical actin fibers after microgravity. Our findings indicate that Fat1 may mediate the rearrangement of cortical actin fibers induced by mechanical unloading.
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Song Y, Gao P, Ding H, Xu G, Hu Y, Tong Y, Xin W, Zhang L, Wu M, Fang L. Underlying mechanism of sorafenib resistance in hepatocellular carcinoma: a bioinformatics study based on validated resistance-related genes. J Gastrointest Oncol 2021; 12:1895-1904. [PMID: 34532137 DOI: 10.21037/jgo-21-377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/17/2021] [Indexed: 11/06/2022] Open
Abstract
Background Sorafenib, the first approved targeted therapy for advanced hepatocellular carcinoma (HCC), is often reported to comprised survival-benefit due to resistance. An underlying mechanism of resistance was proposed using bioinformatics analysis based on differentially expressed genes (DEGs) from microarrays. However, most DEGs were invalidated at both the expression level, and the role in causing resistance. Therefore, we conducted a bioinformatics analysis based on experimentally determined sorafenib-resistance-related genes (SRRGs) to elucidate the mechanism of sorafenib resistance. Methods The SRRGs, which have been experimentally determined to promote or inhibit resistance, were collected from published studies. The Database for Annotation, Visualization and Integrated Discovery (DAVID) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to perform Gene Ontology (GO) and pathway enrichment analysis, respectively. A corresponding protein-protein interaction network (PPI) was created using the Cytoscape software program, and network hub genes were proposed. Results A total of 145 SRRGs, with 117 promoting and 28 inhibiting resistance, were identified. Cell proliferation, migration, development, response to oxygen levels, epithelial-to-mesenchymal transition (EMT), cell skeleton, protein function, and autophagy were all proposed as crucial gene functions related to resistance. The pathways related to cell proliferation or apoptosis, immune function, endocrine metabolism, stem cell function, and differentiation were identified as key resistance-related pathways. A total of 81 hub genes were proposed, including the following top 10 genes: TP53, AKT1, EGFR, STAT3, VEGFA, JUN, MAPK1, IL6, PTEN, and CTNNB1. Conclusions In conclusion, this study gathered experimentally validated genes that determine sorafenib resistance in HCC, provided an overview of the underlying mechanisms of resistance, and further validated sorafenib resistance in HCC.
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Affiliation(s)
- Yu Song
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Peng Gao
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Haiying Ding
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Gaoqi Xu
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yan Hu
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yinghui Tong
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Wenxiu Xin
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Liwen Zhang
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Miaolian Wu
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.,Department of Pharmacy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Luo Fang
- Department of Pharmacy, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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Bosque JR, Gómez-Nieto R, Hormigo S, Herrero-Turrión MJ, Díaz-Casado E, Sancho C, López DE. Molecular tools for the characterization of seizure susceptibility in genetic rodent models of epilepsy. Epilepsy Behav 2021; 121:106594. [PMID: 31685382 DOI: 10.1016/j.yebeh.2019.106594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022]
Abstract
Epilepsy is a chronic neurological disorder characterized by abnormal neuronal activity that arises from imbalances between excitatory and inhibitory synapses, which are highly correlated to functional and structural changes in specific brain regions. The difference between the normal and the epileptic brain may harbor genetic alterations, gene expression changes, and/or protein alterations in the epileptogenic nucleus. It is becoming increasingly clear that such differences contribute to the development of distinct epilepsy phenotypes. The current major challenges in epilepsy research include understanding the disease progression and clarifying epilepsy classifications by searching for novel molecular biomarkers. Thus, the application of molecular techniques to carry out comprehensive studies at deoxyribonucleic acid, messenger ribonucleic acid, and protein levels is of utmost importance to elucidate molecular dysregulations in the epileptic brain. The present review focused on the great diversity of technical approaches available and new research methodology, which are already being used to study molecular alterations underlying epilepsy. We have grouped the different techniques according to each step in the flow of information from DNA to RNA to proteins, and illustrated with specific examples in animal models of epilepsy, some of which are our own. Separately and collectively, the genomic and proteomic techniques, each with its own strengths and limitations, provide valuable information on molecular mechanisms underlying seizure susceptibility and regulation of neuronal excitability. Determining the molecular differences between genetic rodent models of epilepsy and their wild-type counterparts might be a key in determining mechanisms of seizure susceptibility and epileptogenesis as well as the discovery and development of novel antiepileptic agents. This article is part of the Special Issue "NEWroscience 2018".
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Affiliation(s)
- José Ramón Bosque
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain
| | - Ricardo Gómez-Nieto
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain; Department of Neurobiology and Anatomy, Drexel University College of Medicine, United States of America
| | - Sebastián Hormigo
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Department of Cell Biology and Pathology, School of Medicine, University of Salamanca, Salamanca, Spain
| | - M Javier Herrero-Turrión
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; INCYL Neurological Tissue Bank (BTN-INCYL), Spain
| | - Elena Díaz-Casado
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain
| | - Consuelo Sancho
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain
| | - Dolores E López
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain; Department of Neurobiology and Anatomy, Drexel University College of Medicine, United States of America.
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19
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Two distinct skeletal muscle microRNA signatures revealing the complex mechanism of sporadic ALS. Acta Neurol Belg 2021; 122:1499-1509. [PMID: 34241798 DOI: 10.1007/s13760-021-01743-w] [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: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Skeletal muscle pathology is thought to have an important role in the onset and/or progression of amyotrophic lateral sclerosis (ALS), which is a neurodegenerative disorder characterized by progressive muscle weakness. Since miRNAs are recognized as important regulatory factors of essential biological processes, we aimed to identify differentially expressed miRNAs in the skeletal muscle of sporadic ALS patients through the combination of molecular-omic technologies and bioinformatic tools. We analyzed the miRnome profiles of skeletal muscle biopsies acquired from ten sALS patients and five controls with Affymetrix GeneChip miRNA 4.0 Array. To find out differentially expressed miRNAs in patients, data were analyzed by The Institute for Genomic Research-Multi Experiment Viewer (MeV) and miRNAs whose expression difference were statistically significant were identified as candidates. The potential target genes of these miRNAs were predicted by miRWalk 2.0 and were functionally enriched by gene ontology (GO) analysis. The expression level of priority candidates was validated by quantitative real-time PCR (qRT-PCR) analysis. We identified ten differentially expressed miRNAs in patients with a fold change threshold ≥ 2.0, FDR = 0. We identified ten differentially expressed miRNAs in patients with a fold change threshold ≥ 2.0, FDR = 0. Nine out of the ten miRNAs were found to be related to top three enriched ALS-related terms. Based on the qRT-PCR validation of candidate miRNAs, patients were separated into two groups: those with upregulated miR-4429 and miR-1825 expression and those with downregulated miR-638 expression. The different muscle-specific miRNA profiles in sALS patients may indicate the involvement of etiologic heterogeneity, which may allow the development of novel therapeutic strategies.
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20
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Ruskovska T, Budić-Leto I, Corral-Jara KF, Ajdžanović V, Arola-Arnal A, Bravo FI, Deligiannidou GE, Havlik J, Janeva M, Kistanova E, Kontogiorgis C, Krga I, Massaro M, Miler M, Milosevic V, Morand C, Scoditti E, Suárez M, Vauzour D, Milenkovic D. Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans-Evidence from Targeted Nutrigenomic Studies. Nutrients 2021; 13:2326. [PMID: 34371836 PMCID: PMC8308901 DOI: 10.3390/nu13072326] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/14/2022] Open
Abstract
Cardiometabolic disorders are among the leading causes of mortality in the human population. Dietary polyphenols exert beneficial effects on cardiometabolic health in humans. Molecular mechanisms, however, are not completely understood. Aiming to conduct in-depth integrative bioinformatic analyses to elucidate molecular mechanisms underlying the protective effects of polyphenols on cardiometabolic health, we first conducted a systematic literature search to identify human intervention studies with polyphenols that demonstrate improvement of cardiometabolic risk factors in parallel with significant nutrigenomic effects. Applying the predefined inclusion criteria, we identified 58 differentially expressed genes at mRNA level and 5 miRNAs, analyzed in peripheral blood cells with RT-PCR methods. Subsequent integrative bioinformatic analyses demonstrated that polyphenols modulate genes that are mainly involved in the processes such as inflammation, lipid metabolism, and endothelial function. We also identified 37 transcription factors that are involved in the regulation of polyphenol modulated genes, including RELA/NFKB1, STAT1, JUN, or SIRT1. Integrative bioinformatic analysis of mRNA and miRNA-target pathways demonstrated several common enriched pathways that include MAPK signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, focal adhesion, or PPAR signaling pathway. These bioinformatic analyses represent a valuable source of information for the identification of molecular mechanisms underlying the beneficial health effects of polyphenols and potential target genes for future nutrigenetic studies.
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Affiliation(s)
- Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (M.J.)
| | - Irena Budić-Leto
- Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia;
| | - Karla Fabiola Corral-Jara
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
| | - Vladimir Ajdžanović
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Anna Arola-Arnal
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - Francisca Isabel Bravo
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - Georgia-Eirini Deligiannidou
- Department of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece; (G.-E.D.); (C.K.)
| | - Jaroslav Havlik
- Department of Food Science, Czech University of Life Sciences, 16521 Prague, Czech Republic;
| | - Milkica Janeva
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (M.J.)
| | - Elena Kistanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Christos Kontogiorgis
- Department of Medicine, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece; (G.-E.D.); (C.K.)
| | - Irena Krga
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
- Centre of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia
| | - Marika Massaro
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy; (M.M.); (E.S.)
| | - Marko Miler
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Verica Milosevic
- Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, 11060 Belgrade, Serbia; (V.A.); (M.M.); (V.M.)
| | - Christine Morand
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
| | - Egeria Scoditti
- National Research Council (CNR) Institute of Clinical Physiology (IFC), 73100 Lecce, Italy; (M.M.); (E.S.)
| | - Manuel Suárez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain; (A.A.-A.); (F.I.B.); (M.S.)
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - Dragan Milenkovic
- Unité de Nutrition Humaine (UNH), Université Clermont Auvergne, Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Faculté de Médecine, F-63000 Clermont-Ferrand, France; (K.F.C.-J.); (I.K.); (C.M.)
- Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA
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21
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Gene Expression Profile in Different Age Groups and Its Association with Cognitive Function in Healthy Malay Adults in Malaysia. Cells 2021; 10:cells10071611. [PMID: 34199148 PMCID: PMC8304476 DOI: 10.3390/cells10071611] [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: 03/26/2021] [Revised: 06/13/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
The mechanism of cognitive aging at the molecular level is complex and not well understood. Growing evidence suggests that cognitive differences might also be caused by ethnicity. Thus, this study aims to determine the gene expression changes associated with age-related cognitive decline among Malay adults in Malaysia. A cross-sectional study was conducted on 160 healthy Malay subjects, aged between 28 and 79, and recruited around Selangor and Klang Valley, Malaysia. Gene expression analysis was performed using a HumanHT-12v4.0 Expression BeadChip microarray kit. The top 20 differentially expressed genes at p < 0.05 and fold change (FC) = 1.2 showed that PAFAH1B3, HIST1H1E, KCNA3, TM7SF2, RGS1, and TGFBRAP1 were regulated with increased age. The gene set analysis suggests that the Malay adult's susceptibility to developing age-related cognitive decline might be due to the changes in gene expression patterns associated with inflammation, signal transduction, and metabolic pathway in the genetic network. It may, perhaps, have important implications for finding a biomarker for cognitive decline and offer molecular targets to achieve successful aging, mainly in the Malay population in Malaysia.
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22
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Kim J, You S. Effect of samul-tang on female fertility via RAS signaling pathway in ovaries of aged mice. Aging (Albany NY) 2021; 13:14829-14842. [PMID: 34091440 PMCID: PMC8221297 DOI: 10.18632/aging.203150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/20/2021] [Indexed: 05/04/2023]
Abstract
Samul-tang (SM), a traditional herbal medicine, is used to treat age-related human conditions, such as infertility and menstrual irregularities. The mechanism underlying the role of SM in ovary function needs elucidation. In this study, the influence of SM administration on the ovarian reserve of aged mice was investigated. Female BALB/c mice (8 and 40 weeks-old) were administered with distilled water (young or old group) or SM for 4 weeks. SM administration prevented age-related ovarian follicle loss in mice. Quality of oocytes and blastocysts were enhanced in SM-administrated mice compared to those of non-treated old mice. Further, SM administration increased the pregnancy rate and number of litters. SM triggered changes in aging-related genes that are linked to the RAS-mediated pathway. Thus, we demonstrate that SM can be used to increase the oocyte yield in aged women, potentially improving age-related cognitive decline in the ovarian reserve.
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Affiliation(s)
- Jihyun Kim
- Clinical Medicine Division, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Sooseong You
- Clinical Medicine Division, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
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23
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Matta C, Lewis R, Fellows C, Diszhazi G, Almassy J, Miosge N, Dixon J, Uribe MC, May S, Poliska S, Barrett-Jolley R, Fodor J, Szentesi P, Hajdú T, Keller-Pinter A, Henslee E, Labeed FH, Hughes MP, Mobasheri A. Transcriptome-based screening of ion channels and transporters in a migratory chondroprogenitor cell line isolated from late-stage osteoarthritic cartilage. J Cell Physiol 2021; 236:7421-7439. [PMID: 34008188 DOI: 10.1002/jcp.30413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022]
Abstract
Chondrogenic progenitor cells (CPCs) may be used as an alternative source of cells with potentially superior chondrogenic potential compared to mesenchymal stem cells (MSCs), and could be exploited for future regenerative therapies targeting articular cartilage in degenerative diseases such as osteoarthritis (OA). In this study, we hypothesised that CPCs derived from OA cartilage may be characterised by a distinct channelome. First, a global transcriptomic analysis using Affymetrix microarrays was performed. We studied the profiles of those ion channels and transporter families that may be relevant to chondroprogenitor cell physiology. Following validation of the microarray data with quantitative reverse transcription-polymerase chain reaction, we examined the role of calcium-dependent potassium channels in CPCs and observed functional large-conductance calcium-activated potassium (BK) channels involved in the maintenance of the chondroprogenitor phenotype. In line with our very recent results, we found that the KCNMA1 gene was upregulated in CPCs and observed currents that could be attributed to the BK channel. The BK channel inhibitor paxilline significantly inhibited proliferation, increased the expression of the osteogenic transcription factor RUNX2, enhanced the migration parameters, and completely abolished spontaneous Ca2+ events in CPCs. Through characterisation of their channelome we demonstrate that CPCs are a distinct cell population but are highly similar to MSCs in many respects. This study adds key mechanistic data to the in-depth characterisation of CPCs and their phenotype in the context of cartilage regeneration.
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Affiliation(s)
- Csaba Matta
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Department of Veterinary Preclinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Rebecca Lewis
- Department of Veterinary Preclinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Christopher Fellows
- Department of Veterinary Preclinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Gyula Diszhazi
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Janos Almassy
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nicolai Miosge
- Department of Prosthodontics, Tissue Regeneration Work Group, Georg August University, Göttingen, Germany
| | - James Dixon
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre of Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Marcos C Uribe
- The Nottingham Arabidopsis Stock Centre (NASC), School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Sean May
- The Nottingham Arabidopsis Stock Centre (NASC), School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Szilard Poliska
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Richard Barrett-Jolley
- Department of Musculoskeletal Biology, Faculty of Health and Life Sciences, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Janos Fodor
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Szentesi
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tibor Hajdú
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Aniko Keller-Pinter
- Department of Biochemistry, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Erin Henslee
- Department of Mechanical Engineering Sciences, Centre for Biomedical Engineering, University of Surrey, Guildford, UK
| | - Fatima H Labeed
- Department of Mechanical Engineering Sciences, Centre for Biomedical Engineering, University of Surrey, Guildford, UK
| | - Michael P Hughes
- Department of Mechanical Engineering Sciences, Centre for Biomedical Engineering, University of Surrey, Guildford, UK
| | - Ali Mobasheri
- Department of Regenerative Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania.,Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland.,Departments of Orthopedics, Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Joint Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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24
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LncRNAs induce oxidative stress and spermatogenesis by regulating endoplasmic reticulum genes and pathways. Aging (Albany NY) 2021; 13:13764-13787. [PMID: 34001678 PMCID: PMC8202879 DOI: 10.18632/aging.202971] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/08/2020] [Indexed: 12/17/2022]
Abstract
Oligozoospermia or low sperm count is a leading cause of male infertility worldwide. Despite decades of work on non-coding RNAs (ncRNAs) as regulators of spermatogenesis, fertilization, and male fertility, the literature on the function of long non-coding RNAs (lncRNAs) in human oligozoospermia is scarce. We integrated lncRNA and mRNA sequencing data from 12 human normozoospermic and oligozoospermic samples and comprehensively analyzed the function of differentially expressed lncRNAs (DE lncRNAs) and mRNAs (DE mRNAs) in male infertility. The target genes of DE lncRNAs were identified using a Gaussian graphical model. Gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were primarily enriched in protein transport and localization to the endoplasmic reticulum (ER). The lncRNA–mRNA co-expression network revealed cis- and trans-regulated target genes of lncRNAs. The transcriptome data implicated DE lncRNAs and DE mRNAs and their target genes in the accumulation of unfolded proteins in sperm ER, PERK-EIF2 pathway-induced ER stress, oxidative stress, and sperm cell apoptosis in individuals with oligozoospermia. These findings suggest that the identified lncRNAs and pathways could serve as effective therapeutic targets for male infertility.
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25
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Cecati M, Giulietti M, Righetti A, Sabanovic B, Piva F. Effects of CXCL12 isoforms in a pancreatic pre-tumour cellular model: Microarray analysis. World J Gastroenterol 2021; 27:1616-1629. [PMID: 33958847 PMCID: PMC8058651 DOI: 10.3748/wjg.v27.i15.1616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/05/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of death among cancers, it is characterized by poor prognosis and strong chemoresistance. In the PDAC microenvironment, stromal cells release different extracellular components, including CXCL12. The CXCL12 is a chemokine promoting the communication between tumour and stromal cells. Six different splicing isoforms of CXCL12 are known (α, β, γ, δ, ε, θ) but their role in PDAC has not yet been characterized.
AIM To investigate the specific role of α, β, and γ CXCL12 isoforms in PDAC onset.
METHODS We used hTERT-HPNE E6/E7/KRasG12D (Human Pancreatic Nestin-Expressing) cell line as a pancreatic pre-tumour model and exposed it to the α, β, and γ CXCL12 isoforms. The altered expression profiles were assessed by microarray analyses and confirmed by Real-Time polymerase chain reaction. The functional enrichment analyses have been performed by Enrichr tool to highlight Gene Ontology enriched terms. In addition, wound healing assays have been carried out to assess the phenotypic changes, in terms of migration ability, induced by the α, β, and γ CXCL12 isoforms.
RESULTS Microarray analysis of hTERT-HPNE cells treated with the three different CXCL12 isoforms highlighted that the expression of only a few genes was altered. Moreover, the α and β isoforms showed an alteration in expression of different genes, whereas γ isoform affected the expression of genes also common with α and β isoforms. The β isoform altered the expression of genes mainly involved in cell cycle regulation. In addition, all isoforms affected the expression of genes associated to cell migration, adhesion and cytoskeleton. In vitro cell migration assay confirmed that CXCL12 enhanced the migration ability of hTERT-HPNE cells. Among the CXCL12 splicing isoforms, the γ isoform showed higher induction of migration than α and β isoforms.
CONCLUSION Our data suggests an involvement and different roles of CXCL12 isoforms in PDAC onset. However, more investigations are needed to confirm these preliminary observations.
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Affiliation(s)
- Monia Cecati
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60126, Italy
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60126, Italy
| | - Alessandra Righetti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60126, Italy
| | - Berina Sabanovic
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60126, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60126, Italy
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26
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Gilhooley MJ, Hickey DG, Lindner M, Palumaa T, Hughes S, Peirson SN, MacLaren RE, Hankins MW. ON-bipolar cell gene expression during retinal degeneration: Implications for optogenetic visual restoration. Exp Eye Res 2021; 207:108553. [PMID: 33811915 PMCID: PMC8214074 DOI: 10.1016/j.exer.2021.108553] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 03/08/2021] [Accepted: 03/23/2021] [Indexed: 12/28/2022]
Abstract
Purpose Retinal bipolar cells survive even in the later stages of inherited retinal degenerations (IRDs) and so are attractive targets for optogenetic approaches to vision restoration. However, it is not known to what extent the remodelling that these cells undergo during degeneration affects their function. Specifically, it is unclear if they are free from metabolic stress, receptive to adeno-associated viral vectors, suitable for opsin-based optogenetic tools and able to propagate signals by releasing neurotransmitter. Methods Fluorescence activated cell sorting (FACS) was performed to isolate labelled bipolar cells from dissociated retinae of litter-mates with or without the IRD mutation Pde6brd1/rd1 selectively expressing an enhanced yellow fluorescent protein (EYFP) as a marker in ON-bipolar cells. Subsequent mRNA extraction allowed Illumina® microarray comparison of gene expression in bipolar cells from degenerate to those of wild type retinae. Changes in four candidate genes were further investigated at the protein level using retinal immunohistochemistry over the course of degeneration. Results A total of sixty differentially expressed transcripts reached statistical significance: these did not include any genes directly associated with native primary bipolar cell signalling, nor changes consistent with metabolic stress. Four significantly altered genes (Srm2, Slf2, Anxa7 & Cntn1), implicated in synaptic remodelling, neurotransmitter release and viral vector entry had immunohistochemical staining colocalising with ON-bipolar cell markers and varying over the course of degeneration. Conclusion Our findings suggest relatively few gene expression changes in the context of degeneration: that despite remodelling, bipolar cells are likely to remain viable targets for optogenetic vision restoration. In addition, several genes where changes were seen could provide a basis for investigations to enhance the efficacy of optogenetic therapies. Bipolar cells are attractive targets for therapeutic optogenetics in IRDs. This is the first cell specific transcriptomic analysis of bipolar cells in an IRD model. Bipolar cells maintain expression of genes essential to act as targets for optogenetics. Protein staining relating to four candidate genes (Anxa7, Cntn1, Srm2, Sulf2) is confirmed using immunohistochemistry.
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Affiliation(s)
- Michael J Gilhooley
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom; The Oxford Eye Hospital, Oxford, OX3 9DU, United Kingdom; Moorfields Eye Hospital, London, EC1V 2PD, United Kingdom
| | - Doron G Hickey
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom; Royal Victorian Eye and Ear Hospital, Melbourne, 002, Australia
| | - Moritz Lindner
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom; The Oxford Eye Hospital, Oxford, OX3 9DU, United Kingdom; Institute of Physiology and Pathophysiology, Department of Neurophysiology, Philipps University, Deutschhausstrasse 1-2, Marburg, 35037, Germany
| | - Teele Palumaa
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Steven Hughes
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom; Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Stuart N Peirson
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom; The Oxford Eye Hospital, Oxford, OX3 9DU, United Kingdom; Moorfields Eye Hospital, London, EC1V 2PD, United Kingdom
| | - Mark W Hankins
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom; Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, OX1 3RE, United Kingdom.
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Gómez-Carballa A, Barral-Arca R, Cebey-López M, Bello X, Pardo-Seco J, Martinón-Torres F, Salas A. Identification of a Minimal 3-Transcript Signature to Differentiate Viral from Bacterial Infection from Best Genome-Wide Host RNA Biomarkers: A Multi-Cohort Analysis. Int J Mol Sci 2021; 22:ijms22063148. [PMID: 33808774 PMCID: PMC8003556 DOI: 10.3390/ijms22063148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
The fight against the spread of antibiotic resistance is one of the most important challenges facing health systems worldwide. Given the limitations of current diagnostic methods, the development of fast and accurate tests for the diagnosis of viral and bacterial infections would improve patient management and treatment, as well as contribute to reducing antibiotic misuse in clinical settings. In this scenario, analysis of host transcriptomics constitutes a promising target to develop new diagnostic tests based on the host-specific response to infections. We carried out a multi-cohort meta-analysis of blood transcriptomic data available in public databases, including 11 different studies and 1209 samples from virus- (n = 695) and bacteria- (n = 514) infected patients. We applied a Parallel Regularized Regression Model Search (PReMS) on a set of previously reported genes that distinguished viral from bacterial infection to find a minimum gene expression bio-signature. This strategy allowed us to detect three genes, namely BAFT, ISG15 and DNMT1, that clearly differentiate groups of infection with high accuracy (training set: area under the curve (AUC) 0.86 (sensitivity: 0.81; specificity: 0.87); testing set: AUC 0.87 (sensitivity: 0.82; specificity: 0.86)). BAFT and ISG15 are involved in processes related to immune response, while DNMT1 is related to the preservation of methylation patterns, and its expression is modulated by pathogen infections. We successfully tested this three-transcript signature in the 11 independent studies, demonstrating its high performance under different scenarios. The main advantage of this three-gene signature is the low number of genes needed to differentiate both groups of patient categories.
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Affiliation(s)
- Alberto Gómez-Carballa
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Ruth Barral-Arca
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Miriam Cebey-López
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Xabier Bello
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Jacobo Pardo-Seco
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain; (A.G.-C.); (R.B.-A.); (M.C.-L.); (X.B.); (J.P.-S.)
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Galicia, Spain;
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
| | - Antonio Salas
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, 15706 Galicia, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, 15706 Galicia, Spain
- Correspondence:
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RNA-seq and GSEA identifies suppression of ligand-gated chloride efflux channels as the major gene pathway contributing to form deprivation myopia. Sci Rep 2021; 11:5280. [PMID: 33674625 PMCID: PMC7935918 DOI: 10.1038/s41598-021-84338-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
Currently there is no consensus regarding the aetiology of the excessive ocular volume that characterizes high myopia. Thus, we aimed to test whether the gene pathways identified by gene set enrichment analysis of RNA-seq transcriptomics refutes the predictions of the Retinal Ion Driven Efflux (RIDE) hypothesis when applied to the induction of form-deprivation myopia (FDM) and subsequent recovery (post-occluder removal). We found that the induction of profound FDM led to significant suppression in the ligand-gated chloride ion channel transport pathway via suppression of glycine, GABAA and GABAC ionotropic receptors. Post-occluder removal for short term recovery from FDM of 6 h and 24 h, induced significant upregulation of the gene families linked to cone receptor phototransduction, mitochondrial energy, and complement pathways. These findings support a model of form deprivation myopia as a Cl− ion driven adaptive fluid response to the modulation of the visual signal cascade by form deprivation that in turn affects the resultant ionic environment of the outer and inner retinal tissues, axial and vitreal elongation as predicted by the RIDE model. Occluder removal and return to normal light conditions led to return to more normal upregulation of phototransduction, slowed growth rate, refractive recovery and apparent return towards physiological homeostasis.
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Lan Y, Ng CT, Ong CN, Yu LE, Bay BH. Transcriptomic analysis identifies dysregulated genes and functional networks in human small airway epithelial cells exposed to ambient PM 2.5. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111702. [PMID: 33396033 DOI: 10.1016/j.ecoenv.2020.111702] [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: 06/26/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Cellular models exhibiting human physiological features of pseudostratified columnar epithelia, provide a more realistic approach for elucidating detailed mechanisms underlying PM2.5-induced pulmonary toxicity. In this study, we characterized the barrier and mucociliary functions of differentiated human small airway epithelial cells (SAECs), cultured at the air-liquid interface (ALI). Due to the presence of mucociliary protection, particle internalization was reduced, with a concomitant decrease in cytotoxicity in differentiated S-ALI cells, as compared to conventional submerged SAEC cultures. After 24-hour exposure to PM2.5 surrogates, 117 up-regulated genes and 156 down-regulated genes were detected in S-ALI cells, through transcriptomic analysis using the Affymetrix Clariom™ S Human Array. Transcription-level changes in >60 signaling pathways, were revealed by functional annotation of the 273 differentially expressed genes, using the PANTHER Gene List Analysis. These pathways are involved in multiple cellular processes, that include inflammation and apoptosis. Exposure to urban PM2.5 led to complex responses in airway epithelia, including a net induction of downstream pro-inflammatory and pro-apoptotic responses. Collectively, this study highlights the importance of using the more advanced ALI model rather than the undifferentiated submerged model, to avoid over-assessment of inhaled particle toxicity in human. The results of our study also suggest that reduction of ambient PM2.5 concentrations would have a protective effect on respiratory health in humans.
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Affiliation(s)
- Yang Lan
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Cheng Teng Ng
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Choon Nam Ong
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| | - Liya E Yu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Boon Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
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Samul-tang ameliorates oocyte damage due to cyclophosphamide-induced chronic ovarian dysfunction in mice. Sci Rep 2020; 10:21925. [PMID: 33318603 PMCID: PMC7736329 DOI: 10.1038/s41598-020-79013-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/03/2020] [Indexed: 01/27/2023] Open
Abstract
Samul-tang (SM), a traditional herbal medicine, has been used to treat menstrual irregularities and infertility in women. However, the cellular and molecular mechanisms underlying the effects of SM remain elusive. We investigated the potential protective effect of SM against chronic ovarian dysfunction and used bioinformatics analysis to identify its underlying mechanism in a mouse model of cyclophosphamide (CP)-induced diminished ovarian reserve. Female C57BL/6 mice were intraperitoneally injected with CP three times a week, followed by oral administration of distilled water (CP group) or SM (CP + SM group) for 4 weeks. Four weeks later, the effect of SM was assessed by ovarian tissue histological analysis, steroid hormone measurement, oocyte quality, and mRNA and microRNA microarray analysis in the ovaries. Although SM administration did not prevent CP-induced follicle loss in mice, the quality of oocytes was better in CP + SM mice than in CP mice. Gene expression analysis revealed that the expression of fertilisation- and ovarian follicle development-related genes was altered by CP treatment but normalized after SM administration. Further bioinformatics analysis showed possible interactions between differentially expressed mRNAs and microRNAs. Therefore, we demonstrated the protective effects of SM on ovarian function and oocyte maturation against CP-induced damage via multiple epigenetic mechanisms.
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Dodla P, Bhoopalan V, Khoo SK, Miranti C, Sridhar S. Gene expression analysis of human prostate cell lines with and without tumor metastasis suppressor CD82. BMC Cancer 2020; 20:1211. [PMID: 33298014 PMCID: PMC7724878 DOI: 10.1186/s12885-020-07675-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/22/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Tetraspanin CD82 is a tumor metastasis suppressor that is known to down regulate in various metastatic cancers. However, the exact mechanism by which CD82 prevents cancer metastasis is unclear. This study aims to identify genes that are regulated by CD82 in human prostate cell lines. METHODS We used whole human genome microarray to obtain gene expression profiles in a normal prostate epithelial cell line that expressed CD82 (PrEC-31) and a metastatic prostate cell line that does not express CD82 (PC3). Then, siRNA silencing was used to knock down CD82 expression in PrEC-31 while CD82 was re-expressed in PC3 to acquire differentially-expressed genes in the respective cell line. RESULTS Differentially-expressed genes with a P < 0.05 were identified in 3 data sets: PrEC-31 (+CD82) vs PrEC-31(-CD82), PC3-57 (+CD82) vs. PC3-5 V (-CD82), and PC3-29 (+CD82) vs. PC3-5 V (-CD82). Top 25 gene lists did not show overlap within the data sets, except (CALB1) the calcium binding protein calbindin 1 which was significantly up-regulated (2.8 log fold change) in PrEC-31 and PC3-29 cells that expressed CD82. Other most significantly up-regulated genes included serine peptidase inhibitor kazal type 1 (SPINK1) and polypeptide N-acetyl galactosaminyl transferase 14 (GALNT14) and most down-regulated genes included C-X-C motif chemokine ligand 14 (CXCL14), urotensin 2 (UTS2D), and fibroblast growth factor 13 (FGF13). Pathways related with cell proliferation and angiogenesis, migration and invasion, cell death, cell cycle, signal transduction, and metabolism were highly enriched in cells that lack CD82 expression. Expression of two mutually inclusive genes in top 100 gene lists of all data sets, runt-related transcription factor (RUNX3) and trefoil factor 3 (TFF3), could be validated with qRT-PCR. CONCLUSION Identification of genes and pathways regulated by CD82 in this study may provide additional insights into the role that CD82 plays in prostate tumor progression and metastasis, as well as identify potential targets for therapeutic intervention.
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Affiliation(s)
- Pushpaja Dodla
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Vanitha Bhoopalan
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Cindy Miranti
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ, 85724, USA
| | - Suganthi Sridhar
- Department of Integrative Biology, University of South Florida, 140, 7Th Avenue S, University of South Florida, St. Petersburg, FL, 33701, USA.
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lncRNAs Are Involved in Sevoflurane Anesthesia-Related Brain Function Modulation through Affecting Mitochondrial Function and Aging Process. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8841511. [PMID: 33354572 PMCID: PMC7735847 DOI: 10.1155/2020/8841511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 02/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in brain function modulation and neurodegenerative diseases. However, whether lncRNA regulations are involved in the mechanisms of perioperative neurocognitive disorders, especially in anesthesia-related brain dysfunction, remain unknown. Therefore, we explored the expression and regulation pattern profiles of lncRNAs in the hippocampus of aged rats after sevoflurane anesthesia. Three lncRNAs and 772 protein-coding genes were identified by microarray analysis and evidenced by in vitro and in vivo experiments as differentially expressed. Functional annotation and differentially expressed- (DE-) lncRNA-mRNA coexpression networks reveal that DE-lncRNAs are associated with mitochondrial dysfunction and oxidative stress, aging-related metabolism alterations, DNA damage, and apoptosis, as well as neurodegenerative features during sevoflurane anesthesia. These results suggest that lncRNAs play roles in general anesthesia-related brain function modulation during the perioperative context and provide insights into the lncRNA-related modulation mechanisms and targets.
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Panach L, Pertusa C, Martínez-Rojas B, Acebrón Á, Mifsut D, Tarín JJ, Cano A, García-Pérez MÁ. Comparative transcriptome analysis identifies CARM1 and DNMT3A as genes associated with osteoporosis. Sci Rep 2020; 10:16298. [PMID: 33004909 PMCID: PMC7530982 DOI: 10.1038/s41598-020-72870-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
To identify new candidate genes in osteoporosis, mainly involved in epigenetic mechanisms, we compared whole gene-expression in osteoblasts (OBs) obtained from women undergoing hip replacement surgery due to fragility fracture and severe osteoarthritis. Then, we analyzed the association of several SNPs with BMD in 1028 women. Microarray analysis yielded 2542 differentially expressed transcripts belonging to 1798 annotated genes, of which 45.6% (819) were overexpressed, and 54.4% (979) underexpressed (fold-change between - 7.45 and 4.0). Among the most represented pathways indicated by transcriptome analysis were chondrocyte development, positive regulation of bone mineralization, BMP signaling pathway, skeletal system development and Wnt signaling pathway. In the translational stage we genotyped 4 SNPs in DOT1L, HEY2, CARM1 and DNMT3A genes. Raw data analyzed against inheritance patterns showed a statistically significant association between a SNP of DNMT3A and femoral neck-(FN) sBMD and primarily a SNP of CARM1 was correlated with both FN and lumbar spine-(LS) sBMD. Most of these associations remained statistically significant after adjusting for confounders. In analysis with anthropometric and clinical variables, the SNP of CARM1 unexpectedly revealed a close association with BMI (p = 0.000082), insulin (p = 0.000085), and HOMA-IR (p = 0.000078). In conclusion, SNPs of the DNMT3A and CARM1 genes are associated with BMD, in the latter case probably owing to a strong correlation with obesity and fasting insulin levels.
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Affiliation(s)
- Layla Panach
- Research Unit, INCLIVA Health Research Institute, 46010, Valencia, Spain
| | - Clara Pertusa
- Research Unit, INCLIVA Health Research Institute, 46010, Valencia, Spain
| | | | - Álvaro Acebrón
- Orthopedic Surgery and Traumatology, Clinic Hospital, Institute of Health Research INCLIVA, 46010, Valencia, Spain
| | - Damián Mifsut
- Orthopedic Surgery and Traumatology, Clinic Hospital, Institute of Health Research INCLIVA, 46010, Valencia, Spain
| | - Juan J Tarín
- Department of Cellular Biology, Functional Biology and Physical Anthropology, University of Valencia, 46100, Burjassot, Spain
| | - Antonio Cano
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010, Valencia, Spain
| | - Miguel Ángel García-Pérez
- Research Unit, INCLIVA Health Research Institute, 46010, Valencia, Spain.
- Department of Genetics, University of Valencia, 46100, Burjassot, Spain.
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Bleker de Oliveira M, Koshkin V, Liu G, Krylov SN. Analytical Challenges in Development of Chemoresistance Predictors for Precision Oncology. Anal Chem 2020; 92:12101-12110. [PMID: 32790291 DOI: 10.1021/acs.analchem.0c02644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemoresistance, i.e., tumor insensitivity to chemotherapy, shortens life expectancy of cancer patients. Despite the availability of new treatment options, initial systemic regimens for solid tumors are dominated by a set of standard chemotherapy drugs, and alternative therapies are used only when a patient has demonstrated chemoresistance clinically. Chemoresistance predictors use laboratory parameters measured on tissue samples to predict the patient's response to chemotherapy and help to avoid application of chemotherapy to chemoresistant patients. Despite thousands of publications on putative chemoresistance predictors, there are only about a dozen predictors that are sufficiently accurate for precision oncology. One of the major reasons for inaccuracy of predictors is inaccuracy of analytical methods utilized to measure their laboratory parameters: an inaccurate method leads to an inaccurate predictor. The goal of this study was to identify analytical challenges in chemoresistance-predictor development and suggest ways to overcome them. Here we describe principles of chemoresistance predictor development via correlating a clinical parameter, which manifests disease state, with a laboratory parameter. We further classify predictors based on the nature of laboratory parameters and analyze advantages and limitations of different predictors using the reliability of analytical methods utilized for measuring laboratory parameters as a criterion. Our eventual focus is on predictors with known mechanisms of reactions involved in drug resistance (drug extrusion, drug degradation, and DNA damage repair) and using rate constants of these reactions to establish accurate and robust laboratory parameters. Many aspects and conclusions of our analysis are applicable to all types of disease biomarkers built upon the correlation of clinical and laboratory parameters.
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Affiliation(s)
- Mariana Bleker de Oliveira
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto M3J 1P3, Canada
| | - Vasilij Koshkin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto M3J 1P3, Canada
| | - Geoffrey Liu
- Department of Medicine, Medical Oncology, Princess Margaret Cancer Centre, Toronto M5G 2M9, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto M3J 1P3, Canada
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Lü X, Huang Y, Qu Y, Zhang Y, Zhang Z. Integrated transcriptomic and proteomic study on the different molecular mechanisms of PC12 cell growth on chitosan and collagen/chitosan films. Regen Biomater 2020; 7:553-565. [PMID: 33365141 PMCID: PMC7748450 DOI: 10.1093/rb/rbaa030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/25/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022] Open
Abstract
The purpose of this article is to integrate the transcriptomic analysis and the proteomic profiles and to reveal and compare the different molecular mechanisms of PC12 cell growth on the surface of chitosan films and collagen/chitosan films. First, the chitosan films and the collagen/chitosan films were prepared. Subsequently, the cell viability assay was performed; the cell viability of the PC12 cells cultured on the collagen/chitosan films for 24 h was significantly higher than that on the chitosan films. Then, with cDNA microarray, the numbers of differentially expressed genes of PC12 cells on the surface of chitosan and collagen/chitosan films were 13349 and 5165, respectively. Next, the biological pathway analysis indicated that the differentially expressed genes were involved in 40 pathways directly related to cell adhesion and growth. The integrated transcriptomic and our previous proteomic analysis revealed that three biological pathways-extracellular matrix-receptor interaction, focal adhesion and regulation of actin cytoskeleton-were regulated in the processes of protein adsorption, cell adhesion and growth. The adsorbed proteins on the material surfaces further influenced the expression of important downstream genes by regulating the expression of related receptor genes in these three pathways. In comparison, chitosan films had a strong inhibitory effect on PC12 cell adhesion and growth, resulting in the significantly lower cell viability on its surface; on the contrary, collagen/chitosan films were more conducive to promoting PC12 cell adhesion and growth, resulting in higher cell viability.
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Affiliation(s)
- Xiaoying Lü
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yan Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yayun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yiwen Zhang
- SQ Medical Device Co., Ltd, Nanjing 210008, China
| | - Zequn Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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Gao P, Hu Y, Wang J, Ni Y, Zhu Z, Wang H, Yang J, Huang L, Fang L. Underlying Mechanism of Insulin Resistance: A Bioinformatics Analysis Based on Validated Related-Genes from Public Disease Databases. Med Sci Monit 2020; 26:e924334. [PMID: 32651353 PMCID: PMC7370576 DOI: 10.12659/msm.924334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background The underlying mechanism of insulin resistance is complex; bioinformatics analysis is used to explore the mechanism based differential expression genes (DEGs) obtained from omics analysis. However, the expression and role of most DEGs involved in bioinformatics analysis are invalidated. This study aimed to disclose the mechanism of insulin resistance via bioinformatics analysis based on validated insulin resistance-related genes (IRRGs) collected from public disease-gene databases. Material/Methods IRRGs were collected from 4 disease databases including NCBI-Gene, CTD, RGD, and Phenopedia. GO and KEGG analysis of IRRGs were performed by DAVID. Then, the STRING database was employed to construct a protein–protein interaction (PPI) network of IRRGs. The module analysis and hub genes identification were carried out by MCODE and cytoHubba plugin of Cytoscape based on the primary PPI network, respectively. Results A total of 1195 IRRGs were identified. Response to drug, hypoxia, insulin, positive regulation of transcription from RNA polymerase II promoter, cell proliferation, inflammatory response, negative regulation of apoptotic process, glucose homeostasis, cellular response to insulin stimulus, and aging were proposed as the crucial functions related to insulin resistance. Ten insulin resistance-related pathways included the pathways of insulin resistance, pathways in cancer, adipocytokine, prostate cancer, PI3K-Akt, insulin, AMPK, HIF-1, prolactin, and pancreatic cancer signaling pathway were revealed. INS, AKT1, IL-6, TP53, TNF, VEGFA, MAPK3, EGFR, EGF, and SRC were identified as the top 10 hub genes. Conclusions The current study presented a landscape view of possible underlying mechanism of insulin resistance by bioinformatics analysis based on validated IRRGs.
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Affiliation(s)
- Peng Gao
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Yan Hu
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Junyan Wang
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Yinghua Ni
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Zhengyi Zhu
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Huijuan Wang
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Jufei Yang
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Lingfei Huang
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
| | - Luo Fang
- Department of Pharmacy, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China (mainland)
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Prolactin and Estradiol are Epigenetic Modulators in Bovine Mammary Epithelial Cells during Staphylococcus aureus Infection. Pathogens 2020; 9:pathogens9070520. [PMID: 32605209 PMCID: PMC7399903 DOI: 10.3390/pathogens9070520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
Changes in the levels of reproductive hormones compromise the bovine innate immune response (IIR). Changes in 17β-estradiol (E2) and prolactin (bPRL) levels affect the IIR of bovine mammary epithelial cells (bMECs), the target tissue of these hormones. In this work, we explored the effect of the combined hormones on bMEC IIR during Staphylococcus aureus infection, and if they can modulate epigenetic marks. By gentamicin protection assays, we determined that combined hormones (bPRL (5 ng/mL) and E2 (50 pg/mL)] decrease S. aureus internalization into bMECs (~50%), which was associated with a reduction in integrin α5β1 membrane abundance (MA) (~80%) determined by flow cytometry. Additionally, combined hormones increased Toll-like receptor 2 (TLR2) MA (~25%). By RT-qPCR, we showed that combined hormones induce the expression of pro- and anti-inflammatory cytokine genes, as well as up-regulate antimicrobial peptide gene expression. The combined hormones induced H3K9Ac at 12 h of treatment, which coincides with the reduction in histone deacetylase (HDAC, ~15%) activity. In addition, hormones increased the H3K9me2 mark at 12 h, which correlates with a reduction in the expression of KDM4A. In conclusion, bPRL and E2 modulate the IIR of bMECs, an effect that can be related to the regulation of histone H3 modifications such as H3K9Ac and H3K9me2.
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Shaw BI, Cheng DK, Acharya CR, Ettenger RB, Lyerly HK, Cheng Q, Kirk AD, Chambers ET. An age-independent gene signature for monitoring acute rejection in kidney transplantation. Theranostics 2020; 10:6977-6986. [PMID: 32550916 PMCID: PMC7295062 DOI: 10.7150/thno.42110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Acute rejection (AR) remains a significant problem that negatively impacts long-term renal allograft survival. Numerous therapies are used to prevent AR that differ by center and recipient age. This variability confounds diagnostic methods. Methods: To develop an age-independent gene signature for AR effective across a broad array of immunosuppressive regimens, we compiled kidney transplant biopsy (n=1091) and peripheral blood (n=392) gene expression profiles from 12 independent public datasets. After removing genes differentially expressed in pediatric and adult patients, we compared gene expression profiles from biopsy and peripheral blood samples of patients with AR to those who were stable (STA), using Mann-Whitney U Tests with validation in independent testing datasets. We confirmed this signature in pediatric and adult patients (42 AR and 47 STA) from our institutional biorepository. Results: We identified a novel age-independent gene network that identified AR from both kidney and blood samples. We developed a 90-probe set signature targeting 76 genes that differentiated AR from STA and found an 8 gene subset (DIP2C, ENOSF1, FBXO21, KCTD6, PDXDC1, REXO2, HLA-E, and RAB31) that was associated with AR. Conclusion: We used publicly available datasets to create a gene signature of AR that identified AR irrespective of immunosuppression regimen or recipient age. This study highlights a novel model to screen and validate biomarkers across multiple treatment regimens.
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Affiliation(s)
- Brian I Shaw
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Daniel K. Cheng
- Department of Pediatrics, Duke University Medical Center, Durham, United States
| | | | - Robert B Ettenger
- Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, United States
| | - Herbert Kim Lyerly
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Qing Cheng
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Allan D Kirk
- Department of Surgery, Duke University Medical Center, Durham, United States
- Department of Pediatrics, Duke University Medical Center, Durham, United States
| | - Eileen T Chambers
- Department of Surgery, Duke University Medical Center, Durham, United States
- Department of Pediatrics, Duke University Medical Center, Durham, United States
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Wang Y, Qian M, Qu Y, Yang N, Mu B, Liu K, Yang J, Zhou Y, Ni C, Zhong J, Guo X. Genome-Wide Screen of the Hippocampus in Aged Rats Identifies Mitochondria, Metabolism and Aging Processes Implicated in Sevoflurane Anesthesia. Front Aging Neurosci 2020; 12:122. [PMID: 32457595 PMCID: PMC7221025 DOI: 10.3389/fnagi.2020.00122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/14/2020] [Indexed: 01/11/2023] Open
Abstract
Previous studies have shown multiple mechanisms and pathophysiological changes after anesthesia, and genome-wide studies have been implemented in the studies of brain aging and neurodegenerative diseases. However, the genome-wide gene expression patterns and modulation networks after general anesthesia remains to be elucidated. Therefore, whole transcriptome microarray analysis was used to explore the coding gene expression patterns in the hippocampus of aged rats after sevoflurane anesthesia. Six hundred and thirty one upregulated and 183 downregulated genes were screened out, then 44 enriched terms of biological process, 16 of molecular function and 18 of the cellular components were identified by Gene Ontology (GO) and KEGG analysis. Among them, oxidative stress, metabolism, aging, and neurodegeneration were the most enriched biological processes and changed functions. Thus, involved genes of these processes were selected for qPCR verification and a good consistency was confirmed. The potential signaling pathways were further constructed including mitochondrion and oxidative stress-related Hifs-Prkcd-Akt-Nfe2l2-Sod1 signaling, multiple metabolism signaling (Scd2, Scap-Hmgcs2, Aldh18a1-Glul and Igf1r), as well as aging and neurodegeneration related signaling (Spidr-Ercc4-Cdkn1a-Pmaip1 and Map1lc3b). These results provide potential therapeutic gene targets for brain function modulation and memory formation process after inhaled anesthesia in the elderly, which could be valuable for preventing postoperative brain disorders and diseases, such as perioperative neurocognitive disorders (PND), from the genetic level in the future.
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Affiliation(s)
- Yujie Wang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Min Qian
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Yinyin Qu
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Ning Yang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Bing Mu
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kaixi Liu
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Jing Yang
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Yang Zhou
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
| | - Cheng Ni
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhong
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangyang Guo
- Department of Anesthesiology, Peking University Third Hospital, Beijing, China
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Karaer A, Tuncay G, Dogan B, Tecellioglu N, Cigremis Y. Microarray analysis of cumulus cells in women with ovarian endometriosis undergoing intracytoplasmic sperm injection. JOURNAL OF ENDOMETRIOSIS AND PELVIC PAIN DISORDERS 2020. [DOI: 10.1177/2284026520906070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective: The aim of this study was to find the significantly altered genes in cumulus cells of women with ovarian endometriosis by using microarray and quantitative polymerase chain reaction analysis. Methods: Thirty women with ovarian endometriosis and 30 age–body mass index matched controls (women with infertility as a result of pure male factor) were enrolled in this study. Cumulus cells from study participants who underwent controlled ovarian hyperstimulation were isolated mechanically. Microarray comparative genomic hybridization was used to compare the transcriptome of cumulus cells from women with ovarian endometriosis and controls. According to the different expression levels in the microarrays and their putative functions, KRAS, ZNF322, and SDHA were selected and analyzed by real-time quantitative polymerase chain reaction. Results: There was no significant difference in the basal conditions between patients with endometriosis and controls, such as age, body mass index, basal follicle stimulating hormone and estradiol levels, and total gonadotrophin dosage. The gene expression profile of cumulus cells from patients with endometriosis was significantly different from that of controls. A total of 295 genes were significantly up- or down-regulated (p-value < 0.05 and absolute fold change > 1.5). For all of the genes adjusted p-value was found to be 0.999. Polymerase chain reaction analysis showed that KRAS and ZNF322 mRNA levels in the cumulus cells of patients with ovarian endometriosis were significantly up-regulated compared to controls (fold changes: 3.05 and 3.22, respectively). Conclusion: KRAS and ZNF322 mRNA levels in the cumulus cells of patients with ovarian endometriosis were significantly up-regulated.
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Affiliation(s)
- Abdullah Karaer
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, School of Medicine, Inonu University, Malatya, Turkey
| | - Gorkem Tuncay
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, School of Medicine, Inonu University, Malatya, Turkey
| | - Berat Dogan
- Department of Biomedical Engineering, School of Engineering, Inonu University, Malatya, Turkey
| | - Nihan Tecellioglu
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, School of Medicine, Inonu University, Malatya, Turkey
| | - Yilmaz Cigremis
- Department of Medical Biology and Genetics, School of Medicine, Inonu University, Malatya, Turkey
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Han Y, Yoon J, Choi M. Tracing the Anti‐Inflammatory Mechanism/Triggers of
d
‐Allulose: A Profile Study of Microbiome Composition and mRNA Expression in Diet‐Induced Obese Mice. Mol Nutr Food Res 2020; 64:e1900982. [DOI: 10.1002/mnfr.201900982] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/12/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Youngji Han
- Department of Food Science and NutritionKyungpook National University 1370 San‐Kyuk Dong Puk‐Ku 702‐701 Daegu Republic of Korea
- Center for Food and Nutritional Genomics ResearchKyungpook National University 1370 San‐Kyuk Dong Puk‐Ku 702‐701 Daegu Republic of Korea
| | - Joon Yoon
- Harvard University T. H. Chan School of Public Health 655 Huntington Ave Boston MA 02115 USA
| | - Myung‐Sook Choi
- Department of Food Science and NutritionKyungpook National University 1370 San‐Kyuk Dong Puk‐Ku 702‐701 Daegu Republic of Korea
- Center for Food and Nutritional Genomics ResearchKyungpook National University 1370 San‐Kyuk Dong Puk‐Ku 702‐701 Daegu Republic of Korea
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Lin Q, Di YP. Determination and Quantification of Bacterial Virulent Gene Expression Using Quantitative Real-Time PCR. Methods Mol Biol 2020; 2102:177-193. [PMID: 31989555 DOI: 10.1007/978-1-0716-0223-2_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Polymerase chain reaction (PCR) plays significant roles in modern molecular biology. However, it is relatively cumbersome and less accurate to use the traditional PCR method in quantifying gene expression because it requires first generating a standard curve with multiple input controls showing linearity with amplified control PCR products on a electrophoresis gel to compare with the abundance of the to-be-determined gene transcript PCR amplicons. Quantitative real-time PCR (qRT-PCR) is a time-efficient and reliable tool for accurate quantification and comparison of gene (RNA transcript) expression from various biological samples. Current technology has simplified and expedited the qPCR process significantly. However, proper techniques and standard protocols are required in eliminating potentially erroneous experimental outcome. Here, we provide an example from a drug-treated bacterial gene expression study with detailed protocols to demonstrate real-time qPCR with SYBR™ Green and TaqMan®, two of the most adapted and well-established qPCR technologies. Relative quantification of gene (RNA transcript) expression using qRT-PCR is demonstrated in detail from sample preparations to data analysis.
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Affiliation(s)
- Qiao Lin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA.
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Dolinar A, Koritnik B, Glavač D, Ravnik-Glavač M. Circular RNAs as Potential Blood Biomarkers in Amyotrophic Lateral Sclerosis. Mol Neurobiol 2019; 56:8052-8062. [PMID: 31175544 PMCID: PMC6834740 DOI: 10.1007/s12035-019-1627-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are emerging as a novel, yet powerful player in many human diseases. They are involved in several cellular processes and are becoming a noteworthy type of biomarkers. Among other functions, circRNAs can serve as RNA sponges or as scaffolds for RNA-binding proteins. Here, we investigated a microarray expression profile of circRNAs in leukocyte samples from ALS patients and age- and sex-matched healthy controls to identify differentially expressed circRNAs. We selected 10 of them for a qPCR validation of expression on a larger set of samples, identification of their associations with clinical parameters, and evaluation of their diagnostic potential. In total, expression of 7/10 circRNAs was significant in a larger cohort of ALS patients, compared with age- and sex-matched healthy controls. Three of them (hsa_circ_0023919, hsa_circ_0063411, and hsa_circ_0088036) showed the same regulation as in microarray results. These three circRNAs also had AUC > 0.95, and sensitivity and specificity for the optimal threshold point > 90%, showing their potential for using them as diagnostic biomarkers.
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Affiliation(s)
- Ana Dolinar
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Blaž Koritnik
- Institute of Clinical Neurophysiology, Division of Neurology, University Medical Centre Ljubljana, Zaloška cesta 7, 1000, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia.
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Brązert M, Kranc W, Chermuła B, Kowalska K, Jankowski M, Celichowski P, Jeseta M, Piotrowska-Kempisty H, Pawelczyk L, Zabel M, Mozdziak P, Kempisty B. Human Ovarian Granulosa Cells Isolated during an IVF Procedure Exhibit Differential Expression of Genes Regulating Cell Division and Mitotic Spindle Formation. J Clin Med 2019; 8:jcm8122026. [PMID: 31756998 PMCID: PMC6947147 DOI: 10.3390/jcm8122026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Granulosa cells (GCs) are a population of somatic cells whose role after ovulation is progesterone production. GCs were collected from patients undergoing controlled ovarian stimulation during an in vitro fertilization procedure, and they were maintained for 1, 7, 15, and 30 days of in vitro primary culture before collection for further gene expression analysis. A study of genes involved in the biological processes of interest was carried out using expression microarrays. To validate the obtained results, Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) was performed. The direction of changes in the expression of the selected genes was confirmed in most of the examples. Six ontological groups ("cell cycle arrest", "cell cycle process", "mitotic spindle organization", "mitotic spindle assembly checkpoint", "mitotic spindle assembly", and "mitotic spindle checkpoint") were analyzed in this study. The results of the microarrays obtained by us allowed us to identify two groups of genes whose expressions were the most upregulated (FAM64A, ANLN, TOP2A, CTGF, CEP55, BIRC5, PRC1, DLGAP5, GAS6, and NDRG1) and the most downregulated (EREG, PID1, INHA, RHOU, CXCL8, SEPT6, EPGN, RDX, WNT5A, and EZH2) during the culture. The cellular ultrastructure showed the presence of structures characteristic of mitotic cell division: a centrosome surrounded by a pericentric matrix, a microtubule system, and a mitotic spindle connected to chromosomes. The main goal of the study was to identify the genes involved in mitotic division and to identify the cellular ultrastructure of GCs in a long-term in vitro culture. All of the genes in these groups were subjected to downstream analysis, and their function and relation to the ovarian environment are discussed. The obtained results suggest that long-term in vitro cultivation of GCs may lead to their differentiation toward another cell type, including cells with cancer-like characteristics.
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Affiliation(s)
- Maciej Brązert
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, 33 Polna St., 60-535 Poznań, Poland; (M.B.); (B.C.); (L.P.)
| | - Wiesława Kranc
- Department of Anatomy, Poznan University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland; (W.K.); (M.J.)
| | - Błażej Chermuła
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, 33 Polna St., 60-535 Poznań, Poland; (M.B.); (B.C.); (L.P.)
| | - Katarzyna Kowalska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland; (K.K.); (P.C.)
| | - Maurycy Jankowski
- Department of Anatomy, Poznan University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland; (W.K.); (M.J.)
| | - Piotr Celichowski
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland; (K.K.); (P.C.)
| | - Michal Jeseta
- Department of Obstetrics and Gynecology, University Hospital and Masaryk University, 20 Jihlavská St., 625 00 Brno, Czech Republic;
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 30 Dojazd St., 60-631 Poznań, Poland;
| | - Leszek Pawelczyk
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, 33 Polna St., 60-535 Poznań, Poland; (M.B.); (B.C.); (L.P.)
| | - Maciej Zabel
- Department of Histology and Embryology, Wroclaw Medical University, Chałubińskiego St., 50-368 Wrocław, Poland;
- Division of Anatomy and Histology, University of Zielona Gora, 28 Zyty St., 65-046 Zielona Góra, Poland
| | - Paul Mozdziak
- Physiology Graduate Program, North Carolina State University, Campus Box 7608, Raleigh, NC 27695-7608, USA;
| | - Bartosz Kempisty
- Department of Anatomy, Poznan University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland; (W.K.); (M.J.)
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland; (K.K.); (P.C.)
- Department of Obstetrics and Gynecology, University Hospital and Masaryk University, 20 Jihlavská St., 625 00 Brno, Czech Republic;
- Correspondence: ; Tel.: +48-618-546-567; Fax: +48-618-546-568
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Tsai HW, Franklin M, Armoskus C, Taniguchi S, Moder C, Trang K, Santacruz M, Milla A. Androgenic regulation of sexually dimorphic expression of RNA binding motif protein 48 in the developing mouse cortex and hippocampus. Int J Dev Neurosci 2019; 78:33-44. [PMID: 31400491 PMCID: PMC6897302 DOI: 10.1016/j.ijdevneu.2019.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022] Open
Abstract
To further reveal the molecular mechanism underlying sexual differentiation of the mouse cerebral cortex and hippocampus, we reanalyzed our previous microarray study with Gene Ontology (GO) term enrichment and found that the GO term "RNA binding" was over-represented among the 89 sexually dimorphic candidate genes. Thus, we selected 16 autosomal genes annotated to the term RNA binding and profiled their mRNA expression in the developing male and female mouse cortex/hippocampus. During the first three weeks after birth, sex differences in mRNA levels of Khdrbs2, Nanos2, Rbm48, and Tdrd3 were observed in the mouse cortex/hippocampus. Of these genes, only the female-biased expression of Rbm48 in neonates was abolished by prenatal exposure to testosterone propionate (TP), while postnatal treatment of TP three weeks after birth increased Rbm48 and Tdrd3 mRNA levels in both sexes. Regardless of sex, the postnatal cortex/hippocampus also showed a marked increase in the content of androgen receptor (Ar) and estrogen receptor β (Esr2), but a decrease in estrogen receptor α (Esr1) and aromatase (Cyp19a1), which might confer the different responses of Rbm48 to prenatal and postnatal TP. Our results suggest that androgen-regulated, sexually dimorphic Rbm48 expression might present a novel molecular mechanism by which perinatal androgens control development of sexual dimorphism in cortical and hippocampal structure and function.
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Affiliation(s)
- Houng-Wei Tsai
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Michael Franklin
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Chris Armoskus
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Saori Taniguchi
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Courtney Moder
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Kathy Trang
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Marilisa Santacruz
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
| | - Allyson Milla
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA 90840, USA
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Nieto-Taype MA, Garrigós-Martínez J, Sánchez-Farrando M, Valero F, Garcia-Ortega X, Montesinos-Seguí JL. Rationale-based selection of optimal operating strategies and gene dosage impact on recombinant protein production in Komagataella phaffii (Pichia pastoris). Microb Biotechnol 2019; 13:315-327. [PMID: 31657146 PMCID: PMC7017824 DOI: 10.1111/1751-7915.13498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
Its features as a microbial and eukaryotic organism have turned Komagataella phaffii (Pichia pastoris) into an emerging cell factory for recombinant protein production (RPP). As a key step of the bioprocess development, this work aimed to demonstrate the importance of tailor designing the cultivation strategy according to the production kinetics of the cell factory. For this purpose, K. phaffii clones constitutively expressing (PGAP) Candida rugosa lipase 1 (Crl1) with different gene dosage were used as models in continuous and fed‐batch cultures. Production parameters were much greater with a multicopy clone (MCC) than with the single‐copy clone (SCC). Regarding production kinetics, the specific product generation rate (qP) increased linearly with increasing specific growth rate (µ) in SCC; by contrast, qP exhibited saturation in MCC. A transcriptional analysis in chemostat cultures suggested the presence of eventual post‐transcriptional bottlenecks in MCC. After the strain characterization, in order to fulfil overall development of the bioprocess, the performance of both clones was also evaluated in fed‐batch mode. Strikingly, different optimal strategies were determined for both models due to the different production kinetic patterns observed as a trade‐off for product titre, yields and productivity. The combined effect of gene dosage and adequate µ enables rational process development with a view to optimize K. phaffii RPP bioprocesses.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Garrigós-Martínez
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Sánchez-Farrando
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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47
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Gómez-Carballa A, Cebey-López M, Pardo-Seco J, Barral-Arca R, Rivero-Calle I, Pischedda S, Currás-Tuala MJ, Gómez-Rial J, Barros F, Martinón-Torres F, Salas A. A qPCR expression assay of IFI44L gene differentiates viral from bacterial infections in febrile children. Sci Rep 2019; 9:11780. [PMID: 31409879 PMCID: PMC6692396 DOI: 10.1038/s41598-019-48162-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022] Open
Abstract
The diagnosis of bacterial infections in hospital settings is currently performed using bacterial culture from sterile site, but they are lengthy and limited. Transcriptomic biomarkers are becoming promising tools for diagnosis with potential applicability in clinical settings. We evaluated a RT-qPCR assay for a 2-transcript host expression signature (FAM89A and IFI44L genes) inferred from microarray data that allow to differentiate between viral and bacterial infection in febrile children. This assay was able to discriminate viral from bacterial infections (P-value = 1.04 × 10-4; AUC = 92.2%; sensitivity = 90.9%; specificity = 85.7%) and showed very high reproducibility regardless of the reference gene(s) used to normalize the data. Unexpectedly, the monogenic IFI44L expression signature yielded better results than those obtained from the 2-transcript test (P-value = 3.59 × 10-5; AUC = 94.1%; sensitivity = 90.9%; specificity = 92.8%). We validated this IFI44L signature in previously published microarray and whole-transcriptome data from patients affected by different types of viral and bacterial infections, confirming that this gene alone differentiates between both groups, thus saving time, effort, and costs. Herein, we demonstrate that host expression microarray data can be successfully translated into a fast, highly accurate and relatively inexpensive in vitro assay that could be implemented in the clinical routine.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain.
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain.
| | - Miriam Cebey-López
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María José Currás-Tuala
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Barros
- Unidad de Medicina Molecular, Fundación Pública Galega de Medicina Xenómica, CIBERER, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
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48
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Kuznetsov MS, Lisukov AN, Rizvanov AA, Tyapkina OV, Gusev OA, Rezvyakov PN, Kozlovskaya IB, Tomilovskaya ES, Nikolskiy EE, Islamov RR. Bioinformatic Study of Transcriptome Changes in the Mice Lumbar Spinal Cord After the 30-Day Spaceflight and Subsequent 7-Day Readaptation on Earth: New Insights Into Molecular Mechanisms of the Hypogravity Motor Syndrome. Front Pharmacol 2019; 10:747. [PMID: 31354476 PMCID: PMC6637859 DOI: 10.3389/fphar.2019.00747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
The hypogravity motor syndrome (HMS) is one of the deleterious impacts of weightlessness on the human body in orbital space missions. There is a hypothesis that disorders of musculoskeletal system as part of HMS arise in consequence of changes in spinal motor neurons. The study was aimed at bioinformatic analysis of transcriptome changes in lumbar spinal cords of mice after a 30-day spaceflight aboard biosatellite Bion-M1 (space group, S) and subsequent 7-day readaptation to the Earth’s gravity (recovery group, R) when compared with control mice (C group) housed in simulated biosatellite conditions on the Earth. Gene ontology and human phenotype ontology databases were used to detect biological processes, molecular functions, cellular components, and human phenotypes associated with HMS. Our results suggest resemblance of molecular changes developing in space orbit and during the postflight recovery to terrestrial neuromuscular disorders. Remarkably, more prominent transcriptome changes were revealed in R vs. S and R vs. C comparisons that are possibly related to the 7-day recovery period in the Earth’s gravity condition. These data may assist with establishment of HMS pathogenesis and proposing effective preventive and therapeutic options.
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Affiliation(s)
| | | | | | - Oksana Victorovna Tyapkina
- Department of Medical Biology and Genetics, Kazan State Medical University, Kazan, Russia.,Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center" of RAS, Kazan, Russia
| | - Oleg Aleksandrovich Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,RIKEN Institute, Yokohama, Japan
| | | | | | | | - Evgeny Evgenievich Nikolskiy
- Department of Medical Biology and Genetics, Kazan State Medical University, Kazan, Russia.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center" of RAS, Kazan, Russia
| | - Rustem Robertovich Islamov
- Department of Medical Biology and Genetics, Kazan State Medical University, Kazan, Russia.,Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center" of RAS, Kazan, Russia
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49
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Barone V, Bertoldo G, Magro F, Broccanello C, Puglisi I, Baglieri A, Cagnin M, Concheri G, Squartini A, Pizzeghello D, Nardi S, Stevanato P. Molecular and Morphological Changes Induced by Leonardite-based Biostimulant in Beta vulgaris L. PLANTS 2019; 8:plants8060181. [PMID: 31216763 PMCID: PMC6630732 DOI: 10.3390/plants8060181] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 11/16/2022]
Abstract
Humic substances extracted from leonardite are widely considered to be bioactive compounds, influencing the whole-plant physiology and the crop yield. The aim of this work was to evaluate the effect of a new formulate based on leonardite in the early stage of growth of sugar beet (Beta vulgaris L.). A commercial preparation of leonardite (BLACKJAK) was characterized by ionomic analysis, solid-state 13C MAS NMR spectroscopy. Seedlings of sugar beet were grown in Hoagland's solution under controlled conditions. After five days of growth, an aliquot of the concentrated BLACKJAK was added to the solution to obtain a final dilution of 1:1000 (0.5 mg C L-1). The sugar beet response in the early stage of growth was determined by evaluating root morphological traits as well as the changes in the expression of 53 genes related to key morphophysiological processes. Root morphological traits, such as total root length, fine root length (average diameter < 0.5 mm), and number of root tips, were significantly (p < 0.001) increased in plants treated with BLACKJAK, compared to the untreated plants at all sampling times. At the molecular level, BLACKJAK treatment upregulated many of the evaluated genes. Moreover, both Real Time PCR and digital PCR showed that genes involved in hormonal response, such as PIN, ARF3, LOGL 10, GID1, and BRI1, were significantly (p < 0.05) upregulated by treatment with BLACKJAK. Our study provides essential information to understand the effect of a leonardite-based formulate on plant growth hormone metabolism, although the molecular and physiological basis for these complicated regulatory mechanisms deserve further investigations.
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Affiliation(s)
- Valeria Barone
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | | | - Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Ivana Puglisi
- Department of Agriculture, Food and Environment, University of Catania, Via S. Sofia 98, 95123 Catania, Italy.
| | - Andrea Baglieri
- Department of Agriculture, Food and Environment, University of Catania, Via S. Sofia 98, 95123 Catania, Italy.
| | - Massimo Cagnin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Diego Pizzeghello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Serenella Nardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale Università, 16, 35020 Legnaro (PD), Italy.
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50
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Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5387407. [PMID: 31309106 PMCID: PMC6594345 DOI: 10.1155/2019/5387407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/26/2019] [Indexed: 02/07/2023]
Abstract
Neuropathic pain, which is one of the most common forms of chronic pain, seriously increases healthcare costs and impairs patients' quality of life with an incidence of 7–10% worldwide. Microglia cell activation plays a key role in the progression of neuropathic pain. Better understanding of novel molecules modulating microglia cell activation and these underlying functions will extremely benefit the exploration of new treatment. Recent studies suggested long noncoding RNAs may be involved in neuropathic pain. However, its underlying functions and mechanisms in microglia cell activation remain unclear. To identify the differentially expressed lncRNAs and predict their functions in the progression of microglia cell activation, GSE103156 was analyzed using integrated bioinformatics methods. The expression levels of selected lncRNAs and mRNAs were determined by real-time PCR. In the present study, a total of 56 lncRNAs and 298 mRNAs were significantly differentially expressed. The differentially expressed mRNAs were mainly enriched in NF-kappa B signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and NOD-like receptor signaling pathway. The top 10 hub genes were Tnf, Il6, Stat1, Cxcl10, Il1b, Tlr2, Irf1, Ccl2, Irf7, and Ccl5 in the PPI network. Our results showed that Gm8989, Gm8979, and AV051173 may be involved in the progression of microglia cell activation. Taken together, our findings suggest that lots of lncRNAs may be involved in BV2 microglia cell activation in vitro. The findings may provide relevant information for the development of promising targets for the microglial cells activation of neuropathic pain in vivo in the future.
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