1
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Bhattacharya S, Myers JA, Baker C, Guo M, Danopoulos S, Myers JR, Bandyopadhyay G, Romas ST, Huyck HL, Misra RS, Dutra J, Holden-Wiltse J, McDavid AN, Ashton JM, Al Alam D, Potter SS, Whitsett JA, Xu Y, Pryhuber GS, Mariani TJ. Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells. Genes (Basel) 2024; 15:298. [PMID: 38540357 PMCID: PMC10970229 DOI: 10.3390/genes15030298] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/01/2024] Open
Abstract
While animal model studies have extensively defined the mechanisms controlling cell diversity in the developing mammalian lung, there exists a significant knowledge gap with regards to late-stage human lung development. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. Transcriptomic profiling at the single-cell level created a cellular atlas of newborn human lungs. Frozen single-cell isolates obtained from two newborn human lungs from the LungMAP Human Tissue Core Biorepository, were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Transcriptional interrogation of 5500 newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, immune cells and their gene signatures. Computational integration of data from newborn human cells and with 32,000 cells from postnatal days 1 through 10 mouse lungs generated by the LungMAP Cincinnati Research Center facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the newborn human and mouse cellular transcriptomes also demonstrated cell type-specific differences in maturation states of newborn human lung cells. Specifically, newborn human lung matrix fibroblasts could be separated into those representative of younger cells (n = 393), or older cells (n = 158). Cells with each molecular profile were spatially resolved within newborn human lung tissue. This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of maturity.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jacquelyn A. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Cameron Baker
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Minzhe Guo
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - Jason R. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Stephen T. Romas
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Heidie L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Ravi S. Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jennifer Dutra
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
| | - Jeanne Holden-Wiltse
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Andrew N. McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - John M. Ashton
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - S. Steven Potter
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Jeffrey A. Whitsett
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Yan Xu
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Thomas J. Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
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2
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Kaszuba CM, Rodems BJ, Sharma S, Franco EI, Ashton JM, Calvi LM, Bajaj J. Identifying Bone Marrow Microenvironmental Populations in Myelodysplastic Syndrome and Acute Myeloid Leukemia. J Vis Exp 2023:10.3791/66093. [PMID: 38009736 PMCID: PMC10849042 DOI: 10.3791/66093] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/29/2023] Open
Abstract
The bone marrow microenvironment consists of distinct cell populations, such as mesenchymal stromal cells, endothelial cells, osteolineage cells, and fibroblasts, which provide support for hematopoietic stem cells (HSCs). In addition to supporting normal HSCs, the bone marrow microenvironment also plays a role in the development of hematopoietic stem cell disorders, such as myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). MDS-associated mutations in HSCs lead to a block in differentiation and progressive bone marrow failure, especially in the elderly. MDS can often progress to therapy-resistant AML, a disease characterized by a rapid accumulation of immature myeloid blasts. The bone marrow microenvironment is known to be altered in patients with these myeloid neoplasms. Here, a comprehensive protocol to isolate and phenotypically characterize bone marrow microenvironmental cells from murine models of myelodysplastic syndrome and acute myeloid leukemia is described. Isolating and characterizing changes in the bone marrow niche populations can help determine their role in disease initiation and progression and may lead to the development of novel therapeutics targeting cancer-promoting alterations in the bone marrow stromal populations.
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Affiliation(s)
- Christina M Kaszuba
- Wilmot Cancer Institute, University of Rochester Medical Center; Department of Biomedical Engineering, University of Rochester
| | - Benjamin J Rodems
- Wilmot Cancer Institute, University of Rochester Medical Center; Department of Biomedical Genetics, University of Rochester Medical Center
| | - Sonali Sharma
- Wilmot Cancer Institute, University of Rochester Medical Center; Department of Biomedical Genetics, University of Rochester Medical Center
| | - Edgardo I Franco
- Wilmot Cancer Institute, University of Rochester Medical Center; Department of Biomedical Engineering, University of Rochester
| | - John M Ashton
- Wilmot Cancer Institute, University of Rochester Medical Center; Department of Biomedical Genetics, University of Rochester Medical Center; Genomics Research Center, University of Rochester Medical Center
| | - Laura M Calvi
- Wilmot Cancer Institute, University of Rochester Medical Center; Division of Endocrinology and Metabolism, Department of Medicine, University of Rochester Medical Center
| | - Jeevisha Bajaj
- Wilmot Cancer Institute, University of Rochester Medical Center; Department of Biomedical Genetics, University of Rochester Medical Center;
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3
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Liu X, Burke RM, Lighthouse JK, Baker CD, Dirkx RA, Kang B, Chakraborty Y, Mickelsen DM, Twardowski J, Mello SS, Ashton JM, Small EM. p53 Regulates the Extent of Fibroblast Proliferation and Fibrosis in Left Ventricle Pressure Overload. Circ Res 2023; 133:271-287. [PMID: 37409456 PMCID: PMC10361635 DOI: 10.1161/circresaha.121.320324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/22/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Cardiomyopathy is characterized by the pathological accumulation of resident cardiac fibroblasts that deposit ECM (extracellular matrix) and generate a fibrotic scar. However, the mechanisms that control the timing and extent of cardiac fibroblast proliferation and ECM production are not known, hampering the development of antifibrotic strategies to prevent heart failure. METHODS We used the Tcf21 (transcription factor 21)MerCreMer mouse line for fibroblast-specific lineage tracing and p53 (tumor protein p53) gene deletion. We characterized cardiac physiology and used single-cell RNA-sequencing and in vitro studies to investigate the p53-dependent mechanisms regulating cardiac fibroblast cell cycle and fibrosis in left ventricular pressure overload induced by transaortic constriction. RESULTS Cardiac fibroblast proliferation occurs primarily between days 7 and 14 following transaortic constriction in mice, correlating with alterations in p53-dependent gene expression. p53 deletion in fibroblasts led to a striking accumulation of Tcf21-lineage cardiac fibroblasts within the normal proliferative window and precipitated a robust fibrotic response to left ventricular pressure overload. However, excessive interstitial and perivascular fibrosis does not develop until after cardiac fibroblasts exit the cell cycle. Single-cell RNA sequencing revealed p53 null fibroblasts unexpectedly express lower levels of genes encoding important ECM proteins while they exhibit an inappropriately proliferative phenotype. in vitro studies establish a role for p53 in suppressing the proliferative fibroblast phenotype, which facilitates the expression and secretion of ECM proteins. Importantly, Cdkn2a (cyclin-dependent kinase inhibitor 2a) expression and the p16Ink4a-retinoblastoma cell cycle control pathway is induced in p53 null cardiac fibroblasts, which may eventually contribute to cell cycle exit and fulminant scar formation. CONCLUSIONS This study reveals a mechanism regulating cardiac fibroblast accumulation and ECM secretion, orchestrated in part by p53-dependent cell cycle control that governs the timing and extent of fibrosis in left ventricular pressure overload.
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Affiliation(s)
- Xiaoyi Liu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ryan M. Burke
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Janet K. Lighthouse
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Wegmans School of Pharmacy, Department of Pharmaceutical Sciences, St. John Fisher College, Rochester, NY, USA
| | - Cameron D. Baker
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ronald A. Dirkx
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Brian Kang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Yashoswini Chakraborty
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Deanne M. Mickelsen
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jennifer Twardowski
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Stephano S. Mello
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - John M. Ashton
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Eric M. Small
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642
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4
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Kawano Y, Kawano H, Ghoneim D, Fountaine TJ, Byun DK, LaMere MW, Mendler JH, Ho TC, Salama NA, Myers JR, Hussein SE, Frisch BJ, Ashton JM, Azadniv M, Liesveld JL, Kfoury Y, Scadden DT, Becker MW, Calvi LM. Myelodysplastic syndromes disable human CD271+VCAM1+CD146+ niches supporting normal hematopoietic stem/progenitor cells. bioRxiv 2023:2023.04.09.536176. [PMID: 37066307 PMCID: PMC10104201 DOI: 10.1101/2023.04.09.536176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Mesenchymal stem/stromal cells (MSCs) within the bone marrow microenvironment (BMME) support normal hematopoietic stem and progenitor cells (HSPCs). However, the heterogeneity of human MSCs has limited the understanding of their contribution to clonal dynamics and evolution to myelodysplastic syndromes (MDS). We combined three MSC cell surface markers, CD271, VCAM-1 (Vascular Cell Adhesion Molecule-1) and CD146, to isolate distinct subsets of human MSCs from bone marrow aspirates of healthy controls (Control BM). Based on transcriptional and functional analysis, CD271+CD106+CD146+ (NGFR+/VCAM1+/MCAM+/Lin-; NVML) cells display stem cell characteristics, are compatible with murine BM-derived Leptin receptor positive MSCs and provide superior support for normal HSPCs. MSC subsets from 17 patients with MDS demonstrated shared transcriptional changes in spite of mutational heterogeneity in the MDS clones, with loss of preferential support of normal HSPCs by MDS-derived NVML cells. Our data provide a new approach to dissect microenvironment-dependent mechanisms regulating clonal dynamics and progression of MDS.
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5
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Osborn RM, Leach J, Zanche M, Ashton JM, Chu C, Thakar J, Dewhurst S, Rosenberger S, Pavelka M, Pryhuber GS, Mariani TJ, Anderson CS. Preparation of noninfectious scRNAseq samples from SARS-CoV-2-infected epithelial cells. PLoS One 2023; 18:e0281898. [PMID: 36827401 PMCID: PMC9956660 DOI: 10.1371/journal.pone.0281898] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by the SARS coronavirus 2 (SARS-CoV-2) virus. Direct assessment, detection, and quantitative analysis using high throughput methods like single-cell RNA sequencing (scRNAseq) is imperative to understanding the host response to SARS-CoV-2. One barrier to studying SARS-CoV-2 in the laboratory setting is the requirement to process virus-infected cell cultures, and potentially infectious materials derived therefrom, under Biosafety Level 3 (BSL-3) containment. However, there are only 190 BSL3 laboratory facilities registered with the U.S. Federal Select Agent Program, as of 2020, and only a subset of these are outfitted with the equipment needed to perform high-throughput molecular assays. Here, we describe a method for preparing non-hazardous RNA samples from SARS-CoV-2 infected cells, that enables scRNAseq analyses to be conducted safely in a BSL2 facility-thereby making molecular assays of SARS-CoV-2 cells accessible to a much larger community of researchers. Briefly, we infected African green monkey kidney epithelial cells (Vero-E6) with SARS-CoV-2 for 96 hours, trypsin-dissociated the cells, and inactivated them with methanol-acetone in a single-cell suspension. Fixed cells were tested for the presence of infectious SARS-CoV-2 virions using the Tissue Culture Infectious Dose Assay (TCID50), and also tested for viability using flow cytometry. We then tested the dissociation and methanol-acetone inactivation method on primary human lung epithelial cells that had been differentiated on an air-liquid interface. Finally, we performed scRNAseq quality control analysis on the resulting cell populations to evaluate the effects of our virus inactivation and sample preparation protocol on the quality of the cDNA produced. We found that methanol-acetone inactivated SARS-CoV-2, fixed the lung epithelial cells, and could be used to obtain noninfectious, high-quality cDNA libraries. This methodology makes investigating SARS-CoV-2, and related high-containment RNA viruses at a single-cell level more accessible to an expanded community of researchers.
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Affiliation(s)
- Raven M. Osborn
- Translational Biomedical Sciences Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Justin Leach
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Michelle Zanche
- Genomics Research Center, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - John M. Ashton
- Genomics Research Center, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - ChinYi Chu
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Juilee Thakar
- Translational Biomedical Sciences Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Stephen Dewhurst
- Clinical and Translational Sciences Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Sonia Rosenberger
- Department of Environmental Health and Safety, University of Rochester, Rochester, New York, United States of America
- Biosafety Level 3 Facility, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Martin Pavelka
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Biosafety Level 3 Facility, Center for Advanced Research Technologies, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Gloria S. Pryhuber
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- Division of Neonatology, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
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6
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Piekna-Przybylska D, Na D, Zhang J, Baker C, Ashton JM, White PM. Single cell RNA sequencing analysis of mouse cochlear supporting cell transcriptomes with activated ERBB2 receptor indicates a cell-specific response that promotes CD44 activation. Front Cell Neurosci 2023; 16:1096872. [PMID: 36687526 PMCID: PMC9853549 DOI: 10.3389/fncel.2022.1096872] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
Hearing loss caused by the death of cochlear hair cells (HCs) might be restored through regeneration from supporting cells (SCs) via dedifferentiation and proliferation, as observed in birds. In a previous report, ERBB2 activation in a subset of cochlear SCs promoted widespread down-regulation of SOX2 in neighboring cells, proliferation, and the differentiation of HC-like cells. Here we analyze single cell transcriptomes from neonatal mouse cochlear SCs with activated ERBB2, with the goal of identifying potential secreted effectors. ERBB2 induction in vivo generated a new population of cells with de novo expression of a gene network. Called small integrin-binding ligand n-linked glycoproteins (SIBLINGs), these ligands and their regulators can alter NOTCH signaling and promote cell survival, proliferation, and differentiation in other systems. We validated mRNA expression of network members, and then extended our analysis to older stages. ERBB2 signaling in young adult SCs also promoted protein expression of gene network members. Furthermore, we found proliferating cochlear cell aggregates in the organ of Corti. Our results suggest that ectopic activation of ERBB2 signaling in cochlear SCs can alter the microenvironment, promoting proliferation and cell rearrangements. Together these results suggest a novel mechanism for inducing stem cell-like activity in the adult mammalian cochlea.
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Affiliation(s)
- Dorota Piekna-Przybylska
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Daxiang Na
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Jingyuan Zhang
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Cameron Baker
- Genomic Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - John M. Ashton
- Genomic Research Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Patricia M. White
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States,*Correspondence: Patricia M. White,
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7
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Khazan N, Kim KK, Hansen JN, Singh NA, Moore T, Snyder CWA, Pandita R, Strawderman M, Fujihara M, Takamura Y, Jian Y, Battaglia N, Yano N, Teramoto Y, Arnold LA, Hopson R, Kishor K, Nayak S, Ojha D, Sharon A, Ashton JM, Wang J, Milano MT, Miyamoto H, Linehan DC, Gerber SA, Kawar N, Singh AP, Tabdanov ED, Dokholyan NV, Kakuta H, Jurutka PW, Schor NF, Rowswell-Turner RB, Singh RK, Moore RG. Identification of a Vitamin-D Receptor Antagonist, MeTC7, which Inhibits the Growth of Xenograft and Transgenic Tumors In Vivo. J Med Chem 2022; 65:6039-6055. [PMID: 35404047 PMCID: PMC9059124 DOI: 10.1021/acs.jmedchem.1c01878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/12/2021] [Indexed: 12/02/2022]
Abstract
Vitamin-D receptor (VDR) mRNA is overexpressed in neuroblastoma and carcinomas of lung, pancreas, and ovaries and predicts poor prognoses. VDR antagonists may be able to inhibit tumors that overexpress VDR. However, the current antagonists are arduous to synthesize and are only partial antagonists, limiting their use. Here, we show that the VDR antagonist MeTC7 (5), which can be synthesized from 7-dehydrocholesterol (6) in two steps, inhibits VDR selectively, suppresses the viability of cancer cell-lines, and reduces the growth of the spontaneous transgenic TH-MYCN neuroblastoma and xenografts in vivo. The VDR selectivity of 5 against RXRα and PPAR-γ was confirmed, and docking studies using VDR-LBD indicated that 5 induces major changes in the binding motifs, which potentially result in VDR antagonistic effects. These data highlight the therapeutic benefits of targeting VDR for the treatment of malignancies and demonstrate the creation of selective VDR antagonists that are easy to synthesize.
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Affiliation(s)
- Negar Khazan
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Kyu Kwang Kim
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Jeanne N. Hansen
- Department
of Pediatrics, University of Rochester Medical
Center, Rochester, New York 14642, United
States
| | - Niloy A. Singh
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Taylor Moore
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Cameron W. A. Snyder
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Ravina Pandita
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Myla Strawderman
- Department
of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14624, United States
| | - Michiko Fujihara
- Division
of Pharmaceutical Sciences, Okayama University Graduate School of
Medicine, Dentistry and Pharmaceutical Sciences, Kita-ku, Okayama 700-8530, Japan
| | - Yuta Takamura
- Division
of Pharmaceutical Sciences, Okayama University Graduate School of
Medicine, Dentistry and Pharmaceutical Sciences, Kita-ku, Okayama 700-8530, Japan
| | - Ye Jian
- Division
of Surgery and of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14624, United States
| | - Nicholas Battaglia
- Division
of Surgery and of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14624, United States
| | - Naohiro Yano
- Department
of Surgery, Division of Surgical Research, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, Rhode Island 02903, United States
| | - Yuki Teramoto
- Department
of Pathology and Laboratory Medicine, University
of Rochester Medical Center, Rochester, New York 14624, United States
| | - Leggy A. Arnold
- Department
of Chemistry and Biochemistry, University
of Wisconsin Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Russell Hopson
- Department
of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Keshav Kishor
- Department
of Chemistry, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Sneha Nayak
- Department
of Chemistry, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Debasmita Ojha
- Department
of Chemistry, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Ashoke Sharon
- Department
of Chemistry, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - John M. Ashton
- Genomics Core Facility, Wilmot Cancer Center, University of Rochester Medical Center, Rochester, New York 14624, United States
| | - Jian Wang
- Department of Pharmacology and Department of Biochemistry and Molecular
Biology, Penn State College of Medicine, Penn State University, Hershey, Pennsylvania 17036, United States
| | - Michael T. Milano
- Department of Radiation Oncology, University
of Rochester Medical Center, Rochester, New York 16424, United States
| | - Hiroshi Miyamoto
- Department
of Pathology and Laboratory Medicine, University
of Rochester Medical Center, Rochester, New York 14624, United States
| | - David C. Linehan
- Division
of Surgery and of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14624, United States
| | - Scott A. Gerber
- Division
of Surgery and of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14624, United States
- Department of Radiation Oncology, University
of Rochester Medical Center, Rochester, New York 16424, United States
| | - Nada Kawar
- Center for Breast Health and Gynecologic
Oncology, Mercy Medical Center, 271 Carew Street, Springfield, Massachusetts 01104, United States
| | - Ajay P. Singh
- Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08019, United States
| | - Erdem D. Tabdanov
- CytoMechanobiology
Laboratory, Department of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hershey, Pennsylvania 17036, United States
| | - Nikolay V. Dokholyan
- Department of Pharmacology and Department of Biochemistry and Molecular
Biology, Penn State College of Medicine, Penn State University, Hershey, Pennsylvania 17036, United States
| | - Hiroki Kakuta
- Division
of Pharmaceutical Sciences, Okayama University Graduate School of
Medicine, Dentistry and Pharmaceutical Sciences, Kita-ku, Okayama 700-8530, Japan
| | - Peter W. Jurutka
- School of Mathematical and Natural Sciences, Arizona State University, Health Futures Center, Phoenix, Arizona 85054, United States
- University of Arizona College of Medicine, Phoenix, Arizona 85004, United States
| | - Nina F. Schor
- Departments of Pediatrics, Neurology, and Neuroscience, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Rachael B. Rowswell-Turner
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Rakesh K. Singh
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
| | - Richard G. Moore
- Wilmot
Cancer Institute and Division of Gynecologic Oncology, Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester New York 14624, United States
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8
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Morrell CN, Mix D, Aggarwal A, Bhandari R, Godwin M, Owens Iii AP, Lyden SP, Doyle A, Krauel K, Rondina MT, Mohan A, Lowenstein CJ, Shim S, Stauffer S, Josyula VP, Ture SK, Yule DI, Wagner Iii LE, Ashton JM, Elbadawi A, Cameron SJ. Platelet olfactory receptor activation limits platelet reactivity and growth of aortic aneurysms. J Clin Invest 2022; 132:152373. [PMID: 35324479 PMCID: PMC9057618 DOI: 10.1172/jci152373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/16/2022] [Indexed: 11/28/2022] Open
Abstract
As blood transitions from steady laminar flow (S-flow) in healthy arteries to disturbed flow (D-flow) in aneurysmal arteries, platelets are subjected to external forces. Biomechanical platelet activation is incompletely understood and is a potential mechanism behind antiplatelet medication resistance. Although it has been demonstrated that antiplatelet drugs suppress the growth of abdominal aortic aneurysms (AAA) in patients, we found that a certain degree of platelet reactivity persisted in spite of aspirin therapy, urging us to consider additional antiplatelet therapeutic targets. Transcriptomic profiling of platelets from patients with AAA revealed upregulation of a signal transduction pathway common to olfactory receptors, and this was explored as a mediator of AAA progression. Healthy platelets subjected to D-flow ex vivo, platelets from patients with AAA, and platelets in murine models of AAA demonstrated increased membrane olfactory receptor 2L13 (OR2L13) expression. A drug screen identified a molecule activating platelet OR2L13, which limited both biochemical and biomechanical platelet activation as well as AAA growth. This observation was further supported by selective deletion of the OR2L13 ortholog in a murine model of AAA that accelerated aortic aneurysm growth and rupture. These studies revealed that olfactory receptors regulate platelet activation in AAA and aneurysmal progression through platelet-derived mediators of aortic remodeling.
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Affiliation(s)
- Craig N Morrell
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine, Rochester, United States of America
| | - Doran Mix
- Department of Surgery, Division of Vascular Surgery, University of Rochester School of Medicine, Rochester, United States of America
| | - Anu Aggarwal
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
| | - Rohan Bhandari
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
| | - Matthew Godwin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
| | - A Phillip Owens Iii
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Sean P Lyden
- Department of Vascular Surgery, Cleveland Clinic, Cleveland, United States of America
| | - Adam Doyle
- Department of Surgery, Division of Vascular Surgery, University of Rochester School of Medicine, Rochester, United States of America
| | - Krystin Krauel
- Department of Molecular Medicine, University of Utah, Salt Lake City, United States of America
| | - Matthew T Rondina
- Department of Internal Medicine, University of Utah, Salt Lake City, United States of America
| | - Amy Mohan
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine, Rochester, United States of America
| | - Charles J Lowenstein
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, United States of America
| | - Sharon Shim
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
| | - Shaun Stauffer
- Center for Therapeutics Discovery, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
| | - Vara Prasad Josyula
- Center for Therapeutics Discovery, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
| | - Sara K Ture
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine, Rochester, United States of America
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester School of Medicine, Rochester, United States of America
| | - Larry E Wagner Iii
- Department of Pharmacology and Physiology, University of Rochester School of Medicine, Rochester, United States of America
| | - John M Ashton
- Department of Biomedical Genetics, University of Rochester School of Medicine, Rochester, United States of America
| | - Ayman Elbadawi
- Department of Cardiovascular Medicine, University of Texas Medical Branch, Galveston, United States of America
| | - Scott J Cameron
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States of America
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9
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Kallenbach JG, Freeberg MAT, Abplanalp D, Alenchery RG, Ajalik RE, Muscat S, Myers JA, Ashton JM, Loiselle A, Buckley MR, van Wijnen AJ, Awad HA. Altered TGFB1 regulated pathways promote accelerated tendon healing in the superhealer MRL/MpJ mouse. Sci Rep 2022; 12:3026. [PMID: 35194136 PMCID: PMC8863792 DOI: 10.1038/s41598-022-07124-4] [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] [Received: 06/03/2021] [Accepted: 02/11/2022] [Indexed: 12/23/2022] Open
Abstract
To better understand the molecular mechanisms of tendon healing, we investigated the Murphy Roth's Large (MRL) mouse, which is considered a model of mammalian tissue regeneration. We show that compared to C57Bl/6J (C57) mice, injured MRL tendons have reduced fibrotic adhesions and cellular proliferation, with accelerated improvements in biomechanical properties. RNA-seq analysis revealed that differentially expressed genes in the C57 healing tendon at 7 days post injury were functionally linked to fibrosis, immune system signaling and extracellular matrix (ECM) organization, while the differentially expressed genes in the MRL injured tendon were dominated by cell cycle pathways. These gene expression changes were associated with increased α-SMA+ myofibroblast and F4/80+ macrophage activation and abundant BCL-2 expression in the C57 injured tendons. Transcriptional analysis of upstream regulators using Ingenuity Pathway Analysis showed positive enrichment of TGFB1 in both C57 and MRL healing tendons, but with different downstream transcriptional effects. MRL tendons exhibited of cell cycle regulatory genes, with negative enrichment of the cell senescence-related regulators, compared to the positively-enriched inflammatory and fibrotic (ECM organization) pathways in the C57 tendons. Serum cytokine analysis revealed decreased levels of circulating senescence-associated circulatory proteins in response to injury in the MRL mice compared to the C57 mice. These data collectively demonstrate altered TGFB1 regulated inflammatory, fibrosis, and cell cycle pathways in flexor tendon repair in MRL mice, and could give cues to improved tendon healing.
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Affiliation(s)
- Jacob G Kallenbach
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Margaret A T Freeberg
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - David Abplanalp
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Rahul G Alenchery
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Raquel E Ajalik
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Samantha Muscat
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Jacquelyn A Myers
- UR Genomics Research Center (GRC), University of Rochester Medical Center, Rochester, NY, USA
| | - John M Ashton
- UR Genomics Research Center (GRC), University of Rochester Medical Center, Rochester, NY, USA
| | - Alayna Loiselle
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
- Department of Orthopaedics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
| | - Mark R Buckley
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Hani A Awad
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA.
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Orthopaedics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA.
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10
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Misra A, Baker CD, Pritchett EM, Burgos Villar KN, Ashton JM, Small EM. Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics. J Cardiovasc Dev Dis 2021; 9:1. [PMID: 35050211 PMCID: PMC8779463 DOI: 10.3390/jcdd9010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022] Open
Abstract
The neonatal mammalian heart exhibits a remarkable regenerative potential, which includes fibrotic scar resolution and the generation of new cardiomyocytes. To investigate the mechanisms facilitating heart repair after apical resection in neonatal mice, we conducted bulk and spatial transcriptomic analyses at regenerative and non-regenerative timepoints. Importantly, spatial transcriptomics provided near single-cell resolution, revealing distinct domains of atrial and ventricular myocardium that exhibit dynamic phenotypic alterations during postnatal heart maturation. Spatial transcriptomics also defined the cardiac scar, which transitions from a proliferative to secretory phenotype as the heart loses regenerative potential. The resolving scar is characterized by spatially and temporally restricted programs of inflammation, epicardium expansion and extracellular matrix production, metabolic reprogramming, lipogenic scar extrusion, and cardiomyocyte restoration. Finally, this study revealed the emergence of a regenerative border zone defined by immature cardiomyocyte markers and the robust expression of Sprr1a. Taken together, our study defines the spatially and temporally restricted gene programs that underlie neonatal heart regeneration and provides insight into cardio-restorative mechanisms supporting scar resolution.
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Affiliation(s)
- Adwiteeya Misra
- Department of Medicine, Aab Cardiovascular Research Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; (A.M.); (K.N.B.V.)
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA
| | - Cameron D. Baker
- Genomics Research Center, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; (C.D.B.); (E.M.P.); (J.M.A.)
| | - Elizabeth M. Pritchett
- Genomics Research Center, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; (C.D.B.); (E.M.P.); (J.M.A.)
| | - Kimberly N. Burgos Villar
- Department of Medicine, Aab Cardiovascular Research Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; (A.M.); (K.N.B.V.)
- Department of Pathology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - John M. Ashton
- Genomics Research Center, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; (C.D.B.); (E.M.P.); (J.M.A.)
| | - Eric M. Small
- Department of Medicine, Aab Cardiovascular Research Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; (A.M.); (K.N.B.V.)
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
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11
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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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12
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [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
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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13
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Ho TC, Kim HS, Chen Y, Li Y, LaMere MW, Chen C, Wang H, Gong J, Palumbo CD, Ashton JM, Kim HW, Xu Q, Becker MW, Leong KW. Scaffold-mediated CRISPR-Cas9 delivery system for acute myeloid leukemia therapy. Sci Adv 2021; 7:eabg3217. [PMID: 34138728 PMCID: PMC8133753 DOI: 10.1126/sciadv.abg3217] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/23/2021] [Indexed: 05/06/2023]
Abstract
Leukemia stem cells (LSCs) sustain the disease and contribute to relapse in acute myeloid leukemia (AML). Therapies that ablate LSCs may increase the chance of eliminating this cancer in patients. To this end, we used a bioreducible lipidoid-encapsulated Cas9/single guide RNA (sgRNA) ribonucleoprotein [lipidoid nanoparticle (LNP)-Cas9 RNP] to target the critical gene interleukin-1 receptor accessory protein (IL1RAP) in human LSCs. To enhance LSC targeting, we loaded LNP-Cas9 RNP and the chemokine CXCL12α onto mesenchymal stem cell membrane-coated nanofibril (MSCM-NF) scaffolds mimicking the bone marrow microenvironment. In vitro, CXCL12α release induced migration of LSCs to the scaffolds, and LNP-Cas9 RNP induced efficient gene editing. IL1RAP knockout reduced LSC colony-forming capacity and leukemic burden. Scaffold-based delivery increased the retention time of LNP-Cas9 in the bone marrow cavity. Overall, sustained local delivery of Cas9/IL1RAP sgRNA via CXCL12α-loaded LNP/MSCM-NF scaffolds provides an effective strategy for attenuating LSC growth to improve AML therapy.
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Affiliation(s)
- Tzu-Chieh Ho
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Hye Sung Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, Republic of Korea
- Department of Regenerative Dental Medicine, College of Dentistry, Dankook University, Cheonan, Republic of Korea
| | - Yumei Chen
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Yamin Li
- Department of Biomedical Engineering, Tufts University, Boston, MA, USA
| | - Mark W LaMere
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Caroline Chen
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Hui Wang
- Humanized Mouse Core Facility, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Jing Gong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Cal D Palumbo
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
- Genomics Research Center, University of Rochester, Rochester, NY, USA
| | - John M Ashton
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
- Genomics Research Center, University of Rochester, Rochester, NY, USA
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, Republic of Korea
- Department of Regenerative Dental Medicine, College of Dentistry, Dankook University, Cheonan, Republic of Korea
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea
- Cell & Matter Institute, Dankook University, Cheonan, Republic of Korea
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Boston, MA, USA
| | - Michael W Becker
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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14
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Burke RM, Dirkx RA, Quijada P, Lighthouse JK, Mohan A, O'Brien M, Wojciechowski W, Woeller CF, Phipps RP, Alexis JD, Ashton JM, Small EM. Prevention of Fibrosis and Pathological Cardiac Remodeling by Salinomycin. Circ Res 2021; 128:1663-1678. [PMID: 33825488 DOI: 10.1161/circresaha.120.317791] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ryan M Burke
- Aab Cardiovascular Research Institute, Department of Medicine (R.M.B., R.A.D., P.Q., J.K.L., A.M., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Ronald A Dirkx
- Aab Cardiovascular Research Institute, Department of Medicine (R.M.B., R.A.D., P.Q., J.K.L., A.M., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Pearl Quijada
- Aab Cardiovascular Research Institute, Department of Medicine (R.M.B., R.A.D., P.Q., J.K.L., A.M., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Janet K Lighthouse
- Aab Cardiovascular Research Institute, Department of Medicine (R.M.B., R.A.D., P.Q., J.K.L., A.M., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Amy Mohan
- Aab Cardiovascular Research Institute, Department of Medicine (R.M.B., R.A.D., P.Q., J.K.L., A.M., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Meghann O'Brien
- Genomics Research Center (M.O., W.W., J.M.A.), University of Rochester School of Medicine and Dentistry, NY
| | - Wojciech Wojciechowski
- Genomics Research Center (M.O., W.W., J.M.A.), University of Rochester School of Medicine and Dentistry, NY
| | - Collynn F Woeller
- Environmental Medicine (C.F.W., R.P.P.), University of Rochester School of Medicine and Dentistry, NY.,Department of Medicine (C.F.W., R.P.P., J.D.A., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Richard P Phipps
- Environmental Medicine (C.F.W., R.P.P.), University of Rochester School of Medicine and Dentistry, NY.,Department of Medicine (C.F.W., R.P.P., J.D.A., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - Jeffrey D Alexis
- Department of Medicine (C.F.W., R.P.P., J.D.A., E.M.S.), University of Rochester School of Medicine and Dentistry, NY
| | - John M Ashton
- Genomics Research Center (M.O., W.W., J.M.A.), University of Rochester School of Medicine and Dentistry, NY
| | - Eric M Small
- Aab Cardiovascular Research Institute, Department of Medicine (R.M.B., R.A.D., P.Q., J.K.L., A.M., E.M.S.), University of Rochester School of Medicine and Dentistry, NY.,Department of Medicine (C.F.W., R.P.P., J.D.A., E.M.S.), University of Rochester School of Medicine and Dentistry, NY.,Pharmacology and Physiology (E.M.S.), University of Rochester School of Medicine and Dentistry, NY.,Biomedical Engineering, University of Rochester, NY (E.M.S.)
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15
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Schroeder GM, Dutta D, Cavender CE, Jenkins J, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE. Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation. Nucleic Acids Res 2020; 48:8146-8164. [PMID: 32597951 PMCID: PMC7641330 DOI: 10.1093/nar/gkaa546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 03/13/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 01/20/2023] Open
Abstract
Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.
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Affiliation(s)
- Griffin M Schroeder
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Debapratim Dutta
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Chapin E Cavender
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Jermaine L Jenkins
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Elizabeth M Pritchett
- Genomics Research Center, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Cameron D Baker
- Genomics Research Center, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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16
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Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL. A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. J Biomol Tech 2020; 31:11-26. [PMID: 31969795 PMCID: PMC6959150 DOI: 10.7171/jbt.20-3101-003] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and they have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications.
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Affiliation(s)
- Sheenah M. Mische
- New York University (NYU) Langone Medical Center, New
York, New York 10016, USA
| | - Nancy C. Fisher
- University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599, USA
| | - Susan M. Meyn
- Vanderbilt University Medical Center, Nashville,
Tennessee 37212, USA
| | - Katia Sol-Church
- University of Virginia School of Medicine,
Charlottesville, Virginia 22908, USA
| | | | | | - Marie Adams
- Van Andel Institute, Grand Rapids, Michigan 49503,
USA
| | - John M. Ashton
- University of Rochester Medical Center, West
Henrietta, New York 14642, USA
| | - Kym M. Delventhal
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | | | - Laura Holmes
- Stowers Institute for Medical Research, Kansas City,
Missouri 64110, USA
| | - Pratik Jagtap
- University of Minnesota, Minneapolis, Minnesota
55455, USA
| | | | | | - Magnus Palmblad
- Leiden University Medical Center, Leiden 2333, The
Netherlands
| | - Brian C. Searle
- Institute for Systems Biology, Seattle, Washington
98109, USA
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17
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Pei S, Pollyea DA, Gustafson A, Stevens BM, Minhajuddin M, Fu R, Riemondy KA, Gillen AE, Sheridan RM, Kim J, Costello JC, Amaya ML, Inguva A, Winters A, Ye H, Krug A, Jones CL, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers JR, Ashton JM, Nemkov T, D'Alessandro A, Gutman JA, Ramsey HE, Savona MR, Smith CA, Jordan CT. Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia. Cancer Discov 2020; 10:536-551. [PMID: 31974170 PMCID: PMC7124979 DOI: 10.1158/2159-8290.cd-19-0710] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [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: 06/26/2019] [Revised: 12/03/2019] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
Venetoclax-based therapy can induce responses in approximately 70% of older previously untreated patients with acute myeloid leukemia (AML). However, up-front resistance as well as relapse following initial response demonstrates the need for a deeper understanding of resistance mechanisms. In the present study, we report that responses to venetoclax +azacitidine in patients with AML correlate closely with developmental stage, where phenotypically primitive AML is sensitive, but monocytic AML is more resistant. Mechanistically, resistant monocytic AML has a distinct transcriptomic profile, loses expression of venetoclax target BCL2, and relies on MCL1 to mediate oxidative phosphorylation and survival. This differential sensitivity drives a selective process in patients which favors the outgrowth of monocytic subpopulations at relapse. Based on these findings, we conclude that resistance to venetoclax + azacitidine can arise due to biological properties intrinsic to monocytic differentiation. We propose that optimal AML therapies should be designed so as to independently target AML subclones that may arise at differing stages of pathogenesis. SIGNIFICANCE: Identifying characteristics of patients who respond poorly to venetoclax-based therapy and devising alternative therapeutic strategies for such patients are important topics in AML. We show that venetoclax resistance can arise due to intrinsic molecular/metabolic properties of monocytic AML cells and that such properties can potentially be targeted with alternative strategies.
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Affiliation(s)
- Shanshan Pei
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Daniel A Pollyea
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Annika Gustafson
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Brett M Stevens
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Mohammad Minhajuddin
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado
| | - Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado
| | - Austin E Gillen
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado
| | - Ryan M Sheridan
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado
| | - Jihye Kim
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Maria L Amaya
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, Colorado
| | - Anagha Inguva
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Amanda Winters
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Haobin Ye
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Anna Krug
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Courtney L Jones
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Biniam Adane
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Nabilah Khan
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Jessica Ponder
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Jeffrey Schowinsky
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado
| | - Diana Abbott
- Center for Innovative Design and Analysis, Colorado School of Public Health, Aurora, Colorado
| | - Andrew Hammes
- Center for Innovative Design and Analysis, Colorado School of Public Health, Aurora, Colorado
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, New York
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Angelo D'Alessandro
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Jonathan A Gutman
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Haley E Ramsey
- Department of Internal Medicine, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Michael R Savona
- Department of Internal Medicine, Vanderbilt University School of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Clayton A Smith
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado
| | - Craig T Jordan
- Division of Hematology, University of Colorado School of Medicine, Aurora, Colorado.
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18
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Wang W, Friedland SC, Guo B, O’Dell MR, Alexander WB, Whitney-Miller CL, Agostini-Vulaj D, Huber AR, Myers JR, Ashton JM, Dunne RF, Steiner LA, Hezel AF. ARID1A, a SWI/SNF subunit, is critical to acinar cell homeostasis and regeneration and is a barrier to transformation and epithelial-mesenchymal transition in the pancreas. Gut 2019; 68:1245-1258. [PMID: 30228219 PMCID: PMC6551318 DOI: 10.1136/gutjnl-2017-315541] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Here, we evaluate the contribution of AT-rich interaction domain-containing protein 1A (ARID1A), the most frequently mutated member of the SWItch/sucrose non-fermentable (SWI/SNF) complex, in pancreatic homeostasis and pancreatic ductal adenocarcinoma (PDAC) pathogenesis using mouse models. DESIGN Mice with a targeted deletion of Arid1a in the pancreas by itself and in the context of two common genetic alterations in PDAC, Kras and p53, were followed longitudinally. Pancreases were examined and analysed for proliferation, response to injury and tumourigenesis. Cancer cell lines derived from these models were analysed for clonogenic, migratory, invasive and transcriptomic changes. RESULTS Arid1a deletion in the pancreas results in progressive acinar-to-ductal metaplasia (ADM), loss of acinar mass, diminished acinar regeneration in response to injury and ductal cell expansion. Mutant Kras cooperates with homozygous deletion of Arid1a, leading to intraductal papillary mucinous neoplasm (IPMN). Arid1a loss in the context of mutant Kras and p53 leads to shorter tumour latency, with the resulting tumours being poorly differentiated. Cancer cell lines derived from Arid1a-mutant tumours are more mesenchymal, migratory, invasive and capable of anchorage-independent growth; gene expression analysis showed activation of epithelial-mesenchymal transition (EMT) and stem cell identity pathways that are partially dependent on Arid1a loss for dysregulation. CONCLUSIONS ARID1A plays a key role in pancreatic acinar homeostasis and response to injury. Furthermore, ARID1A restrains oncogenic KRAS-driven formation of premalignant proliferative IPMN. Arid1a-deficient PDACs are poorly differentiated and have mesenchymal features conferring migratory/invasive and stem-like properties.
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Affiliation(s)
- Wenjia Wang
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Scott C Friedland
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
| | - Bing Guo
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Michael R O’Dell
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - William B Alexander
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
| | - Christa L Whitney-Miller
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Diana Agostini-Vulaj
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Aaron R Huber
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Richard F Dunne
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Laurie A Steiner
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Aram F Hezel
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
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19
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Bandyopadhyay G, Lillis J, Misra RS, Myers JR, Ashton JM, Huyck HL, Krenitsky D, Romas ST, Poole CJ, Holden‐Wiltse J, Katzman PJ, Deutsch G, Bhattacharya S, Mariani TJ, Pryhuber GS. Identification and Characterization of Cellular Heterogeneity within Human Late Developmental Stage Dissociated Lung by CITE‐Seq. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.847.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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)
| | - Jacquelyn Lillis
- Genomics Research CenterUniversity of Rochester Medical CenterRochesterNY
| | - Ravi S Misra
- PediatricsUniversity of Rochester Medical CenterRochesterNY
| | - Jason R Myers
- Genomics Research CenterUniversity of Rochester Medical CenterRochesterNY
| | - John M Ashton
- Genomics Research CenterUniversity of Rochester Medical CenterRochesterNY
| | - Heidie L Huyck
- PediatricsUniversity of Rochester Medical CenterRochesterNY
| | | | | | - Cory J Poole
- PediatricsUniversity of Rochester Medical CenterRochesterNY
| | | | - Philip J Katzman
- Pathology & Lab MedicineUniversity of Rochester Medical CenterRochesterNY
| | - Gail Deutsch
- PathologySeattle Childrens Hospital, University of WashingtonSeattleWA
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20
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Ye H, Adane B, Khan N, Alexeev E, Nusbacher N, Minhajuddin M, Stevens BM, Winters AC, Lin X, Ashton JM, Purev E, Xing L, Pollyea DA, Lozupone CA, Serkova NJ, Colgan SP, Jordan CT. Subversion of Systemic Glucose Metabolism as a Mechanism to Support the Growth of Leukemia Cells. Cancer Cell 2018; 34:659-673.e6. [PMID: 30270124 PMCID: PMC6177322 DOI: 10.1016/j.ccell.2018.08.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/18/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
From an organismal perspective, cancer cell populations can be considered analogous to parasites that compete with the host for essential systemic resources such as glucose. Here, we employed leukemia models and human leukemia samples to document a form of adaptive homeostasis, where malignant cells alter systemic physiology through impairment of both host insulin sensitivity and insulin secretion to provide tumors with increased glucose. Mechanistically, tumor cells induce high-level production of IGFBP1 from adipose tissue to mediate insulin sensitivity. Further, leukemia-induced gut dysbiosis, serotonin loss, and incretin inactivation combine to suppress insulin secretion. Importantly, attenuated disease progression and prolonged survival are achieved through disruption of the leukemia-induced adaptive homeostasis. Our studies provide a paradigm for systemic management of leukemic disease.
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Affiliation(s)
- Haobin Ye
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Biniam Adane
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Nabilah Khan
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Erica Alexeev
- Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Nichole Nusbacher
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Mohammad Minhajuddin
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Brett M Stevens
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Amanda C Winters
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, 13123 E 16th Avenue, Aurora, CO 80045, USA
| | - Xi Lin
- Department of Pathology and Laboratory Medicine, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - John M Ashton
- Functional Genomics Center, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Enkhtsetseg Purev
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Lianping Xing
- Department of Pathology and Laboratory Medicine, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Daniel A Pollyea
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Catherine A Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Natalie J Serkova
- Department of Radiology, Animal Imaging Shared Resources, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Sean P Colgan
- Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado Anschutz Medical Campus, 12700 E 19(th) Avenue, Aurora, CO 80045, USA.
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21
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Pei S, Minhajuddin M, Adane B, Khan N, Stevens BM, Mack SC, Lai S, Rich JN, Inguva A, Shannon KM, Kim H, Tan AC, Myers JR, Ashton JM, Neff T, Pollyea DA, Smith CA, Jordan CT. AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells. Cell Stem Cell 2018; 23:86-100.e6. [PMID: 29910151 DOI: 10.1016/j.stem.2018.05.021] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [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: 10/24/2017] [Revised: 03/30/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022]
Abstract
Leukemia stem cells (LSCs) are thought to drive the genesis of acute myeloid leukemia (AML) as well as relapse following chemotherapy. Because of their unique biology, developing effective methods to eradicate LSCs has been a significant challenge. In the present study, we demonstrate that intrinsic overexpression of the mitochondrial dynamics regulator FIS1 mediates mitophagy activity that is essential for primitive AML cells. Depletion of FIS1 attenuates mitophagy and leads to inactivation of GSK3, myeloid differentiation, cell cycle arrest, and a profound loss of LSC self-renewal potential. Further, we report that the central metabolic stress regulator AMPK is also intrinsically activated in LSC populations and is upstream of FIS1. Inhibition of AMPK signaling recapitulates the biological effect of FIS1 loss. These data suggest a model in which LSCs co-opt AMPK/FIS1-mediated mitophagy as a means to maintain stem cell properties that may be otherwise compromised by the stresses induced by oncogenic transformation.
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Affiliation(s)
- Shanshan Pei
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | | | - Biniam Adane
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | - Nabilah Khan
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | - Brett M Stevens
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | - Stephen C Mack
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sisi Lai
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anagha Inguva
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | - Kevin M Shannon
- Department of Pediatrics, University of California - San Francisco, San Francisco, CA 94143, USA
| | - Hyunmin Kim
- Division of Medical Oncology, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Aik-Choon Tan
- Division of Medical Oncology, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester, NY 14642, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, NY 14642, USA
| | - Tobias Neff
- Department of Pediatrics, Section of Pediatric Hematology/Oncology/Bone Marrow Transplantation, University of Colorado Denver, Aurora, CO 80045, USA
| | - Daniel A Pollyea
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | - Clayton A Smith
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado, Aurora, CO 80045, USA.
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22
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Schott EM, Farnsworth CW, Grier A, Lillis JA, Soniwala S, Dadourian GH, Bell RD, Doolittle ML, Villani DA, Awad H, Ketz JP, Kamal F, Ackert-Bicknell C, Ashton JM, Gill SR, Mooney RA, Zuscik MJ. Targeting the gut microbiome to treat the osteoarthritis of obesity. JCI Insight 2018; 3:95997. [PMID: 29669931 DOI: 10.1172/jci.insight.95997] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [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: 06/28/2017] [Accepted: 03/14/2018] [Indexed: 01/07/2023] Open
Abstract
Obesity is a risk factor for osteoarthritis (OA), the greatest cause of disability in the US. The impact of obesity on OA is driven by systemic inflammation, and increased systemic inflammation is now understood to be caused by gut microbiome dysbiosis. Oligofructose, a nondigestible prebiotic fiber, can restore a lean gut microbial community profile in the context of obesity, suggesting a potentially novel approach to treat the OA of obesity. Here, we report that - compared with the lean murine gut - obesity is associated with loss of beneficial Bifidobacteria, while key proinflammatory species gain in abundance. A downstream systemic inflammatory signature culminates with macrophage migration to the synovium and accelerated knee OA. Oligofructose supplementation restores the lean gut microbiome in obese mice, in part, by supporting key commensal microflora, particularly Bifidobacterium pseudolongum. This is associated with reduced inflammation in the colon, circulation, and knee and protection from OA. This observation of a gut microbiome-OA connection sets the stage for discovery of potentially new OA therapeutics involving strategic manipulation of specific microbial species inhabiting the intestinal space.
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Affiliation(s)
- Eric M Schott
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | | | - Alex Grier
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Jacquelyn A Lillis
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Sarah Soniwala
- Center for Musculoskeletal Research.,Department of Biology and
| | - Gregory H Dadourian
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
| | - Richard D Bell
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - Madison L Doolittle
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - David A Villani
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - Hani Awad
- Center for Musculoskeletal Research.,Department of Biomedical Engineering, University of Rochester, Rochester, New York, USA
| | - John P Ketz
- Center for Musculoskeletal Research.,Department of Orthopaedics & Rehabilitation and
| | - Fadia Kamal
- Center for Musculoskeletal Research.,Department of Orthopaedics & Rehabilitation and
| | | | - John M Ashton
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Steven R Gill
- Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Robert A Mooney
- Center for Musculoskeletal Research.,Department of Pathology & Laboratory Medicine, and
| | - Michael J Zuscik
- Center for Musculoskeletal Research.,Department of Orthopaedics & Rehabilitation and
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23
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Scheible KM, Emo J, Laniewski N, Baran AM, Peterson DR, Holden-Wiltse J, Bandyopadhyay S, Straw AG, Huyck H, Ashton JM, Tripi KS, Arul K, Werner E, Scalise T, Maffett D, Caserta M, Ryan RM, Reynolds AM, Ren CL, Topham DJ, Mariani TJ, Pryhuber GS. T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy. JCI Insight 2018; 3:96724. [PMID: 29467329 DOI: 10.1172/jci.insight.96724] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 08/07/2017] [Accepted: 01/17/2018] [Indexed: 12/31/2022] Open
Abstract
The inverse relationship between gestational age at birth and postviral respiratory morbidity suggests that infants born preterm (PT) may miss a critical developmental window of T cell maturation. Despite a continued increase in younger PT survivors with respiratory complications, we have limited understanding of normal human fetal T cell maturation, how ex utero development in premature infants may interrupt normal T cell development, and whether T cell development has an effect on infant outcomes. In our longitudinal cohort of 157 infants born between 23 and 42 weeks of gestation, we identified differences in T cells present at birth that were dependent on gestational age and differences in postnatal T cell development that predicted respiratory outcome at 1 year of age. We show that naive CD4+ T cells shift from a CD31-TNF-α+ bias in mid gestation to a CD31+IL-8+ predominance by term gestation. Former PT infants discharged with CD31+IL8+CD4+ T cells below a range similar to that of full-term born infants were at an over 3.5-fold higher risk for respiratory complications after NICU discharge. This study is the first to our knowledge to identify a pattern of normal functional T cell development in later gestation and to associate abnormal T cell development with health outcomes in infants.
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Affiliation(s)
| | | | | | - Andrea M Baran
- Department of Biostatistics and Computational Biology, and
| | | | | | | | - Andrew G Straw
- Department of Biostatistics and Computational Biology, and
| | | | | | | | - Karan Arul
- Undergraduate Campus, University of Rochester, Rochester, New York, USA
| | | | | | | | | | - Rita M Ryan
- Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Anne Marie Reynolds
- Department of Pediatrics, State University of New York, University at Buffalo, Buffalo, New York, USA
| | - Clement L Ren
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
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24
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Elbarbary RA, Miyoshi K, Myers JR, Du P, Ashton JM, Tian B, Maquat LE. Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G 1/S phase transition. Science 2018; 356:859-862. [PMID: 28546213 DOI: 10.1126/science.aai9372] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/16/2016] [Accepted: 04/21/2017] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression. The pathways that mediate mature miRNA decay are less well understood than those that mediate miRNA biogenesis. We found that functional miRNAs are degraded in human cells by the endonuclease Tudor-SN (TSN). In vitro, recombinant TSN initiated the decay of both protein-free and Argonaute 2-loaded miRNAs via endonucleolytic cleavage at CA and UA dinucleotides, preferentially at scissile bonds located more than five nucleotides away from miRNA ends. Cellular targets of TSN-mediated decay defined using microRNA sequencing followed this rule. Inhibiting TSN-mediated miRNA decay by CRISPR-Cas9 knockout of TSN inhibited cell cycle progression by up-regulating a cohort of miRNAs that down-regulates mRNAs that encode proteins critical for the G1-to-S phase transition. Our study indicates that targeting TSN nuclease activity could inhibit pathological cell proliferation.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Keita Miyoshi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, NY 14642, USA
| | - Peicheng Du
- Office of Advanced Research Computing, Rutgers University, Piscataway, NJ 08854, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, NY 14642, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.,Department of Oncology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
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25
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Wong EL, Lutz NM, Hogan VA, Lamantia CE, McMurray HR, Myers JR, Ashton JM, Majewska AK. Developmental alcohol exposure impairs synaptic plasticity without overtly altering microglial function in mouse visual cortex. Brain Behav Immun 2018; 67:257-278. [PMID: 28918081 PMCID: PMC5696045 DOI: 10.1016/j.bbi.2017.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/23/2017] [Accepted: 09/04/2017] [Indexed: 12/26/2022] Open
Abstract
Fetal alcohol spectrum disorder (FASD), caused by gestational ethanol (EtOH) exposure, is one of the most common causes of non-heritable and life-long mental disability worldwide, with no standard treatment or therapy available. While EtOH exposure can alter the function of both neurons and glia, it is still unclear how EtOH influences brain development to cause deficits in sensory and cognitive processing later in life. Microglia play an important role in shaping synaptic function and plasticity during neural circuit development and have been shown to mount an acute immunological response to EtOH exposure in certain brain regions. Therefore, we hypothesized that microglial roles in the healthy brain could be permanently altered by early EtOH exposure leading to deficits in experience-dependent plasticity. We used a mouse model of human third trimester high binge EtOH exposure, administering EtOH twice daily by subcutaneous injections from postnatal day 4 through postnatal day 9 (P4-:P9). Using a monocular deprivation model to assess ocular dominance plasticity, we found an EtOH-induced deficit in this type of visually driven experience-dependent plasticity. However, using a combination of immunohistochemistry, confocal microscopy, and in vivo two-photon microscopy to assay microglial morphology and dynamics, as well as fluorescence activated cell sorting (FACS) and RNA-seq to examine the microglial transcriptome, we found no evidence of microglial dysfunction in early adolescence. We also found no evidence of microglial activation in visual cortex acutely after early ethanol exposure, possibly because we also did not observe EtOH-induced neuronal cell death in this brain region. We conclude that early EtOH exposure caused a deficit in experience-dependent synaptic plasticity in the visual cortex that was independent of changes in microglial phenotype or function. This demonstrates that neural plasticity can remain impaired by developmental ethanol exposure even in a brain region where microglia do not acutely assume nor maintain an activated phenotype.
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Affiliation(s)
- Elissa L. Wong
- Dept. of Environmental Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Nina M. Lutz
- Dept. of Neuroscience, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Victoria A. Hogan
- Dept. of Neuroscience, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Cassandra E. Lamantia
- Dept. of Neuroscience, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Helene R. McMurray
- Dept. of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY14642, USA,Inst. For Innovative Education, Miner Libraries, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jason R. Myers
- Genomics Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA,Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John M. Ashton
- Genomics Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA,Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ania K. Majewska
- Dept. of Neuroscience, University of Rochester Medical Center, Rochester, NY 14642, USA,Corresponding author: Ania K. Majewska:
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26
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Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR. Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness. Sci Rep 2017; 7:6548. [PMID: 28747714 PMCID: PMC5529430 DOI: 10.1038/s41598-017-06738-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [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: 12/09/2016] [Accepted: 06/16/2017] [Indexed: 02/02/2023] Open
Abstract
Lower respiratory tract infection (LRTI) commonly causes hospitalization in adults. Because bacterial diagnostic tests are not accurate, antibiotics are frequently prescribed. Peripheral blood gene expression to identify subjects with bacterial infection is a promising strategy. We evaluated whole blood profiling using RNASeq to discriminate infectious agents in adults with microbiologically defined LRTI. Hospitalized adults with LRTI symptoms were recruited. Clinical data and blood was collected, and comprehensive microbiologic testing performed. Gene expression was measured using RNASeq and qPCR. Genes discriminatory for bacterial infection were identified using the Bonferroni-corrected Wilcoxon test. Constrained logistic models to predict bacterial infection were fit using screened LASSO. We enrolled 94 subjects who were microbiologically classified; 53 as “non-bacterial” and 41 as “bacterial”. RNAseq and qPCR confirmed significant differences in mean expression for 10 genes previously identified as discriminatory for bacterial LRTI. A novel dimension reduction strategy selected three pathways (lymphocyte, α-linoleic acid metabolism, IGF regulation) including eleven genes as optimal markers for discriminating bacterial infection (naïve AUC = 0.94; nested CV-AUC = 0.86). Using these genes, we constructed a classifier for bacterial LRTI with 90% (79% CV) sensitivity and 83% (76% CV) specificity. This novel, pathway-based gene set displays promise as a method to distinguish bacterial from nonbacterial LRTI.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Alex F Rosenberg
- Division of Allergy Immunology & Rheumatology, Department of Medicine, University of Rochester School Medicine, Rochester, NY, USA
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Katherine Grzesik
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester School Medicine, Rochester, NY, USA
| | - Steven R Gill
- Genomics Research Center, University of Rochester School Medicine, Rochester, NY, USA
| | - Anthony M Corbett
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - Jeanne Holden-Wiltse
- Department of Biostatistics and Computational Biology, University of Rochester School Medicine, Rochester, NY, USA
| | - David J Topham
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester School Medicine, Rochester, NY, USA.,Department of Microbiology and Immunology, University of Rochester School Medicine, Rochester, NY, USA
| | - Edward E Walsh
- Division of Infectious Diseases, Department of Medicine, University of Rochester School Medicine and Rochester General Hospital, Rochester, NY, USA
| | - Thomas J Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester School Medicine, Rochester, NY, USA
| | - Ann R Falsey
- Division of Infectious Diseases, Department of Medicine, University of Rochester School Medicine and Rochester General Hospital, Rochester, NY, USA.
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27
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Hilimire TA, Chamberlain JM, Anokhina V, Bennett RP, Swart O, Myers JR, Ashton JM, Stewart RA, Featherston AL, Gates K, Helms ED, Smith HC, Dewhurst S, Miller BL. HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells. ACS Chem Biol 2017; 12:1674-1682. [PMID: 28448121 PMCID: PMC5477779 DOI: 10.1021/acschembio.7b00052] [Citation(s) in RCA: 37] [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] [Indexed: 02/05/2023]
Abstract
![]()
The
HIV-1 frameshift-stimulating (FSS) RNA, a regulatory RNA of
critical importance in the virus’ life cycle, has been posited
as a novel target for anti-HIV drug development. We report the synthesis
and evaluation of triazole-containing compounds able to bind the FSS
with high affinity and selectivity. Readily accessible synthetically,
these compounds are less toxic than previously reported olefin congeners.
We show for the first time that FSS-targeting compounds have antiviral
activity against replication-competent HIV in human cells, including
a highly cytopathic, multidrug-resistant strain. These results support
the viability of the HIV-1 FSS RNA as a therapeutic target and more
generally highlight opportunities for synthetic molecule-mediated
interference with protein recoding in a wide range of organisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Eric D. Helms
- Department of Chemistry, SUNY Geneseo, Geneseo, New York 14454, United States
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28
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Shen J, Wang C, Li D, Xu T, Myers J, Ashton JM, Wang T, Zuscik MJ, McAlinden A, O'Keefe RJ. DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. JCI Insight 2017; 2:93612. [PMID: 28614801 DOI: 10.1172/jci.insight.93612] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/10/2017] [Indexed: 01/05/2023] Open
Abstract
Osteoarthritis (OA) is the most common form of arthritis worldwide. It is a complex disease affecting the whole joint but is generally characterized by progressive degradation of articular cartilage. Recent genome-wide association screens have implicated distinct DNA methylation signatures in OA patients. We show that the de novo DNA methyltransferase (Dnmt) 3b, but not Dnmt3a, is present in healthy murine and human articular chondrocytes and its expression decreases in OA mouse models and in chondrocytes from human OA patients. Targeted deletion of Dnmt3b in murine articular chondrocytes results in an early-onset and progressive postnatal OA-like pathology. RNA-Seq and methylC-Seq analyses of Dnmt3b loss-of-function chondrocytes show that cellular metabolic processes are affected. Specifically, TCA metabolites and mitochondrial respiration are elevated. Importantly, a chondroprotective effect was found following Dnmt3b gain of function in murine articular chondrocytes in vitro and in vivo. This study shows that Dnmt3b plays a significant role in regulating postnatal articular cartilage homeostasis. Cellular pathways regulated by Dnmt3b in chondrocytes may provide novel targets for therapeutic approaches to treat OA.
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Affiliation(s)
- Jie Shen
- Department of Orthopaedic Surgery and
| | | | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Taotao Xu
- Department of Orthopaedic Surgery and.,Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jason Myers
- Genomics Research Center, School of Medicine and Dentistry, and
| | - John M Ashton
- Genomics Research Center, School of Medicine and Dentistry, and.,Department of Microbiology and Immunology, School of Medicine and Dentistry, and
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, School of Medicine, Washington University, St. Louis, Missouri, USA
| | - Michael J Zuscik
- Department of Orthopaedics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery and.,Department of Cell Biology & Physiology, School of Medicine, Washington University, St. Louis, Missouri, USA
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29
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Gasparetto M, Pei S, Minhajuddin M, Khan N, Pollyea DA, Myers JR, Ashton JM, Becker MW, Vasiliou V, Humphries KR, Jordan CT, Smith CA. Targeted therapy for a subset of acute myeloid leukemias that lack expression of aldehyde dehydrogenase 1A1. Haematologica 2017; 102:1054-1065. [PMID: 28280079 PMCID: PMC5451337 DOI: 10.3324/haematol.2016.159053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 11/02/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
Aldehyde dehydrogenase 1A1 (ALDH1A1) activity is high in hematopoietic stem cells and functions in part to protect stem cells from reactive aldehydes and other toxic compounds. In contrast, we found that approximately 25% of all acute myeloid leukemias expressed low or undetectable levels of ALDH1A1 and that this ALDH1A1− subset of leukemias correlates with good prognosis cytogenetics. ALDH1A1− cell lines as well as primary leukemia cells were found to be sensitive to treatment with compounds that directly and indirectly generate toxic ALDH substrates including 4-hydroxynonenal and the clinically relevant compounds arsenic trioxide and 4-hydroperoxycyclophosphamide. In contrast, normal hematopoietic stem cells were relatively resistant to these compounds. Using a murine xenotransplant model to emulate a clinical treatment strategy, established ALDH1A1− leukemias were also sensitive to in vivo treatment with cyclophosphamide combined with arsenic trioxide. These results demonstrate that targeting ALDH1A1− leukemic cells with toxic ALDH1A1 substrates such as arsenic and cyclophosphamide may be a novel targeted therapeutic strategy for this subset of acute myeloid leukemias.
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Affiliation(s)
| | - Shanshan Pei
- Division of Hematology, University of Colorado, Aurora, CO, USA
| | | | - Nabilah Khan
- Division of Hematology, University of Colorado, Aurora, CO, USA
| | | | - Jason R Myers
- Genomics Research Center, University of Rochester, NY, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, NY, USA
| | - Michael W Becker
- Department of Medicine, University of Rochester Medical Center, NY, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale University, New Haven, CT, USA
| | - Keith R Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Craig T Jordan
- Division of Hematology, University of Colorado, Aurora, CO, USA
| | - Clayton A Smith
- Division of Hematology, University of Colorado, Aurora, CO, USA
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30
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Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT. Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells. J Biol Chem 2016; 291:25280. [PMID: 27888238 DOI: 10.1074/jbc.a116.750653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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31
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Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT. Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. J Biol Chem 2016; 291:21984-22000. [PMID: 27573247 DOI: 10.1074/jbc.m116.750653] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Indexed: 12/22/2022] Open
Abstract
Although multidrug approaches to cancer therapy are common, few strategies are based on rigorous scientific principles. Rather, drug combinations are largely dictated by empirical or clinical parameters. In the present study we developed a strategy for rational design of a regimen that selectively targets human acute myelogenous leukemia (AML) stem cells. As a starting point, we used parthenolide, an agent shown to target critical mechanisms of redox balance in primary AML cells. Next, using proteomic, genomic, and metabolomic methods, we determined that treatment with parthenolide leads to induction of compensatory mechanisms that include up-regulated NADPH production via the pentose phosphate pathway as well as activation of the Nrf2-mediated oxidative stress response pathway. Using this knowledge we identified 2-deoxyglucose and temsirolimus as agents that can be added to a parthenolide regimen as a means to inhibit such compensatory events and thereby further enhance eradication of AML cells. We demonstrate that the parthenolide, 2-deoxyglucose, temsirolimus (termed PDT) regimen is a potent means of targeting AML stem cells but has little to no effect on normal stem cells. Taken together our findings illustrate a comprehensive approach to designing combination anticancer drug regimens.
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Affiliation(s)
| | | | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045
| | | | | | | | | | - Vinod K Yadav
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado 80045, and
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado 80045, and
| | - John M Ashton
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York 14642
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045
| | | | | | - Peter A Crooks
- Department of Pharmaceutical Sciences, University of Arkansas, Little Rock, Arkansas 72205
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32
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Yoshida T, Myers JR, Ashton JM, De Benedetto A, Gill SR, Philpot C, David G, Leung DY, Beck LA. Novel Gene Signatures Observed in the Nonlesional Skin from European American Atopic Dermatitis Subjects Who Are Colonized with Staphyloccoccus Aureus. J Allergy Clin Immunol 2016. [DOI: 10.1016/j.jaci.2015.12.730] [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: 11/30/2022]
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33
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Baras AS, Mitchell CJ, Myers JR, Gupta S, Weng LC, Ashton JM, Cornish TC, Pandey A, Halushka MK. miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy. PLoS One 2015; 10:e0143066. [PMID: 26571139 PMCID: PMC4646525 DOI: 10.1371/journal.pone.0143066] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/30/2015] [Indexed: 02/02/2023] Open
Abstract
Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM). Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA) are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html.
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Affiliation(s)
- Alexander S. Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher J. Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jason R. Myers
- Genomics Research Center, University of Rochester, Rochester, New York, United States of America
| | - Simone Gupta
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lien-Chun Weng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John M. Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, United States of America
| | - Toby C. Cornish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Pei S, Minhajuddin M, Callahan KP, Balys M, Ashton JM, Neering SJ, Lagadinou ED, Corbett C, Ye H, Liesveld JL, O'Dwyer KM, Li Z, Shi L, Greninger P, Settleman J, Benes C, Hagen FK, Munger J, Crooks PA, Becker MW, Jordan CT. Targeting aberrant glutathione metabolism to eradicate human acute myelogenous leukemia cells. J Biol Chem 2013; 288:33542-33558. [PMID: 24089526 PMCID: PMC3837103 DOI: 10.1074/jbc.m113.511170] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [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] [Received: 08/17/2013] [Revised: 10/01/2013] [Indexed: 12/14/2022] Open
Abstract
The development of strategies to eradicate primary human acute myelogenous leukemia (AML) cells is a major challenge to the leukemia research field. In particular, primitive leukemia cells, often termed leukemia stem cells, are typically refractory to many forms of therapy. To investigate improved strategies for targeting of human AML cells we compared the molecular mechanisms regulating oxidative state in primitive (CD34(+)) leukemic versus normal specimens. Our data indicate that CD34(+) AML cells have elevated expression of multiple glutathione pathway regulatory proteins, presumably as a mechanism to compensate for increased oxidative stress in leukemic cells. Consistent with this observation, CD34(+) AML cells have lower levels of reduced glutathione and increased levels of oxidized glutathione compared with normal CD34(+) cells. These findings led us to hypothesize that AML cells will be hypersensitive to inhibition of glutathione metabolism. To test this premise, we identified compounds such as parthenolide (PTL) or piperlongumine that induce almost complete glutathione depletion and severe cell death in CD34(+) AML cells. Importantly, these compounds only induce limited and transient glutathione depletion as well as significantly less toxicity in normal CD34(+) cells. We further determined that PTL perturbs glutathione homeostasis by a multifactorial mechanism, which includes inhibiting key glutathione metabolic enzymes (GCLC and GPX1), as well as direct depletion of glutathione. These findings demonstrate that primitive leukemia cells are uniquely sensitive to agents that target aberrant glutathione metabolism, an intrinsic property of primary human AML cells.
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Affiliation(s)
- Shanshan Pei
- Department of Biomedical Genetics, University of Rochester School of Medicine, Rochester, New York 14642; Department of Medicine, University of Colorado Denver, Aurora, Colorado 80045
| | | | - Kevin P Callahan
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Marlene Balys
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - John M Ashton
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Sarah J Neering
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Eleni D Lagadinou
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Cheryl Corbett
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Haobin Ye
- Department of Medicine, University of Colorado Denver, Aurora, Colorado 80045; Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Jane L Liesveld
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Kristen M O'Dwyer
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Zheng Li
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021; Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10021
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129
| | - Jeffrey Settleman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129
| | - Cyril Benes
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129
| | - Fred K Hagen
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, University of Arkansas, Little Rock, Arkansas 72205
| | - Michael W Becker
- Department of Medicine, University of Rochester School of Medicine, Rochester, New York 14642
| | - Craig T Jordan
- Department of Biomedical Genetics, University of Rochester School of Medicine, Rochester, New York 14642; Department of Medicine, University of Colorado Denver, Aurora, Colorado 80045.
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35
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Lagadinou ED, Sach A, Callahan K, Rossi RM, Neering SJ, Minhajuddin M, Ashton JM, Pei S, Grose V, O'Dwyer KM, Liesveld JL, Brookes PS, Becker MW, Jordan CT. BCL-2 inhibition targets oxidative phosphorylation and selectively eradicates quiescent human leukemia stem cells. Cell Stem Cell 2013; 12:329-41. [PMID: 23333149 DOI: 10.1016/j.stem.2012.12.013] [Citation(s) in RCA: 888] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 11/05/2012] [Accepted: 12/17/2012] [Indexed: 12/17/2022]
Abstract
Most forms of chemotherapy employ mechanisms involving induction of oxidative stress, a strategy that can be effective due to the elevated oxidative state commonly observed in cancer cells. However, recent studies have shown that relative redox levels in primary tumors can be heterogeneous, suggesting that regimens dependent on differential oxidative state may not be uniformly effective. To investigate this issue in hematological malignancies, we evaluated mechanisms controlling oxidative state in primary specimens derived from acute myelogenous leukemia (AML) patients. Our studies demonstrate three striking findings. First, the majority of functionally defined leukemia stem cells (LSCs) are characterized by relatively low levels of reactive oxygen species (termed "ROS-low"). Second, ROS-low LSCs aberrantly overexpress BCL-2. Third, BCL-2 inhibition reduced oxidative phosphorylation and selectively eradicated quiescent LSCs. Based on these findings, we propose a model wherein the unique physiology of ROS-low LSCs provides an opportunity for selective targeting via disruption of BCL-2-dependent oxidative phosphorylation.
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Affiliation(s)
- Eleni D Lagadinou
- James P. Wilmot Cancer Center, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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36
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Ashton JM, Balys M, Neering SJ, Hassane DC, Cowley G, Root DE, Miller PG, Ebert BL, McMurray HR, Land H, Jordan CT. Gene sets identified with oncogene cooperativity analysis regulate in vivo growth and survival of leukemia stem cells. Cell Stem Cell 2012; 11:359-72. [PMID: 22863534 DOI: 10.1016/j.stem.2012.05.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 04/23/2012] [Accepted: 05/18/2012] [Indexed: 01/29/2023]
Abstract
Leukemia stem cells (LSCs) represent a biologically distinct subpopulation of myeloid leukemias, with reduced cell cycle activity and increased resistance to therapeutic challenge. To better characterize key properties of LSCs, we employed a strategy based on identification of genes synergistically dysregulated by cooperating oncogenes. We hypothesized that such genes, termed "cooperation response genes" (CRGs), would represent regulators of LSC growth and survival. Using both a primary mouse model and human leukemia specimens, we show that CRGs comprise genes previously undescribed in leukemia pathogenesis in which multiple pathways modulate the biology of LSCs. In addition, our findings demonstrate that the CRG expression profile can be used as a drug discovery tool for identification of compounds that selectively target the LSC population. We conclude that CRG-based analyses provide a powerful means to characterize the basic biology of LSCs as well as to identify improved methods for therapeutic targeting.
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Affiliation(s)
- John M Ashton
- James P. Wilmot Cancer Center, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
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Delvecchio VG, Connolly JP, Alefantis TG, Walz A, Quan MA, Patra G, Ashton JM, Whittington JT, Chafin RD, Liang X, Grewal P, Khan AS, Mujer CV. Proteomic profiling and identification of immunodominant spore antigens of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Appl Environ Microbiol 2006; 72:6355-63. [PMID: 16957262 PMCID: PMC1563598 DOI: 10.1128/aem.00455-06] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Differentially expressed and immunogenic spore proteins of the Bacillus cereus group of bacteria, which includes Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis, were identified. Comparative proteomic profiling of their spore proteins distinguished the three species from each other as well as the virulent from the avirulent strains. A total of 458 proteins encoded by 232 open reading frames were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analysis for all the species. A number of highly expressed proteins, including elongation factor Tu (EF-Tu), elongation factor G, 60-kDa chaperonin, enolase, pyruvate dehydrogenase complex, and others exist as charge variants on two-dimensional gels. These charge variants have similar masses but different isoelectric points. The majority of identified proteins have cellular roles associated with energy production, carbohydrate transport and metabolism, amino acid transport and metabolism, posttranslational modifications, and translation. Novel vaccine candidate proteins were identified using B. anthracis polyclonal antisera from humans postinfected with cutaneous anthrax. Fifteen immunoreactive proteins were identified in B. anthracis spores, whereas 7, 14, and 7 immunoreactive proteins were identified for B. cereus and in the virulent and avirulent strains of B. thuringiensis spores, respectively. Some of the immunodominant antigens include charge variants of EF-Tu, glyceraldehyde-3-phosphate dehydrogenase, dihydrolipoamide acetyltransferase, Delta-1-pyrroline-5-carboxylate dehydrogenase, and a dihydrolipoamide dehydrogenase. Alanine racemase and neutral protease were uniquely immunogenic to B. anthracis. Comparative analysis of the spore immunome will be of significance for further nucleic acid- and immuno-based detection systems as well as next-generation vaccine development.
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MESH Headings
- Antigens, Bacterial/genetics
- Antigens, Bacterial/isolation & purification
- Bacillus anthracis/chemistry
- Bacillus anthracis/genetics
- Bacillus anthracis/immunology
- Bacillus cereus/chemistry
- Bacillus cereus/genetics
- Bacillus cereus/immunology
- Bacillus thuringiensis/chemistry
- Bacillus thuringiensis/genetics
- Bacillus thuringiensis/immunology
- Bacterial Proteins/genetics
- Bacterial Proteins/immunology
- Bacterial Proteins/isolation & purification
- Electrophoresis, Gel, Two-Dimensional
- Genes, Bacterial
- Immunodominant Epitopes/genetics
- Immunodominant Epitopes/isolation & purification
- Open Reading Frames
- Proteomics
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Spores, Bacterial/chemistry
- Spores, Bacterial/genetics
- Spores, Bacterial/immunology
- Virulence/immunology
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38
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Ashton JM, Bolme P, Zerihun G. Protein binding of salicylic and salicyluric acid in serum from malnourished children: the influence of albumin, competitive binding and non-esterified fatty acids. J Pharm Pharmacol 1989; 41:474-80. [PMID: 2570853 DOI: 10.1111/j.2042-7158.1989.tb06503.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The serum protein binding of salicylic and salicyluric acid has been determined by ultrafiltration in 60 children after administration of oral salicylate. The children were classified according to nutritional status: well-nourished (n = 12), underweight (n = 12), marasmic (n = 17) marasmic-kwashiorkor (n = 7) and kwashiorkor (n = 12). Salicylic acid free fractions were 0.106 +/- 0.026, 0.114 +/- 0.069, 0.141 +/- 0.037, 0.285 +/- 0.279 and 0.438 +/- 0.190 in the five groups, respectively. Salicyluric acid free fractions were 0.184 +/- 0.057, 0.280 +/- 0.282, 0.236 +/- 0.114, 0.484 +/- 0.497 and 0.646 +/- 0.261, respectively. The degree of binding was dependent on serum albumin levels, ligand concentrations and non-esterified fatty acids (NEFA). The NEFA/albumin ratio ranged from 0.05 to 6.6. The fitting of a one-site Scatchard binding model to the collective data was improved when a decrease was allowed for in the number of binding sites in proportion to NEFA concentrations. Salicyluric acid binding could be fitted only when inhibition of the parent compound was included. Binding was not affected by age or sex. The major determinants of salicylate binding in sera from malnourished children have thus been identified.
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Affiliation(s)
- J M Ashton
- Dept. of Biopharmaceutics and Pharmacokinetics, Biomedical Centre, Uppsala University, Sweden
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Abstract
A survey was conducted by postal questionnaire among 1200 residents of metropolitan Adelaide, South Australia, to determine public opinion on various policies and procedures concerned with the selection of medical students. There were 712 respondents, reflecting closely the metropolitan population in age and sex distribution but having a significant bias toward higher status occupational groups. Responses were examined separately for three broad occupational groups and were found to be quite consistent across each group. A clear majority preference was indicated for selecting medical students not only from those completing secondary school but including others with different educational and occupational backgrounds, and for using a variety of selection procedures in addition to examination results.
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