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Panner Selvam MK, Kanagaraj V, Kathaperumal K, Nissly RH, Daly JM, Kuchipudi SV. Comparative transcriptome analysis of spleen of Newcastle Disease Virus (NDV) infected chicken and Japanese quail: a potential role of NF-κβ pathway activation in NDV resistance. Virusdisease 2023; 34:402-409. [PMID: 37780899 PMCID: PMC10533468 DOI: 10.1007/s13337-023-00833-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 10/03/2023] Open
Abstract
Newcastle disease (ND) affects a few hundred avian species including chicken and several species of domestic and wild birds. The clinical outcome of Newcastle disease virus (NDV) infection ranges from mild to severe fatal disease depending on the NDV pathotype and the host species involved. Japanese quails serve as natural reservoirs of NDV and play important role in NDV epidemiology. While infection of chicken with velogenic NDV results in severe often fatal illness, the same infection in Japanese quails results in inapparent infection. The molecular basis of this contrasting clinical outcomes of NDV infection is not yet clearly known. We compared global gene expression in spleen of chicken and Japanese quails infected with lentogenic and velogenic NDVs. We found contrasting regulation of key genes associated with NF-κB pathway and T-cell activation between chicken and Japanese quails. Our data suggests association of NDV resistance in Japanese quails to activation of NF-κB pathway and T cell proliferation. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00833-y.
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Affiliation(s)
- Manesh Kumar Panner Selvam
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Vijayrani Kanagaraj
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Kumanan Kathaperumal
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
| | - Janet M. Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Nottingham, UK
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
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Cisse AM, Erber JE, McHale BJ, Gato WE. Hepatic genomic assessment of dietary ingestion of 2-aminoanthracene in Sprague Dawley rats. J Environ Sci Health B 2023; 58:229-238. [PMID: 36880702 DOI: 10.1080/03601234.2023.2185023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
This research aims to investigate the effects of 2-aminoanthracene (2-AA), a polycyclic aromatic hydrocarbon (PAH), on the liver. PAH is a by-product of the incomplete combustion of fossil fuels. Specifically, the impact of 2-AA on different body tissues in animals has been reported. The liver is an organ central to the metabolism of PAHs, including 2-AA. Sprague Dawley rats ingested a well-defined dose of 2-AA in their diet (0, 50, and 100 mg/kg 2-AA) for 12 weeks. Hepatic global gene expression using Affymetrix Rat Genome 230 2.0 microarray was performed. Overall, more than 17,000 genes were expressed. Approximately 70 genes were upregulated, while 65 were downregulated when control rats were compared with low-dose animals. Similarly, 103 genes were upregulated and 49 downregulated when the high-concentration 2-AA group was compared with the control group rats. This result suggests that the magnitude of gene expression fold change depends on the dose of 2-AA ingested. Several differentially expressed genes are involved in biological processes such as gene transcription, cell cycle, and immune system function, indicating that the ingestion of 2-AA could impact these processes. The over-expression of genes related to liver inflammation, nonalcoholic liver disease, hepatic glucose processing, and PAH metabolism were noted.
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Affiliation(s)
- Awa M Cisse
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Jody E Erber
- Department of Chemistry and Biochemistry, Georgia Southern University, Statesboro, Georgia, USA
| | - Brittany J McHale
- Department of Pathology, College of Veterinary Medicine, The University of Georgia, Athens. United States
| | - Worlanyo E Gato
- Department of Chemistry and Biochemistry, Georgia Southern University, Statesboro, Georgia, USA
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Wang P, Meng X, Xue J, Fan C, Wang J. Genome-wide analysis for nanofiber induced global gene expression profile: A study in MC3T3-E1 cells by RNA-Seq. Colloids Surf B Biointerfaces 2023; 223:113143. [PMID: 36682297 DOI: 10.1016/j.colsurfb.2023.113143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Nanofibers are one of the attractive biomaterials that can provide unique environments to direct cell behaviors. However, how nanofiber structure affects the global gene expression of laden cells remains unclear. Herein, high-throughput mRNA sequencing (RNA-seq) is applied to analyze the transcriptome of the MC3T3-E1 cells (a model osteoblast cell line) cultured on electrospun nanofibers. The cell-adhesive poly(L-lactide) nanofibers and membranes are developed by the mussel-inspired coating of gelatin-dopamine conjugate under H2O2-mediated oxidation. The MC3T3-E1 cells cultured on nanofibers exhibit elongated morphology and increased proliferation compared with those on membranes. The differences in global gene expression profiles are determined by RNA-seq, in which 905 differentially expressed genes (DEGs) are identified. Significantly, the DEGs related to cytoskeleton, promotion of cell cycle progression, cell adhesion, and cell proliferation, are higher expressed in the cells on nanofibers, while the DEGs involved in cell-cycle arrest and osteoblast mineralization are up-regulated in the cells on membranes. This study elucidates the roles of nanofiber structure in affecting gene expression of laden cells at the whole transcriptome level, and it will lay the foundation for understanding nanofiber-guided cell behaviors.
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Affiliation(s)
- Peiyan Wang
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, Shandong, PR China
| | - Xinyue Meng
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China
| | - Junqiang Xue
- Department of Rehabilitation Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266000, Shandong, PR China
| | - Changjiang Fan
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, Shandong, PR China.
| | - Jianxun Wang
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, PR China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, Shandong, PR China.
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Sasaki K, Ferdousi F, Fukumitsu S, Kuwata H, Isoda H. Antidepressant- and anxiolytic-like activities of Rosmarinus officinalis extract in rodent models: Involvement of oxytocinergic system. Biomed Pharmacother 2021; 144:112291. [PMID: 34653760 DOI: 10.1016/j.biopha.2021.112291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Oxytocin (OXT), a neuropeptide involved in mammal reproductive and prosocial behaviors, has been reported to interact with various stressor-provoked neurobiological changes, including neuroendocrine, neurotransmitter, and inflammatory processes. In view of disturbances in psychosocial relationships due to social isolation and physical distancing measures amid the COVID-19 pandemic, being one of the triggering factors for the recent rise in depression and anxiety, OXT is a potential candidate for a new antidepressant. METHODS In this present study, we have aimed to investigate the effects of oral administration of Rosmarinus officinalis extract (RE), extracted from distillation residue of rosemary essential oil, on central OXT level in the context of other stress biomarkers and neurotransmitter levels in mice models. Tail suspension test (TST) and elevated plus maze test (EPMT) following LPS injection were employed to assess depressive- and anxiety-like behavior in mice, respectively. FINDINGS Pretreatment with RE for seven days significantly improved behavior in TST and EPMT. Whole-genome microarray analysis reveals that RE significantly reversed TST stress-induced alterations in gene expressions related to oxytocinergic and neurotransmitter pathways and inflammatory processes. In both models, RE significantly increased central Oxt and Oxtr expressions, as well as OXT protein levels. RE also significantly attenuated stress-induced changes in serum corticosterone, brain and serum BDNF levels, and brain neurotransmitters levels in both models. INTERPRETATION Altogether, our study is the first to report antidepressant- and anxiolytic-like activities of RE through modulating oxytocinergic system in mice brain and thus highlights the prospects of RE in the treatment of depressive disorders of psychosocial nature.
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Affiliation(s)
- Kazunori Sasaki
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Open Innovation Laboratory for Food and Medicinal Resource Engineering, National Institute of Advanced Industrial Science and Technology (AIST) and University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Farhana Ferdousi
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Open Innovation Laboratory for Food and Medicinal Resource Engineering, National Institute of Advanced Industrial Science and Technology (AIST) and University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Satoshi Fukumitsu
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Tsukuba Life Science Innovation Program (T-LSI), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8577 Ibaraki, Japan
| | - Hidetoshi Kuwata
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroko Isoda
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Open Innovation Laboratory for Food and Medicinal Resource Engineering, National Institute of Advanced Industrial Science and Technology (AIST) and University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Tsukuba Life Science Innovation Program (T-LSI), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8577 Ibaraki, Japan.
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Sewelam N, Brilhaus D, Bräutigam A, Alseekh S, Fernie AR, Maurino VG. Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes. J Exp Bot 2020; 71:5098-5112. [PMID: 32442250 DOI: 10.1093/jxb/eraa250] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/19/2020] [Indexed: 05/22/2023]
Abstract
Environmental stresses such as drought, heat, and salinity limit plant development and agricultural productivity. While individual stresses have been studied extensively, much less is known about the molecular interaction of responses to multiple stresses. To address this problem, we investigated molecular responses of Arabidopsis to single, double, and triple combinations of salt, osmotic, and heat stresses. A metabolite profiling analysis indicated the production of specific compatible solutes depending on the nature of the stress applied. We found that in combination with other stresses, heat has a dominant effect on global gene expression and metabolite level patterns. Treatments that include heat stress lead to strongly reduced transcription of genes coding for abundant photosynthetic proteins and proteins regulating the cell life cycle, while genes involved in protein degradation are up-regulated. Under combined stress conditions, the plants shifted their metabolism to a survival state characterized by low productivity. Our work provides molecular evidence for the dangers for plant productivity and future world food security posed by heat waves resulting from global warming. We highlight candidate genes, many of which are functionally uncharacterized, for engineering plant abiotic stress tolerance.
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Affiliation(s)
- Nasser Sewelam
- Institute of Developmental and Molecular Biology of Plants, and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Dominik Brilhaus
- Institute of Plant Biochemistry, and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center for Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Center for Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Veronica G Maurino
- Institute of Developmental and Molecular Biology of Plants, and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Molecular Plant Physiology, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Bonn, Germany
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Liu Q, Yang J, Huang X, Liu Y, Han K, Zhao D, Zhang L, Li Y. Global gene expression analysis data of chicken dendritic cells infected with H9N2 avian influenza virus. Data Brief 2020; 30:105430. [PMID: 32300615 PMCID: PMC7152653 DOI: 10.1016/j.dib.2020.105430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023] Open
Abstract
This data article reports the global gene expression analysis data of chicken DCs infected with H9N2 avian influenza virus (AIV) compared with mock infection. The differentially expressed genes (DEGs), and the data of GO enrichment analysis and KEGG pathway analysis for DEGs were reported here. In addition, some of these DEGs associated with innate immune response and antigen presentation were also verified by qPCR. The replication of H9N2 AIV in DCs, and the viability kinetic of DCs during H9N2 AIV infection, and the primers for qPCR were also reported in this data article. The data presented here was used on the research article entitled “Transcriptomic profile of chicken bone marrow-derive dendritic cells in response to H9N2 avianinfluenza A virus”.
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Abstract
Global gene expression analyses in bacteria have undergone a dramatic transformation. Prior to the development of high-throughput sequencing technologies, real-time PCR or microarray studies were the mainstay of assessing differences in gene expression in bacteria. Real-time PCR remains a critical tool for targeted gene expression analyses. However, microarray studies have given way to the plethora of advantages in RNA sequencing (RNA-seq) for the determination of global gene expression (i.e., transcriptome). Increased accessibility to high-throughput sequencing and user-friendly bioinformatics data analysis software have made RNA-seq technology use more widespread. Here, we provide comprehensive methods to perform RNA sequencing of Streptococcus pyogenes strains grown in vitro in standard laboratory media, including cell growth, RNA extraction, ribosomal RNA depletion, and library construction. Considerations for library sequencing and data analysis are also provided.
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Affiliation(s)
- Misú Sanson
- Division of Infectious Diseases, Department of Pediatrics, Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Sciences Center at Houston, Houston, TX, USA.
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Proestou DA, Sullivan ME. Variation in global transcriptomic response to Perkinsus marinus infection among eastern oyster families highlights potential mechanisms of disease resistance. Fish Shellfish Immunol 2020; 96:141-151. [PMID: 31809834 DOI: 10.1016/j.fsi.2019.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Dermo disease, caused by the protozoan parasite Perkinsus marinus, negatively impacts wild and cultured Eastern oyster populations, yet our knowledge of the mechanistic bases for parasite pathogenicity and the Eastern oyster's response to it is limited. To better understand host responses to the parasite and identify molecular mechanisms underlying disease-resistance phenotypes, we experimentally challenged two families exhibiting divergent Dermo-resistance phenotypes with the parasite, generated global expression profiles using RNAseq and identified differentially expressed transcripts between control and challenged oysters from each family at multiple time points post-parasite injection. The susceptible and resistant families exhibited strikingly different transcriptomic responses to the parasite over a 28-day time period. The resistant family exhibited a strong, focused, early response to P. marinus infection, where many significantly upregulated transcripts were associated with the biological processes "regulation of proteolysis" and "oxidation-reduction process." P. marinus virulence factors are mainly comprised of proteases that facilitate parasite invasion and weaken host humoral defenses, thus host upregulation of transcripts associated with negative regulation of proteolysis is consistent with a Dermo-resistant phenotype. In contrast, the susceptible family mounted a very weak, disorganized, initial response to the parasite. Few transcripts were differentially expressed between control and injected oysters, and no functional enrichment was detected among them. At the final 28 d time point 2450 differentially expressed transcripts were identified and were associated with either "G-protein coupled receptor activity" (upregulated) or "microtubule-based process" (downregulated). A handful of protease inhibitors were differentially expressed between control and injected susceptible oysters, but this function was not enriched in the susceptible data set. The differential expression patterns observed in this study provide valuable insight into the functional basis of Dermo resistance and suggest that the timing of expression is just as important as the transcripts being expressed.
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Affiliation(s)
- Dina A Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
| | - Mary E Sullivan
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA; University of Rhode Island, Department of Fisheries, Animal and Veterinary Science, 460 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
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Yazdimamaghani M, Moos PJ, Ghandehari H. Time- and dose-dependent gene expression analysis of macrophage response as a function of porosity of silica nanoparticles. Nanomedicine 2019; 21:102041. [PMID: 31228603 DOI: 10.1016/j.nano.2019.102041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
There is a limited amount of information available on gene expression regulation of macrophages in response to changing the time of exposure, concentration, and physicochemical properties of nanomaterials. In this study, RAW264.7 macrophages were treated with spherical nonporous and mesoporous silica nanoparticles of similar size at different incubation times and concentrations. RNA-sequencing was used to study transcriptional profiles. Bioinformatics analyses, functional annotation clustering, and network analyses were employed to understand signaling pathways of cellular response as a function of porosity, incubation time, and concentration. Porosity introduced drastic changes to the genomic response of macrophages at equitoxic concentrations and incubation times. Direct relations between increases in time and concentration with an increased number of differentially expressed genes were observed.
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Affiliation(s)
- Mostafa Yazdimamaghani
- Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA; Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Philip J Moos
- Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA; Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Hamidreza Ghandehari
- Utah Center for Nanomedicine, Nano Institute of Utah, University of Utah, Salt Lake City, UT 84112, USA; Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112, USA; Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA.
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Abstract
High-throughput transcriptome sequencing (RNASeq) represents one of the most comprehensive and scalable methods to analyze global gene expression. It allows for absolute quantification of gene expression and also enables the discovery of novel transcripts and alternatively spliced isoforms. This chapter provides hand-on tools and a step-by-step procedure to analyze RNASeq data from punctures of two different retinal tissues (retina and RPE-choroid-sclera) at two different locations (periphery and macular region) from eight individuals. The procedure described in this chapter will use various programs from the free, open-source Tuxedo Suite software package to analyze sequencing data and to ascertain genes that are differentially expressed between retina and RPE-choroid-sclera.
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Affiliation(s)
- Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany.
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
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Castillo C, Carrillo I, Libisch G, Juiz N, Schijman A, Robello C, Kemmerling U. Host-parasite interaction: changes in human placental gene expression induced by Trypanosoma cruzi. Parasit Vectors 2018; 11:479. [PMID: 30143027 DOI: 10.1186/s13071-018-2988-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/02/2018] [Indexed: 01/20/2023] Open
Abstract
Background Chagas disease is caused by Trypanosoma cruzi, a parasite endemic to Latin America. Most infections occur in children by vector or congenital transmission. Trypanosoma cruzi establishes a complexity of specific molecular parasite-host cell interactions to invade the host. However, most studies have been mainly focused on the interaction between the parasite and different cell types, but not on the infection and invasion on a tissue level. During congenital transmission, T. cruzi must cross the placental barrier, composed of epithelial and connective tissues, in order to infect the developing fetus. Here we aimed to study the global changes of transcriptome in the placental tissue after a T. cruzi challenge. Results Strong changes in gene expression profiling were found in the different experimental conditions, involving the reprogramming of gene expression in genes involved in the innate immune response. Conclusions Trypanosoma cruzi induces strong changes in genes involved in a wide range of pathways, especially those involved in immune response against infections. Electronic supplementary material The online version of this article (10.1186/s13071-018-2988-0) contains supplementary material, which is available to authorized users.
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Rangan P, Furtado A, Henry RJ. The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. BMC Genomics 2017; 18:766. [PMID: 29020946 PMCID: PMC5637334 DOI: 10.1186/s12864-017-4154-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat is one of the three major cereals that have been domesticated to feed human populations. The composition of the wheat grain determines the functional properties of wheat including milling efficiency, bread making, and nutritional value. Transcriptome analysis of the developing wheat grain provides key insights into the molecular basis for grain development and quality. RESULTS The transcriptome of 35 genotypes was analysed by RNA-Seq at two development stages (14 and 30 days-post-anthesis, dpa) corresponding to the mid stage of development (stage Z75) and the almost mature seed (stage Z85). At 14dpa, most of the transcripts were associated with the synthesis of the major seed components including storage proteins and starch. At 30dpa, a diverse range of genes were expressed at low levels with a predominance of genes associated with seed defence and stress tolerance. RNA-Seq analysis of changes in expression between 14dpa and 30dpa stages revealed 26,477 transcripts that were significantly differentially expressed at a FDR corrected p-value cut-off at ≤0.01. Functional annotation and gene ontology mapping was performed and KEGG pathway mapping allowed grouping based upon biochemical linkages. This analysis demonstrated that photosynthesis associated with the pericarp was very active at 14dpa but had ceased by 30dpa. Recently reported genes for flour yield in milling and bread quality were found to influence wheat quality largely due to expression patterns at the earlier seed development stage. CONCLUSIONS This study serves as a resource providing an overview of gene expression during wheat grain development at the early (14dpa) and late (30dpa) grain filling stages for use in studies of grain quality and nutritional value and in understanding seed biology.
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Affiliation(s)
- Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia.,Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia.
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Kaufmann SHE, Fortune S, Pepponi I, Ruhwald M, Schrager LK, Ottenhoff THM. TB biomarkers, TB correlates and human challenge models: New tools for improving assessment of new TB vaccines. Tuberculosis (Edinb) 2016; 99 Suppl 1:S8-S11. [PMID: 27402312 DOI: 10.1016/j.tube.2016.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 4th Global Forum on TB Vaccines, convened in Shanghai, China, from 21 - 24 April 2015, brought together a wide and diverse community involved in tuberculosis vaccine research and development to discuss the current status of, and future directions for this critical effort. This paper summarizes the sessions on Biomarkers and Correlates, and Human Challenge Models. Summaries of all sessions from the 4th Global Forum are compiled in a special supplement of Tuberculosis. [August 2016, Vol 99, Supp S1, S1-S30].
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Affiliation(s)
| | - Sarah Fortune
- Harvard Chan School of Public Health, Boston, MA, USA
| | - Ilaria Pepponi
- Jenner Institute, University of Oxford, UK; Animal and Plant Health Agency, Surrey, UK
| | | | | | - Tom H M Ottenhoff
- Leiden University Medical Center, Leiden, The Netherlands; TuBerculosis Vaccine Initiative (TBVI), Lelystad, The Netherlands
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Longhin E, Capasso L, Battaglia C, Proverbio MC, Cosentino C, Cifola I, Mangano E, Camatini M, Gualtieri M. Integrative transcriptomic and protein analysis of human bronchial BEAS-2B exposed to seasonal urban particulate matter. Environ Pollut 2016; 209:87-98. [PMID: 26647171 DOI: 10.1016/j.envpol.2015.11.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Exposure to particulate matter (PM) is associated with various health effects. Physico-chemical properties influence the toxicological impact of PM, nonetheless the mechanisms underlying PM-induced effects are not completely understood. OBJECTIVES Human bronchial epithelial cells were used to analyse the pathways activated after exposure to summer and winter urban PM and to identify possible markers of exposure. METHODS BEAS-2B cells were exposed for 24 h to 10 μg/cm(2) of winter PM2.5 (wPM) and summer PM10 (sPM) sampled in Milan. A microarray technology was used to profile the cells gene expression. Genes and microRNAs were analyzed by bioinformatics technique to identify pathways involved in cellular responses. Selected genes and pathways were validated at protein level (western blot, membrane protein arrays and ELISA). RESULTS The molecular networks activated by the two PM evidenced a correlation among oxidative stress, inflammation and DNA damage responses. sPM induced the release of pro-inflammatory mediators, although miR-146a and genes related to inflammation resulted up-regulated by both PM. Moreover both PM affected a set of genes, proteins and miRNAs related to antioxidant responses, cancer development, extracellular matrix remodeling and cytoskeleton organization, while miR-29c, implicated in epigenetic modification, resulted up-regulated only by wPM. sPM effects may be related to biological and inorganic components, while wPM apparently related to the high content of organic compounds. CONCLUSIONS These results may be helpful for the individuation of biomarkers for PM exposure, linked to the specific PM physico-chemical properties.
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Affiliation(s)
- Eleonora Longhin
- Department of Earth and Environmental Sciences, POLARIS Research Centre, University of Milano-Bicocca, Piazza della Scienza 1, Milano 20126, Italy
| | - Laura Capasso
- Department of Earth and Environmental Sciences, POLARIS Research Centre, University of Milano-Bicocca, Piazza della Scienza 1, Milano 20126, Italy
| | - Cristina Battaglia
- Department of medical biotechnology and translational medicine (BIOMETRA), Università degli Studi di Milano, 93 via F.lli Cervi, Segrate 20900, Italy; Institute of biomedical technology, CNR, Via F.lli Cervi, Segrate 20900, Italy.
| | - Maria Carla Proverbio
- Department of Physiopathology and Transplantation, Università degli Studi di Milano, 20090, Italy
| | - Cristina Cosentino
- Department of medical biotechnology and translational medicine (BIOMETRA), Università degli Studi di Milano, 93 via F.lli Cervi, Segrate 20900, Italy
| | - Ingrid Cifola
- Department of Physiopathology and Transplantation, Università degli Studi di Milano, 20090, Italy
| | - Eleonora Mangano
- Institute of biomedical technology, CNR, Via F.lli Cervi, Segrate 20900, Italy
| | - Marina Camatini
- Department of Earth and Environmental Sciences, POLARIS Research Centre, University of Milano-Bicocca, Piazza della Scienza 1, Milano 20126, Italy
| | - Maurizio Gualtieri
- ENEA-UTTS/SSPT-MET-INAT, Strada per Crescentino 41, 13040, Saluggia (VC), Italy.
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Zacapala-Gómez AE, Del Moral-Hernández O, Villegas-Sepúlveda N, Hidalgo-Miranda A, Romero-Córdoba SL, Beltrán-Anaya FO, Leyva-Vázquez MA, Alarcón-Romero LDC, Illades-Aguiar B. Changes in global gene expression profiles induced by HPV 16 E6 oncoprotein variants in cervical carcinoma C33-A cells. Virology 2015; 488:187-95. [PMID: 26655236 DOI: 10.1016/j.virol.2015.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 01/03/2023]
Abstract
We analyzed the effects of the expression of HPV 16 E6 oncoprotein variants (AA-a, AA-c, E-A176/G350, E-C188/G350, E-G350), and the E-Prototype in global gene expression profiles in an in vitro model. E6 gene was cloned into an expression vector fused to GFP and was transfected in C33-A cells. Affymetrix GeneChip Human Transcriptome Array 2.0 platform was used to analyze the expression of over 245,000 coding transcripts. We found that HPV16 E6 variants altered the expression of 387 different genes in comparison with E-Prototype. The altered genes are involved in cellular processes related to the development of cervical carcinoma, such as adhesion, angiogenesis, apoptosis, differentiation, cell cycle, proliferation, transcription and protein translation. Our results show that polymorphic changes in HPV16 E6 natural variants are sufficient to alter the overall gene expression profile in C33-A cells, explaining in part the observed differences in oncogenic potential of HPV16 variants.
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Affiliation(s)
- Ana Elvira Zacapala-Gómez
- Laboratorio de Biomedicina Molecular, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Gro., México.
| | - Oscar Del Moral-Hernández
- Laboratorio de Biomedicina Molecular, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Gro., México.
| | - Nicolás Villegas-Sepúlveda
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), México, D.F., México.
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., México.
| | | | - Fredy Omar Beltrán-Anaya
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., México.
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Gro., México.
| | - Luz Del Carmen Alarcón-Romero
- Laboratorio de Investigación en Citopatología e Histoquímica, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Gro., México.
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Gro., México.
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16
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Andrade FDO, de Assis S, Jin L, Fontelles CC, Barbisan LF, Purgatto E, Hilakivi-Clarke L, Ong TP. Lipidomic fatty acid profile and global gene expression pattern in mammary gland of rats that were exposed to lard-based high fat diet during fetal and lactation periods associated to breast cancer risk in adulthood. Chem Biol Interact 2015; 239:118-28. [PMID: 26115784 DOI: 10.1016/j.cbi.2015.06.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 06/05/2015] [Accepted: 06/23/2015] [Indexed: 02/07/2023]
Abstract
The persistent effects of animal fat consumption during pregnancy and nursing on the programming of breast cancer risk among female offspring were studied here. We have previously found that female offspring of rat dams that consumed a lard-based high-fat (HF) diet (60% fat-derived energy) during pregnancy, or during pregnancy and lactation, were at a reduced risk of developing mammary cancer. To better understand the unexpected protective effects of early life lard exposure, we have applied lipidomics and nutrigenomics approaches to investigate the fatty acid profile and global gene expression patterns in the mammary tissue of the female offspring. Consumption of this HF diet during gestation had few effects on the mammary tissue fatty acids profile of young adult offspring, while exposure from gestation throughout nursing promoted significant alterations in the fatty acids profile. Major differences were related to decreases in saturated fatty acids (SFA) and increases in omega-6 polyunsaturated fatty acids (PUFAs), monounsaturated fatty acids (MUFAs) and conjugated linolenic acid (CLA) concentrations. In addition several differences in gene expression patterns by microarray analysis between the control and in utero or in utero and during lactation HF exposed offspring were identified. Differential dependency network (DDN) analysis indicated that many of the genes exhibited unique connections to other genes only in the HF offspring. These unique connections included Hrh1-Ythdf1 and Repin1-Elavl2 in the in utero HF offspring, and Rnf213-Htr3b and Klf5-Chrna4 in the in utero and lactation HF offspring, compared with the control offspring. We conclude that an exposure to a lard-based HF diet during early life changes the fatty acid profile and transcriptional network in mammary gland in young adult rats, and these changes appear to be consistent with reduced mammary cancer risk observed in our previous study.
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Affiliation(s)
- Fábia de Oliveira Andrade
- Departament of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, Bloco 14, 05508-900 São Paulo, SP, Brazil
| | - Sonia de Assis
- Department of Oncology, Georgetown University Lombardi Comprehensive Cancer Center, Research Building, Room E407, Georgetown University School of Medicine, 3970 Reservoir Road NW, Washington, DC 20007, USA
| | - Lu Jin
- Department of Oncology, Georgetown University Lombardi Comprehensive Cancer Center, Research Building, Room E407, Georgetown University School of Medicine, 3970 Reservoir Road NW, Washington, DC 20007, USA
| | - Camile Castilho Fontelles
- Departament of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, Bloco 14, 05508-900 São Paulo, SP, Brazil
| | - Luís Fernando Barbisan
- Department of Morphology, Botucatu Bioscience Institute, State University of São Paulo Botucatu, Distrito de Rubião Júnior, s/n. Rubião Júnior, 18618000 Botucatu, SP, Brazil
| | - Eduardo Purgatto
- Departament of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, Bloco 14, 05508-900 São Paulo, SP, Brazil
| | - Leena Hilakivi-Clarke
- Department of Oncology, Georgetown University Lombardi Comprehensive Cancer Center, Research Building, Room E407, Georgetown University School of Medicine, 3970 Reservoir Road NW, Washington, DC 20007, USA
| | - Thomas Prates Ong
- Departament of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, Bloco 14, 05508-900 São Paulo, SP, Brazil; Food Research Center (NAPAN), Av. Prof. Lineu Prestes 580, Bloco 14, 05508-900 São Paulo, SP, Brazil.
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17
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Abstract
The database of Gene Co-Regulation (dGCR) is a web tool for the analysis of gene relationships based on correlated patterns of gene expression over publicly available transcriptional data. The motivation behind dGCR is that genes whose expression patterns correlate across many experiments tend to be co-regulated and hence share biological function. In addition to revealing functional connections between individual gene pairs, extended sets of co-regulated genes can also be assessed for enrichment of gene ontology classes and interaction pathways. This functionality provides an insight into the biological function of the query gene itself. The dGCR web tool extends the range of expression data curated by existing co-regulation databases and provides additional insights into gene function through the analysis of pathways, gene ontology classes and co-regulation modules.
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Affiliation(s)
- Gareth Williams
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London SE1 1UL, UK
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18
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Doumatey AP, Xu H, Huang H, Trivedi NS, Lei L, Elkahloun A, Adeyemo A, Rotimi CN. Global Gene Expression Profiling in Omental Adipose Tissue of Morbidly Obese Diabetic African Americans. J Endocrinol Metab 2015; 5:199-210. [PMID: 26504501 DOI: 10.14740/jem286w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Adipose tissues play important role in the pathophysiology of obesity-related diseases including type 2 diabetes (T2D). To describe gene expression patterns and functional pathways in obesity-related T2D, we performed global transcript profiling of omental adipose tissue (OAT) in morbidly obese individuals with or without T2D. METHODS Twenty morbidly obese (mean BMI: about 54 kg/m2) subjects were studied, including 14 morbidly obese individuals with T2D (cases) and 6 morbidly obese individuals without T2D (reference group). Gene expression profiling was performed using the Affymetrix U133 Plus 2.0 human genome expression array. Analysis of covariance was performed to identify differentially expressed genes (DEGs). Bioinformatics tools including PANTHER and Ingenuity Pathway Analysis (IPA) were applied to the DEGs to determine biological functions, networks and canonical pathways that were overrepresented in these individuals. RESULTS At an absolute fold-change threshold of 2 and false discovery rate (FDR) < 0.05, 68 DEGs were identified in cases compared to the reference group. Myosin X (MYO10) and transforming growth factor beta regulator 1 (TBRG1) were upregulated. MYO10 encodes for an actin-based motor protein that has been associated with T2D. Telomere extension by telomerase (HNRNPA1, TNKS2), D-myo-inositol (1, 4, 5)-trisphosphate biosynthesis (PIP5K1A, PIP4K2A), and regulation of actin-based motility by Rho (ARPC3) were the most significant canonical pathways and overlay with T2D signaling pathway. Upstream regulator analysis predicted 5 miRNAs (miR-320b, miR-381-3p, miR-3679-3p, miR-494-3p, and miR-141-3p,) as regulators of the expression changes identified. CONCLUSION This study identified a number of transcripts and miRNAs in OAT as candidate novel players in the pathophysiology of T2D in African Americans.
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Affiliation(s)
- Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Huichun Xu
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD ; University of Maryland, School of Medicine, Baltimore, MD
| | - Hanxia Huang
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Niraj S Trivedi
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Lin Lei
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Abdel Elkahloun
- Core laboratory-Cancer Genetics, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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19
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Kulkarni KK, Bankar KG, Shukla RN, Das C, Banerjee A, Dasgupta D, Vasudevan M. Global gene expression profiling data analysis reveals key gene families and biological processes inhibited by Mithramycin in sarcoma cell lines. Genom Data 2014; 3:8-14. [PMID: 26484141 PMCID: PMC4535529 DOI: 10.1016/j.gdata.2014.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/03/2023]
Abstract
The role of Mithramycin as an anticancer drug has been well studied. Sarcoma is a type of cancer arising from cells of mesenchymal origin. Though incidence of sarcoma is not of significant percentage, it becomes vital to understand the role of Mithramycin in controlling tumor progression of sarcoma. In this article, we have analyzed the global gene expression profile changes induced by Mithramycin in two different sarcoma lines from whole genome gene expression profiling microarray data. We have found that the primary mode of action of Mithramycin is by global repression of key cellular processes and gene families like phosphoproteins, kinases, alternative splicing, regulation of transcription, DNA binding, regulation of histone acetylation, negative regulation of gene expression, chromosome organization or chromatin assembly and cytoskeleton.
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Affiliation(s)
- Kirti K Kulkarni
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
| | - Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
| | - Rohit Nandan Shukla
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Amrita Banerjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Dipak Dasgupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd., Bangalore 560043, India
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20
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Chandran S, Cairns MT, O'Brien M, Smith TJ. Transcriptomic effects of estradiol treatment on cultured human uterine smooth muscle cells. Mol Cell Endocrinol 2014; 393:16-23. [PMID: 24942541 DOI: 10.1016/j.mce.2014.05.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/07/2014] [Accepted: 05/22/2014] [Indexed: 11/20/2022]
Abstract
Contractility of the myometrial smooth muscle cells during the estrous cycle and pregnancy is modulated by estrogen but the temporal expression of estrogen (relative to progesterone) and the type of contraction involved are distinctly different in pregnancy and estrous. This in vitro cell culture study investigated the global gene expression profile of human uterine smooth muscle cells (hUtSMCs) following 17β-estradiol (E2) treatment. In response to E2 treatment 540 genes, many of which have not been previously described as estrogen responsive, were identified as significantly differentially expressed. These genes are involved in biological processes that include muscle contraction, cell migration and adhesion, apoptosis and phosphorylation. Evidence from this study suggests that 17β-estradiol may have effects that are contrary to an overall contraction phenotype. The hUtSMC in vitro culture system is a useful model to investigate steroid effects on smooth muscle cells and may provide additional clues as to how smooth muscle cells behave in vivo.
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Affiliation(s)
- Sreenath Chandran
- National Centre for Biomedical Engineering Science, NUI Galway, Galway, Ireland
| | - Michael T Cairns
- National Centre for Biomedical Engineering Science, NUI Galway, Galway, Ireland
| | - Margaret O'Brien
- National Centre for Biomedical Engineering Science, NUI Galway, Galway, Ireland
| | - Terry J Smith
- National Centre for Biomedical Engineering Science, NUI Galway, Galway, Ireland.
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21
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Talwar S, Jain N, Shivashankar GV. The regulation of gene expression during onset of differentiation by nuclear mechanical heterogeneity. Biomaterials 2014; 35:2411-9. [PMID: 24388387 DOI: 10.1016/j.biomaterials.2013.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/08/2013] [Indexed: 12/11/2022]
Abstract
Embryonic stem (ES) cells exhibit plasticity in nuclear organization as well as variability in gene expression. Although such physicochemical features are important in lineage commitment, mechanistic insights coupling nuclear plasticity and gene expression have not been elucidated. To probe this, we developed single cell micro-patterned assay to map nuclear deformation and its correlation with gene expression. We found an inherent heterogeneity in nuclear pliability of ES cells. Softer nuclei deformed to the underlying substrate geometry while the stiffer ones remained spherical. Stiffer nuclei were strongly correlated with decreased global histone (H3) acetylation and an increase in Lamin A/C expression. Interestingly, these cells also have higher nuclear accumulation of the transcription cofactor MRTF-A (myocardin-related transcription factor A) and an upregulation of its downstream target genes. Taken together, our results provide compelling evidence to show that the mechanical heterogeneity of stem cell nucleus can regulate transcriptional programs during onset of cellular differentiation.
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