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Hernandez R, Shi J, Liu J, Li X, Wu J, Zhao L, Zhou T, Chen Q, Zhou C. PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice. J Lipid Res 2023; 64:100352. [PMID: 36871792 PMCID: PMC10119612 DOI: 10.1016/j.jlr.2023.100352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/08/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Small noncoding RNAs (sncRNAs) play diverse roles in numerous biological processes. While the widely used RNA sequencing (RNA-Seq) method has advanced sncRNA discovery, RNA modifications can interfere with the complementary DNA library construction process, preventing the discovery of highly modified sncRNAs including transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) that may have important functions in disease development. To address this technical obstacle, we recently developed a novel PANDORA-Seq (Panoramic RNA Display by Overcoming RNA Modification Aborted Sequencing) method to overcome RNA modification-elicited sequence interferences. To identify novel sncRNAs associated with atherosclerosis development, LDL receptor-deficient (LDLR-/-) mice were fed a low-cholesterol diet or high-cholesterol diet (HCD) for 9 weeks. Total RNAs isolated from the intima were subjected to PANDORA-Seq and traditional RNA-Seq. By overcoming RNA modification-elicited limitations, PANDORA-Seq unveiled an rsRNA/tsRNA-enriched sncRNA landscape in the atherosclerotic intima of LDLR-/- mice, which was strikingly different from that detected by traditional RNA-Seq. While microRNAs were the dominant sncRNAs detected by traditional RNA-Seq, PANDORA-Seq substantially increased the reads of rsRNAs and tsRNAs. PANDORA-Seq also detected 1,383 differentially expressed sncRNAs induced by HCD feeding, including 1,160 rsRNAs and 195 tsRNAs. One of HCD-induced intimal tsRNAs, tsRNA-Arg-CCG, may contribute to atherosclerosis development by regulating the proatherogenic gene expression in endothelial cells. Overall, PANDORA-Seq revealed a hidden rsRNA and tsRNA population associated with atherosclerosis development. These understudied tsRNAs and rsRNAs, which are much more abundant than microRNAs in the atherosclerotic intima of LDLR-/- mice, warrant further investigations.
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Affiliation(s)
- Rebecca Hernandez
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Jingwei Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Xiuchun Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Jake Wu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA; Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
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Mohr AE, Reiss RA, Beaudet M, Sena J, Naik JS, Walker BR, Sweazea KL. Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study. PeerJ 2021; 9:e11714. [PMID: 34285833 PMCID: PMC8274493 DOI: 10.7717/peerj.11714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/11/2021] [Indexed: 11/20/2022] Open
Abstract
Background Diet-induced metabolic dysfunction precedes multiple disease states including diabetes, heart disease, and vascular dysfunction. The critical role of the vasculature in disease progression is established, yet the details of how gene expression changes in early cardiovascular disease remain an enigma. The objective of the current pilot project was to evaluate whether a quantitative assessment of gene expression within the aorta of six-week old healthy male Sprague-Dawley rats compared to those exhibiting symptoms of metabolic dysfunction could reveal potential mediators of vascular dysfunction. Methods RNA was extracted from the aorta of eight rats from a larger experiment; four animals fed a high-fat diet (HFD) known to induce symptoms of metabolic dysfunction (hypertension, increased adiposity, fasting hyperglycemia) and four age-matched healthy animals fed a standard chow diet (CHOW). The bioinformatic workflow included Gene Ontology (GO) biological process enrichment and network analyses. Results The resulting network contained genes relevant to physiological processes including fat and protein metabolism, oxygen transport, hormone regulation, vascular regulation, thermoregulation, and circadian rhythm. The majority of differentially regulated genes were downregulated, including several associated with circadian clock function. In contrast, leptin and 3-hydroxy-3-methylglutaryl-CoA synthase 2 (Hmgcs2) were notably upregulated. Leptin is involved in several major energy balance signaling pathways and Hmgcs2 is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis. Conclusion Together, these data describe changes in gene expression within the aortic wall of HFD rats with early metabolic dysfunction and highlight potential pathways and signaling intermediates that may impact the development of early vascular dysfunction.
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Affiliation(s)
- Alex E Mohr
- College of Health Solutions, Arizona State University, Phoenix, AZ, United States
| | - Rebecca A Reiss
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, United States
| | - Monique Beaudet
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, United States
| | - Johnny Sena
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Jay S Naik
- The Department of Cell Biology and Physiology, University of New Mexico, Albuquerque, NM, United States
| | - Benjimen R Walker
- The Department of Cell Biology and Physiology, University of New Mexico, Albuquerque, NM, United States
| | - Karen L Sweazea
- College of Health Solutions & School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Xie H, Zhang JF, Li Q. Identification and analysis of genes associated with lung adenocarcinoma by integrated bioinformatics methods. Ann Hum Genet 2021; 85:125-137. [PMID: 33847374 DOI: 10.1111/ahg.12418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/14/2021] [Accepted: 03/08/2021] [Indexed: 01/21/2023]
Abstract
Lung adenocarcinoma (LUAD) is one of the most common forms of lung cancer, with a very high mortality rate. Although the treatments available for LUAD have become more effective in recent years, significant improvement is still needed. Advances in sequencing technologies and bioinformatics analysis have enabled new approaches to be developed for identifying drug targets. In this work we utilized data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to identify hub genes related to LUAD through Weighted Gene Correlation Network Analysis (WGCNA) and other bioinformatics methods, with the goal of identifying new drug targets for cancer treatment.
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Affiliation(s)
- Hui Xie
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, P. R. China.,Key Laboratory of Medical Imaging and Artifical Intelligence of Hunan Province, Chenzhou, 423000, P. R. China
| | - Jian-Fang Zhang
- Department of Physical examination, Beihu Centers for Disease Control and Prevention, Chenzhou, 423000, P. R. China
| | - Qing Li
- Key Laboratory of Medical Imaging and Artifical Intelligence of Hunan Province, Chenzhou, 423000, P. R. China.,Department of Interventional vascular surgery, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, P. R. China
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Busnelli M, Manzini S, Chiara M, Colombo A, Fontana F, Oleari R, Potì F, Horner D, Bellosta S, Chiesa G. Aortic Gene Expression Profiles Show How ApoA-I Levels Modulate Inflammation, Lysosomal Activity, and Sphingolipid Metabolism in Murine Atherosclerosis. Arterioscler Thromb Vasc Biol 2021; 41:651-667. [PMID: 33327742 PMCID: PMC7837693 DOI: 10.1161/atvbaha.120.315669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 12/01/2020] [Indexed: 01/16/2023]
Abstract
OBJECTIVE HDL (high-density lipoprotein) particles are known to possess several antiatherogenic properties that include the removal of excess cholesterol from peripheral tissues, the maintenance of endothelial integrity, antioxidant, and anti-inflammatory activities. ApoA-I overexpression in apoE-deficient (EKO) mice has been shown to increase HDL levels and to strongly reduce atherosclerosis development. The aim of the study was to investigate gene expression patterns associated with atherosclerosis development in the aorta of EKO mice and how HDL plasma levels relate to gene expression patterns at different stages of atherosclerosis development and with different dietary treatments. Approach and Results: Eight-week-old EKO mice, EKO mice overexpressing human apoA-I, and wild-type mice as controls were fed either normal laboratory or Western diet for 6 or 22 weeks. Cholesterol distribution among lipoproteins was evaluated, and atherosclerosis of the aorta was quantified. High-throughput sequencing technologies were used to analyze the transcriptome of the aorta of the 3 genotypes in each experimental condition. In addition to the well-known activation of inflammation and immune response, the impairment of sphingolipid metabolism, phagosome-lysosome system, and osteoclast differentiation emerged as relevant players in atherosclerosis development. The reduced atherosclerotic burden in the aorta of EKO mice expressing high levels of apoA-I was accompanied by a reduced activation of immune system markers, as well as reduced perturbation of lysosomal activity and a better regulation of the sphingolipid synthesis pathway. CONCLUSIONS ApoA-I modulates atherosclerosis development in the aorta of EKO mice affecting the expression of pathways additional to those associated with inflammation and immune response.
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Affiliation(s)
- Marco Busnelli
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Stefano Manzini
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Matteo Chiara
- Department of Biosciences (M.C., D.H.), Università degli Studi di Milano, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy (M.C., D.H.)
| | - Alice Colombo
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Fabrizio Fontana
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Francesco Potì
- Department of Medicine and Surgery—Unit of Neurosciences, University of Parma, Italy (F.P.)
| | - David Horner
- Department of Biosciences (M.C., D.H.), Università degli Studi di Milano, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy (M.C., D.H.)
| | - Stefano Bellosta
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
| | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences (M.B., S.M., A.C., F.F., R.O., S.B., G.C.), Università degli Studi di Milano, Italy
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Schanstra JP, Luong TT, Makridakis M, Van Linthout S, Lygirou V, Latosinska A, Alesutan I, Boehme B, Schelski N, Von Lewinski D, Mullen W, Nicklin S, Delles C, Feuillet G, Denis C, Lang F, Pieske B, Bascands JL, Mischak H, Saulnier-Blache JS, Voelkl J, Vlahou A, Klein J. Systems biology identifies cytosolic PLA2 as a target in vascular calcification treatment. JCI Insight 2019; 4:125638. [PMID: 31092728 DOI: 10.1172/jci.insight.125638] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/17/2019] [Indexed: 01/15/2023] Open
Abstract
Although cardiovascular disease (CVD) is the leading cause of morbimortality worldwide, promising new drug candidates are lacking. We compared the arterial high-resolution proteome of patients with advanced versus early-stage CVD to predict, from a library of small bioactive molecules, drug candidates able to reverse this disease signature. Of the approximately 4000 identified proteins, 100 proteins were upregulated and 52 were downregulated in advanced-stage CVD. Arachidonyl trifluoromethyl ketone (AACOCF3), a cytosolic phospholipase A2 (cPLA2) inhibitor was predicted as the top drug able to reverse the advanced-stage CVD signature. Vascular cPLA2 expression was increased in patients with advanced-stage CVD. Treatment with AACOCF3 significantly reduced vascular calcification in a cholecalciferol-overload mouse model and inhibited osteoinductive signaling in vivo and in vitro in human aortic smooth muscle cells. In conclusion, using a systems biology approach, we have identified a potentially new compound that prevented typical vascular calcification in CVD in vivo. Apart from the clear effect of this approach in CVD, such strategy should also be able to generate novel drug candidates in other complex diseases.
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Affiliation(s)
- Joost P Schanstra
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Trang Td Luong
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Manousos Makridakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Sophie Van Linthout
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Vasiliki Lygirou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Ioana Alesutan
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Institute for Physiology and Pathophysiology, Johannes Kepler University Linz, Linz, Austria
| | - Beate Boehme
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Nadeshda Schelski
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Stuart Nicklin
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Guylène Feuillet
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Colette Denis
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Florian Lang
- Department of Physiology I, University of Tubingen, Tubingen, Germany
| | - Burkert Pieske
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Jean-Loup Bascands
- INSERM, U1188, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | | | - Jean-Sebastien Saulnier-Blache
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jakob Voelkl
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany.,Institute for Physiology and Pathophysiology, Johannes Kepler University Linz, Linz, Austria
| | - Antonia Vlahou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Julie Klein
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
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