1
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Mathai C, Jourd'heuil F, Pham LGC, Gilliard K, Howard D, Balnis J, Jaitovich A, Chittur SV, Rilley M, Peredo-Wende R, Ammoura I, Shin SJ, Barroso M, Barra J, Shishkova E, Coon JJ, Lopez-Soler RI, Jourd'heuil D. Regulation of DNA damage and transcriptional output in the vasculature through a cytoglobin-HMGB2 axis. Redox Biol 2023; 65:102838. [PMID: 37573836 PMCID: PMC10428073 DOI: 10.1016/j.redox.2023.102838] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023] Open
Abstract
Identifying novel regulators of vascular smooth muscle cell function is necessary to further understand cardiovascular diseases. We previously identified cytoglobin, a hemoglobin homolog, with myogenic and cytoprotective roles in the vasculature. The specific mechanism of action of cytoglobin is unclear but does not seem to be related to oxygen transport or storage like hemoglobin. Herein, transcriptomic profiling of injured carotid arteries in cytoglobin global knockout mice revealed that cytoglobin deletion accelerated the loss of contractile genes and increased DNA damage. Overall, we show that cytoglobin is actively translocated into the nucleus of vascular smooth muscle cells through a redox signal driven by NOX4. We demonstrate that nuclear cytoglobin heterodimerizes with the non-histone chromatin structural protein HMGB2. Our results are consistent with a previously unknown function by which a non-erythrocytic hemoglobin inhibits DNA damage and regulates gene programs in the vasculature by modulating the genome-wide binding of HMGB2.
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Affiliation(s)
- Clinton Mathai
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Frances Jourd'heuil
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Le Gia Cat Pham
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Kurrim Gilliard
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Dennis Howard
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Joseph Balnis
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA; Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, NY, USA
| | - Ariel Jaitovich
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA; Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, NY, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Cancer Research Center, University at Albany, New York, 12144, USA
| | - Mark Rilley
- Division of Rheumatology, Department of Medicine, Samuel Stratton VA Medical Center, Albany, NY, 12208, USA
| | - Ruben Peredo-Wende
- Division of Rheumatology, Department of Medicine, Samuel Stratton VA Medical Center, Albany, NY, 12208, USA
| | - Ibrahim Ammoura
- Department of Pathology and Medicine, Albany Medical Center, Albany, NY, 12208, USA
| | - Sandra J Shin
- Department of Pathology and Medicine, Albany Medical Center, Albany, NY, 12208, USA
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Jonathan Barra
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53506, USA
| | - Joshua J Coon
- Department of Pathology and Medicine, Albany Medical Center, Albany, NY, 12208, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53506, USA; Morgridge Institute for Research, Madison, WI, 53515, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53506, USA
| | - Reynold I Lopez-Soler
- Section of Renal Transplantation, Edward Hines VA Jr. Hospital, Hines, IL, 60141, USA; Department of Surgery, Division of Intra-Abdominal Transplantation, Stritch School of Medicine, Maywood, IL, 60153, USA
| | - David Jourd'heuil
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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2
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Mathai C, Jourd'heuil F, Pham LGC, Gilliard K, Howard D, Balnis J, Jaitovich A, Chittur SV, Rilley M, Peredo-Wende R, Ammoura I, Shin SJ, Barroso M, Barra J, Shishkova E, Coon JJ, Lopez-Soler RI, Jourd'heuil D. Nuclear cytoglobin associates with HMGB2 and regulates DNA damage and genome-wide transcriptional output in the vasculature. bioRxiv 2023:2023.05.10.540045. [PMID: 37214992 PMCID: PMC10197644 DOI: 10.1101/2023.05.10.540045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Identifying novel regulators of vascular smooth muscle cell function is necessary to further understand cardiovascular diseases. We previously identified cytoglobin, a hemoglobin homolog, with myogenic and cytoprotective roles in the vasculature. The specific mechanism of action of cytoglobin is unclear but does not seem to be related to oxygen transport or storage like hemoglobin. Herein, transcriptomic profiling of injured carotid arteries in cytoglobin global knockout mice revealed that cytoglobin deletion accelerated the loss of contractile genes and increased DNA damage. Overall, we show that cytoglobin is actively translocated into the nucleus of vascular smooth muscle cells through a redox signal driven by NOX4. We demonstrate that nuclear cytoglobin heterodimerizes with the non-histone chromatin structural protein HMGB2. Our results are consistent with a previously unknown function by which a non-erythrocytic hemoglobin inhibits DNA damage and regulates gene programs in the vasculature by modulating the genome-wide binding of HMGB2.
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3
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Glinsky GV, Godugu K, Sudha T, Rajabi M, Chittur SV, Hercbergs AA, Mousa SA, Davis PJ. Effects of Anticancer Agent P-bi-TAT on Gene Expression Link the Integrin Thyroid Hormone Receptor to Expression of Stemness and Energy Metabolism Genes in Cancer Cells. Metabolites 2022; 12:metabo12040325. [PMID: 35448512 PMCID: PMC9029602 DOI: 10.3390/metabo12040325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 12/10/2022] Open
Abstract
Chemically modified forms of tetraiodothyroacetic acid (tetrac), an L-thyroxine derivative, have been shown to exert their anticancer activity at plasma membrane integrin αvβ3 of tumor cells. Via a specific hormone receptor on the integrin, tetrac-based therapeutic agents modulate expression of genes relevant to cancer cell proliferation, survival and energy metabolism. P-bi-TAT, a novel bivalent tetrac-containing synthetic compound has anticancer activity in vitro and in vivo against glioblastoma multiforme (GBM) and other types of human cancers. In the current study, microarray analysis was carried out on a primary culture of human GBM cells exposed to P-bi-TAT (10−6 tetrac equivalent) for 24 h. P-bi-TAT significantly affected expression of a large panel of genes implicated in cancer cell stemness, growth, survival and angiogenesis. Recent interest elsewhere in ATP synthase as a target in GBM cells caused us to focus attention on expression of genes involved in energy metabolism. Significantly downregulated transcripts included multiple energy-metabolism-related genes: electron transport chain genes ATP5A1 (ATP synthase 1), ATP51, ATP5G2, COX6B1 (cytochrome c oxidase subunit 6B1), NDUFA8 (NADH dehydrogenase (ubiquinone) FA8), NDUFV2I and other NDUF genes. The NDUF and ATP genes are also relevant to control of oxidative phosphorylation and transcription. Qualitatively similar actions of P-bi-TAT on expression of subsets of energy-metabolism-linked genes were also detected in established human GBM and pancreatic cancer cell lines. In conclusion, acting at αvβ3 integrin, P-bi-TAT caused downregulation in human cancer cells of expression of a large number of genes involved in electron transport and oxidative phosphorylation. These observations suggest that cell surface thyroid hormone receptors on αvβ3 regulate expression of genes relevant to tumor cell stemness and energy metabolism.
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Affiliation(s)
- Gennadi V. Glinsky
- Institute of Engineering in Medicine, University of California San Diego, San Diego, CA 92037, USA
- Correspondence: (G.V.G.); (P.J.D.); Tel.: +1-858-401-3470 (G.V.G.); +1-518-428-7848 (P.J.D.); Fax: +1-518-694-7567 (P.J.D.)
| | - Kavitha Godugu
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, One Discovery Drive, Rensselaer, NY 12144, USA; (K.G.); (T.S.); (M.R.); (S.A.M.)
| | - Thangirala Sudha
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, One Discovery Drive, Rensselaer, NY 12144, USA; (K.G.); (T.S.); (M.R.); (S.A.M.)
| | - Mehdi Rajabi
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, One Discovery Drive, Rensselaer, NY 12144, USA; (K.G.); (T.S.); (M.R.); (S.A.M.)
| | - Sridar V. Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, NY 12144, USA;
| | | | - Shaker A. Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, One Discovery Drive, Rensselaer, NY 12144, USA; (K.G.); (T.S.); (M.R.); (S.A.M.)
| | - Paul J. Davis
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, One Discovery Drive, Rensselaer, NY 12144, USA; (K.G.); (T.S.); (M.R.); (S.A.M.)
- Department of Medicine, Albany Medical College, Albany, NY 12208, USA
- Correspondence: (G.V.G.); (P.J.D.); Tel.: +1-858-401-3470 (G.V.G.); +1-518-428-7848 (P.J.D.); Fax: +1-518-694-7567 (P.J.D.)
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4
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Das S, Saqib M, Meng RC, Chittur SV, Guan Z, Wan F, Sun W. Hemochromatosis drives acute lethal intestinal responses to hyperyersiniabactin-producing Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 2022; 119:e2110166119. [PMID: 34969677 PMCID: PMC8764673 DOI: 10.1073/pnas.2110166119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/19/2022] Open
Abstract
Hemachromatosis (iron-overload) increases host susceptibility to siderophilic bacterial infections that cause serious complications, but the underlying mechanisms remain elusive. The present study demonstrates that oral infection with hyperyersiniabactin (Ybt) producing Yersinia pseudotuberculosis Δfur mutant (termed Δfur) results in severe systemic infection and acute mortality to hemochromatotic mice due to rapid disruption of the intestinal barrier. Transcriptome analysis of Δfur-infected intestine revealed up-regulation in cytokine-cytokine receptor interactions, the complement and coagulation cascade, the NF-κB signaling pathway, and chemokine signaling pathways, and down-regulation in cell-adhesion molecules and Toll-like receptor signaling pathways. Further studies indicate that dysregulated interleukin (IL)-1β signaling triggered in hemachromatotic mice infected with Δfur damages the intestinal barrier by activation of myosin light-chain kinases (MLCK) and excessive neutrophilia. Inhibiting MLCK activity or depleting neutrophil infiltration reduces barrier disruption, largely ameliorates immunopathology, and substantially rescues hemochromatotic mice from lethal Δfur infection. Moreover, early intervention of IL-1β overproduction can completely rescue hemochromatotic mice from the lethal infection.
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Affiliation(s)
- Shreya Das
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Mohd Saqib
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Ryan C Meng
- Center for Functional Genomics, University at Albany-State University of New York, Rensselaer, NY 12144
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany-State University of New York, Rensselaer, NY 12144
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Fengyi Wan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205
| | - Wei Sun
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208;
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5
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Ashton JM, Rehrauer H, Myers J, Myers J, Zanche M, Balys M, Foox J, Mason CE, Steen R, Kuentzel M, Aquino C, Garcia-Reyero N, Chittur SV. Comparative Analysis of Single-Cell RNA Sequencing Platforms and Methods. J Biomol Tech 2021; 32:3fc1f5fe.3eccea01. [PMID: 35837267 PMCID: PMC9258609 DOI: 10.7171/3fc1f5fe.3eccea01] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) offers great new opportunities for increasing our understanding of complex biological processes. In particular, development of an accurate Human Cell Atlas is largely dependent on the rapidly advancing technologies and molecular chemistries employed in scRNA-seq. These advances have already allowed an increase in throughput for scRNA-seq from 96 to 80,000 cells on a single instrument run by capturing cells within nanoliter droplets. Although this increase in throughput is critical for many experimental questions, a thorough comparison between microfluidic-based, plate-based, and droplet-based technologies or between multiple available platforms utilizing these technologies is largely lacking. Here, we report scRNA-seq data from SUM149PT cells treated with the histone deacetylase inhibitor trichostatin A versus untreated controls across several scRNA-seq platforms (Fluidigm C1, WaferGen iCell8, 10x Genomics Chromium Controller, and Illumina/BioRad ddSEQ). The primary goal of this project was to demonstrate RNA sequencing methods for profiling the ultra-low amounts of RNA present in individual cells, and this report discusses the results of the study, as well as technical challenges and lessons learned and present general guidelines for best practices in sample preparation and analysis.
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Affiliation(s)
- John M. Ashton
- University of Rochester Medical Center,
University of Rochester, West Henrietta, New York 14642, USA
| | - Hubert Rehrauer
- Functional Genomics Center Zurich,
ETH and University of Zurich, CH-8057 Zurich, Switzerland
| | - Jason Myers
- University of Rochester Medical Center,
University of Rochester, West Henrietta, New York 14642, USA
| | - Jacqueline Myers
- University of Rochester Medical Center,
University of Rochester, West Henrietta, New York 14642, USA
| | - Michelle Zanche
- University of Rochester Medical Center,
University of Rochester, West Henrietta, New York 14642, USA
| | - Malene Balys
- University of Rochester Medical Center,
University of Rochester, West Henrietta, New York 14642, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics,
Weill Cornell Medicine, New York, NY10065, USA
| | - Chistopher E. Mason
- Department of Physiology and Biophysics,
Weill Cornell Medicine, New York, NY10065, USA
| | - Robert Steen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marcy Kuentzel
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA
| | - Catharine Aquino
- Functional Genomics Center Zurich,
ETH and University of Zurich, CH-8057 Zurich, Switzerland
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA
| | - Sridar V. Chittur
- Center for Functional Genomics,
University at Albany-SUNY, Rensselaer, New York 12144, USA
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6
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Ropri AS, DeVaux RS, Eng J, Chittur SV, Herschkowitz JI. Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer. Breast Cancer Res 2021; 23:101. [PMID: 34717732 PMCID: PMC8557595 DOI: 10.1186/s13058-021-01479-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Increased breast cancer screening over the past four decades has led to a substantial rise in the diagnosis of ductal carcinoma in situ (DCIS). Although DCIS lesions precede invasive ductal carcinoma (IDC), they do not always transform into cancer. The current standard-of-care for DCIS is an aggressive course of therapy to prevent invasive and metastatic disease resulting in over-diagnosis and over-treatment. Thus, there is a critical need to identify functional determinants of progression of DCIS to IDC to allow discrimination between indolent and aggressive disease. Recent studies show that super-enhancers, in addition to promoting other gene transcription, are themselves transcribed producing super-enhancer associated long noncoding RNAs (SE-lncRNAs). These SE-lncRNAs can interact with their associated enhancer regions in cis and influence activities and expression of neighboring genes. Furthermore, they represent a novel, untapped group of therapeutic targets. METHODS With an integrative analysis of enhancer loci with global expression of SE-lncRNAs in the MCF10A progression series, we have identified differentially expressed SE-lncRNAs which can identify mechanisms for DCIS to IDC progression. Furthermore, cross-referencing these SE-lncRNAs with patient samples in the The Cancer Genome Atlas (TCGA) database, we have unveiled 27 clinically relevant SE-lncRNAs that potentially interact with their enhancer to regulate nearby gene expression. To complement SE-lncRNA expression studies, we conducted an unbiased global analysis of super-enhancers that are acquired or lost in progression. RESULTS Here we designate SE-lncRNAs RP11-379F4.4 and RP11-465B22.8 as potential markers of progression of DCIS to IDC through regulation of the expression of their neighboring genes (RARRES1 and miR-200b, respectively). Moreover, we classified 403 super-enhancer regions in MCF10A normal cells, 627 in AT1, 1053 in DCIS, and 320 in CA1 cells. Comparison analysis of acquired/lost super-enhancer regions with super-enhancer regions classified in 47 ER positive patients, 10 triple negative breast cancer (TNBC) patients, and 11 TNBC cell lines reveal critically acquired pathways including STAT signaling and NF-kB signaling. In contrast, protein folding, and local estrogen production are identified as major pathways lost in progression. CONCLUSION Collectively, these analyses identify differentially expressed SE-lncRNAs and acquired/lost super-enhancers in progression of breast cancer important for promoting DCIS lesions to IDC.
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MESH Headings
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Cell Line
- Disease Progression
- Enhancer Elements, Genetic/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Membrane Proteins/genetics
- MicroRNAs/genetics
- RNA, Long Noncoding/genetics
- Receptors, Estrogen/metabolism
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/pathology
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Affiliation(s)
- Ali S Ropri
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, 1 Discovery Drive, Suite 317, Rensselaer, NY, 12144, USA.
| | - Rebecca S DeVaux
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, 1 Discovery Drive, Suite 317, Rensselaer, NY, 12144, USA
| | - Jonah Eng
- Bethlehem Central High School, Bethlehem Central School District, Delmar, NY, 12054, USA
| | - Sridar V Chittur
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, 1 Discovery Drive, Suite 317, Rensselaer, NY, 12144, USA
- Center for Functional Genomics, Cancer Research Center, University at Albany, Rensselaer, NY, 12144, USA
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, 1 Discovery Drive, Suite 317, Rensselaer, NY, 12144, USA
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7
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D’Souza SS, Zhang Y, Bailey JT, Fung ITH, Kuentzel ML, Chittur SV, Yang Q. Type I Interferon signaling controls the accumulation and transcriptomes of monocytes in the aged lung. Aging Cell 2021; 20:e13470. [PMID: 34547174 PMCID: PMC8520712 DOI: 10.1111/acel.13470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/15/2021] [Revised: 07/18/2021] [Accepted: 08/20/2021] [Indexed: 12/21/2022] Open
Abstract
Aging is paradoxically associated with a deteriorated immune defense (immunosenescence) and increased basal levels of tissue inflammation (inflammaging). The lung is particularly sensitive to the effects of aging. The immune cell mechanisms underlying physiological lung aging remain poorly understood. Here we reveal that aging leads to increased interferon signaling and elevated concentrations of chemokines in the lung, which is associated with infiltration of monocytes into the lung parenchyma. scRNA‐seq identified a novel Type‐1 interferon signaling dependent monocyte subset (MO‐ifn) that upregulated IFNAR1 expression and exhibited greater transcriptomal changes with aging than the other monocytes. Blockade of type‐1 interferon signaling by treatment with anti‐IFNAR1 neutralizing antibodies rapidly ablated MO‐ifn cells. Treatment with anti‐IFNAR1 antibodies also reduced airway chemokine concentrations and repressed the accumulation of the overall monocyte population in the parenchyma of the aged lung. Together, our work suggests that physiological aging is associated with increased basal level of airway monocyte infiltration and inflammation in part due to elevated type‐1 interferon signaling.
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Affiliation(s)
- Shanti S. D’Souza
- Department of Immunology and Microbial Disease Albany Medical College Albany NY USA
| | - Yuanyue Zhang
- Department of Immunology and Microbial Disease Albany Medical College Albany NY USA
| | - Jacob T. Bailey
- Department of Immunology and Microbial Disease Albany Medical College Albany NY USA
| | - Ivan T. H. Fung
- Department of Immunology and Microbial Disease Albany Medical College Albany NY USA
| | - Marcy L. Kuentzel
- Center for Functional Genomics University at Albany‐SUNY Rensselaer NY USA
| | - Sridar V. Chittur
- Center for Functional Genomics University at Albany‐SUNY Rensselaer NY USA
| | - Qi Yang
- Department of Immunology and Microbial Disease Albany Medical College Albany NY USA
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8
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Abstract
Here we present an inexpensive, rapid, and robust reverse-transcription loop-mediated isothermal amplification (RT-LAMP)-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection method that is easily scalable, enabling point-of-care facilities and clinical labs to determine results from patients' saliva directly in 30 minutes for less than $2 per reaction. The method uses a novel combination of widely available reagents that can be prepared in bulk, plated, and frozen and remain stable until samples are received. This innovation dramatically reduces preparation time, enabling high-throughput automation and testing with time to results (including setup) in less than 1 hour for 96 patient samples simultaneously when using a 384-well format. By using a dual reporter (phenol red pH indicator for end-point detection and SYTO-9 fluorescent dye for real time), the assay also provides internal validation of results and redundancy in the event of an instrument malfunction.
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Affiliation(s)
- Andrew Hayden
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - Marcy Kuentzel
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, New York, USA
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9
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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10
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Tighe SW, Hayden AF, Kuentzel ML, Eckstrom KM, Foox J, Vellone DL, Finstad KH, Laaguiby PK, Hoffman JJ, Chittur SV. Molecular Characterization of Increased Amplicon Lengths in SARS-CoV-2 Reverse Transcription Loop-Mediated Isothermal Amplification Assays. J Biomol Tech 2021; 32:199-205. [PMID: 35027877 PMCID: PMC8730522 DOI: 10.7171/jbt.21-3203-015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a power tool for the amplification of specific RNA and DNA targets. Much like PCR, LAMP requires primers that surround a target amplification region and generates exponential product through a unique highly specific daisy-chain single-temperature amplification reaction. However, until recently, attempts to amplify targets of greater than 200 base pairs (bp) have been mostly unsuccessful and limited to short amplicon targets of less than 150 bp. Although short amplicons have the benefit of a rapid detection (<40 min), they do not allow for the prediction of RNA integrity based on RNA length and possible intactness. In this study, 8 primer sets were developed using 2 LAMP primer-specific software packages against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid gene with insert lengths ranging from 262 to 945 bp in order to amplify and infer the integrity of viral RNA. Because these amplification lengths are greater than the current methods that use an insert length of 130 or less, they require a longer incubation, modified primer and temperature strategies, and the addition of specific adjuncts to prevent nonspecific amplification. This proof of concept study resulted in successful reverse transcription LAMP reactions for amplicon targets of 262, 687, 693, and 945 bp using a clinical nasopharyngeal NP sample, purified SARS-CoV-2 RNA, and crude lysate containing inactivated virus.
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Affiliation(s)
- Scott W. Tighe
- University of Vermont, Vermont Integrative Genomics, Burlington, Vermont 05405, USA
| | - Andrew F. Hayden
- Center for Functional Genomics, University at Albany—State University of New York, Rensselaer, NY 12144, USA
| | - Marcy L. Kuentzel
- Center for Functional Genomics, University at Albany—State University of New York, Rensselaer, NY 12144, USA
| | - Korin M. Eckstrom
- University of Vermont, Vermont Integrative Genomics, Burlington, Vermont 05405, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Daniel L. Vellone
- University of Vermont, Vermont Integrative Genomics, Burlington, Vermont 05405, USA
| | - Kristiaan H. Finstad
- University of Vermont, Vermont Integrative Genomics, Burlington, Vermont 05405, USA
| | - Pheobe K. Laaguiby
- University of Vermont, Vermont Integrative Genomics, Burlington, Vermont 05405, USA
| | - Jessica J. Hoffman
- University of Vermont, Vermont Integrative Genomics, Burlington, Vermont 05405, USA
| | - Sridar V. Chittur
- Center for Functional Genomics, University at Albany—State University of New York, Rensselaer, NY 12144, USA
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11
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Box A, DeLay M, Tighe S, Chittur SV, Bergeron A, Cochran M, Lopez P, Meyer EM, Saluk A, Thornton S, Brundage K. Evaluating the Effects of Cell Sorting on Gene Expression. J Biomol Tech 2021; 31:100-111. [PMID: 32982601 DOI: 10.7171/jbt.20-3103-004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cell sorting is a commonly used technology to isolate highly purified cell populations for downstream applications. Because the sorted cells are destined for further analysis, i.e., gene expression assays or functional assays, ensuring that the sorting process itself has little effect on the cells is of utmost importance. Previous studies examining the effects of sorting on cellular function have primarily focused on a specific cell type or condition. One of the goals of the Flow Cytometry Research Group of the Association of Biomolecular Resource Facilities is to establish best practice guidelines for cell sorting conditions that minimize cell stress, perturbation, or injury to the sorted cell population. In this study, the effects of nozzle size, sample pressure, UV exposure, and instrument type were evaluated for their effects on gene expression and cell cycle using both established cell lines and primary cells across several flow cytometry shared facilities. Results indicate that nozzle size and pressure, as well as UV exposure and instrument type, have only minor effects on gene expression, which were diminished by subsequent culturing of the sorted cells. In this assessment, these data demonstrate that cell sorting itself, regardless of instrumentation used, has minimal effects on downstream cellular applications.
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Affiliation(s)
- Andrew Box
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Monica DeLay
- Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Scott Tighe
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Albany, New York, USA
| | | | - Matthew Cochran
- University of Rochester Medical Center, West Henrietta, New York, USA
| | - Peter Lopez
- New York University Langone Medical Center, New York City, New York, USA
| | - E Michael Meyer
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Alan Saluk
- The Scripps Research Institute, San Diego, California, USA
| | - Sherry Thornton
- Department of Pediatrics and Cincinnati Children's Hospital, University of Cincinnati Medical Center, Cincinnati, Ohio, USA; and
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12
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Fung ITH, Zhang Y, Shin DS, Sankar P, Sun X, D'Souza SS, Song R, Kuentzel ML, Chittur SV, Zuloaga KL, Yang Q. Group 2 innate lymphoid cells are numerically and functionally deficient in the triple transgenic mouse model of Alzheimer's disease. J Neuroinflammation 2021; 18:152. [PMID: 34229727 PMCID: PMC8261980 DOI: 10.1186/s12974-021-02202-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/23/2021] [Indexed: 01/02/2023] Open
Abstract
Background The immune pathways in Alzheimer’s disease (AD) remain incompletely understood. Our recent study indicates that tissue-resident group 2 innate lymphoid cells (ILC2) accumulate in the brain barriers of aged mice and that their activation alleviates aging-associated cognitive decline. The regulation and function of ILC2 in AD, however, remain unknown. Methods In this study, we examined the numbers and functional capability of ILC2 from the triple transgenic AD mice (3xTg-AD) and control wild-type mice. We investigated the effects of treatment with IL-5, a cytokine produced by ILC2, on the cognitive function of 3xTg-AD mice. Results We demonstrate that brain-associated ILC2 are numerically and functionally defective in the triple transgenic AD mouse model (3xTg-AD). The numbers of brain-associated ILC2 were greatly reduced in 7-month-old 3xTg-AD mice of both sexes, compared to those in age- and sex-matched control wild-type mice. The remaining ILC2 in 3xTg-AD mice failed to efficiently produce the type 2 cytokine IL-5 but gained the capability to express a number of proinflammatory genes. Administration of IL-5, a cytokine produced by ILC2, transiently improved spatial recognition and learning in 3xTg-AD mice. Conclusion Our results collectively indicate that numerical and functional deficiency of ILC2 might contribute to the cognitive impairment of 3xTg-AD mice. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-021-02202-2.
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Affiliation(s)
- Ivan Ting Hin Fung
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Yuanyue Zhang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Damian S Shin
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, 12208, USA
| | - Poornima Sankar
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Xiangwan Sun
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Shanti S D'Souza
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA
| | - Renjie Song
- Biochemistry & Immunology Core Facility at Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Marcy L Kuentzel
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, NY, 12144, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, NY, 12144, USA
| | - Kristen L Zuloaga
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, 12208, USA
| | - Qi Yang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, 12208, USA.
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13
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Fung ITH, Sankar P, Zhang Y, Robison LS, Zhao X, D'Souza SS, Salinero AE, Wang Y, Qian J, Kuentzel ML, Chittur SV, Temple S, Zuloaga KL, Yang Q. Activation of group 2 innate lymphoid cells alleviates aging-associated cognitive decline. J Exp Med 2020; 217:133697. [PMID: 32022838 PMCID: PMC7144523 DOI: 10.1084/jem.20190915] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/28/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence has challenged the traditional view about the immune privilege of the brain, but the precise roles of immune cells in regulating brain physiology and function remain poorly understood. Here, we report that tissue-resident group 2 innate lymphoid cells (ILC2) accumulate in the choroid plexus of aged brains. ILC2 in the aged brain are long-lived, are relatively resistant to cellular senescence and exhaustion, and are capable of switching between cell cycle dormancy and proliferation. They are functionally quiescent at homeostasis but can be activated by IL-33 to produce large amounts of type 2 cytokines and other effector molecules in vitro and in vivo. Intracerebroventricular transfer of activated ILC2 revitalized the aged brain and enhanced the cognitive function of aged mice. Administration of IL-5, a major ILC2 product, was sufficient to repress aging-associated neuroinflammation and alleviate aging-associated cognitive decline. Targeting ILC2 in the aged brain may provide new avenues to combat aging-associated neurodegenerative disorders.
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Affiliation(s)
- Ivan Ting Hin Fung
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY
| | - Poornima Sankar
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY
| | - Yuanyue Zhang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY
| | - Lisa S Robison
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY
| | - Xiuli Zhao
- Neural Stem Cell Institute, Rensselaer, NY
| | - Shanti S D'Souza
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY
| | - Abigail E Salinero
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY
| | - Yue Wang
- Neural Stem Cell Institute, Rensselaer, NY
| | - Jiang Qian
- Department of Pathology, Albany Medical College, Albany, NY
| | - Marcy L Kuentzel
- Center for Functional Genomics, University at Albany-State University of New York, Rensselaer, NY
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany-State University of New York, Rensselaer, NY
| | | | - Kristen L Zuloaga
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY
| | - Qi Yang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY.,Department of Medicine, Albany Medical College, Albany, NY
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14
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Box A, DeLay M, Tighe S, Chittur SV, Bergeron A, Cochran M, Lopez P, Meyer EM, Saluk A, Thornton S, Brundage K. Evaluating the Effects of Cell Sorting on Gene Expression. J Biomol Tech 2020; 31:jbt.20-3103-004. [PMID: 32831654 DOI: 10.7171/jbt.2020-3103-004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cell sorting is a commonly used technology to isolate highly purified cell populations for downstream applications. Because the sorted cells are destined for further analysis, i.e., gene expression assays or functional assays, ensuring that the sorting process itself has little effect on the cells is of utmost importance. Previous studies examining the effects of sorting on cellular function have primarily focused on a specific cell type or condition. One of the goals of the Flow Cytometry Research Group of the Association of Biomolecular Resource Facilities is to establish best practice guidelines for cell sorting conditions that minimize cell stress, perturbation, or injury to the sorted cell population. In this study, the effects of nozzle size, sample pressure, UV exposure, and instrument type were evaluated for their effects on gene expression and cell cycle using both established cell lines and primary cells across several flow cytometry shared facilities. Results indicate that nozzle size and pressure, as well as UV exposure and instrument type, have only minor effects on gene expression, which were diminished by subsequent culturing of the sorted cells. In this assessment, these data demonstrate that cell sorting itself, regardless of instrumentation used, has minimal effects on downstream cellular applications.
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Affiliation(s)
- Andrew Box
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Monica DeLay
- Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Scott Tighe
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Albany, New York, USA
| | | | - Matthew Cochran
- University of Rochester Medical Center, West Henrietta, New York, USA
| | - Peter Lopez
- New York University Langone Medical Center, New York City, New York, USA
| | - E Michael Meyer
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Alan Saluk
- The Scripps Research Institute, San Diego, California, USA
| | - Sherry Thornton
- Department of Pediatrics and Cincinnati Children's Hospital, University of Cincinnati Medical Center, Cincinnati, Ohio, USA; and
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15
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Zhang Y, Fung ITH, Sankar P, Chen X, Robison LS, Ye L, D'Souza SS, Salinero AE, Kuentzel ML, Chittur SV, Zhang W, Zuloaga KL, Yang Q. Depletion of NK Cells Improves Cognitive Function in the Alzheimer Disease Mouse Model. J Immunol 2020; 205:502-510. [PMID: 32503894 DOI: 10.4049/jimmunol.2000037] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022]
Abstract
Despite mounting evidence suggesting the involvement of the immune system in regulating brain function, the specific role of immune and inflammatory cells in neurodegenerative diseases remain poorly understood. In this study, we report that depletion of NK cells, a type of innate lymphocytes, alleviates neuroinflammation, stimulates neurogenesis, and improves cognitive function in a triple-transgenic Alzheimer disease (AD) mouse model. NK cells in the brains of triple-transgenic AD mouse model (3xTg-AD) mice exhibited an enhanced proinflammatory profile. Depletion of NK cells by anti-NK1.1 Abs drastically improved cognitive function of 3xTg-AD mice. NK cell depletion did not affect amyloid β concentrations but enhanced neurogenesis and reduced neuroinflammation. Notably, in 3xTg-AD mice depleted of NK cells, microglia demonstrated a homeostatic-like morphology, decreased proliferative response and reduced expression of neurodestructive proinflammatory cytokines. Together, our results suggest a proinflammatory role for NK cells in 3xTg-AD mice and indicate that targeting NK cells might unlock novel strategies to combat AD.
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Affiliation(s)
- Yuanyue Zhang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Ivan Ting Hin Fung
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Poornima Sankar
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Xiangyu Chen
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Lisa S Robison
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208
| | - Longyun Ye
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Shanti S D'Souza
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Abigail E Salinero
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208
| | - Marcy L Kuentzel
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, NY 12144; and
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, NY 12144; and
| | - Wenzheng Zhang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
| | - Kristen L Zuloaga
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208;
| | - Qi Yang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208;
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16
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D’Souza S, Shen X, Fung ITH, Ye L, Kuentzel M, Chittur SV, Furuya Y, Siebel CW, Maillard IP, Metzger DW, Yang Q. Compartmentalized effects of aging on group 2 innate lymphoid cell development and function. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.234.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The effects of aging on innate immunity and the resulting impacts on immunosenescence remain poorly understood. Here, we report that aging induces compartmentalized changes to the development and function of group 2 innate lymphoid cells (ILC2), an ILC subset implicated in pulmonary homeostasis and tissue repair. Aging enhances bone marrow early ILC2 development through Notch signaling, but the newly generated circulating ILC2 are unable to settle in the lungs to replenish the concomitantly declining mature lung ILC2 pool in aged mice. Aged lung ILC2 are transcriptomically heterogeneous and functionally compromised, failing to produce cytokines at homeostasis and during influenza infection. They have reduced expression of Cyp2e1, a cytochrome P450 oxidase required for optimal ILC2 function. Transfer of lung ILC2 from young mice enhances resistance to influenza infection in old mice. These data highlight compartmentalized effects of aging on ILC and indicate that targeting tissue-resident ILCs might unlock therapies to enhance resistance to infections and diseases in the elderly.
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17
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Frye CA, Chittur SV. Mating Enhances Expression of Hormonal and Trophic Factors in the Midbrain of Female Rats. Front Behav Neurosci 2020; 14:21. [PMID: 32351369 PMCID: PMC7176275 DOI: 10.3389/fnbeh.2020.00021] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/31/2020] [Indexed: 11/23/2022] Open
Abstract
Among female rats, mating enhances neurosteroid formation in the midbrain ventral tegmental area (VTA; independent of peripheral steroid-secreting glands, ovaries, and adrenals). The sources/targets for these actions are not well understood. In Experiment 1, proestrous rats engaged in a mating paradigm, or did not, and the midbrains had been assessed via the Affymetrix rat genome microarrays. In Experiment 2, the influence of gonadal and adrenal glands on the expression of these genes was assessed in rats that were proestrous, ovariectomized (OVX), or OVX and adrenalectomized (ADX). The microarrays revealed 53 target genes that were significantly up-regulated (>2.0-fold change) in response to mating. Mating significantly enhanced the midbrain mRNA expression of genes involved in hormonal and trophic actions: Gh1, S100g, and Klk1b3 in proestrous, but not OVX and/or ADX, rats; Fshb in all but OVX/ADX rats; and lutenizing hormone β and thyroid-stimulating hormone (TSH) β in all rats. Thus, mating enhances midbrain gene expression independent and dependent of peripheral glands.
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Affiliation(s)
- Cheryl A Frye
- Department of Psychology, The University at Albany-SUNY, Albany, NY, United States.,Department of Biological Sciences, The University at Albany-SUNY, Albany, NY, United States.,Center for Neuroscience Research, The University at Albany-SUNY, Albany, NY, United States.,Center for Life Sciences Research, The University at Albany-SUNY, Albany, NY, United States
| | - Sridar V Chittur
- Center for Functional Genomics, The University at Albany-SUNY, Albany, NY, United States
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18
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Fung ITH, Sankar P, Zhang Y, Robison LS, Zhao X, D’Souza S, Salinero AE, Wang Y, Qian J, Kuentzel M, Chittur SV, Temple S, Zuloaga KL, Yang Q. Accumulation and activation of group 2 innate lymphoid cells in the aged brain alleviate aging associated cognitive decline. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.148.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Increasing evidence has challenged the traditional view about the immune privilege of the brain, but the precise roles of immune cells in regulating brain physiology and function remain poorly understood. Here we report that tissue-resident group 2 innate lymphoid cells (ILC2) accumulate in the choroid plexus of aged brains. ILC2 in the aged brain are long-lived, relatively resistant to cellular senescence and exhaustion, and are capable of switching between cell cycle dormancy and proliferation. They are functionally quiescent at homeostasis but can be activated by IL-33 to produce large amounts of type-2 cytokines and other effector molecules in vitro and in vivo. Intracerebroventricular transfer of activated ILC2 revitalized the aged brain and enhanced the cognitive function of aged mice. Administration of IL-5, a major ILC2 product, was sufficient to repress aging-associated neuroinflammation and alleviate aging-associated cognitive decline. Targeting ILC2 in the aged brain may provide new avenues to combat aging-associated neurodegenerative disorders.
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Affiliation(s)
- Ivan Ting Hin Fung
- 1Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Poornima Sankar
- 1Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Yuanyue Zhang
- 1Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Lisa S. Robison
- 2Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - Xiuli Zhao
- 3Neural Stem Cell Institute, Rensselaer, New York, USA
| | - Shanti D’Souza
- 1Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
| | - Abigail E. Salinero
- 2Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - Yue Wang
- 3Neural Stem Cell Institute, Rensselaer, New York, USA
| | - Jiang Qian
- 4Department of Pathology, Albany Medical College, Albany, New York, USA
| | - Marcy Kuentzel
- 5Center for Functional Genomics, University at Albany-SUNY, Rensselaer, New York, USA
| | - Sridar V. Chittur
- 5Center for Functional Genomics, University at Albany-SUNY, Rensselaer, New York, USA
| | - Sally Temple
- 3Neural Stem Cell Institute, Rensselaer, New York, USA
| | - Kristen L. Zuloaga
- 2Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York, USA
| | - Qi Yang
- 1Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
- 6Department of Medicine, Albany Medical College, Albany, New York, USA
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19
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DeVaux RS, Ropri AS, Grimm SL, Hall PA, Herrera EO, Chittur SV, Smith WP, Coarfa C, Behbod F, Herschkowitz JI. Long noncoding RNA BHLHE40-AS1 promotes early breast cancer progression through modulating IL-6/STAT3 signaling. J Cell Biochem 2020; 121:3465-3478. [PMID: 31907974 DOI: 10.1002/jcb.29621] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 08/26/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a nonobligate precursor to invasive breast cancer. Only a small percentage of DCIS cases are predicted to progress; however, there is no method to determine which DCIS lesions will remain innocuous from those that will become invasive disease. Therefore, DCIS is treated aggressively creating a current state of overdiagnosis and overtreatment. There is a critical need to identify functional determinants of progression of DCIS to invasive ductal carcinoma (IDC). Interrogating biopsies from five patients with contiguous DCIS and IDC lesions, we have shown that expression of the long noncoding RNA BHLHE40-AS1 increases with disease progression. BHLHE40-AS1 expression supports DCIS cell proliferation, motility, and invasive potential. Mechanistically, BHLHE40-AS1 modulates interleukin (IL)-6/signal transducer and activator of transcription 3 (STAT3) activity and a proinflammatory cytokine signature, in part through interaction with interleukin enhancer-binding factor 3. These data suggest that BHLHE40-AS1 supports early breast cancer progression by engaging STAT3 signaling, creating an immune-permissive microenvironment.
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Affiliation(s)
- Rebecca S DeVaux
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-SUNY, Rensselaer, New York
| | - Ali S Ropri
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-SUNY, Rensselaer, New York
| | - Sandra L Grimm
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Peter A Hall
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | | | - Sridar V Chittur
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, New York
| | - William P Smith
- Department of Radiology, Hays Medical Center, University of Kansas Health System, Kansas City, Kansas
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Fariba Behbod
- Division of Cancer and Developmental Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-SUNY, Rensselaer, New York
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20
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Boehlke C, Rupf S, Tenniswood M, Chittur SV, Hannig C, Zierau O. Caries and periodontitis associated bacteria are more abundant in human saliva compared to other great apes. Arch Oral Biol 2020; 111:104648. [PMID: 31927405 DOI: 10.1016/j.archoralbio.2020.104648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Received: 08/23/2019] [Revised: 11/29/2019] [Accepted: 01/01/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Caries and periodontitis are uncommon in free ranging great apes but a major oral disease in humans. The aim was to analyze abundance and diversity of oral bacteria of western humans and their closest relatives, to examine if zoo apes feeding on diet other than in their natural habitat show caries and periodontitis associated salivary bacteria and comparable susceptibility for oral civilization diseases as humans. DESIGN Bacterial composition of human and great ape saliva samples were compared by analyzing the V3 region of the bacteria 16S rRNA gene by Next Generation Sequencing with Ion Torrent. RESULTS Results show species-specific differences in the salivary bacteria phyla and genera composition among all apes. Moreover, salivary bacterial composition within non-human apes showed higher intra-individual differences than within humans. Human saliva exhibited lowest bacteria diversity. Different behavioral patterns including (oral) hygiene standards of humans and non-human apes might cause differences. All species differed in diversity and abundance of caries associated bacteria genera. Human saliva revealed higher abundance of caries and periodontitis relevant bacteria in contrast to other great apes, which might be supported by higher consume of refined cariogenic food items, possibly raising their risk for oral disease susceptibility. CONCLUSIONS The study offers first clues on caries and periodontitis relevant bacteria of captive great ape species in comparison to humans. Higher susceptibility to oral diseases for humans than for their closest relatives, leads to the question, if the oral microbiome changed during evolution and how it is influenced by the human life style.
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Affiliation(s)
- Carolin Boehlke
- Faculty of Biology, Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01217 Dresden, Germany; Policlinic of Operative and Pediatric Dentistry, Faculty of Medicine ´Carl Gustav Carus´, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66424 Homburg/Saar, Germany.
| | - Martin Tenniswood
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144-2345, USA.
| | - Sridar V Chittur
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144-2345, USA; Center for Functional Genomics, University at Albany, Rensselaer, NY, 12144-2345, USA.
| | - Christian Hannig
- Policlinic of Operative and Pediatric Dentistry, Faculty of Medicine ´Carl Gustav Carus´, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Oliver Zierau
- Faculty of Biology, Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01217 Dresden, Germany.
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21
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Nallanthighal S, Tierney L, Cady NC, Murray TM, Chittur SV, Reliene R. Surface coatings alter transcriptional responses to silver nanoparticles following oral exposure. NanoImpact 2020; 17:100205. [PMID: 32864508 PMCID: PMC7453744 DOI: 10.1016/j.impact.2019.100205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Silver nanoparticles (AgNPs) are used in food packaging materials, dental care products and other consumer goods and can result in oral exposure. To determine whether AgNP coatings modulate transcriptional responses to AgNP exposure, we exposed mice orally to 20 nm citrate (cit)-coated AgNPs (cit-AgNPs) or polyvinylpyrrolidone (PVP)-coated AgNPs (PVP-AgNPs) at a 4 mg/kg dose for 7 consecutive days and analyzed changes in the expression of protein-coding genes and long noncoding RNAs (lncRNAs), a new class of regulatory RNAs, in the liver. We identified unique and common expression signatures of protein-coding and lncRNA genes, altered biological processes and signaling pathways, and coding-non-coding gene interactions for cit-AgNPs and PVP-AgNPs. Commonly regulated genes comprised only about 10 and 20 percent of all differentially expressed genes in PVP-AgNP and cit-AgNP exposed mice, respectively. Commonly regulated biological processes included glutathione metabolic process and cellular oxidant detoxification. Commonly regulated pathways included Keap-Nrf2, PPAR, MAPK and IL-6 signaling pathways. The coding-non-coding gene co-expression analysis revealed that protein-coding genes were co-expressed with a variable number of lncRNAs ranging from one to twenty three and may share functional roles with the protein-coding genes. PVP-AgNP exposure induced a more robust transcriptional response than cit-AgNP exposure characterized by more than two-fold higher number of differentially expressed both protein- coding and lncRNA genes. Our data demonstrate that the surface coating strongly modulates the spectrum and the number of differentially expressed genes after oral AgNP exposure. On the other hand, our data suggest that AgNP exposure can alter drug and chemical sensitivity, metabolic homeostasis and cancer risk irrespective of the coating type, warranting further investigations.
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Affiliation(s)
- Sameera Nallanthighal
- Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Lukas Tierney
- Colleges of Nanoscale Sciences and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Nathaniel C. Cady
- Colleges of Nanoscale Sciences and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Thomas M. Murray
- Colleges of Nanoscale Sciences and Engineering, SUNY Polytechnic Institute, Albany, NY, USA
| | - Sridar V. Chittur
- Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Ramune Reliene
- Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA
- Department of Environmental Health Sciences, University at Albany, State University of New York, Albany, NY, USA
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22
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D'Souza SS, Shen X, Fung ITH, Ye L, Kuentzel M, Chittur SV, Furuya Y, Siebel CW, Maillard IP, Metzger DW, Yang Q. Compartmentalized effects of aging on group 2 innate lymphoid cell development and function. Aging Cell 2019; 18:e13019. [PMID: 31429526 PMCID: PMC6826140 DOI: 10.1111/acel.13019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 02/14/2019] [Revised: 06/20/2019] [Accepted: 07/14/2019] [Indexed: 01/03/2023] Open
Abstract
The effects of aging on innate immunity and the resulting impacts on immunosenescence remain poorly understood. Here, we report that aging induces compartmentalized changes to the development and function of group 2 innate lymphoid cells (ILC2), an ILC subset implicated in pulmonary homeostasis and tissue repair. Aging enhances bone marrow early ILC2 development through Notch signaling, but the newly generated circulating ILC2 are unable to settle in the lungs to replenish the concomitantly declining mature lung ILC2 pool in aged mice. Aged lung ILC2 are transcriptomically heterogeneous and functionally compromised, failing to produce cytokines at homeostasis and during influenza infection. They have reduced expression of Cyp2e1, a cytochrome P450 oxidase required for optimal ILC2 function. Transfer of lung ILC2 from young mice enhances resistance to influenza infection in old mice. These data highlight compartmentalized effects of aging on ILC and indicate that targeting tissue-resident ILCs might unlock therapies to enhance resistance to infections and diseases in the elderly.
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Affiliation(s)
- Shanti S. D'Souza
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
| | - Xiaofei Shen
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
| | - Ivan T. H. Fung
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
| | - Longyun Ye
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
| | - Marcy Kuentzel
- Center for Functional Genomics University at Albany‐SUNY Rensselaer New York USA
| | - Sridar V. Chittur
- Center for Functional Genomics University at Albany‐SUNY Rensselaer New York USA
| | - Yoichi Furuya
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
| | - Christian W. Siebel
- Department of Discovery Oncology Genentech South San Francisco California USA
| | - Ivan P. Maillard
- Division of Hematology‐Oncology, Department of Medicine & Abramson Family Cancer Research Institute University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Dennis W. Metzger
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
| | - Qi Yang
- Department of Immunology and Microbial Disease Albany Medical College Albany New York USA
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23
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Mubaid S, Ma JF, Omer A, Ashour K, Lian XJ, Sanchez BJ, Robinson S, Cammas A, Dormoy-Raclet V, Di Marco S, Chittur SV, Tenenbaum SA, Gallouzi IE. HuR counteracts miR-330 to promote STAT3 translation during inflammation-induced muscle wasting. Proc Natl Acad Sci U S A 2019; 116:17261-17270. [PMID: 31405989 PMCID: PMC6717253 DOI: 10.1073/pnas.1905172116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Debilitating cancer-induced muscle wasting, a syndrome known as cachexia, is lethal. Here we report a posttranscriptional pathway involving the RNA-binding protein HuR as a key player in the onset of this syndrome. Under these conditions, HuR switches its function from a promoter of muscle fiber formation to become an inducer of muscle loss. HuR binds to the STAT3 (signal transducer and activator of transcription 3) mRNA, which encodes one of the main effectors of this condition, promoting its expression both in vitro and in vivo. While HuR does not affect the stability and the cellular movement of this transcript, HuR promotes the translation of the STAT3 mRNA by preventing miR-330 (microRNA 330)-mediated translation inhibition. To achieve this effect, HuR directly binds to a U-rich element in the STAT3 mRNA-3'untranslated region (UTR) located within the vicinity of the miR-330 seed element. Even though the binding sites of HuR and miR-330 do not overlap, the recruitment of either one of them to the STAT3-3'UTR negatively impacts the binding and the function of the other factor. Therefore, together, our data establish the competitive interplay between HuR and miR-330 as a mechanism via which muscle fibers modulate, in part, STAT3 expression to determine their fate in response to promoters of muscle wasting.
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Affiliation(s)
- Souad Mubaid
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Jennifer F Ma
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Amr Omer
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Kholoud Ashour
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Xian J Lian
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Brenda J Sanchez
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Samantha Robinson
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
- Université Toulouse III Paul Sabatier, 31330 Toulouse, France
- Laboratoire d'Excellence "TOUCAN," 31037 Toulouse, France
| | - Virginie Dormoy-Raclet
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux Cedex, France
| | - Sergio Di Marco
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sridar V Chittur
- College of Nanoscale Sciences, State University of New York (SUNY) Polytechnic Institute, Albany, NY 12203
- College of Engineering, SUNY Polytechnic Institute, Albany, NY 12203
| | - Scott A Tenenbaum
- College of Nanoscale Sciences, State University of New York (SUNY) Polytechnic Institute, Albany, NY 12203
- College of Engineering, SUNY Polytechnic Institute, Albany, NY 12203
| | - Imed-Eddine Gallouzi
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada;
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24
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He T, Chittur SV, Musah RA. Impact on Glioblastoma U87 Cell Gene Expression of a Carborane Cluster-Bearing Amino Acid: Implications for Carborane Toxicity in Mammalian Cells. ACS Chem Neurosci 2019; 10:1524-1534. [PMID: 30475580 DOI: 10.1021/acschemneuro.8b00512] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 12/31/2022] Open
Abstract
Carboranes have been extensively investigated as potential drugs for the treatment of malignant human brain tumors by boron neutron capture therapy (BNCT). This noninvasive treatment modality utilizes compounds containing the nonradioactive isotope 10B which has a high propensity to capture slow neutrons. In response, it emits high energy α-particles that kill the cell. We have successfully synthesized a boron delivery agent by installing a boron-rich m-carborane within the amino acid cysteine. Rapid uptake of this compound into U87 glioblastoma cells within 5 min of exposure was observed, and fluorescence microscopy studies showed that it was retained intracellularly after 48 h. In the absence of thermal neutrons, a cytostatic effect in U87 cells was observed at exposures ranging from 1 μM to 1 mM relative to the control, while no change was observed at 1-0.01 μM. Microarray studies unveiled a wide range of unique changes in the gene expression profile of the U87 cells, particularly for the genes associated with cell cycle, which were observed to be greatly suppressed after treatment with the compound. These results were validated by qPCR studies. Although the compound was designed for BNCT, its distinctive impacts on gene regulation reveal that it and other carborane-containing cluster molecules may exert unique heretofore unknown effects on the transcriptome, even in the absence of applied radiation.
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Affiliation(s)
- Tianyu He
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Sridar V. Chittur
- Center for Functional Genomics, University at Albany, State University of New York, 1 Discovery Drive, Rensselaer, New York 12144, United States
| | - Rabi A. Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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25
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Narvaez CJ, Mall SK, Fountain A, Parr BA, Chittur SV, Kokorin BI, Botsford SF, Startari JF. Specifically Targeted Electromagnetic Fields Arrest Proliferation of Glioblastoma Multiforme U-87 Cells in Culture. Anticancer Res 2018; 38:3255-3266. [PMID: 29848672 DOI: 10.21873/anticanres.12590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/06/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Glioblastoma multiforme is an aggressive primary tumor that arises in the glial cells of the brain. Standardized first-line treatment has considerable morbidity and less than one-year median survival after intervention. Ultra-low intensity electromagnetic fields have been shown to interact with biological organisms without anticipated deleterious side-effects. The aim of the study was to determine if a novel, non-invasive application of non-ionizing radiation has an inhibitory effect on proliferation of glioblastoma multiforme cells. MATERIALS AND METHODS U-87 MG cells were continuously exposed for 54 h to an electromagnetic field tuned to simultaneously interact with DNA/RNA oligonucleotides (mutated alpha-kinase 2 gene/Hsa-miR-381-5p respectively) and proteins (HSP70/CHI3L1). RESULTS Exposed cells demonstrated a significant inhibition of cell growth and concurrent increase in cell death. CONCLUSION This technology induces cell death by novel non-cytotoxic mechanisms unlikely to induce side-effects in patients; can be customized for individual tumors and may contribute to the emerging strategy of personalized medicine.
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Affiliation(s)
- Carmen J Narvaez
- Center for Functional Genomics, Rensselaer, NY, U.S.A.,University at Albany, Rensselaer, NY, U.S.A
| | - Samantha K Mall
- University at Albany, Rensselaer, NY, U.S.A.,Anapole Technologies Inc., Burlington, IA, U.S.A
| | - Aaron Fountain
- Center for Functional Genomics, Rensselaer, NY, U.S.A.,Anapole Technologies Inc., Burlington, IA, U.S.A.,Department of Chemistry and Biology, Ryerson University, Toronto, Canada
| | - Brian A Parr
- Center for Functional Genomics, Rensselaer, NY, U.S.A.,University at Albany, Rensselaer, NY, U.S.A
| | - Sridar V Chittur
- Center for Functional Genomics, Rensselaer, NY, U.S.A.,University at Albany, Rensselaer, NY, U.S.A
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26
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Helle J, Keiler AM, Zierau O, Dörfelt P, Vollmer G, Lehmann L, Chittur SV, Tenniswood M, Welsh J, Kretzschmar G. Effects of the aryl hydrocarbon receptor agonist 3-methylcholanthrene on the 17β-estradiol regulated mRNA transcriptome of the rat uterus. J Steroid Biochem Mol Biol 2017; 171:133-143. [PMID: 28285017 DOI: 10.1016/j.jsbmb.2017.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 11/18/2016] [Revised: 03/01/2017] [Accepted: 03/06/2017] [Indexed: 10/20/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are products of incomplete combustion of organic compounds, abundant in exhaust fumes and cigarette smoke. They act by binding to the aryl hydrocarbon receptor (AHR) which induces expression of phase 1 and phase 2 enzymes in the liver. PAH induced AHR activation may also lead to adverse effects by modulating other pathways, for example estrogen receptor (ER) signaling in the female reproductive tract. We have investigated the effects of the PAH 3-methylcholanthrene (3-MC) on 17β-estradiol (E2) dependent signaling in the uterus of ovariectomized rats to characterize the cross talk between AHR and ER on an mRNA transcriptome wide scale. A standard three day uterotrophic assay was performed in young adult Lewis rats. Treatment induced effects were analyzed using histology, immunohistochemistry and gene expression analysis by microarray and qPCR. 3-MC shows broad E2 antagonistic effects on uterine mRNA transcription of the vast majority of E2 regulated genes, significantly altering prostaglandin biosynthesis, complement activation, coagulation pathways and other inflammatory response pathways. The regulation of ER expression in the uterus, but not the regulation of E2 metabolism in the liver, was identified as a potentially important factor in mediating this general antiestrogenic effect. The regulation of prostaglandin biosynthesis by E2 is important for inflammation-like events during pregnancy including the initiation of birth. Our results suggest that adverse effects of PAHs on prostaglandin related pathways are likely caused by the interference with E2 signaling, specifically by inhibiting the E2 mediated downregulation of PGF2α. Characterization of the generalized antagonistic effect of 3-MC on E2 dependent signaling in the rat uterus thus contributes to a better understanding of molecular mechanisms of the toxicity of PAHs in female reproductive organs.
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Affiliation(s)
- Janina Helle
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Annekathrin M Keiler
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Oliver Zierau
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Peggy Dörfelt
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Günter Vollmer
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01062, Dresden, Germany
| | - Leane Lehmann
- Institute of Pharmacy and Food Chemistry, Universität Würzburg, 97070 Würzburg, Germany
| | - Sridar V Chittur
- Cancer Research Center and Department of Biomedical Sciences, University at Albany, NY 12144-2345, United States
| | - Martin Tenniswood
- Cancer Research Center and Department of Biomedical Sciences, University at Albany, NY 12144-2345, United States
| | - JoEllen Welsh
- Cancer Research Center and Department of Biomedical Sciences, University at Albany, NY 12144-2345, United States
| | - Georg Kretzschmar
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01062, Dresden, Germany.
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27
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Longmate WM, Lyons SP, Chittur SV, Pumiglia KM, Van De Water L, DiPersio CM. Suppression of integrin α3β1 by α9β1 in the epidermis controls the paracrine resolution of wound angiogenesis. J Cell Biol 2017; 216:1473-1488. [PMID: 28416479 PMCID: PMC5412555 DOI: 10.1083/jcb.201510042] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/10/2017] [Accepted: 03/14/2017] [Indexed: 12/02/2022] Open
Abstract
The development of novel therapies to promote wound healing is hindered by our poor understanding of how different integrins function together in the epidermis. Longmate et al. show that cross-suppression by integrins within the epidermis controls paracrine signals that regulate wound angiogenesis. Integrin α9β1 suppresses the proangiogenic functions of α3β1 during late-stage wound healing, leading to the normalization of blood vessel density in the wound bed. Development of wound therapies is hindered by poor understanding of combinatorial integrin function in the epidermis. In this study, we generated mice with epidermis-specific deletion of α3β1, α9β1, or both integrins as well as keratinocyte lines expressing these integrin combinations. Consistent with proangiogenic roles for α3β1, α3-null keratinocytes showed reduced paracrine stimulation of endothelial cell migration and survival, and wounds of epidermis-specific α3 knockout mice displayed impaired angiogenesis. Interestingly, α9β1 in keratinocytes suppressed α3β1-mediated stimulation of endothelial cells, and wounds of epidermis-specific α9 knockout mice displayed delayed vascular normalization and reduced endothelial apoptosis, indicating that α9β1 cross-suppresses α3β1 proangiogenic functions. Moreover, α9β1 inhibited α3β1 signaling downstream of focal adhesion kinase (FAK) autoactivation at the point of Src-mediated phosphorylation of FAK Y861/Y925. Finally, α9β1 cross-suppressed many α3β1-dependent genes, including the gene that encodes MMP-9, which we implicated as a regulator of integrin-dependent cross talk to endothelial cells. Our findings identify a novel physiological context for combinatorial integrin signaling, laying the foundation for therapeutic strategies that manipulate α9β1 and/or α3β1 during wound healing.
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Affiliation(s)
- Whitney M Longmate
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
| | - Scott P Lyons
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, NY 12144
| | - Kevin M Pumiglia
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
| | - Livingston Van De Water
- Department of Surgery, Albany Medical College, Albany, NY 12208.,Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
| | - C Michael DiPersio
- Department of Surgery, Albany Medical College, Albany, NY 12208 .,Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
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Helle J, Bader MI, Keiler AM, Zierau O, Vollmer G, Chittur SV, Tenniswood M, Kretzschmar G. Cross-Talk in the Female Rat Mammary Gland: Influence of Aryl Hydrocarbon Receptor on Estrogen Receptor Signaling. Environ Health Perspect 2016; 124:601-610. [PMID: 26372666 PMCID: PMC4858405 DOI: 10.1289/ehp.1509680] [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] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Cross-talk between the aryl hydrocarbon receptor (AHR) and the estrogen receptor (ER) plays a major role in signaling processes in female reproductive organs. OBJECTIVES We investigated the influence of the AHR ligand 3-methylcholanthrene (3-MC) on ER-mediated signaling in mammary gland tissue of ovariectomized (ovx) rats. METHODS After 14 days of hormonal decline, ovx rats were treated for 3 days with 4 μg/kg 17β-estradiol (E2), 15 mg/kg 8-prenylnaringenin (8-PN), 15 mg/kg 3-MC, or a combination of these compounds (E2 + 3-MC, 8-PN + 3-MC). Whole-mount preparations of the mammary gland were used to count terminal end buds (TEBs). Protein expression studies (immunohistochemistry, immunofluorescence), a cDNA microarray, pathway analyses, and quantitative real-time polymerase chain reaction (qPCR) were performed to evaluate the interaction between AHR- and ER-mediated signaling pathways. RESULTS E2 treatment increased the number of TEBs and the levels of Ki-67 protein and progesterone receptor (PR); this treatment also changed the expression of 325 genes by more than 1.5-fold. Although 3-MC treatment alone had marginal impact on gene or protein expression, when rats were co-treated with 3-MC and E2, 3-MC strongly inhibited E2-induced TEB development, protein synthesis, and the expression of nearly half of E2-induced genes. This inhibitory effect of 3-MC was partially mirrored when 8-PN was used as an ER ligand. The anti-estrogenicity of ligand-activated AHR was at least partly due to decreased protein levels of ERα in ductal epithelial cells. CONCLUSION Our data show transcriptome-wide anti-estrogenic properties of ligand-activated AHR on ER-mediated processes in the mammary gland, thereby contributing an explanation for the chemopreventive and endocrine-disrupting potential of AHR ligands. CITATION Helle J, Bader MI, Keiler AM, Zierau O, Vollmer G, Chittur SV, Tenniswood M, Kretzschmar G. 2016. Cross-talk in the female rat mammary gland: influence of aryl hydrocarbon receptor on estrogen receptor signaling. Environ Health Perspect 124:601-610; http://dx.doi.org/10.1289/ehp.1509680.
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Affiliation(s)
- Janina Helle
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, Dresden, Germany
| | - Manuela I. Bader
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, Dresden, Germany
| | - Annekathrin M. Keiler
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, Dresden, Germany
| | - Oliver Zierau
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, Dresden, Germany
| | - Günter Vollmer
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, Dresden, Germany
| | - Sridar V. Chittur
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Martin Tenniswood
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Georg Kretzschmar
- Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, Dresden, Germany
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Gorski JP, Huffman NT, Vallejo J, Brotto L, Chittur SV, Breggia A, Stern A, Huang J, Mo C, Seidah NG, Bonewald L, Brotto M. Deletion of Mbtps1 (Pcsk8, S1p, Ski-1) Gene in Osteocytes Stimulates Soleus Muscle Regeneration and Increased Size and Contractile Force with Age. J Biol Chem 2015; 291:4308-22. [PMID: 26719336 DOI: 10.1074/jbc.m115.686626] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 08/18/2015] [Indexed: 12/28/2022] Open
Abstract
Conditional deletion of Mbtps1 (cKO) protease in bone osteocytes leads to an age-related increase in mass (12%) and in contractile force (30%) in adult slow twitch soleus muscles (SOL) with no effect on fast twitch extensor digitorum longus muscles. Surprisingly, bone from 10-12-month-old cKO animals was indistinguishable from controls in size, density, and morphology except for a 25% increase in stiffness. cKO SOL exhibited increased expression of Pax7, Myog, Myod1, Notch, and Myh3 and 6-fold more centralized nuclei, characteristics of postnatal regenerating muscle, but only in type I myosin heavy chain-expressing cells. Increased expression of gene pathways mediating EGF receptor signaling, circadian exercise, striated muscle contraction, and lipid and carbohydrate oxidative metabolism were also observed in cKO SOL. This muscle phenotype was not observed in 3-month-old mice. Although Mbtps1 mRNA and protein expression was reduced in cKO bone osteocytes, no differences in Mbtps1 or cre recombinase expression were observed in cKO SOL, explaining this age-related phenotype. Understanding bone-muscle cross-talk may provide a fresh and novel approach to prevention and treatment of age-related muscle loss.
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Affiliation(s)
- Jeff P Gorski
- From the Department of Oral and Craniofacial Sciences, University of Missouri-Kansas City Center of Excellence in the Study of Dental and Musculoskeletal Tissues, School of Dentistry,
| | - Nichole T Huffman
- From the Department of Oral and Craniofacial Sciences, University of Missouri-Kansas City Center of Excellence in the Study of Dental and Musculoskeletal Tissues, School of Dentistry
| | - Julian Vallejo
- Muscle Biology Research Group, School of Nursing and Health Studies, and
| | - Leticia Brotto
- Muscle Biology Research Group, School of Nursing and Health Studies, and
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, New York 12144
| | | | - Amber Stern
- School of Computing and Engineering, University of Missouri-Kansas City, Kansas City, Missouri 64108, Engineering Systems, Inc., Charlotte, North Carolina 28277, and
| | - Jian Huang
- Muscle Biology Research Group, School of Nursing and Health Studies, and
| | - Chenglin Mo
- Muscle Biology Research Group, School of Nursing and Health Studies, and
| | - Nabil G Seidah
- Institut de Recherches Cliniques Montreal, Montreal, Quebec H2W IR7, Canada
| | - Lynda Bonewald
- From the Department of Oral and Craniofacial Sciences, University of Missouri-Kansas City Center of Excellence in the Study of Dental and Musculoskeletal Tissues, School of Dentistry
| | - Marco Brotto
- Muscle Biology Research Group, School of Nursing and Health Studies, and
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Lopez-Dee ZP, Chittur SV, Patel H, Chinikaylo A, Lippert B, Patel B, Lawler J, Gutierrez LS. Thrombospondin-1 in a Murine Model of Colorectal Carcinogenesis. PLoS One 2015; 10:e0139918. [PMID: 26461935 PMCID: PMC4603676 DOI: 10.1371/journal.pone.0139918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/19/2015] [Indexed: 12/12/2022] Open
Abstract
Colorectal Cancer (CRC) is one of the late complications observed in patients suffering from inflammatory bowel diseases (IBD). Carcinogenesis is promoted by persistent chronic inflammation occurring in IBD. Understanding the mechanisms involved is essential in order to ameliorate inflammation and prevent CRC. Thrombospondin 1 (TSP-1) is a multidomain glycoprotein with important roles in angiogenesis. The effects of TSP-1 in colonic tumor formation and growth were analyzed in a model of inflammation-induced carcinogenesis. WT and TSP-1 deficient mice (TSP-1-/-) of the C57BL/6 strain received a single injection of azoxymethane (AOM) and multiple cycles of dextran sodium sulfate (DSS) to induce chronic inflammation-related cancers. Proliferation and angiogenesis were histologically analyzed in tumors. The intestinal transcriptome was also analyzed using a gene microarray approach. When the area containing tumors was compared with the entire colonic area of each mouse, the tumor burden was decreased in AOM/DSS-treated TSP-1-/- versus wild type (WT) mice. However, these lesions displayed more angiogenesis and proliferation rates when compared with the WT tumors. AOM-DSS treatment of TSP-1-/- mice resulted in significant deregulation of genes involved in transcription, canonical Wnt signaling, transport, defense response, regulation of epithelial cell proliferation and metabolism. Microarray analyses of these tumors showed down-regulation of 18 microRNAs in TSP-1-/- tumors. These results contribute new insights on the controversial role of TSP-1 in cancer and offer a better understanding of the genetics and pathogenesis of CRC.
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Affiliation(s)
- Zenaida P. Lopez-Dee
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Sridar V. Chittur
- Center for Functional Genomics, University of Albany, State University of New York, Renssaeler, New York, United States of America
| | - Hiral Patel
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Aleona Chinikaylo
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Brittany Lippert
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Bhumi Patel
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Jack Lawler
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Linda S. Gutierrez
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
- * E-mail:
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Kokabee L, Wang X, Sevinsky CJ, Wang WLW, Cheu L, Chittur SV, Karimipoor M, Tenniswood M, Conklin DS. Bruton's tyrosine kinase is a potential therapeutic target in prostate cancer. Cancer Biol Ther 2015; 16:1604-15. [PMID: 26383180 DOI: 10.1080/15384047.2015.1078023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 10/23/2022] Open
Abstract
Bruton's tyrosine kinase (BTK) is a non-receptor tyrosine kinase that has mainly been studied in haematopoietic cells. We have investigated whether BTK is a potential therapeutic target in prostate cancer. We find that BTK is expressed in prostate cells, with the alternate BTK-C isoform predominantly expressed in prostate cancer cells and tumors. This isoform is transcribed from an alternative promoter and results in a protein with an amino-terminal extension. Prostate cancer cell lines and prostate tumors express more BTK-C transcript than the malignant NAMALWA B-cell line or human lymphomas. BTK protein expression is also observed in tumor tissue from prostate cancer patients. Down regulation of this protein with RNAi or inhibition with BTK-specific inhibitors, Ibrutinib, AVL-292 or CGI-1746 decrease cell survival and induce apoptosis in prostate cancer cells. Microarray results show that inhibiting BTK under these conditions increases expression of apoptosis related genes, while overexpression of BTK-C is associated with elevated expression of genes with functions related to cell adhesion, cytoskeletal structure and the extracellular matrix. These results are consistent with studies that show that BTK signaling is important for adhesion and migration of B cells and suggest that BTK-C may confer similar properties to prostate cancer cells. Since BTK-C is a survival factor for these cells, it represents both a potential biomarker and novel therapeutic target for prostate cancer.
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Affiliation(s)
- Leila Kokabee
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA.,b Department of Molecular Medicine ; Pasteur Institute of Iran; Tehran, Iran
| | - Xianhui Wang
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
| | - Christopher J Sevinsky
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
| | - Wei Lin Winnie Wang
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
| | - Lindsay Cheu
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
| | - Sridar V Chittur
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
| | - Morteza Karimipoor
- b Department of Molecular Medicine ; Pasteur Institute of Iran; Tehran, Iran
| | - Martin Tenniswood
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
| | - Douglas S Conklin
- a Cancer Research Center and Department of Biomedical Sciences ; State University of New York; University at Albany ; Rensselaer , NY USA
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Van Ee J, Chien AS, Chittur SV, Martin L, White N, Knudtson KL, Hunter TC, Perera AG, Reyero Vinas NG. ABRF 2015: Outstanding Scientific Poster Awards. J Biomol Tech 2015. [DOI: 10.7171/jbt.15-2602-007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Missan DS, Chittur SV, DiPersio CM. Regulation of fibulin-2 gene expression by integrin α3β1 contributes to the invasive phenotype of transformed keratinocytes. J Invest Dermatol 2014; 134:2418-2427. [PMID: 24694902 PMCID: PMC4134363 DOI: 10.1038/jid.2014.166] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/18/2014] [Accepted: 02/28/2014] [Indexed: 11/09/2022]
Abstract
The laminin-binding integrin α3β1 is highly expressed in epidermal keratinocytes, where it regulates both cell-autonomous and paracrine functions that promote wound healing and skin tumorigenesis. However, the roles for α3β1 in regulating gene expression programs that control the behaviors of immortalized or transformed keratinocytes remain underexplored. In the current study, we used a microarray approach to identify genes that are regulated by α3β1 in immortalized keratinocytes. α3β1-Responsive genes included several genes that are involved in extracellular matrix proteolysis or remodeling, including fibulin-2 and secreted protein acidic and rich in cysteine. However, α3β1-dependent induction of specific target genes was influenced by the genetic lesion that triggered immortalization, as α3β1-dependent fibulin-2 expression occurred in cells immortalized by either SV40 large T antigen or p53-null mutation, whereas α3β1-dependent expression of secreted protein acidic and rich in cysteine occurred only in the former cells. Interestingly, quantitative PCR arrays did not reveal strong patterns of α3β1-dependent gene expression in freshly isolated primary keratinocytes, suggesting that this regulation is acquired during immortalization. p53-null keratinocytes transformed with oncogenic RasV12 retained α3β1-dependent fibulin-2 expression, and RNAi-mediated knockdown of fibulin-2 in these cells reduced invasion, although not their tumorigenic potential. These findings demonstrate a prominent role for α3β1 in immortalized/transformed keratinocytes in regulating fibulin-2 and other genes that promote matrix remodeling and invasion.
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Affiliation(s)
- Dara S Missan
- Center for Cell Biology and Cancer Research, Albany Medical College, Albany, New York, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - C Michael DiPersio
- Center for Cell Biology and Cancer Research, Albany Medical College, Albany, New York, USA.
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Subbaram S, Lyons SP, Svenson KB, Hammond SL, McCabe LG, Chittur SV, DiPersio CM. Integrin α3β1 controls mRNA splicing that determines Cox-2 mRNA stability in breast cancer cells. J Cell Sci 2014; 127:1179-89. [PMID: 24434582 DOI: 10.1242/jcs.131227] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 01/10/2023] Open
Abstract
It is unknown how cues from the tumor microenvironment can regulate post-transcriptional mechanisms, such as alternative splicing, that control genes that drive malignant growth. The induction of cyclooxygenase 2 (Cox-2) by integrin α3β1 in breast cancer cells can promote tumor progression. We have used RNAi to suppress α3β1 in human MDA-MB-231 breast cancer cells and then investigated changes in global gene expression. Numerous mRNAs, including Cox-2, show altered expression and/or alternative exon usage (AEU) in α3β1-deficient cells. AEU included patterns predicted to render an mRNA susceptible to degradation, such as 3'-UTR variations or retention of elements that target an mRNA for nonsense-mediated decay (NMD). PCR-based analysis of α3β1-deficient cells confirmed changes in Cox-2 mRNA that might target it for NMD, including retention of an intron that harbors premature termination codons and changes within the 3'-UTR. Moreover, Cox-2 mRNA has reduced stability in α3β1-deficient cells, which is partially reversed by knockdown of the essential NMD factor UPF1. Our study identifies α3β1-mediated AEU as a novel paradigm of integrin-dependent gene regulation that has potential for exploitation as a therapeutic target.
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Affiliation(s)
- Sita Subbaram
- Center for Cell Biology and Cancer Research, Albany Medical College, MC-165, 47 New Scotland Avenue, Albany, NY 12208, USA
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Narvaez CJ, Simmons KM, Brunton J, Salinero A, Chittur SV, Welsh JE. Induction of STEAP4 correlates with 1,25-dihydroxyvitamin D3 stimulation of adipogenesis in mesenchymal progenitor cells derived from human adipose tissue. J Cell Physiol 2013; 228:2024-36. [PMID: 23553608 DOI: 10.1002/jcp.24371] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/15/2013] [Indexed: 01/01/2023]
Abstract
The vitamin D receptor (VDR) is expressed in human adipocytes and is transiently induced during early adipogenesis in mesenchymal progenitor cell models. VDR null mice exhibit enhanced energy expenditure and reduced adiposity even when fed high fat diets. Adipocyte-specific transgenic-expression of human VDR in mice enhances adipose tissue mass, indicating that VDR activation in adipocytes enhances lipid storage in vivo. In these studies, we conducted genomic profiling and differentiation assays in primary cultures of human adipose-derived mesenchymal progenitor cells to define the role of the VDR and its ligand 1,25-dihydroxyvitamin D3 (1,25D) in adipogenesis. In the presence of adipogenic media, 1,25D promoted lipid accumulation and enhanced the expression of FABP4, FASN, and PPARγ. Mesenchymal cells derived from 6-month old VDR null mice exhibited impaired adipogenesis ex vivo but differentiation was restored by stable expression of human VDR. STEAP4, a gene that encodes a metalloreductase linked to obesity, insulin sensitivity, metabolic homeostasis and inflammation, was highly induced in human adipose cells differentiated in the presence of 1,25D but was minimally affected by 1,25D in undifferentiated precursors. These studies provide a molecular basis for recent epidemiological associations between vitamin D status, body weight and insulin resistance which may have relevance for prevention or treatment of metabolic syndrome and obesity.
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Affiliation(s)
- C J Narvaez
- Department of Biomedical Sciences, University at Albany, Albany, NY 12144, USA
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36
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Oliver JC, Linger RS, Chittur SV, Davisson VJ. Substrate activation and conformational dynamics of guanosine 5'-monophosphate synthetase. Biochemistry 2013; 52:5225-35. [PMID: 23841499 DOI: 10.1021/bi3017075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glutamine amidotransferases catalyze the amination of a wide range of molecules using the amide nitrogen of glutamine. The family provides numerous examples for study of multi-active-site regulation and interdomain communication in proteins. Guanosine 5'-monophosphate synthetase (GMPS) is one of three glutamine amidotransferases in de novo purine biosynthesis and is responsible for the last step in the guanosine branch of the pathway, the amination of xanthosine 5'-monophosphate (XMP). In several amidotransferases, the intramolecular path of ammonia from glutamine to substrate is understood; however, the crystal structure of GMPS only hinted at the details of such transfer. Rapid kinetics studies provide insight into the mechanism of the substrate-induced changes in this complex enzyme. Rapid mixing of GMPS with substrates also manifests absorbance changes that report on the kinetics of formation of a reactive intermediate as well as steps in the process of rapid transfer of ammonia to this intermediate. Isolation and use of the adenylylated nucleotide intermediate allowed the study of the amido transfer reaction distinct from the ATP-dependent reaction. Changes in intrinsic tryptophan fluorescence upon mixing of enzyme with XMP suggest a conformational change upon substrate binding, likely the ordering of a highly conserved loop in addition to global domain motions. In the GMPS reaction, all forward rates before product release appear to be faster than steady-state turnover, implying that release is likely rate-limiting. These studies establish the functional role of a substrate-induced conformational change in the GMPS catalytic cycle and provide a kinetic context for the formation of an ammonia channel linking the distinct active sites.
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Affiliation(s)
- Justin C Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University , West Lafayette, Indiana 47907, United States
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Gorski J, Huffman NT, Breggia A, Rosen CJ, Chittur SV, Stern A, Dallas M, Seidah NG, Brotto L, Bonewald LF, Brotto M. DELETION OF MBTPS1 IN BONE LEADS TO ENHANCEMENT OF MUSCLE MASS AND FUNCTION IN MATURE MICE. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.942.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jeffrey Gorski
- Oral Biology‐Bone Biology Research ProgramUniversity of Missouri‐Kansas CityKansas CityMO
| | - NT Huffman
- Oral Biology‐Bone Biology Research ProgramUniversity of Missouri‐Kansas CityKansas CityMO
| | - Anne Breggia
- Maine Medical Center Research InstituteScarboroughME
| | - Cliff J. Rosen
- Maine Medical Center Research InstituteScarboroughME
- School of MedicineTufts UniversityBostonMA
| | | | - Amber Stern
- Oral Biology‐Bone Biology Research ProgramUniversity of Missouri‐Kansas CityKansas CityMO
| | - Mark Dallas
- School of DentistryUniversity of Missouri‐Kansas CityKansas CityMO
| | - N G Seidah
- Clinical Research Institute of MontrealMontrealQCCanada
| | - Leticia Brotto
- School of NursingUniversity of Missouri‐Kansas CityKansas CityMO
| | - Lynda F. Bonewald
- Oral Biology‐Bone Biology Research ProgramUniversity of Missouri‐Kansas CityKansas CityMO
- School of DentistryUniversity of Missouri‐Kansas CityKansas CityMO
| | - Marco Brotto
- School of NursingUniversity of Missouri‐Kansas CityKansas CityMO
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Subbaram S, Svenson KK, Hammond SL, Craig L, Chittur SV, DiPersio CM. Abstract A68: Integrin α3β1-dependent regulation of Cox2 in human breast cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.tim2013-a68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
During the process of gene transcription, inclusion or exclusion of exons can have profound effects on the stability of messenger RNA and affect many aspects of tumorigenesis such as growth, migration and invasion. Changes in cell adhesion are important during cancer progression and metastasis. In this process, integrins are implicated in tumor growth and cancer cell invasion from the primary tumor as well as tumor cell attachment at distant sites of metastasis. Integrins are heterodimeric cell surface receptors consisting of an α and a β subunit which interact with the extracellular matrix (ECM) and mediate inside-out and outside-in signaling. Integrin α3β1 is expressed in a variety of different cell types and its expression is enhanced in breast cancer. Experiments performed with breast cancer cell lines suggests that laminin-332, which is a major ligand for α3β1, is secreted from mammary epithelial cells and enhances the motility and aggressive features of breast cancer cells indicating the importance of α3β1 signaling in invasion. Using MDA-MB-231 breast cancer cell line, which was stably transduced with lentivirus encoding either control shRNA or α3-targeting shRNA, we performed microarray analysis using the Affymetrix GeneChip® Human Exon 1.0 ST Array platform. We identified 72 genes that were upregulated at least 2-fold and 329 genes that were downregulated at least 2-fold, when α3β1 was suppressed. Cox2 mRNA expression levels as well as differential exon inclusion in the mRNA was affected by the presence or absence of α3β1. We were able to identify and validate differential exon inclusion in the mRNA of Cox2 using RT-PCR and real time PCR assays. In addition, stability of Cox2 mRNA was shown to be regulated by α3β1 expression in a mRNA decay assay using RT-PCR as an end-point readout. The presence of differing exons as well as extended 3'-UTR has been shown to confer Cox2 mRNA susceptibility to nonsense-mediated mRNA decay (NMD). Knocking down UPF1, a key regulator of NMD, stabilized Cox2 mRNA in an α3β1-dependent manner as determined by both RT-PCR and RNAse protection assays. In addition, the NMD pathway appears to be repressed in the presence of α3β1 as determined by phosphorylation status of eIF2α. Taken together, α3β1 is a key factor that determines the splice variant of Cox2 mRNA that is generated in MDA-MB-231 cells. It also affects the process of NMD thereby affecting Cox2 mRNA turnover and protein expression thus affecting angiogenesis and tumor progression. Understanding the role that α3β1 plays in various molecular events leading to differential exon usage and mRNA stability of specific breast cancer genes such as Cox2 could be vital to the development of therapies to target metastatic breast cancer.
Citation Format: Sita Subbaram, Kimberly K. Svenson, Sean L. Hammond, Lorena Craig, Sridar V. Chittur, C. Michael DiPersio. Integrin α3β1-dependent regulation of Cox2 in human breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr A68.
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Shirode AB, Kovvuru P, Chittur SV, Henning SM, Heber D, Reliene R. Antiproliferative effects of pomegranate extract in MCF-7 breast cancer cells are associated with reduced DNA repair gene expression and induction of double strand breaks. Mol Carcinog 2013; 53:458-70. [DOI: 10.1002/mc.21995] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/06/2012] [Accepted: 12/08/2012] [Indexed: 01/10/2023]
Affiliation(s)
- Amit B. Shirode
- Department of Environmental Health Sciences; University at Albany; State University of New York; Albany New York
- Cancer Research Center; University at Albany; Rensselaer New York
| | - Prasad Kovvuru
- Department of Environmental Health Sciences; University at Albany; State University of New York; Albany New York
- Cancer Research Center; University at Albany; Rensselaer New York
| | - Sridar V. Chittur
- Cancer Research Center; University at Albany; Rensselaer New York
- Department of Biomedical Sciences; University at Albany; State University of New York; Albany New York
| | - Susanne M. Henning
- Center for Human Nutrition; David Geffen School of Medicine; University of California; Los Angeles California
| | - David Heber
- Center for Human Nutrition; David Geffen School of Medicine; University of California; Los Angeles California
| | - Ramune Reliene
- Department of Environmental Health Sciences; University at Albany; State University of New York; Albany New York
- Cancer Research Center; University at Albany; Rensselaer New York
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Perrone CE, Mattocks DAL, Plummer JD, Chittur SV, Mohney R, Vignola K, Orentreich DS, Orentreich N. Genomic and metabolic responses to methionine-restricted and methionine-restricted, cysteine-supplemented diets in Fischer 344 rat inguinal adipose tissue, liver and quadriceps muscle. J Nutrigenet Nutrigenomics 2012; 5:132-57. [PMID: 23052097 DOI: 10.1159/000339347] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 05/04/2012] [Indexed: 01/26/2023]
Abstract
BACKGROUND/AIMS Methionine restriction (MR) is a dietary intervention that increases lifespan, reduces adiposity and improves insulin sensitivity. These effects are reversed by supplementation of the MR diet with cysteine (MRC). Genomic and metabolomic studies were conducted to identify potential mechanisms by which MR induces favorable metabolic effects, and that are reversed by cysteine supplementation. METHODS Gene expression was examined by microarray analysis and TaqMan quantitative PCR. Levels of selected proteins were measured by Western blot and metabolic intermediates were analyzed by mass spectrometry. RESULTS MR increased lipid metabolism in inguinal adipose tissue and quadriceps muscle while it decreased lipid synthesis in liver. In inguinal adipose tissue, MR not only caused the transcriptional upregulation of genes associated with fatty acid synthesis but also of Lpin1, Pc, Pck1 and Pdk1, genes that are associated with glyceroneogenesis. MR also upregulated lipolysis-associated genes in inguinal fat and led to increased oxidation in this tissue, as suggested by higher levels of methionine sulfoxide and 13-HODE + 9-HODE compared to control-fed (CF) rats. Moreover, MR caused a trend toward the downregulation of inflammation-associated genes in inguinal adipose tissue. MRC reversed most gene and metabolite changes induced by MR in inguinal adipose tissue, but drove the expression of Elovl6, Lpin1, Pc, and Pdk1 below CF levels. In liver, MR decreased levels of a number of long-chain fatty acids, glycerol and glycerol-3-phosphate corresponding with the gene expression data. Although MR increased the expression of genes associated with carbohydrate metabolism, levels of glycolytic intermediates were below CF levels. MR, however, stimulated gluconeogenesis and ketogenesis in liver tissue. As previously reported, sulfur amino acids derived from methionine were decreased in liver by MR, but homocysteine levels were elevated. Increased liver homocysteine levels by MR were associated with decreased cystathionine β-synthase (CBS) protein levels and lowered vitamin B6 and 5-methyltetrahydrofolate (5MeTHF) content. Finally, MR upregulated fibroblast growth factor 21 (FGF21) gene and protein levels in both liver and adipose tissues. MRC reversed some of MR's effects in liver and upregulated the transcription of genes associated with inflammation and carcinogenesis such as Cxcl16, Cdh17, Mmp12, Mybl1, and Cav1 among others. In quadriceps muscle, MR upregulated lipid metabolism-associated genes and increased 3-hydroxybutyrate levels suggesting increased fatty acid oxidation as well as stimulation of gluconeogenesis and glycogenolysis in this tissue. CONCLUSION Increased lipid metabolism in inguinal adipose tissue and quadriceps muscle, decreased triglyceride synthesis in liver and the downregulation of inflammation-associated genes are among the factors that could favor the lean phenotype and increased insulin sensitivity observed in MR rats.
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Affiliation(s)
- Carmen E Perrone
- Orentreich Foundation for the Advancement of Science, Inc, Cold Spring-on-Hudson, NY, USA.
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Lopez-Dee ZP, Chittur SV, Patel B, Stanton R, Wakeley M, Lippert B, Menaker A, Eiche B, Terry R, Gutierrez LS. Thrombospondin-1 type 1 repeats in a model of inflammatory bowel disease: transcript profile and therapeutic effects. PLoS One 2012; 7:e34590. [PMID: 22509329 PMCID: PMC3318003 DOI: 10.1371/journal.pone.0034590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/02/2012] [Indexed: 12/31/2022] Open
Abstract
Thrombospondin-1 (TSP-1) is a matricellular protein with regulatory functions in inflammation and cancer. The type 1 repeats (TSR) domains of TSP-1 have been shown to interact with a wide range of proteins that result in the anti-angiogenic and anti-tumor properties of TSP-1. To ascertain possible functions and evaluate potential therapeutic effects of TSRs in inflammatory bowel disease, we conducted clinical, histological and microarray analyses on a mouse model of induced colitis. We used dextran sulfate sodium (DSS) to induce colitis in wild-type (WT) mice for 7 days. Simultaneously, mice were injected with either saline or one form of TSP-1 derived recombinant proteins, containing either (1) the three type 1 repeats of the TSP-1 (3TSR), (2) the second type 1 repeat (TSR2), or (3) TSR2 with the RFK sequence (TSR2+RFK). Total RNA isolated from the mice colons were processed and hybridized to mouse arrays. Array data were validated by real-time qPCR and immunohistochemistry. Histological and disease indices reveal that the mice treated with the TSRs show different patterns of leukocytic infiltration and that 3TSR treatment was the most effective in decreasing inflammation in DSS-induced colitis. Transcriptional profiling revealed differentially expressed (DE) genes, with the 3TSR-treated mice showing the least deviation from the WT-water controls. In conclusion, this study shows that 3TSR treatment is effective in attenuating the inflammatory response to DSS injury. In addition, the transcriptomics work unveils novel genetic data that suggest beneficial application of the TSR domains in inflammatory bowel disease.
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Affiliation(s)
- Zenaida P. Lopez-Dee
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Sridar V. Chittur
- Center for Functional Genomics, University at Albany, State University of New York, Rensselaer, New York, United States of America
| | - Bhumi Patel
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Rebecca Stanton
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Michelle Wakeley
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Brittany Lippert
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Anastasya Menaker
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Bethany Eiche
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Robert Terry
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Linda S. Gutierrez
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
- * E-mail:
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Tsumagari K, Chang SC, Lacey M, Baribault C, Chittur SV, Sowden J, Tawil R, Crawford GE, Ehrlich M. Gene expression during normal and FSHD myogenesis. BMC Med Genomics 2011; 4:67. [PMID: 21951698 PMCID: PMC3204225 DOI: 10.1186/1755-8794-4-67] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 09/27/2011] [Indexed: 01/31/2023] Open
Abstract
Background Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. Within each repeat unit is a gene, DUX4, that can encode a protein containing two homeodomains. A DUX4 transcript derived from the last repeat unit in a contracted array is associated with pathogenesis but it is unclear how. Methods Using exon-based microarrays, the expression profiles of myogenic precursor cells were determined. Both undifferentiated myoblasts and myoblasts differentiated to myotubes derived from FSHD patients and controls were studied after immunocytochemical verification of the quality of the cultures. To further our understanding of FSHD and normal myogenesis, the expression profiles obtained were compared to those of 19 non-muscle cell types analyzed by identical methods. Results Many of the ~17,000 examined genes were differentially expressed (> 2-fold, p < 0.01) in control myoblasts or myotubes vs. non-muscle cells (2185 and 3006, respectively) or in FSHD vs. control myoblasts or myotubes (295 and 797, respectively). Surprisingly, despite the morphologically normal differentiation of FSHD myoblasts to myotubes, most of the disease-related dysregulation was seen as dampening of normal myogenesis-specific expression changes, including in genes for muscle structure, mitochondrial function, stress responses, and signal transduction. Other classes of genes, including those encoding extracellular matrix or pro-inflammatory proteins, were upregulated in FSHD myogenic cells independent of an inverse myogenesis association. Importantly, the disease-linked DUX4 RNA isoform was detected by RT-PCR in FSHD myoblast and myotube preparations only at extremely low levels. Unique insights into myogenesis-specific gene expression were also obtained. For example, all four Argonaute genes involved in RNA-silencing were significantly upregulated during normal (but not FSHD) myogenesis relative to non-muscle cell types. Conclusions DUX4's pathogenic effect in FSHD may occur transiently at or before the stage of myoblast formation to establish a cascade of gene dysregulation. This contrasts with the current emphasis on toxic effects of experimentally upregulated DUX4 expression at the myoblast or myotube stages. Our model could explain why DUX4's inappropriate expression was barely detectable in myoblasts and myotubes but nonetheless linked to FSHD.
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Affiliation(s)
- Koji Tsumagari
- Human Genetics Program, Tulane Medical School, New Orleans, LA, USA
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Wang WLW, Chatterjee N, Chittur SV, Welsh J, Tenniswood MP. Effects of 1α,25 dihydroxyvitamin D3 and testosterone on miRNA and mRNA expression in LNCaP cells. Mol Cancer 2011; 10:58. [PMID: 21592394 PMCID: PMC3112430 DOI: 10.1186/1476-4598-10-58] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/18/2011] [Indexed: 02/07/2023] Open
Abstract
Background There is evidence from epidemiological and in vitro studies that the biological effects of testosterone (T) on cell cycle and survival are modulated by 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) in prostate cancer. To investigate the cross talk between androgen- and vitamin D-mediated intracellular signaling pathways, the individual and combined effects of T and 1,25(OH)2D3 on global gene expression in LNCaP prostate cancer cells were assessed. Results Stringent statistical analysis identifies a cohort of genes that lack one or both androgen response elements (AREs) or vitamin D response elements (VDREs) in their promoters, which are nevertheless differentially regulated by both steroids (either additively or synergistically). This suggests that mechanisms in addition to VDR- and AR-mediated transcription are responsible for the modulation of gene expression. Microarray analysis shows that fifteen miRNAs are also differentially regulated by 1,25(OH)2D3 and T. Among these miR-22, miR-29ab, miR-134, miR-1207-5p and miR-371-5p are up regulated, while miR-17 and miR-20a, members of the miR-17/92 cluster are down regulated. A number of genes implicated in cell cycle progression, lipid synthesis and accumulation and calcium homeostasis are among the mRNA targets of these miRNAs. Thus, in addition to their well characterized effects on transcription, mediated by either or both cognate nuclear receptors, 1,25(OH)2D3 and T regulate the steady state mRNA levels by modulating miRNA-mediated mRNA degradation, generating attenuation feedback loops that result in global changes in mRNA and protein levels. Changes in genes involved in calcium homeostasis may have specific clinical importance since the second messenger Ca2+ is known to modulate various cellular processes, including cell proliferation, cell death and cell motility, which affects prostate cancer tumor progression and responsiveness to therapy. Conclusions These data indicate that these two hormones combine to drive a differentiated phenotype, and reinforce the idea that the age dependent decline in both hormones results in the de-differentiation of prostate tumor cells, which results in increased proliferation, motility and invasion common to aggressive tumors. These studies also reinforce the potential importance of miRNAs in prostate cancer progression and therapeutic outcomes.
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Affiliation(s)
- Wei-Lin W Wang
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
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Dyavaiah M, Rooney JP, Chittur SV, Lin Q, Begley TJ. Autophagy-dependent regulation of the DNA damage response protein ribonucleotide reductase 1. Mol Cancer Res 2011; 9:462-75. [PMID: 21343333 DOI: 10.1158/1541-7786.mcr-10-0473] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein synthesis and degradation are posttranscriptional pathways used by cells to regulate protein levels. We have developed a systems biology approach to identify targets of posttranscriptional regulation and we have employed this system in Saccharomyces cerevisiae to study the DNA damage response. We present evidence that 50% to 75% of the transcripts induced by alkylation damage are regulated posttranscriptionally. Significantly, we demonstrate that two transcriptionally-induced DNA damage response genes, RNR1 and RNR4, fail to show soluble protein level increases after DNA damage. To determine one of the associated mechanisms of posttranscriptional regulation, we tracked ribonucleotide reductase 1 (Rnr1) protein levels during the DNA damage response. We show that RNR1 is actively translated after damage and that a large fraction of the corresponding Rnr1 protein is packaged into a membrane-bound structure and transported to the vacuole for degradation, with these last two steps dependent on autophagy proteins. We found that inhibition of target of rapamycin (TOR) signaling and subsequent induction of autophagy promoted an increase in targeting of Rnr1 to the vacuole and a decrease in soluble Rnr1 protein levels. In addition, we demonstrate that defects in autophagy result in an increase in soluble Rnr1 protein levels and a DNA damage phenotype. Our results highlight roles for autophagy and TOR signaling in regulating a specific protein and demonstrate the importance of these pathways in optimizing the DNA damage response.
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Affiliation(s)
- Madhu Dyavaiah
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer, New York 12144, USA
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Abstract
Throughout the vertebrate subphylum, the regenerative potential of central nervous system axons is greatest in embryonic stages and declines as development progresses. For example, Xenopus laevis can functionally recover from complete transection of the spinal cord as a tadpole but is unable to do so after metamorphosing into a frog. Neurons of the reticular formation and raphe nucleus are among those that regenerate axons most reliably in tadpole and that lose this ability after metamorphosis. To identify molecular factors associated with the success and failure of spinal cord axon regeneration, we pharmacologically manipulated thyroid hormone (TH) levels using methimazole or triiodothyronine, to either keep tadpoles in a permanently larval state or induce precocious metamorphosis, respectively. Following complete spinal cord transection, serotonergic axons crossed the lesion site and tadpole swimming ability was restored when metamorphosis was inhibited, but these events failed to occur when metamorphosis was prematurely induced. Thus, the metamorphic events controlled by TH led directly to the loss of regenerative potential. Microarray analysis identified changes in hindbrain gene expression that accompanied regeneration-permissive and -inhibitory conditions, including many genes in the permissive condition that have been previously associated with axon outgrowth and neuroprotection. These data demonstrate that changes in gene expression occur within regenerating neurons in response to axotomy under regeneration-permissive conditions in which normal development has been suspended, and they identify candidate genes for future studies of how central nervous system axons can successfully regenerate in some vertebrates.
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Affiliation(s)
- Kurt M Gibbs
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
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Abstract
Protein-protein interactions (PPIs) have been widely studied to understand the biological processes or molecular functions associated with different disease systems like cancer. While focused studies on individual cancers have generated valuable information, global and comparative analysis of datasets from different cancer types has not been done. In this work, we carried out bioinformatic analysis of PPIs corresponding to differentially expressed genes from microarrays of various tumor tissues (belonging to bladder, colon, kidney and thyroid cancers) and compared their associated biological processes and molecular functions (based on Gene Ontology terms). We identified a set of processes or functions that are common to all these cancers, as well as those that are specific to only one or partial cancer types. Similarly, protein interaction networks in nucleic acid metabolism were compared to identify the common/specific clusters of proteins across different cancer types. Our results provide a basis for further experimental investigations to study protein interaction networks associated with cancer. The methodology developed in this work can also be applied to study similar disease systems.
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Affiliation(s)
- Purnima Guda
- GenNYsis Center for Excellence in Cancer Genomics and Department of Epidemiology & Biostatistics, State University of New York at Albany, Rensselaer, NY 12144-3456, USA
| | - Sridar V. Chittur
- Center for Functional Genomics and Department of Biomedical Sciences, State University of New York at Albany, Rensselaer, NY 12144-3456, USA
| | - Chittibabu Guda
- GenNYsis Center for Excellence in Cancer Genomics and Department of Epidemiology & Biostatistics, State University of New York at Albany, Rensselaer, NY 12144-3456, USA
- Corresponding author.
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Mousa SA, Sudha T, Dyskin E, Dier U, Gallati C, Hanko C, Chittur SV, Rebbaa A. Stress resistant human embryonic stem cells as a potential source for the identification of novel cancer stem cell markers. Cancer Lett 2009; 289:208-16. [PMID: 19733430 DOI: 10.1016/j.canlet.2009.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 08/11/2009] [Accepted: 08/12/2009] [Indexed: 01/06/2023]
Abstract
Cancer stem cells are known for their inherent resistance to therapy. Here we investigated whether normal stem cells with acquired resistance to stress can be used to identify novel markers of cancer stem cells. For this, we generated a human embryonic stem cell line resistant to Trichostatin A and analyzed changes in its gene expression. The resistant cells over-expressed various genes associated with tumor aggressiveness, many of which are also expressed in the CD133+ glioma cancer stem cells. These findings suggest that stress-resistant stem cells generated in vitro may be useful for the discovery of novel markers of cancer stem cells.
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Affiliation(s)
- Shaker A Mousa
- The Pharmaceutical Research Institute at Albany, Albany College of Pharmacy and Health Sciences, Albany, NY, USA
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Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a common cardiac disease of Great Dane dogs, yet very little is known about the underlying molecular abnormalities that contribute to disease. OBJECTIVE Discover a set of genes that are differentially expressed in Great Dane dogs with DCM as a way to identify candidate genes for further study as well as to better understand the molecular abnormalities that underlie the disease. ANIMALS Three Great Dane dogs with end-stage DCM and 3 large breed control dogs. METHODS Prospective study. Transcriptional activity of 42,869 canine DNA sequences was determined with a canine-specific oligonucleotide microarray. Genome expression patterns of left ventricular tissue samples from affected Great Dane dogs were evaluated by measuring the relative amount of complementary RNA hybridization to the microarray probes and comparing it with expression from large breed dogs with noncardiac disease. RESULTS Three hundred and twenty-three transcripts were differentially expressed (> or = 2-fold change). The transcript with the greatest degree of upregulation (+61.3-fold) was calstabin2 (FKBP12.6), whereas the transcript with the greatest degree of downregulation (-9.07-fold) was triadin. Calstabin2 and triadin are both regulatory components of the cardiac ryanodine receptor (RyR2) and are critical to normal intracellular Ca2+ release and excitation-contraction coupling. CONCLUSION AND CLINICAL IMPORTANCE Great Dane dogs with DCM demonstrate abnormal calstabin2 and triadin expression. These changes likely affect Ca2+ flux within cardiac cells and may contribute to the pathophysiology of disease. Microarray-based analysis identifies calstabin2, triadin, and RyR2 function as targets of future study.
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Affiliation(s)
- M A Oyama
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Chittur SV, Sangster-Guity N, McCormick PJ. Histone deacetylase inhibitors: a new mode for inhibition of cholesterol metabolism. BMC Genomics 2008; 9:507. [PMID: 18959802 PMCID: PMC2613157 DOI: 10.1186/1471-2164-9-507] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 10/29/2008] [Indexed: 11/12/2022] Open
Abstract
Background Eukaryotic gene expression is a complex process involving multiple cis and trans activating molecules to either facilitate or inhibit transcription. In recent years, many studies have focused on the role of acetylation of histone proteins in modulating transcription, whereas deacetylation of these same proteins is associated with inactivation or repression of gene expression. This study explores gene expression in HepG2 and F9 cell lines treated with Trichostatin A (TSA), a potent histone deacetylase inhibitor. Results These experiments show that TSA treatment results in clear repression of genes involved in the cholesterol biosynthetic pathway as well as other associated pathways including fatty acid biosynthesis and glycolysis. TSA down regulates 9 of 15 genes in this pathway in the F9 embryonal carcinoma model and 11 of 15 pathway genes in the HepG2 cell line. A time course study on the effect of TSA on gene expression of various enzymes and transcription factors involved in these pathways suggests that down regulation of Srebf2 may be the triggering factor for down regulation of the cholesterol biosynthesis pathway. Conclusion Our results provide new insights in the effects of histone deacetylases on genes involved in primary metabolism. This observation suggests that TSA, and other related histone deacetylase inhibitors, may be useful as potential therapeutic entities for the control of cholesterol levels in humans.
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Affiliation(s)
- Sridar V Chittur
- Center for Functional Genomics, University at Albany, State University of New York, Cancer Research Center, One Discovery Drive, Rm 310, Rensselaer, NY 12144, USA.
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Oyama MA, Reiken S, Lehnart SE, Chittur SV, Meurs KM, Stern J, Marks AR. Arrhythmogenic right ventricular cardiomyopathy in Boxer dogs is associated with calstabin2 deficiency. J Vet Cardiol 2008; 10:1-10. [PMID: 18515204 DOI: 10.1016/j.jvc.2008.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 03/19/2008] [Accepted: 04/02/2008] [Indexed: 01/27/2023]
Abstract
OBJECTIVE To examine the presence and effect of calstabin2-deficiency in Boxer dogs with arrhythmogenic right ventricular cardiomyopathy (ARVC). ANIMALS Thirteen Boxer dogs with ARVC. MATERIALS AND METHODS Tissue samples were collected for histopathology, oligonucleotide microarray, PCR, immunoelectrophoresis, ryanodine channel immunoprecipitation and single-channel recordings, and calstabin2 DNA sequencing. RESULTS In cardiomyopathic Boxer dogs, myocardial calstabin2 mRNA and protein were significantly decreased as compared to healthy control dogs (calstabin2 protein normalized to tetrameric cardiac ryanodine receptor (RyR2) complex: affected, 0.51+/-0.04; control, 3.81+/-0.22; P<0.0001). Calstabin2 deficiency in diseased dog hearts was associated with a significantly increased open probability of single RyR2 channels indicating intracellular Ca(2+) leak. PCR-based sequencing of the promoter, exonic and splice site regions of the canine calstabin2 gene did not identify any causative mutations. CONCLUSIONS Calstabin2 deficiency is a potential mechanism of Ca(2+) leak-induced ventricular arrhythmias and heart disease in Boxer dogs with ARVC.
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Affiliation(s)
- Mark A Oyama
- University of Pennsylvania, Philadelphia, PA, USA, USA.
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