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Romero G, González S, Royero W, González A. Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean. Genet Mol Biol 2024; 47:e20220263. [PMID: 38593425 PMCID: PMC11003654 DOI: 10.1590/1678-4685-gmb-2022-0263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development.
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Affiliation(s)
- German Romero
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
| | - Sandra González
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Wendy Royero
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Adriana González
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
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Xu Z, Lee MC, Sheehan K, Fujii K, Rabl K, Rader G, Varney S, Sharma M, Eilers H, Kober K, Miaskowski C, Levine JD, Schumacher MA. Chemotherapy for pain: reversing inflammatory and neuropathic pain with the anticancer agent mithramycin A. Pain 2024; 165:54-74. [PMID: 37366593 PMCID: PMC10723648 DOI: 10.1097/j.pain.0000000000002972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/08/2023] [Accepted: 04/25/2023] [Indexed: 06/28/2023]
Abstract
ABSTRACT The persistence of inflammatory and neuropathic pain is poorly understood. We investigated a novel therapeutic paradigm by targeting gene networks that sustain or reverse persistent pain states. Our prior observations found that Sp1-like transcription factors drive the expression of TRPV1, a pain receptor, that is blocked in vitro by mithramycin A (MTM), an inhibitor of Sp1-like factors. Here, we investigate the ability of MTM to reverse in vivo models of inflammatory and chemotherapy-induced peripheral neuropathy (CIPN) pain and explore MTM's underlying mechanisms. Mithramycin reversed inflammatory heat hyperalgesia induced by complete Freund adjuvant and cisplatin-induced heat and mechanical hypersensitivity. In addition, MTM reversed both short-term and long-term (1 month) oxaliplatin-induced mechanical and cold hypersensitivity, without the rescue of intraepidermal nerve fiber loss. Mithramycin reversed oxaliplatin-induced cold hypersensitivity and oxaliplatin-induced TRPM8 overexpression in dorsal root ganglion (DRG). Evidence across multiple transcriptomic profiling approaches suggest that MTM reverses inflammatory and neuropathic pain through broad transcriptional and alternative splicing regulatory actions. Mithramycin-dependent changes in gene expression following oxaliplatin treatment were largely opposite to and rarely overlapped with changes in gene expression induced by oxaliplatin alone. Notably, RNAseq analysis revealed MTM rescue of oxaliplatin-induced dysregulation of mitochondrial electron transport chain genes that correlated with in vivo reversal of excess reactive oxygen species in DRG neurons. This finding suggests that the mechanism(s) driving persistent pain states such as CIPN are not fixed but are sustained by ongoing modifiable transcription-dependent processes.
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Affiliation(s)
- Zheyun Xu
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Man-Cheung Lee
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Kayla Sheehan
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Keisuke Fujii
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Anesthesiology, Wakayama Medical University, Wakayama, Japan
| | - Katalin Rabl
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Gabriella Rader
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Scarlett Varney
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Manohar Sharma
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Helge Eilers
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
| | - Kord Kober
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA, United States
| | - Christine Miaskowski
- Department of Physiological Nursing, School of Nursing, University of California, San Francisco, CA, United States
| | - Jon D. Levine
- Division of Neuroscience, Departments of Medicine and Oral and Maxillofacial Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Mark A. Schumacher
- Department of Anesthesia and Perioperative Care and the UCSF Pain and Addiction Research Center, University of California, San Francisco, San Francisco, CA, United States
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Resnick JD, Beer MA, Pekosz A. Early transcriptional responses of human nasal epithelial cells to infection with Influenza A and SARS-CoV-2 virus differ and are influenced by physiological temperature. bioRxiv 2023:2023.03.07.531609. [PMID: 36945583 PMCID: PMC10028862 DOI: 10.1101/2023.03.07.531609] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Influenza A (IAV) and SARS-CoV-2 (SCV2) viruses represent an ongoing threat to public health. Both viruses target the respiratory tract, which consists of a gradient of cell types, receptor expression, and temperature. Environmental temperature has been an un-derstudied contributor to infection susceptibility and understanding its impact on host responses to infection could help uncover new insights into severe disease risk factors. As the nasal passageways are the initial site of respiratory virus infection, in this study we investigated the effect of temperature on host responses in human nasal epithelial cells (hNECs) utilizing IAV and SCV2 in vitro infection models. We demonstrate that temperature affects SCV2, but not IAV, viral replicative fitness and that SCV2 infected cultures are slower to mount an infection-induced response, likely due to suppression by the virus. Additionally, we show that that temperature not only changes the basal transcriptomic landscape of epithelial cells, but that it also impacts the response to infection. The induction of interferon and other innate immune responses were not drastically affected by temperature, suggesting that while the baseline antiviral response at different temperatures remains consistent, there may be metabolic or signaling changes that affect how well the cultures are able to adapt to new pressures such as infection. Finally, we show that hNECs respond differently to IAV and SCV2 infection in ways that give insight into how the virus is able to manipulate the cell to allow for replication and release. Taken together, these data give new insight into the innate immune response to respiratory infections and can assist in identifying new treatment strategies for respiratory infections.
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Affiliation(s)
- Jessica D Resnick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- McKusick- Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Beer
- McKusick- Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Jetti SK, Crane AB, Akbergenova Y, Aponte-Santiago NA, Cunningham KL, Whittaker CA, Littleton JT. Molecular Logic of Synaptic Diversity Between Drosophila Tonic and Phasic Motoneurons. bioRxiv 2023:2023.01.17.524447. [PMID: 36711745 PMCID: PMC9882338 DOI: 10.1101/2023.01.17.524447] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although neuronal subtypes display unique synaptic organization and function, the underlying transcriptional differences that establish these features is poorly understood. To identify molecular pathways that contribute to synaptic diversity, single neuron PatchSeq RNA profiling was performed on Drosophila tonic and phasic glutamatergic motoneurons. Tonic motoneurons form weaker facilitating synapses onto single muscles, while phasic motoneurons form stronger depressing synapses onto multiple muscles. Super-resolution microscopy and in vivo imaging demonstrated synaptic active zones in phasic motoneurons are more compact and display enhanced Ca 2+ influx compared to their tonic counterparts. Genetic analysis identified unique synaptic properties that mapped onto gene expression differences for several cellular pathways, including distinct signaling ligands, post-translational modifications and intracellular Ca 2+ buffers. These findings provide insights into how unique transcriptomes drive functional and morphological differences between neuronal subtypes.
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Affiliation(s)
- Suresh K Jetti
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Andrés B Crane
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Yulia Akbergenova
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Nicole A Aponte-Santiago
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Karen L Cunningham
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Charles A Whittaker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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Rajagopala SV, Strickland BA, Pakala SB, Kimura KS, Shilts MH, Rosas-Salazar C, Brown HM, Freeman MH, Wessinger BC, Gupta V, Phillips E, Mallal SA, Turner JH, Das SR. Mucosal gene expression in response to SARS-CoV-2 is associated with early viral load. bioRxiv 2022:2022.08.23.504908. [PMID: 36052371 PMCID: PMC9435401 DOI: 10.1101/2022.08.23.504908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Little is known about the relationships between symptomatic early-time SARS-CoV-2 viral load and upper airway mucosal gene expression and immune response. To examine the association of symptomatic SARS-CoV-2 early viral load with upper airway mucosal gene expression, we profiled the host mucosal transcriptome from nasopharyngeal swab samples from 68 adults with symptomatic, mild-to-moderate COVID-19. We measured SARS-CoV-2 viral load using qRT-PCR. We then examined the association of SARS-CoV-2 viral load with upper airway mucosal immune response. We detected SARS-CoV-2 in all samples and recovered >80% of the genome from 85% of the samples from symptomatic COVID-19 adults. The respiratory virome was dominated by SARS-CoV-2, with limited co-detection of common respiratory viruses i.e., only the human Rhinovirus (HRV) being identified in 6% of the samples. We observed a significant positive correlation between SARS-CoV-2 viral load and interferon signaling (OAS2, OAS3, IFIT1, UPS18, ISG15, ISG20, IFITM1, and OASL), chemokine signaling (CXCL10 and CXCL11), and adaptive immune system (IFITM1, CD300E, and SIGLEC1) genes in symptomatic, mild-to-moderate COVID-19 adults, when adjusted for age, sex and race. Interestingly, the expression levels of most of these genes plateaued at a CT value of ~25. Overall, our data shows that early nasal mucosal immune response to SARS-CoV-2 infection is viral load dependent, which potentially could modify COVID-19 outcomes. AUTHOR SUMMARY Several prior studies have shown that SARS-CoV-2 viral load can predict the likelihood of disease spread and severity. A higher detectable SARS-CoV-2 plasma viral load was associated with worse respiratory disease severity. However, the relationship between SARS-CoV-2 viral load and airway mucosal gene expression and immune response remains elusive. We profiled the nasal mucosal transcriptome from nasal samples collected from adults infected with SARS-CoV-2 during Spring 2020 with mild-to-moderate symptoms using a comprehensive metatranscriptomics method. We observed a positive correlation between SARS-CoV-2 viral load with interferon signaling, chemokine signaling, and adaptive immune system in adults with COVID-19. Our data suggest that early nasal mucosal immune response to SARS-CoV-2 infection was viral load-dependent and may modify COVID-19 outcomes.
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Affiliation(s)
| | - Britton A. Strickland
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman B. Pakala
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Kyle S. Kimura
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
| | - Meghan H. Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | | | - Hunter M. Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Michael H. Freeman
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
| | | | - Veerain Gupta
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Simon A. Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Justin H. Turner
- Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman R. Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
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Casu A, Grippo PJ, Wasserfall C, Sun Z, Linsley PS, Hamerman JA, Fife BT, Lacy-Hulbert A, Toledo FGS, Hart PA, Papachristou GI, Bellin MD, Yadav D, Laughlin MR, Goodarzi MO, Speake C. Evaluating the Immunopathogenesis of Diabetes After Acute Pancreatitis in the Diabetes RElated to Acute Pancreatitis and Its Mechanisms Study: From the Type 1 Diabetes in Acute Pancreatitis Consortium. Pancreas 2022; 51:580-585. [PMID: 36206462 PMCID: PMC9555855 DOI: 10.1097/mpa.0000000000002076] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
ABSTRACT The association between acute pancreatitis (AP) and diabetes mellitus (DM) has long been established, with the initial descriptions of AP patients presenting with DM after a bout of AP published in the 1940s and 50s. However, the potential mechanisms involved, particularly those components related to the immune system, have not been well defined. The Diabetes RElated to Acute pancreatitis and its Mechanisms (DREAM) study is a multicenter clinical study designed to understand the frequency and phenotype of DM developing after AP. This article describes one objective of the DREAM study: to determine the immunologic mechanisms of DM after AP, including the contribution of β-cell autoimmunity. This component of the study will assess the presence of islet autoimmunity, as well as the magnitude and kinetics of the innate and adaptive immune response at enrollment and during longitudinal follow-up after 1 or more episodes of AP. Finally, DREAM will evaluate the relationship between immune features, DM development, and pancreatitis etiology and severity.
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Affiliation(s)
- Anna Casu
- From the Translational Research Institute, AdventHealth Orlando, Orlando, FL
| | - Paul J Grippo
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois-Chicago, Chicago, IL
| | - Clive Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL
| | - Zhaoli Sun
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Peter S Linsley
- Center for Systems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Jessica A Hamerman
- Center for Fundamental Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Brian T Fife
- Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Adam Lacy-Hulbert
- Center for Fundamental Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Frederico G S Toledo
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Phil A Hart
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Georgios I Papachristou
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | | | - Dhiraj Yadav
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Maren R Laughlin
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Cate Speake
- Diabetes Clinical Research Program, Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA
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Higazy D, Lin X, Xie T, Wang K, Gao X, Cui M. Altered gene expression in human brain microvascular endothelial cells in response to the infection of influenza H1N1 virus. Animal Diseases 2022; 2:25. [PMID: 36345345 PMCID: PMC9631584 DOI: 10.1186/s44149-022-00053-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/08/2022] [Indexed: 11/06/2022] Open
Abstract
Influenza viruses not only cause respiratory illness, but also have been reported to elicit neurological manifestations following acute viral infection. The central nervous system (CNS) has a specific defense mechanism against pathogens structured by cerebral microvasculature lined with brain endothelial cells to form the blood–brain barrier (BBB). To investigate the response of human brain microvascular endothelial cells (hBMECs) to the Influenza A virus (IAV), we inoculated the cells with the A/WSN/33 (H1N1) virus. We then conducted an RNAseq experiment to determine the changes in gene expression levels and the activated disease pathways following infection. The analysis revealed an effective activation of the innate immune defense by inducing the pattern recognition receptors (PRRs). Along with the production of proinflammatory cytokines, we detected an upregulation of interferons and interferon-stimulated genes, such as IFN-β/λ, ISG15, CXCL11, CXCL3 and IL-6, etc. Moreover, infected hBMECs exhibited a disruption in the cytoskeletal structure both on the transcriptomic and cytological levels. The RNAseq analysis showed different pathways and candidate genes associated with the neuroactive ligand-receptor interaction, neuroinflammation, and neurodegenerative diseases, together with a predicted activation of the neuroglia. Likewise, some genes linked with the mitochondrial structure and function displayed a significantly altered expression. En masse, this data supports that hBMECs could be infected by the IAV, which induces the innate and inflammatory immune response. The results suggest that the influenza virus infection could potentially induce a subsequent aggravation of neurological disorders.
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Affiliation(s)
- Doaa Higazy
- grid.7776.10000 0004 0639 9286Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613 Egypt ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.424020.00000 0004 0369 1054International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St. Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xianwu Lin
- grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.424020.00000 0004 0369 1054International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St. Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Tanghui Xie
- grid.35155.370000 0004 1790 4137College of Informatics, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Ke Wang
- grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.424020.00000 0004 0369 1054International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St. Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xiaochen Gao
- grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.424020.00000 0004 0369 1054International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St. Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Min Cui
- grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.424020.00000 0004 0369 1054International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St. Huazhong Agricultural University, Wuhan, 430070 Hubei China
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8
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Piffer AC, Santos FMD, Thomé MP, Diehl C, Garcia AWA, Kinskovski UP, Schneider RDO, Gerber A, Feltes BC, Schrank A, Vasconcelos ATR, Lenz G, Kmetzsch L, Vainstein MH, Staats CC. Transcriptomic analysis reveals that mTOR pathway can be modulated in macrophage cells by the presence of cryptococcal cells. Genet Mol Biol 2021; 44:e20200390. [PMID: 34352067 PMCID: PMC8341293 DOI: 10.1590/1678-4685-gmb-2020-0390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/05/2021] [Indexed: 11/21/2022] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are the etiological agents of cryptococcosis, a high mortality disease. The development of such disease depends on the interaction of fungal cells with macrophages, in which they can reside and replicate. In order to dissect the molecular mechanisms by which cryptococcal cells modulate the activity of macrophages, a genome-scale comparative analysis of transcriptional changes in macrophages exposed to Cryptococcus spp. was conducted. Altered expression of nearly 40 genes was detected in macrophages exposed to cryptococcal cells. The major processes were associated with the mTOR pathway, whose associated genes exhibited decreased expression in macrophages incubated with cryptococcal cells. Phosphorylation of p70S6K and GSK-3β was also decreased in macrophages incubated with fungal cells. In this way, Cryptococci presence could drive the modulation of mTOR pathway in macrophages possibly to increase the survival of the pathogen.
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Affiliation(s)
- Alícia C Piffer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Francine M Dos Santos
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Marcos P Thomé
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Camila Diehl
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Ane Wichine Acosta Garcia
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Uriel Perin Kinskovski
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Rafael de Oliveira Schneider
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Alexandra Gerber
- Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil
| | - Bruno César Feltes
- Universidade Federal do Rio Grande do Sul, Instituto de Informática, Porto Alegre, RS, Brazil
| | - Augusto Schrank
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | | | - Guido Lenz
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Lívia Kmetzsch
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Marilene H Vainstein
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Charley C Staats
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Porto Alegre, RS, Brazil
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9
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Wang Y, Guo R, Chen B, Rahman T, Cai L, Li Y, Dong Y, Tseng GC, Fang J, Seney ML, Huang YH. Cocaine-induced neural adaptations in the lateral hypothalamic melanin-concentrating hormone neurons and the role in regulating rapid eye movement sleep after withdrawal. Mol Psychiatry 2021; 26:3152-68. [PMID: 33093653 DOI: 10.1038/s41380-020-00921-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022]
Abstract
Sleep abnormalities are often a prominent contributor to withdrawal symptoms following chronic drug use. Notably, rapid eye movement (REM) sleep regulates emotional memory, and persistent REM sleep impairment after cocaine withdrawal negatively impacts relapse-like behaviors in rats. However, it is not understood how cocaine experience may alter REM sleep regulatory machinery, and what may serve to improve REM sleep after withdrawal. Here, we focus on the melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus (LH), which regulate REM sleep initiation and maintenance. Using adult male Sprague-Dawley rats trained to self-administer intravenous cocaine, we did transcriptome profiling of LH MCH neurons after long-term withdrawal using RNA-sequencing, and performed functional assessment using slice electrophysiology. We found that 3 weeks after withdrawal from cocaine, LH MCH neurons exhibit a wide range of gene expression changes tapping into cell membrane signaling, intracellular signaling, and transcriptional regulations. Functionally, they show reduced membrane excitability and decreased glutamatergic receptor activity, consistent with increased expression of voltage-gated potassium channel gene Kcna1 and decreased expression of metabotropic glutamate receptor gene Grm5. Finally, chemogenetic or optogenetic stimulations of LH MCH neural activity increase REM sleep after long-term withdrawal with important differences. Whereas chemogenetic stimulation promotes both wakefulness and REM sleep, optogenetic stimulation of these neurons in sleep selectively promotes REM sleep. In summary, cocaine exposure persistently alters gene expression profiles and electrophysiological properties of LH MCH neurons. Counteracting cocaine-induced hypoactivity of these neurons selectively in sleep enhances REM sleep quality and quantity after long-term withdrawal.
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10
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Hwang JW, Jang SK, Lee DJ. Genomic analysis of pancreatic cancer reveals 3 molecular subtypes with different clinical outcomes. Medicine (Baltimore) 2021; 100:e24969. [PMID: 33832071 PMCID: PMC8036077 DOI: 10.1097/md.0000000000024969] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT Pancreatic cancer has a very high mortality with a 5-year survival of <5%. The purpose of this study was to classify specific molecular subtypes associated with prognosis of pancreatic cancer using The Cancer Genome Atlas (TCGA) multiplatform genomic data.Multiplatform genomic data (N = 178), including gene expression, copy number alteration, and somatic mutation data, were obtained from cancer browser (https://genome-cancer.ucsc.edu, cohort: TCGA Pancreatic Cancer). Clinical data including survival results were analyzed. We also used validation cohort (GSE50827) to confirm the robustness of these molecular subtypes in pancreatic cancer.When we performed unsupervised clustering using TCGA gene expression data, we found three distinct molecular subtypes associated with different survival results. Copy number alteration and somatic mutation data showed different genomic patterns for these three subtypes. Ingenuity pathway analysis revealed that each subtype showed differentially altered pathways. Using each subtype-specific genes (200 were selected), we could predict molecular subtype in another cohort, confirming the robustness of these molecular subtypes of pancreatic cancer. Cox regression analysis revealed that molecular subtype is the only significant prognostic factor for pancreatic cancer (P = .042, 95% confidence interval 0.523-0.98).Genomic analysis of pancreatic cancer revealed 3 distinct molecular subtypes associated with different survival results. Using these subtype-specific genes and prediction model, we could predict molecular subtype associated with prognosis of pancreatic cancer.
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Affiliation(s)
- Ji Woong Hwang
- Department of Surgery, Kangnam Sacred Heart Hospital, Hallym University College of Medicine
| | - Soo Kyung Jang
- Department of Otolaryngology-Head and Neck Surgery, Division of Precision Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Dong Jin Lee
- Department of Otolaryngology-Head and Neck Surgery, Division of Precision Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
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11
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Maniatis S, Petrescu J, Phatnani H. Spatially resolved transcriptomics and its applications in cancer. Curr Opin Genet Dev 2021; 66:70-77. [PMID: 33434721 PMCID: PMC7969406 DOI: 10.1016/j.gde.2020.12.002] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023]
Abstract
Spatially resolved transcriptomics (SRT) offers the promise of understanding cells and their modes of dysfunction in the context of intact tissues. Technologies for SRT have advanced rapidly with a large number being published in recent years. Diverse methods for SRT produce data at widely varying depth, throughput, accessibility and cost. Many published SRT methods have been demonstrated only in their labs of origin, while others have matured to the point of commercialization and widespread availability. Here we review technologies for SRT, and their application in studies of tumor heterogeneity.
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Affiliation(s)
- Silas Maniatis
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Joana Petrescu
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA; Department of Neurology, Division of Neuromuscular Medicine, Columbia University, New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA; Department of Neurology, Division of Neuromuscular Medicine, Columbia University, New York, NY, USA.
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12
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Yasin H, Stowe R, Wong CK, Jithesh PV, Zahir FR. First Whole Transcriptome RNAseq on CHD8 Haploinsufficient Patient and Meta-Analyses Across Cellular Models Uncovers Likely Key Pathophysiological Target Genes. Cureus 2020; 12:e11571. [PMID: 33282601 PMCID: PMC7710346 DOI: 10.7759/cureus.11571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In 2019, we confirmed that the haploinsufficiency of CHD8 does indeed cause the novel syndromic neurodevelopmental disease we first discovered a dozen years before. Here, we report the first whole transcriptome RNAseq gene expression profiling for a patient with this new syndrome, as a preliminary exploration of potential pathophysiological mechanisms. We compared our patient transcriptome profile with that of all publicly available RNAseq datasets from human cellular models including neuronal progenitor cells, neurons and organoids. We compared differential gene expression profiles overall and conducted phenotype-informed data filtration based on the characteristic syndrome presentation. We found that concordance among differential gene expression profiles was poor across all datasets. Nevertheless, remarkably, we show that the patient blood differential gene expression profile most resembled that of the neuronal cell model, a finding that encourages further transcriptome profiling using patient blood samples. In addition, our custom phenotype-informed analyses yielded important, differentially expressed syndrome pathophysiology target genes. Finally, we note that genes dysregulated due to CHD8 heterozygous deletion are linked to known neurological as well as oncological pathways.
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Affiliation(s)
- Heba Yasin
- Life Science, Hamad Bin Khalifa University, Doha, QAT
| | - Robert Stowe
- Psychiatry and Neurology, University of British Columbia, Vancouver, CAN
| | - Chi Kin Wong
- Medical Genetics, University of British Columbia, Vancouver, CAN
| | | | - Farah R Zahir
- Medical Genetics, University of British Columbia, Vancouver, CAN
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13
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Zhang Z, Schlamp F, Huang L, Clark H, Brayboy L. Inflammaging is associated with shifted macrophage ontogeny and polarization in the aging mouse ovary. Reproduction 2020; 159:325-337. [PMID: 31940276 PMCID: PMC7066623 DOI: 10.1530/rep-19-0330] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [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] [Received: 07/30/2019] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
The fertility of women declines sharply after age 35 and is essentially lost upon menopause at age 51. The ovary plays an important part in aging-associated changes in women's physiology since it is an essential component of both the reproductive and endocrine systems. Several previous studies in mice have shown that the ovarian tissue goes through drastic changes over the course of aging and exhibits signs of aging-associated chronic inflammation (inflammaging), which may contribute to the marked decline of oocyte quality in aged individuals. To further examine aging-associated gene expression changes in the ovary and to characterize the development of inflammaging, we performed detailed transcriptomic analysis of whole ovaries from mice of six different age groups over the mouse reproductive lifespan and identified more than 5000 genes with significant expression change over the course of aging. Intriguingly, we found aging-associated changes in the expression of several markers that indicate alterations in the composition of ovarian macrophages, which are known to be central players of inflammaging. Using flow cytometry, we analyzed and compared macrophage populations and polarization in young and old ovaries and found a significant increase in monocyte recruitment and macrophage alternative activation (M2) in the old ovaries compared to those in young. Our results are consistent with previous findings of aging-associated increase of fibrosis in the ovarian stromal extracellular matrix, and they provide new clues about the development of inflammaging in the mammalian ovary.
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Affiliation(s)
- Zijing Zhang
- Department of Obstetrics and Gynecology, Division of Research, Women & Infants Hospital of Rhode Island, 101 Dudley Street, Providence, RI 02905, USA
| | - Florencia Schlamp
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Lu Huang
- Department of Microbiology and immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Haley Clark
- Department of Obstetrics and Gynecology, Division of Research, Women & Infants Hospital of Rhode Island, 101 Dudley Street, Providence, RI 02905, USA
| | - Lynae Brayboy
- Department of Obstetrics and Gynecology, Division of Research, Women & Infants Hospital of Rhode Island, 101 Dudley Street, Providence, RI 02905, USA
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Women & Infants Hospital of Rhode Island, 101 Dudley Street, Providence, RI 02905, USA
- Alpert Medical School of Brown University, 222 Richmond Street Providence, RI 02903, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University 185 Meeting Street, Providence, RI 02912, USA
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14
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Winer BY, Gaska JM, Lipkowitz G, Bram Y, Parekh A, Parsons L, Leach R, Jindal R, Cho CH, Shrirao A, Novik E, Schwartz RE, Ploss A. Analysis of Host Responses to Hepatitis B and Delta Viral Infections in a Micro-scalable Hepatic Co-culture System. Hepatology 2020; 71:14-30. [PMID: 31206195 PMCID: PMC6917996 DOI: 10.1002/hep.30815] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/05/2019] [Indexed: 12/30/2022]
Abstract
Hepatitis B virus (HBV) remains a major global health problem with 257 million chronically infected individuals worldwide, of whom approximately 20 million are co-infected with hepatitis delta virus (HDV). Progress toward a better understanding of the complex interplay between these two viruses and the development of novel therapies have been hampered by the scarcity of suitable cell culture models that mimic the natural environment of the liver. Here, we established HBV and HBV/HDV co-infections and super-infections in self-assembling co-cultured primary human hepatocytes (SACC-PHHs) for up to 28 days in a 384-well format and highlight the suitability of this platform for high-throughput drug testing. We performed RNA sequencing at days 8 and 28 on SACC-PHHs, either HBV mono-infected or HBV/HDV co-infected. Our transcriptomic analysis demonstrates that hepatocytes in SACC-PHHs maintain a mature hepatic phenotype over time, regardless of infection condition. We confirm that HBV is a stealth virus, as it does not induce a strong innate immune response; rather, oxidative phosphorylation and extracellular matrix-receptor interactions are dysregulated to create an environment that promotes persistence. Notably, HDV co-infection also did not lead to statistically significant transcriptional changes across multiple donors and replicates. The lack of innate immune activation is not due to SACC-PHHs being impaired in their ability to induce interferon stimulated genes (ISGs). Rather, polyinosinic:polycytidylic acid exposure activates ISGs, and this stimulation significantly inhibits HBV infection, yet only minimally affects the ability of HDV to infect and persist. Conclusion: These data demonstrate that the SACC-PHH system is a versatile platform for studying HBV/HDV co-infections and holds promise for performing chemical library screens and improving our understanding of the host response to such infections.
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Affiliation(s)
- Benjamin Y. Winer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jenna M. Gaska
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gabriel Lipkowitz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yaron Bram
- Division of Gastroenterology & Hepatology, Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Amit Parekh
- Hurel® Corporation, North Brunswick, NJ 08902, USA
| | - Lance Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Robert Leach
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rohit Jindal
- Hurel® Corporation, North Brunswick, NJ 08902, USA
| | - Cheul H. Cho
- Hurel® Corporation, North Brunswick, NJ 08902, USA
| | - Anil Shrirao
- Hurel® Corporation, North Brunswick, NJ 08902, USA
| | - Eric Novik
- Hurel® Corporation, North Brunswick, NJ 08902, USA
| | - Robert E. Schwartz
- Division of Gastroenterology & Hepatology, Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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15
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Kompa B, Coker B. Learning a Latent Space of Highly Multidimensional Cancer Data. Pac Symp Biocomput 2020; 25:379-390. [PMID: 31797612 PMCID: PMC6934353] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We introduce a Unified Disentanglement Network (UFDN) trained on The Cancer Genome Atlas (TCGA), which we refer to as UFDN-TCGA. We demonstrate that UFDN-TCGA learns a biologically relevant, low-dimensional latent space of high-dimensional gene expression data by applying our network to two classification tasks of cancer status and cancer type. UFDN-TCGA performs comparably to random forest methods. The UFDN allows for continuous, partial interpolation between distinct cancer types. Furthermore, we perform an analysis of differentially expressed genes between skin cutaneous melanoma (SKCM) samples and the same samples interpolated into glioblastoma (GBM). We demonstrate that our interpolations consist of relevant metagenes that recapitulate known glioblastoma mechanisms.
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Affiliation(s)
- Benjamin Kompa
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA,
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16
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Bushnell GG, Hardas TP, Hartfield RM, Zhang Y, Oakes RS, Ronquist S, Chen H, Rajapakse I, Wicha MS, Jeruss JS, Shea LD. Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor Cells In Vivo. Cancer Res 2019; 79:2042-2053. [PMID: 30808673 PMCID: PMC6467791 DOI: 10.1158/0008-5472.can-18-2502] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/21/2018] [Accepted: 02/18/2019] [Indexed: 12/28/2022]
Abstract
For most cancers, metastasis is the point at which clinical treatment shifts from curative intent to extending survival. Biomaterial implants acting as a synthetic premetastatic niche recruit metastatic cancer cells and provide a survival advantage, and their use as a diagnostic platform requires assessing their relevance to disease progression. Here, we showed that scaffold-captured tumor cells (SCAF) were 30 times more metastatic to the lung than primary tumor (PT) cells, similar to cells derived from lung micrometastases (LUNG). SCAF cells were more aggressive in vitro, demonstrated higher levels of migration, invasion, and mammosphere formation, and had a greater proportion of cancer stem cells than PT. SCAF cells were highly enriched for gene expression signatures associated with metastasis and had associated genomic structural changes, including globally enhanced entropy. Collectively, our findings demonstrate that SCAF cells are distinct from PT and more closely resemble LUNG, indicating that tumor cells retrieved from scaffolds are reflective of cells at metastatic sites. SIGNIFICANCE: These findings suggest that metastatic tumor cells captured by a biomaterial scaffold may serve as a diagnostic for molecular staging of metastasis.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/8/2042/F1.large.jpg.
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Affiliation(s)
- Grace G Bushnell
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Tejaswini P Hardas
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Rachel M Hartfield
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Yining Zhang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Robert S Oakes
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Scott Ronquist
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Haiming Chen
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Indika Rajapakse
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan
| | - Max S Wicha
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jacqueline S Jeruss
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
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17
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Hernandez I, Luna G, Rauch JN, Reis SA, Giroux M, Karch CM, Boctor D, Sibih YE, Storm NJ, Diaz A, Kaushik S, Zekanowski C, Kang AA, Hinman CR, Cerovac V, Guzman E, Zhou H, Haggarty SJ, Goate AM, Fisher SK, Cuervo AM, Kosik KS. A farnesyltransferase inhibitor activates lysosomes and reduces tau pathology in mice with tauopathy. Sci Transl Med 2019; 11:eaat3005. [PMID: 30918111 PMCID: PMC7961212 DOI: 10.1126/scitranslmed.aat3005] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 08/15/2018] [Accepted: 11/30/2018] [Indexed: 11/02/2022]
Abstract
Tau inclusions are a shared feature of many neurodegenerative diseases, among them frontotemporal dementia caused by tau mutations. Treatment approaches for these conditions include targeting posttranslational modifications of tau proteins, maintaining a steady-state amount of tau, and preventing its tendency to aggregate. We discovered a new regulatory pathway for tau degradation that operates through the farnesylated protein, Rhes, a GTPase in the Ras family. Here, we show that treatment with the farnesyltransferase inhibitor lonafarnib reduced Rhes and decreased brain atrophy, tau inclusions, tau sumoylation, and tau ubiquitination in the rTg4510 mouse model of tauopathy. In addition, lonafarnib treatment attenuated behavioral abnormalities in rTg4510 mice and reduced microgliosis in mouse brain. Direct reduction of Rhes in the rTg4510 mouse by siRNA reproduced the results observed with lonafarnib treatment. The mechanism of lonafarnib action mediated by Rhes to reduce tau pathology was shown to operate through activation of lysosomes. We finally showed in mouse brain and in human induced pluripotent stem cell-derived neurons a normal developmental increase in Rhes that was initially suppressed by tau mutations. The known safety of lonafarnib revealed in human clinical trials for cancer suggests that this drug could be repurposed for treating tauopathies.
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Affiliation(s)
- Israel Hernandez
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Gabriel Luna
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jennifer N Rauch
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Surya A Reis
- Department of Neurology, Massachusetts General Hospital, Chemical Neurobiology Lab, and Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Michel Giroux
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Daniel Boctor
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Youssef E Sibih
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Nadia J Storm
- Department of Developmental and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Antonio Diaz
- Department of Developmental and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Cezary Zekanowski
- Laboratory of Neurogenetics, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106 Warsaw, Poland
| | - Alexander A Kang
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Cassidy R Hinman
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Vesna Cerovac
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elmer Guzman
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Honjun Zhou
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stephen J Haggarty
- Department of Neurology, Massachusetts General Hospital, Chemical Neurobiology Lab, and Center for Genomic Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven K Fisher
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ana M Cuervo
- Department of Developmental and Molecular Biology and Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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18
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Liu X, Duan X, Holmes JA, Li W, Lee SH, Tu Z, Zhu C, Salloum S, Lidofsky A, Schaefer EA, Cai D, Li S, Wang H, Huang Y, Zhao Y, Yu ML, Xu Z, Chen L, Hong J, Lin W, Chung RT. A Long Noncoding RNA Regulates Hepatitis C Virus Infection Through Interferon Alpha-Inducible Protein 6. Hepatology 2019; 69:1004-1019. [PMID: 30199576 PMCID: PMC6393205 DOI: 10.1002/hep.30266] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 02/22/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) play a critical role in the regulation of many important cellular processes. However, the mechanisms by which lncRNAs regulate viral infection and host immune responses are not well understood. We sought to explore lncRNA regulation of hepatitis C virus (HCV) infection and interferon response. We performed RNA sequencing (RNAseq) in Huh7.5.1 cells with or without interferon alpha (IFNα) treatment. Clustered regularly interspaced short palindromic repeats/Cas9 guide RNA (gRNA) was used to knock out selected genes. The promoter clones were constructed, and the activity of related interferon-stimulated genes (ISGs) were detected by the secrete-pair dual luminescence assay. We constructed the full-length and four deletion mutants of an interferon-induced lncRNA RP11-288L9.4 (lncRNA-IFI6) based on predicted secondary structure. Selected gene mRNAs and their proteins, together with HCV infection, in Huh7.5.1 cells and primary human hepatocytes (PHHs) were monitored by quantitative real-time PCR (qRT-PCR) and western blot. We obtained 7,901 lncRNAs from RNAseq. A total of 1,062 host-encoded lncRNAs were significantly differentially regulated by IFNα treatment. We found that lncRNA-IFI6 gRNA significantly inhibited HCV infection compared with negative gRNA control. The expression of the antiviral ISG IFI6 was significantly increased following lncRNA-IFI6 gRNA editing compared with negative gRNA control in Japanese fulminant hepatitis 1 (JFH1)-infected Huh7.5.1 cells and PHHs. We observed that lncRNA-IFI6 regulation of HCV was independent of Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling. lncRNA-IFI6 negatively regulated IFI6 promoter function through histone modification. Overexpression of the truncated spatial domain or full-length lncRNA-IFI6 inhibited IFI6 expression and increased HCV replication. Conclusion: A lncRNA, lncRNA-IFI6, regulates antiviral innate immunity in the JFH1 HCV infection model. lncRNA-IFI6 regulates HCV infection independently of the JAK-STAT pathway. lncRNA-IFI6 exerts its regulatory function via promoter activation and histone modification of IFI6 through its spatial domain.
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Affiliation(s)
- Xiao Liu
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, 610052 Chengdu, China
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jacinta A. Holmes
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Wenting Li
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, Anhui Provincial Hospital, Anhui Medical University, Hefei, China
| | - Sae Hwan Lee
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Soonchunhyang University College of Medicine, Cheonan Hospital, 330721 Dongnamgu Cheonan, Republic of Korea
| | - Zeng Tu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of microbiology, College of Basic Medical Science, Chongqing Medical University, 400715 Chongqing, China
| | - Chuanlong Zhu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shadi Salloum
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Anna Lidofsky
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Esperance A. Schaefer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Dachuan Cai
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Department of Infectious Disease, Chongqing Medical University, 400715 Chongqing, China
| | - Shilin Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China
| | - Haoju Wang
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China
| | - Yongfu Huang
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China
| | - Yongju Zhao
- Southwest University, College of Animal Science and technology, 400715 Chongqing, China
| | - Ming-Lung Yu
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Division of Hepatobiliary, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung, Kaohsiung Medical University, Taiwan
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, 610052 Chengdu, China
| | - Limin Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China
| | - Jian Hong
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Wenyu Lin
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, 610052 Chengdu, China,Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Corresponding authors Correspondence address: Gastrointestinal Unit, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Tel.: +1 617 726 2061; fax: +1 617 643 0446. , or
| | - Raymond T. Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA,Corresponding authors Correspondence address: Gastrointestinal Unit, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Tel.: +1 617 726 2061; fax: +1 617 643 0446. , or
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Goggin DE, Kaur P, Owen MJ, Powles SB. 2,4-D and dicamba resistance mechanisms in wild radish: subtle, complex and population specific? Ann Bot 2018; 122:627-640. [PMID: 29893784 PMCID: PMC6153477 DOI: 10.1093/aob/mcy097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 05/11/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Resistance to synthetic auxin herbicides such as 2,4-dichlorophenoxyacetic acid (2,4-D) is increasing in weed populations worldwide, which is of concern given the recent introduction of synthetic auxin-resistant transgenic crops. Due to the complex mode of action of the auxinic herbicides, the mechanisms of evolved resistance remain largely uncharacterized. The aims of this study were to assess the level of diversity in resistance mechanisms in 11 populations of the problem weed Raphanus raphanistrum, and to use a high-throughput, whole-genome transcriptomic analysis on one resistant and one susceptible population to identify important changes in gene expression in response to 2,4-D. METHODS Levels of 2,4-D and dicamba (3,6-dichloro-2-methoxybenzoic acid) resistance were quantified in a dose-response study and the populations were further screened for auxin selectivity, 2,4-D translocation and metabolism, expression of key 2,4-D-responsive genes and activation of the mitogen-activated proein kinase (MAPK) pathway. Potential links between resistance levels and mechanisms were assessed using correlation analysis. KEY RESULTS The transcriptomic study revealed early deployment of the plant defence response in the 2,4-D-treated resistant population, and there was a corresponding positive relationship between auxinic herbicide resistance and constitutive MAPK phosphorylation across all populations. Populations with shoot-wide translocation of 2,4-D had similar resistance levels to those with restricted translocation, suggesting that reduced translocation may not be as strong a resistance mechanism as originally thought. Differences in auxin selectivity between populations point to the likelihood of different resistance-conferring alterations in auxin signalling and/or perception in the different populations. CONCLUSIONS 2,4-D resistance in wild radish appears to result from subtly different auxin signalling alterations in different populations, supplemented by an enhanced defence response and, in some cases, reduced 2,4-D translocation. This study highlights the dangers of applying knowledge generated from a few populations of a weed species to the species as a whole.
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Affiliation(s)
- Danica E Goggin
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- For correspondence. E-mail
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, Australia
- Telethon Kids Institute, Subiaco, Australia
| | - Mechelle J Owen
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
| | - Stephen B Powles
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
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20
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Birnbaum SSL, Rinker DC, Abbot P. Maintaining Biological Cultures and Measuring Gene Expression in Aphis nerii: A Non-model System for Plant-insect Interactions. J Vis Exp 2018:58044. [PMID: 30222148 PMCID: PMC6235080 DOI: 10.3791/58044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Aphids are excellent experimental models for a variety of biological questions ranging from the evolution of symbioses and the development of polyphenisms to questions surrounding insect's interactions with their host plants. Genomic resources are available for several aphid species, and with advances in the next-generation sequencing, transcriptomic studies are being extended to non-model organisms that lack genomes. Furthermore, aphid cultures can be collected from the field and reared in the laboratory for the use in organismal and molecular experiments to bridge the gap between ecological and genetic studies. Last, many aphids can be maintained in the laboratory on their preferred host plants in perpetual, parthenogenic life cycles allowing for comparisons of asexually reproducing genotypes. Aphis nerii, the milkweed-oleander aphid, provides one such model to study insect interactions with toxic plants using both organismal and molecular experiments. Methods for the generation and maintenance of the plant and aphid cultures in the greenhouse and laboratory, DNA and RNA extractions, microsatellite analysis, de novo transcriptome assembly and annotation, transcriptome differential expression analysis, and qPCR verification of differentially expressed genes are outlined and discussed here.
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Affiliation(s)
| | | | - Patrick Abbot
- Biological Sciences Department, Vanderbilt University;
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21
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Pantazatos SP, Huang YY, Rosoklija GB, Dwork AJ, Arango V, Mann JJ. Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity. Mol Psychiatry 2017; 22:760-773. [PMID: 27528462 PMCID: PMC5313378 DOI: 10.1038/mp.2016.130] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/04/2016] [Accepted: 06/07/2016] [Indexed: 12/30/2022]
Abstract
Brain gene expression profiling studies of suicide and depression using oligonucleotide microarrays have often failed to distinguish these two phenotypes. Moreover, next generation sequencing approaches are more accurate in quantifying gene expression and can detect alternative splicing. Using RNA-seq, we examined whole-exome gene and exon expression in non-psychiatric controls (CON, N=29), DSM-IV major depressive disorder suicides (MDD-S, N=21) and MDD non-suicides (MDD, N=9) in the dorsal lateral prefrontal cortex (Brodmann Area 9) of sudden death medication-free individuals post mortem. Using small RNA-seq, we also examined miRNA expression (nine samples per group). DeSeq2 identified 35 genes differentially expressed between groups and surviving adjustment for false discovery rate (adjusted P<0.1). In depression, altered genes include humanin-like-8 (MTRNRL8), interleukin-8 (IL8), and serpin peptidase inhibitor, clade H (SERPINH1) and chemokine ligand 4 (CCL4), while exploratory gene ontology (GO) analyses revealed lower expression of immune-related pathways such as chemokine receptor activity, chemotaxis and cytokine biosynthesis, and angiogenesis and vascular development in (adjusted P<0.1). Hypothesis-driven GO analysis suggests lower expression of genes involved in oligodendrocyte differentiation, regulation of glutamatergic neurotransmission, and oxytocin receptor expression in both suicide and depression, and provisional evidence for altered DNA-dependent ATPase expression in suicide only. DEXSEq analysis identified differential exon usage in ATPase, class II, type 9B (adjusted P<0.1) in depression. Differences in miRNA expression or structural gene variants were not detected. Results lend further support for models in which deficits in microglial, endothelial (blood-brain barrier), ATPase activity and astrocytic cell functions contribute to MDD and suicide, and identify putative pathways and mechanisms for further study in these disorders.
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Affiliation(s)
- Spiro P. Pantazatos
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY,Department of Psychiatry, New York, NY
| | - Yung-yu Huang
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY,Department of Psychiatry, New York, NY
| | - Gorazd B. Rosoklija
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY,Department of Psychiatry, New York, NY
| | | | - Victoria Arango
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY,Department of Psychiatry, New York, NY
| | - J. John Mann
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY,Department of Psychiatry, New York, NY,To whom correspondence should be addressed:
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22
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Derrick T, Last AR, Burr SE, Roberts CH, Nabicassa M, Cassama E, Bailey RL, Mabey DCW, Burton MJ, Holland MJ. Inverse relationship between microRNA-155 and -184 expression with increasing conjunctival inflammation during ocular Chlamydia trachomatis infection. BMC Infect Dis 2016; 16:60. [PMID: 26842862 PMCID: PMC4739388 DOI: 10.1186/s12879-016-1367-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Trachoma, a preventable blinding eye disease, is initiated by ocular infection with Chlamydia trachomatis (Ct). We previously showed that microRNAs (miR) -147b and miR-1285 were up-regulated in inflammatory trachomatous scarring. During the initial stage of disease, follicular trachoma with current Ct infection, the differential expression of miR has not yet been investigated. METHODS Conjunctival samples were collected from 163 children aged 1-9 years old living in a trachoma-endemic region of Guinea Bissau, West Africa. Small RNA sequencing (RNAseq) was carried out on samples from five children with follicular trachoma and current Ct infection and five children with healthy conjunctivae and no Ct infection. Small RNAseq was also carried out on human epithelial cell lines infected with ocular Ct strains A2497 and isogenic plasmid-free A2497 in vitro. Results were validated by quantitative PCR (qPCR) in 163 clinical samples. RESULTS Differential expression of RNAseq data identified 12 miR with changes in relative expression during follicular trachoma, of which 9 were confirmed as differentially expressed by qPCR (miR-155, miR-150, miR-142, miR-181b, miR-181a, miR-342, miR-132, miR-4728 and miR-184). MiR-155 and miR-184 expression had a direct relationship with the degree of clinical inflammation. MiR-155 was up-regulated (OR = 2.533 ((95 % CI = 1.291-4.971); P = 0.0069) and miR-184 was down-regulated (OR = 0.416 ((95 % CI = 0.300-0.578); P = 1.61*10(-7)) as the severity of clinical inflammation increased. Differential miR expression was not detected in HEp-2 or HCjE epithelial cells 48 h post infection with Ct in vitro. HCjE cells, a conjunctival epithelial cell line, had a markedly different miR background expression compared to HEp-2 cells. CONCLUSIONS In follicular trachoma, expression of miR-155 and miR-184 is correlated with the severity of inflammation. This likely reflects host regulation of the immune response and a prolonged period of wound healing following the clearance of Ct. Prolonged healing may be associated with subsequent development of scarring trachoma.
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Affiliation(s)
- Tamsyn Derrick
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Anna R Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Sarah E Burr
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.
| | - Chrissy H Roberts
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Meno Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea Bissau.
| | - Eunice Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea Bissau.
| | - Robin L Bailey
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - David C W Mabey
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Matthew J Burton
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Martin J Holland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015; 16:395. [PMID: 25986459 PMCID: PMC4437557 DOI: 10.1186/s12864-015-1627-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 05/11/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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Fu L, Minton DR, Zhang T, Nanus DM, Gudas LJ. Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome. Mol Cancer Res 2015; 13:870-8. [PMID: 25715653 PMCID: PMC4433424 DOI: 10.1158/1541-7786.mcr-14-0423] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 07/29/2014] [Accepted: 02/18/2015] [Indexed: 12/26/2022]
Abstract
UNLABELLED Renal cell carcinoma (RCC) is the most common cancer arising from the kidney in adults, with clear cell RCC (ccRCC) representing the majority of all RCCs. Expression of a human HIF1α triple-mutant (P402A, P564A, and N803A) construct in the proximal tubule cells of C57BL/6 mice [TRAnsgenic model of Cancer of the Kidney (TRACK); ref. 1] mimics the histologic changes found in early stage human ccRCC. To better understand the genomic landscape, a high-throughput sequence analysis was performed with cDNA libraries (RNAseq) derived from TRACK transgenic positive (TG(+)) kidney cortex along with human ccRCC transcripts from the Oncomine and The Cancer Genome Atlas databases. Importantly, the expression profiles of TRACK TG(+) kidneys show significant similarities with those observed in human ccRCC, including increased expression of genes involved in glycolysis and the tricarboxylic acid cycle. Some of the transcripts overexpressed in both the TRACK mouse model and human ccRCC include ANKRD37, CA9, EGLN3, HK2, NDUFA4L2, and SLC16A3. These data suggest that constitutive activation of HIF1α in kidney proximal tubule cells transcriptionally reprograms the regulation of metabolic pathways in the kidney and that HIF1α is a major contributor to the altered metabolism observed in human ccRCC. IMPLICATIONS TRACK (GGT-HIF1αM3) kidney mRNA profiles show similarities to human ccRCC transcriptome and phenotypes associated with the Warburg effect.
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Affiliation(s)
- Leiping Fu
- Department of Pharmacology, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York. Weill Cornell Meyer Cancer Center, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York
| | - Denise R Minton
- Department of Pharmacology, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York. Weill Cornell Meyer Cancer Center, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York
| | - David M Nanus
- Weill Cornell Meyer Cancer Center, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York. Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York. Weill Cornell Meyer Cancer Center, Weill Cornell Medical College (WCMC) of Cornell University, New York, New York.
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25
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Slattery ML, Herrick JS, Mullany LE, Gertz J, Wolff RK. Improved survival among colon cancer patients with increased differentially expressed pathways. BMC Med 2015; 13:75. [PMID: 25890236 PMCID: PMC4389992 DOI: 10.1186/s12916-015-0292-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/11/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Studies of colorectal cancer (CRC) have shown that hundreds to thousands of genes are differentially expressed in tumors when compared to normal tissue samples. In this study, we evaluate how genes that are differentially expressed in colon versus normal tissue influence survival. METHODS We performed RNA-seq on tumor/normal paired samples from 175 colon cancer patients. We implemented a cross validation strategy to determine genes that were significantly differentially expressed between tumor and normal samples. Differentially expressed genes were evaluated with Ingenuity Pathway Analysis to identify key pathways that were de-regulated. A summary differential pathway expression score (DPES) was developed to summarize hazard of dying while adjusting for age, American Joint Committee on Cancer (AJCC) stage, sex, and tumor molecular phenotype, i.e., MSI, TP53, KRAS, and CIMP. RESULTS A total of 1,138 genes were up-regulated and 695 were down-regulated. These de-regulated genes were enriched for 19 Ingenuity Canonical Pathways, with the most significant pathways involving cell signaling and growth. Of the enriched pathways, 16 were significantly associated with CRC-specific mortality, including 1 metabolic pathway and 15 signaling pathways. In all instances, having a higher DPES (i.e., more de-regulated genes) was associated with better survival. Further assessment showed that individuals diagnosed at AJCC Stage 1 had more de-regulated genes than individuals diagnosed at AJCC Stage 4. CONCLUSIONS Our data suggest that having more de-regulated pathways is associated with a good prognosis and may be a reaction to key events that are disabling to tumor progression. Please see related article: http://dx.doi.org/10.1186/s12916-015-0307-6 .
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Affiliation(s)
- Martha L Slattery
- Department of Internal Medicine, University of Utah School of Medicine, 383 Colorow, Salt Lake City, 84018, USA.
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah School of Medicine, 383 Colorow, Salt Lake City, 84018, USA.
| | - Lila E Mullany
- Department of Internal Medicine, University of Utah School of Medicine, 383 Colorow, Salt Lake City, 84018, USA.
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, 1950 Circle of Hope, Salt Lake City, 84112, USA.
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah School of Medicine, 383 Colorow, Salt Lake City, 84018, USA.
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Abstract
The crosstalk between tumor cells and cells of the tumor stroma dictate malignant progression and represent an intriguing and viable anticancer therapeutic target. The successful development of therapeutics targeting tumor-stroma interactions is tied to the insight provided by basic research on such crosstalk. Tumor-stroma interactions can be transient and dynamic, and they occur within defined spatiotemporal contexts among genetically and compositionally heterogeneous populations of cells, yet methods currently applied to study the said crosstalk do not sufficiently address these features. Emerging imaging and genetic methods, however, can overcome limitations of traditional approaches and provide unprecedented insight into tumor-stroma crosstalk with unparalleled accuracy. The comprehensive data obtained by applying emerging methods will require processing and analysis by multidisciplinary teams, but the efforts will ultimately rejuvenate hope in developing novel therapies against pro-tumorigenic tumor-stroma crosstalk.
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Affiliation(s)
- Ian H Guldner
- Department of Biological Science, Harper Cancer Research Institute, University of Notre Dame, A130 Harper Hall, Notre Dame, IN 46556, USA.
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Liu R, Loraine AE, Dickerson JA. Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. BMC Bioinformatics 2014; 15:364. [PMID: 25511303 PMCID: PMC4271460 DOI: 10.1186/s12859-014-0364-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [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: 05/31/2014] [Accepted: 10/29/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Alternative Splicing (AS) as a post-transcription regulation mechanism is an important application of RNA-seq studies in eukaryotes. A number of software and computational methods have been developed for detecting AS. Most of the methods, however, are designed and tested on animal data, such as human and mouse. Plants genes differ from those of animals in many ways, e.g., the average intron size and preferred AS types. These differences may require different computational approaches and raise questions about their effectiveness on plant data. The goal of this paper is to benchmark existing computational differential splicing (or transcription) detection methods so that biologists can choose the most suitable tools to accomplish their goals. RESULTS This study compares the eight popular public available software packages for differential splicing analysis using both simulated and real Arabidopsis thaliana RNA-seq data. All software are freely available. The study examines the effect of varying AS ratio, read depth, dispersion pattern, AS types, sample sizes and the influence of annotation. Using a real data, the study looks at the consistences between the packages and verifies a subset of the detected AS events using PCR studies. CONCLUSIONS No single method performs the best in all situations. The accuracy of annotation has a major impact on which method should be chosen for AS analysis. DEXSeq performs well in the simulated data when the AS signal is relative strong and annotation is accurate. Cufflinks achieve a better tradeoff between precision and recall and turns out to be the best one when incomplete annotation is provided. Some methods perform inconsistently for different AS types. Complex AS events that combine several simple AS events impose problems for most methods, especially for MATS. MATS stands out in the analysis of real RNA-seq data when all the AS events being evaluated are simple AS events.
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Affiliation(s)
- Ruolin Liu
- Department of Electrical and Computational Engineering, Iowa State University, Howe Hall, Ames, 50011-3060, USA.
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, 600 Laureate Way, Kannapolis, 28081, NC, USA.
| | - Julie A Dickerson
- Department of Electrical and Computational Engineering, Iowa State University, Howe Hall, Ames, 50011-3060, USA.
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van Wyk SG, Du Plessis M, Cullis CA, Kunert KJ, Vorster BJ. Cysteine protease and cystatin expression and activity during soybean nodule development and senescence. BMC Plant Biol 2014; 14:294. [PMID: 25404209 PMCID: PMC4243279 DOI: 10.1186/s12870-014-0294-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/17/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Nodules play an important role in fixing atmospheric nitrogen for soybean growth. Premature senescence of nodules can negatively impact on nitrogen availability for plant growth and, as such, we need a better understanding of nodule development and senescence. Cysteine proteases are known to play a role in nodule senescence, but knowledge is still fragmented regarding the function their inhibitors (cystatins) during the development and senescence of soybean nodules. This study provides the first data with regard to cystatin expression during nodule development combined with biochemical characterization of their inhibition strength. RESULTS Seventy nine non-redundant cysteine protease gene sequences with homology to papain, belonging to different subfamilies, and several legumain-like cysteine proteases (vacuole processing enzymes) were identified from the soybean genome assembly with eighteen of these cysteine proteases actively transcribed during nodule development and senescence. In addition, nineteen non-redundant cystatins similar to oryzacystatin-I and belonging to cystatin subgroups A and C were identified from the soybean genome assembly with seven actively transcribed in nodules. Most cystatins had preferential affinity to cathepsin L-like cysteine proteases. Transcription of cystatins Glyma05g28250, Glyma15g12211, Glyma15g36180 particularly increased during onset of senescence, possibly regulating proteolysis when nodules senesce and undergo programmed cell death. Both actively transcribed and non-actively transcribed nodule cystatins inhibited cathepsin-L- and B-like activities in different age nodules and they also inhibited papain and cathepsin-L activity when expressed and purified from bacterial cells. CONCLUSIONS Overlap in activities and specificities of actively and non-actively transcribed cystatins raises the question if non-transcribed cystatins provide a reservoir for response to particular environments. This data might be applicable to the development of strategies to extend the active life span of nodules or prevent environmentally induced senescence.
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Affiliation(s)
- Stefan George van Wyk
- />Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Magdeleen Du Plessis
- />Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | | | - Karl Josef Kunert
- />Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Barend Juan Vorster
- />Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
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Abstract
This review, the first of an occasional series, tries to make sense of the concepts and uses of deep sequencing of polynucleic acids (DNA and RNA). Deep sequencing, synonymous with next-generation sequencing, high-throughput sequencing and massively parallel sequencing, includes whole genome sequencing but is more often and diversely applied to specific parts of the genome captured in different ways, for example the highly expressed portion of the genome known as the exome and portions of the genome that are epigenetically marked either by DNA methylation, the binding of proteins including histones, or that are in different configurations and thus more or less accessible to enzymes that cleave DNA. Deep sequencing of RNA (RNASeq) reverse-transcribed to complementary DNA is invaluable for measuring RNA expression and detecting changes in RNA structure. Important concepts in deep sequencing include the length and depth of sequence reads, mapping and assembly of reads, sequencing error, haplotypes, and the propensity of deep sequencing, as with other types of 'big data', to generate large numbers of errors, requiring monitoring for methodologic biases and strategies for replication and validation. Deep sequencing yields a unique genetic fingerprint that can be used to identify a person, and a trove of predictors of genetic medical diseases. Deep sequencing to identify epigenetic events including changes in DNA methylation and RNA expression can reveal the history and impact of environmental exposures. Because of the power of sequencing to identify and deliver biomedically significant information about a person and their blood relatives, it creates ethical dilemmas and practical challenges in research and clinical care, for example the decision and procedures to report incidental findings that will increasingly and frequently be discovered.
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Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D'Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M, Valle G. A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol 2014; 14:99. [PMID: 24739459 PMCID: PMC4108029 DOI: 10.1186/1471-2229-14-99] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/07/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. RESULTS We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. Several gene structures have been improved and alternative splicing was described for about 30% of the genes. A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. CONCLUSIONS As described in Arabidopsis, also grape displays a marked AS tissue-specificity, while stress conditions produce splicing changes to a minor extent. Surprisingly, some distinctive splicing features were also observed between genotypes. This was further supported by the observation that the panel of Serine/Arginine-rich splicing factors show a few, but very marked differences between genotypes. The finding that a part the splicing machinery can change in closely related organisms can lead to some interesting hypotheses for evolutionary adaptation, that could be particularly relevant in the response to sudden and strong selective pressures.
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Affiliation(s)
- Nicola Vitulo
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Claudio Forcato
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | | | - Andrea Telatin
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | | | | | | | - Massimiliano Corso
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padua, Padua, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padua, Padua, Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padua, Padua, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padua, Padua, Italy
- CIRVE, Centre for Research in Viticulture and Enology, University of Padua, Padua, Italy
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
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Feldmesser E, Rosenwasser S, Vardi A, Ben-Dor S. Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. BMC Genomics 2014; 15:148. [PMID: 24559402 PMCID: PMC4028052 DOI: 10.1186/1471-2164-15-148] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated. RESULTS Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20% versus any of the read-based approaches alone. CONCLUSIONS To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.
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Affiliation(s)
- Ester Feldmesser
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shilo Rosenwasser
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Vardi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shifra Ben-Dor
- Department of Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel
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Soetaert SSA, Van Neste CMF, Vandewoestyne ML, Head SR, Goossens A, Van Nieuwerburgh FCW, Deforce DLD. Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua. BMC Plant Biol 2013; 13:220. [PMID: 24359620 PMCID: PMC3878173 DOI: 10.1186/1471-2229-13-220] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 12/12/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The medicinal plant Artemisia annua is covered with filamentous trichomes and glandular, artemisinin producing trichomes. A high artemisinin supply is needed at a reduced cost for treating malaria. Artemisinin production in bioreactors can be facilitated if a better insight is obtained in the biosynthesis of artemisinin and other metabolites. Therefore, metabolic activities of glandular and filamentous trichomes were investigated at the transcriptome level. RESULTS By laser pressure catapulting, glandular and filamentous trichomes as well as apical and sub-apical cells from glandular trichomes were collected and their transcriptome was sequenced using Illumina RNA-Seq. A de novo transcriptome was assembled (Trinity) and studied with a differential expression analysis (edgeR).A comparison of the transcriptome from glandular and filamentous trichomes shows that MEP, MVA, most terpene and lipid biosynthesis pathways are significantly upregulated in glandular trichomes. Conversely, some transcripts coding for specific sesquiterpenoid and triterpenoid enzymes such as 8-epi-cedrol synthase and an uncharacterized oxidosqualene cyclase were significantly upregulated in filamentous trichomes. All known artemisinin biosynthesis genes are upregulated in glandular trichomes and were detected in both the apical and sub-apical cells of the glandular trichomes. No significant differential expression could be observed between the apical and sub-apical cells. CONCLUSIONS Our results underscore the vast metabolic capacities of A. annua glandular trichomes but nonetheless point to the existence of specific terpene metabolic pathways in the filamentous trichomes. Candidate genes that might be involved in artemisinin biosynthesis are proposed based on their putative function and their differential expression level.
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Affiliation(s)
- Sandra SA Soetaert
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Christophe MF Van Neste
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Mado L Vandewoestyne
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute, 10550N. Torrey Pines Rd, La Jolla, CA 92037 United States of America
| | - Alain Goossens
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Filip CW Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Dieter LD Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
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Kao D, Felix D, Aboobaker A. The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics 2013; 14:797. [PMID: 24238224 PMCID: PMC4046745 DOI: 10.1186/1471-2164-14-797] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 11/11/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Planarians can regenerate entire animals from a small fragment of the body. The regenerating fragment is able to create new tissues and remodel existing tissues to form a complete animal. Thus different fragments with very different starting components eventually converge on the same solution. In this study, we performed an extensive RNA-seq time-course on regenerating head and tail fragments to observe the differences and similarities of the transcriptional landscape between head and tail fragments during regeneration. RESULTS We have consolidated existing transcriptomic data for S. mediterranea to generate a high confidence set of transcripts for use in genome wide expression studies. We performed a RNA-seq time-course on regenerating head and tail fragments from 0 hours to 3 days. We found that the transcriptome profiles of head and tail regeneration were very different at the start of regeneration; however, an unexpected convergence of transcriptional profiles occurred at 48 hours when head and tail fragments are still morphologically distinct. By comparing differentially expressed transcripts at various time-points, we revealed that this divergence/convergence pattern is caused by a shared regulatory program that runs early in heads and later in tails.Additionally, we also performed RNA-seq on smed-prep(RNAi) tail fragments which ultimately fail to regenerate anterior structures. We find the gene regulation program in response to smed-prep(RNAi) to display the opposite regulatory trend compared to the previously mentioned share regulatory program during regeneration. Using annotation data and comparative approaches, we also identified a set of approximately 4,800 triclad specific transcripts that were enriched amongst the genes displaying differential expression during the regeneration time-course. CONCLUSION The regeneration transcriptome of head and tail regeneration provides us with a rich resource for investigating the global expression changes that occurs during regeneration. We show that very different regenerative scenarios utilize a shared core regenerative program. Furthermore, our consolidated transcriptome and annotations allowed us to identity triclad specific transcripts that are enriched within this core regulatory program. Our data support the hypothesis that both conserved aspects of animal developmental programs and recent evolutionarily innovations work in concert to control regeneration.
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Affiliation(s)
- Damian Kao
- />School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Daniel Felix
- />Fundación CNIC Carlos III- Centro Nacional de Investigaciones Cardiovasculares, Melchor Fernández Almagro, 3, Madrid, Código Postal 28029 Spain
| | - Aziz Aboobaker
- />Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS UK
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Rinker DC, Zhou X, Pitts RJ. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. BMC Genomics 2013; 14:749. [PMID: 24182346 PMCID: PMC3833343 DOI: 10.1186/1471-2164-14-749] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [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: 07/11/2013] [Accepted: 10/22/2013] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Two sibling members of the Anopheles gambiae species complex display notable differences in female blood meal preferences. An. gambiae s.s. has a well-documented preference for feeding upon human hosts, whereas An. quadriannulatus feeds on vertebrate/mammalian hosts, with only opportunistic feeding upon humans. Because mosquito host-seeking behaviors are largely driven by the sensory modality of olfaction, we hypothesized that hallmarks of these divergent host seeking phenotypes will be in evidence within the transcriptome profiles of the antennae, the mosquito's principal chemosensory appendage. RESULTS To test this hypothesis, we have sequenced antennal mRNA of non-bloodfed females from each species and observed a number of distinct quantitative and qualitative differences in their chemosensory gene repertoires. In both species, these gene families show higher rates of sequence polymorphisms than the overall rates in their respective transcriptomes, with potentially important divergences between the two species. Moreover, quantitative differences in odorant receptor transcript abundances have been used to model potential distinctions in volatile odor receptivity between the two sibling species of anophelines. CONCLUSION This analysis suggests that the anthropophagic behavior of An. gambiae s.s. reflects the differential distribution of olfactory receptors in the antenna, likely resulting from a co-option and refinement of molecular components common to both species. This study improves our understanding of the molecular evolution of chemoreceptors in closely related anophelines and suggests possible mechanisms that underlie the behavioral distinctions in host seeking that, in part, account for the differential vectorial capacity of these mosquitoes.
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Affiliation(s)
- David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Ronald Jason Pitts
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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Wu D, Pang Y, Wilkerson MD, Wang D, Hammerman PS, Liu JS. Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity. Br J Cancer 2013; 109:1599-608. [PMID: 24002593 PMCID: PMC3776976 DOI: 10.1038/bjc.2013.452] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 03/17/2013] [Revised: 07/06/2013] [Accepted: 07/12/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Squamous cell lung cancer (SqCC) is the second most common type of lung cancer in the United States. Previous studies have used gene-expression data to classify SqCC samples into four subtypes, including the primitive, classical, secretory and basal subtypes. These subtypes have different survival outcomes, although it is unknown whether these molecular subtypes predict response to therapy. METHODS Here, we analysed RNAseq data of 178 SqCC tumour samples and characterised the features of the different SqCC subtypes to define signature genes and pathway alterations specific to each subtype. Further, we compared the gene-expression features of each molecular subtype to specific time points in models of airway development. We also classified SqCC-derived cell lines and their reported therapeutic vulnerabilities. RESULTS We found that the primitive subtype may come from a later stage of differentiation, whereas the basal subtype may be from an early time. Most SqCC cell lines responded to one of five anticancer drugs (Panobinostat, 17-AAG, Irinotecan, Topotecan and Paclitaxel), whereas the basal-type cell line EBC-1 was sensitive to three other drugs (PF2341066, AZD6244 and PD-0325901). CONCLUSION Compared with the other three subtypes of cell lines, the secretory-type cell lines were significantly less sensitive to the five most effective drugs, possibly because of their low proliferation activity. We provide a bioinformatics framework to explore drug repurposing for cancer subtypes based on the available genomic profiles of tumour samples, normal cell types, cancer cell lines and data of drug sensitivity in cell lines.
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Affiliation(s)
- D Wu
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - Y Pang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - M D Wilkerson
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Wang
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Clayton, Victoria, Australia
| | - P S Hammerman
- The Eli and Edythe L. Broad Institute of Massachusetts, Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
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St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P. VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biol 2013; 14:R73. [PMID: 23876380 PMCID: PMC4053963 DOI: 10.1186/gb-2013-14-7-r73] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [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: 11/05/2012] [Accepted: 07/22/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs. RESULTS Here we identify 2,147 vlincRNAs covering 10 percent of our genome. We show they are present not only in cancerous cells, but also in primary cells and normal human tissues, and are controlled by canonical promoters. Furthermore, vlincRNA promoters frequently originate from within endogenous retroviral sequences. Strikingly, the number of vlincRNAs expressed from endogenous retroviral promoters strongly correlates with pluripotency or the degree of malignant transformation. These results suggest a previously unknown connection between the pluripotent state and cancer via retroviral repeat-driven expression of vlincRNAs. Finally, we show that vlincRNAs can be syntenically conserved in humans and mouse and their depletion using RNAi can cause apoptosis in cancerous cells. CONCLUSIONS These intriguing observations suggest that vlincRNAs could create a framework that combines many existing short ESTs and lincRNAs into a landscape of very long transcripts functioning in the regulation of gene expression in the nucleus. Certain types of vlincRNAs participate at specific stages of normal development and, based on analysis of a limited set of cancerous and primary cell lines, they appear to be co-opted by cancer-associated transcriptional programs. This provides additional understanding of transcriptome regulation during the malignant state, and could lead to additional targets and options for its reversal.
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Affiliation(s)
- Georges St Laurent
- St. Laurent Institute, One Kendall Square, Cambridge, MA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI
| | - Dmitry Shtokalo
- St. Laurent Institute, One Kendall Square, Cambridge, MA
- A.P.Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev ave., Novosibirsk 630090, Russia
| | - Biao Dong
- Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, PA
| | | | - Xiaoxuan Fan
- Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, PA
| | - Sandra Lazorthes
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France
- CNRS, LBCMCP, F-31062 Toulouse, France
| | - Estelle Nicolas
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France
- CNRS, LBCMCP, F-31062 Toulouse, France
| | - Nianli Sang
- Department of Biology, Drexel University, 3245 Chestnut St, PISB 417, Philadelphia, PA
| | - Timothy J Triche
- Department of Pathology, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA
| | - Timothy A McCaffrey
- The George Washington University Medical Center, Department of Medicine, Division of Genomic Medicine, 2300 I St. NW, Washington, D.C
| | - Weidong Xiao
- Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, PA
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Macklaim JM, Fernandes AD, Di Bella JM, Hammond JA, Reid G, Gloor GB. Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis. Microbiome 2013; 1:12. [PMID: 24450540 PMCID: PMC3971606 DOI: 10.1186/2049-2618-1-12] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/13/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND Bacterial vaginosis (BV), the most common vaginal condition of reproductive-aged women, is associated with a highly diverse and heterogeneous microbiota. Here we present a proof-of-principle analysis to uncover the function of the microbiota using meta-RNA-seq to uncover genes and pathways that potentially differentiate healthy vaginal microbial communities from those in the dysbiotic state of bacterial vaginosis (BV). RESULTS The predominant organism, Lactobacillus iners, was present in both conditions and showed a differing expression profile in BV compared to healthy. Despite its minimal genome, L. iners differentially expressed over 10% of its gene complement. Notably, in a BV environment L. iners increased expression of a cholesterol-dependent cytolysin, and of mucin and glycerol transport and related metabolic enzymes. Genes belonging to a CRISPR system were greatly upregulated suggesting that bacteriophage influence the community. Reflective of L. iners, the bacterial community as a whole demonstrated a preference for glycogen and glycerol as carbon sources under BV conditions. The predicted end-products of metabolism under BV conditions include an abundance of succinate and other short-chain fatty-acids, while healthy conditions are predicted to largely contain lactic acid. CONCLUSIONS Our study underscores the importance of understanding the functional activity of the bacterial community in addition to characterizing the population structure when investigating the human microbiome.
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Affiliation(s)
- Jean M Macklaim
- Department of Biochemistry, The University of Western Ontario, London N6A 5C1, Canada
- Canadian Research & Development Centre for Probiotics, Lawson Health Research Institute, London, ON, N6A 4V2, Canada
| | | | - Julia M Di Bella
- Department of Microbiology and Immunology, The University of Western Ontario, London, N6A 5C1, Canada
| | - Jo-Anne Hammond
- Department of Family Medicine, The University of Western Ontario, London, N6A 5C1, Canada
| | - Gregor Reid
- Canadian Research & Development Centre for Probiotics, Lawson Health Research Institute, London, ON, N6A 4V2, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, N6A 5C1, Canada
- Department of Surgery, The University of Western Ontario, London, N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, The University of Western Ontario, London N6A 5C1, Canada
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Abstract
We provide here a protocol for the preparation of cap-analysis gene expression (CAGE) libraries, which allows for measuring the expression of eukaryotic capped RNAs and simultaneously map the promoter regions. The presented protocol simplifies the previously published ones and moreover produces tags that are 27 nucleotides long, which facilitates mapping to the genome. The protocol takes less than 5 days to complete and presents a notable improvement compared to previously published versions.
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Manful T, Fadda A, Clayton C. The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA 2011; 17:2039-2047. [PMID: 21947264 PMCID: PMC3198596 DOI: 10.1261/rna.2837311] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/16/2011] [Indexed: 05/31/2023]
Abstract
The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation and mRNA abundance on a transcriptome-wide scale. The model organism used was the bloodstream form of Trypanosoma brucei, a protist that lacks regulation of RNA polymerase II initiation. The mRNA half-lives varied over two orders of magnitude, with a median half-life of 13 min for total (rRNA-depleted) mRNA. Data for poly(A)+ RNA yielded shorter half-lives than for total RNA, indicating that removal of the poly(A) tail was usually the first step in degradation. Depletion of the major 5'-3' exoribonuclease, XRNA, resulted in the stabilization of most mRNAs with half-lives under 30 min. Thus, on a transcriptome-wide scale, degradation of most mRNAs is initiated by deadenylation. Trypanosome mRNA levels are strongly influenced by gene copy number and mRNA half-life: Very abundant mRNAs that are required throughout the life-cycle may be encoded by multicopy genes and have intermediate-to-long half-lives; those encoding ribosomal proteins, with one to two gene copies, are exceptionally stable. Developmentally regulated transcripts with a lower abundance in the bloodstream forms than the procyclic forms had half-lives around the median, whereas those with a higher abundance in the bloodstream forms than the procyclic forms, such as those encoding glycolytic enzymes, had longer half-lives.
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Affiliation(s)
- Theresa Manful
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D69120 Heidelberg, Germany
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