1
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Imbiakha B, Ezzatpour S, Buchholz DW, Sahler J, Ye C, Olarte-Castillo XA, Zou A, Kwas C, O’Hare K, Choi A, Adeleke RA, Khomandiak S, Goodman L, Jager MC, Whittaker GR, Martinez-Sobrido L, August A, Aguilar HC. Age-dependent acquisition of pathogenicity by SARS-CoV-2 Omicron BA.5. SCIENCE ADVANCES 2023; 9:eadj1736. [PMID: 37738347 PMCID: PMC10516498 DOI: 10.1126/sciadv.adj1736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Abstract
Pathology studies of SARS-CoV-2 Omicron variants of concern (VOC) are challenged by the lack of pathogenic animal models. While Omicron BA.1 and BA.2 replicate in K18-hACE2 transgenic mice, they cause minimal to negligible morbidity and mortality, and less is known about more recent Omicron VOC. Here, we show that in contrast to Omicron BA.1, BA.5-infected mice exhibited high levels of morbidity and mortality, correlating with higher early viral loads. Neither Omicron BA.1 nor BA.5 replicated in brains, unlike most prior VOC. Only Omicron BA.5-infected mice exhibited substantial weight loss, high pathology scores in lungs, and high levels of inflammatory cells and cytokines in bronchoalveolar lavage fluid, and 5- to 8-month-old mice exhibited 100% fatality. These results identify a rodent model for pathogenesis or antiviral countermeasure studies for circulating SARS-CoV-2 Omicron BA.5. Further, differences in morbidity and mortality between Omicron BA.1 and BA.5 provide a model for understanding viral determinants of pathogenicity.
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Affiliation(s)
- Brian Imbiakha
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Shahrzad Ezzatpour
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | - David W. Buchholz
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Julie Sahler
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ximena A. Olarte-Castillo
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Anna Zou
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Cole Kwas
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Katelyn O’Hare
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Annette Choi
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Richard Ayomide Adeleke
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Solomiia Khomandiak
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Goodman
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Mason C. Jager
- Department of Population Medicine and Diagnostic Sciences, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | | | - Avery August
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
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2
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Deacon AM, Blouin R, Thibault C, Lacasse P. Mechanism underlying the modulation of milk production by incomplete milking. J Dairy Sci 2022; 106:783-791. [DOI: 10.3168/jds.2022-22164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022]
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3
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Shapira T, Monreal IA, Dion SP, Buchholz DW, Imbiakha B, Olmstead AD, Jager M, Désilets A, Gao G, Martins M, Vandal T, Thompson CAH, Chin A, Rees WD, Steiner T, Nabi IR, Marsault E, Sahler J, Diel DG, Van de Walle GR, August A, Whittaker GR, Boudreault PL, Leduc R, Aguilar HC, Jean F. A TMPRSS2 inhibitor acts as a pan-SARS-CoV-2 prophylactic and therapeutic. Nature 2022; 605:340-348. [PMID: 35344983 PMCID: PMC9095466 DOI: 10.1038/s41586-022-04661-w] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/18/2022] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus remains a global public health crisis. Although widespread vaccination campaigns are underway, their efficacy is reduced owing to emerging variants of concern1,2. Development of host-directed therapeutics and prophylactics could limit such resistance and offer urgently needed protection against variants of concern3,4. Attractive pharmacological targets to impede viral entry include type-II transmembrane serine proteases (TTSPs) such as TMPRSS2; these proteases cleave the viral spike protein to expose the fusion peptide for cell entry, and thus have an essential role in the virus lifecycle5,6. Here we identify and characterize a small-molecule compound, N-0385, which exhibits low nanomolar potency and a selectivity index of higher than 106 in inhibiting SARS-CoV-2 infection in human lung cells and in donor-derived colonoids7. In Calu-3 cells it inhibits the entry of the SARS-CoV-2 variants of concern B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta). Notably, in the K18-human ACE2 transgenic mouse model of severe COVID-19, we found that N-0385 affords a high level of prophylactic and therapeutic benefit after multiple administrations or even after a single administration. Together, our findings show that TTSP-mediated proteolytic maturation of the spike protein is critical for SARS-CoV-2 infection in vivo, and suggest that N-0385 provides an effective early treatment option against COVID-19 and emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - I Abrrey Monreal
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Sébastien P Dion
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - David W Buchholz
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Brian Imbiakha
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Andrea D Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mason Jager
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Antoine Désilets
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Guang Gao
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Thierry Vandal
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Connor A H Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aaleigha Chin
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - William D Rees
- Department of Medicine, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Theodore Steiner
- Department of Medicine, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Marsault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Julie Sahler
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Gerlinde R Van de Walle
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Avery August
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Hector C Aguilar
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA.
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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4
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Lauzier A, Bossanyi MF, Larcher R, Nassari S, Ugrankar R, Henne WM, Jean S. Snazarus and its human ortholog SNX25 modulate autophagic flux. J Cell Sci 2022; 135:273525. [PMID: 34821359 DOI: 10.1242/jcs.258733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
Macroautophagy, the degradation and recycling of cytosolic components in the lysosome, is an important cellular mechanism. It is a membrane-mediated process that is linked to vesicular trafficking events. The sorting nexin (SNX) protein family controls the sorting of a large array of cargoes, and various SNXs impact autophagy. To improve our understanding of their functions in vivo, we screened all Drosophila SNXs using inducible RNA interference in the fat body. Significantly, depletion of Snazarus (Snz) led to decreased autophagic flux. Interestingly, we observed altered distribution of Vamp7-positive vesicles with Snz depletion, and the roles of Snz were conserved in human cells. SNX25, the closest human ortholog to Snz, regulates both VAMP8 endocytosis and lipid metabolism. Through knockout-rescue experiments, we demonstrate that these activities are dependent on specific SNX25 domains and that the autophagic defects seen upon SNX25 loss can be rescued by ethanolamine addition. We also demonstrate the presence of differentially spliced forms of SNX14 and SNX25 in cancer cells. This work identifies a conserved role for Snz/SNX25 as a regulator of autophagic flux and reveals differential isoform expression between paralogs.
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Affiliation(s)
- Annie Lauzier
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Marie-France Bossanyi
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Raphaëlle Larcher
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Sonya Nassari
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Rupali Ugrankar
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Hary Lines Boulevard, Dallas, TX 75390, USA
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Hary Lines Boulevard, Dallas, TX 75390, USA
| | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
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5
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Jia Y, Han J, Wang H, Hong W, Wang H, Zhang M, Li Z. Ultrasensitive quantification of multiplexed mRNA variants via splice-junction anchored DNA probes and SplintR ligase-initiated PCR. Chem Commun (Camb) 2021; 57:10011-10014. [PMID: 34498616 DOI: 10.1039/d1cc03033g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A method based on mRNA-templated ligation of splice-junction anchored DNA probes followed by PCR amplification of the ligated product has been developed for multiplexed detection of mRNA splice variants with high sensitivity and specificity. The proposed assay can detect as low as 10 aM mRNA splicing variants and has been successfully applied to detect real samples.
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Affiliation(s)
- Yuting Jia
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biology Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Jun Han
- National Textile and Leather Product Quality Supervision Testing Center, Beijing 100025, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biology Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Weixiang Hong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biology Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biology Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Mai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biology Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biology Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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6
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Guo J, Starr D, Guo H. Classification and review of free PCR primer design software. Bioinformatics 2021; 36:5263-5268. [PMID: 33104196 DOI: 10.1093/bioinformatics/btaa910] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Polymerase chain reaction (PCR) has been a revolutionary biomedical advancement. However, for PCR to be appropriately used, one must spend a significant amount of effort on PCR primer design. Carefully designed PCR primers not only increase sensitivity and specificity, but also decrease effort spent on experimental optimization. Computer software removes the human element by performing and automating the complex and rigorous calculations required in PCR primer design. Classification and review of the available software options and their capabilities should be a valuable resource for any PCR application. RESULTS This article focuses on currently available free PCR primer design software and their major functions (https://pcrprimerdesign.github.io/). The software are classified according to their PCR applications, such as Sanger sequencing, reverse transcription quantitative PCR, single nucleotide polymorphism detection, splicing variant detection, methylation detection, microsatellite detection, multiplex PCR and targeted next generation sequencing, and conserved/degenerate primers to clone orthologous genes from related species, new gene family members in the same species, or to detect a group of related pathogens. Each software is summarized to provide a technical review of their capabilities and utilities.
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Affiliation(s)
- Jingwen Guo
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - David Starr
- Department of Pathology, Saint Louis University, St. Louis, MO 63104, USA
| | - Huazhang Guo
- Department of Pathology, Saint Louis University, St. Louis, MO 63104, USA
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7
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Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB. PRMT5 inhibition disrupts splicing and stemness in glioblastoma. Nat Commun 2021; 12:979. [PMID: 33579912 PMCID: PMC7881162 DOI: 10.1038/s41467-021-21204-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is a deadly cancer in which cancer stem cells (CSCs) sustain tumor growth and contribute to therapeutic resistance. Protein arginine methyltransferase 5 (PRMT5) has recently emerged as a promising target in GBM. Using two orthogonal-acting inhibitors of PRMT5 (GSK591 or LLY-283), we show that pharmacological inhibition of PRMT5 suppresses the growth of a cohort of 46 patient-derived GBM stem cell cultures, with the proneural subtype showing greater sensitivity. We show that PRMT5 inhibition causes widespread disruption of splicing across the transcriptome, particularly affecting cell cycle gene products. We identify a GBM splicing signature that correlates with the degree of response to PRMT5 inhibition. Importantly, we demonstrate that LLY-283 is brain-penetrant and significantly prolongs the survival of mice with orthotopic patient-derived xenografts. Collectively, our findings provide a rationale for the clinical development of brain penetrant PRMT5 inhibitors as treatment for GBM.
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Affiliation(s)
- Patty Sachamitr
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Jolene C Ho
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Felipe E Ciamponi
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, Brazil
- The Structural Genomics Consortium, University of Campinas (UNICAMP), Campinas, Brazil
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Fiona J Coutinho
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle M Kushida
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lilian Lee
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Naghmeh Rastegar
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - María Sánchez-Osuna
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | | | - Evgeny Kanshin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Heather Whetstone
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mathieu Durand
- RNomics Platform, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Kirsten Hart
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Maria Mangos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Joseph Veyhl
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Wenjun Chen
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Nhat Tran
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Bang-Chi Duong
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Ahmed M Aman
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Xinghui Che
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xiaoyang Lan
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Owen Whitley
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Olga Zaslaver
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Laura M Richards
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Ian Restall
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Amy Caudy
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Maple Flavored Solutions, LLC, Stony Brook, NY, USA
| | - Hannes L Röst
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Sunit Das
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Cusimano
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, Toronto, ON, Canada
| | - Julian Spears
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Department of Medical Imaging, St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - H Artee Luchman
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- Clark H. Smith Brain Tumor Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samuel Weiss
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
- Clark H. Smith Brain Tumor Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katlin B Massirer
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, Brazil
- The Structural Genomics Consortium, University of Campinas (UNICAMP), Campinas, Brazil
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.
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8
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Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production. PLoS Pathog 2020; 16:e1008593. [PMID: 33180834 PMCID: PMC7707522 DOI: 10.1371/journal.ppat.1008593] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/01/2020] [Accepted: 10/04/2020] [Indexed: 12/11/2022] Open
Abstract
Despite the existence of a preventive vaccine, chronic infection with Hepatitis B virus (HBV) affects more than 250 million people and represents a major global cause of hepatocellular carcinoma (HCC) worldwide. Current clinical treatments, in most of cases, do not eliminate viral genome that persists as a DNA episome in the nucleus of hepatocytes and constitutes a stable template for the continuous expression of viral genes. Several studies suggest that, among viral factors, the HBV core protein (HBc), well-known for its structural role in the cytoplasm, could have critical regulatory functions in the nucleus of infected hepatocytes. To elucidate these functions, we performed a proteomic analysis of HBc-interacting host-factors in the nucleus of differentiated HepaRG, a surrogate model of human hepatocytes. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs), which are involved in various aspects of mRNA metabolism. Among them, we focused our studies on SRSF10, a RBP that was previously shown to regulate alternative splicing (AS) in a phosphorylation-dependent manner and to control stress and DNA damage responses, as well as viral replication. Functional studies combining SRSF10 knockdown and a pharmacological inhibitor of SRSF10 phosphorylation (1C8) showed that SRSF10 behaves as a restriction factor that regulates HBV RNAs levels and that its dephosphorylated form is likely responsible for the anti-viral effect. Surprisingly, neither SRSF10 knock-down nor 1C8 treatment modified the splicing of HBV RNAs but rather modulated the level of nascent HBV RNA. Altogether, our work suggests that in the nucleus of infected cells HBc interacts with multiple RBPs that regulate viral RNA metabolism. Our identification of SRSF10 as a new anti-HBV restriction factor offers new perspectives for the development of new host-targeted antiviral strategies. Chronic infection with Hepatitis B virus (HBV) affects more than 250 million of people world-wide and is a major global cause of liver cancer. Current treatments lead to a significant reduction of viremia in patients. However, viral clearance is rarely obtained and the persistence of the HBV genome in the hepatocyte’s nucleus generates a stable source of viral RNAs and subsequently proteins which play important roles in immune escape mechanisms and liver disease progression. Therapies aiming at efficiently and durably eliminating viral gene expression are still required. In this study, we identified the nuclear partners of the HBV Core protein (HBc) to understand how this structural protein, responsible for capsid assembly in the cytoplasm, could also regulate viral gene expression. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs). One of these RBPs, SRSF10, was demonstrated to restrict HBV RNA levels and a drug, able to alter its phosphorylation, behaved as an antiviral compound capable of reducing viral gene expression. Altogether, this study sheds new light on novel regulatory functions of HBc and provides information relevant for the development of antiviral strategies aiming at preventing viral gene expression.
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Vasianovich Y, Bajon E, Wellinger RJ. Telomerase biogenesis requires a novel Mex67 function and a cytoplasmic association with the Sm 7 complex. eLife 2020; 9:60000. [PMID: 33095156 PMCID: PMC7644208 DOI: 10.7554/elife.60000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
The templating RNA is the core of the telomerase reverse transcriptase. In Saccharomyces cerevisiae, the complex life cycle and maturation of telomerase includes a cytoplasmic stage. However, timing and reason for this cytoplasmic passage are poorly understood. Here, we use inducible RNA tagging experiments to show that immediately after transcription, newly synthesized telomerase RNAs undergo one round of nucleo-cytoplasmic shuttling. Their export depends entirely on Crm1/Xpo1, whereas re-import is mediated by Kap122 plus redundant, kinetically less efficient import pathways. Strikingly, Mex67 is essential to stabilize newly transcribed RNA before Xpo1-mediated nuclear export. The results further show that the Sm7 complex associates with and stabilizes the telomerase RNA in the cytoplasm and promotes its nuclear re-import. Remarkably, after this cytoplasmic passage, the nuclear stability of telomerase RNA no longer depends on Mex67. These results underscore the utility of inducible RNA tagging and challenge current models of telomerase maturation.
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Affiliation(s)
- Yulia Vasianovich
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Emmanuel Bajon
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
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Sage M, See W, Nault S, Morin C, Michalski C, Chabot B, Marouan S, Lavoie PM, Micheau P, Praud JP, Fortin-Pellerin É. Effect of Low Versus High Tidal-Volume Total Liquid Ventilation on Pulmonary Inflammation. Front Physiol 2020; 11:603. [PMID: 32625110 PMCID: PMC7315809 DOI: 10.3389/fphys.2020.00603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/14/2020] [Indexed: 01/28/2023] Open
Abstract
Animal experiments suggest that total liquid ventilation (TLV) induces less ventilator-induced lung injury (VILI) than conventional mechanical gas ventilation. However, TLV parameters that optimally minimize VILI in newborns remain unknown. Our objective was to compare lung inflammation between low (L-VT) and high (H-VT) liquid tidal volume and evaluate impacts on the weaning process. Sixteen anesthetized and paralyzed newborn lambs were randomized in an L-VT group (initial tidal volume of 10 mL/kg at 10/min) and an H-VT group (initial tidal volume of 20 mL/kg at 5/min). Five unventilated newborn lambs served as controls. After 4 h of TLV in the supine position, the lambs were weaned in the prone position for another 4 h. The levels of respiratory support needed during the 4 h post-TLV were compared. The anterior and posterior lung regions were assessed by a histological score and real-time quantitative PCR for IL1B, IL6, and TNF plus 12 other exploratory VILI-associated genes. All but one lamb were successfully extubated within 2 h post-TLV (72 ± 26 min vs. 63 ± 25 min, p = 0.5) with similar FiO2 at 4 h post-TLV (27 ± 6% vs. 33 ± 7%, p = 0.3) between the L-VT and H-VT lambs. No significant differences were measured in histological inflammation scores between L-VT and H-VT lambs, although lambs in both groups exhibited slightly higher scores than the control lambs. The L-VT group displayed higher IL1B mRNA expression than the H-VT group in both anterior (2.8 ± 1.5-fold increase vs. 1.3 ± 0.4-fold increase, p = 0.02) and posterior lung regions (3.0 ± 1.0-fold change increase vs. 1.1 ± 0.3-fold increase, p = 0.002), respectively. No significant differences were found in IL6 and TNF expression levels. Gene expression changes overall indicated that L-VT was associated with a qualitatively distinct inflammatory gene expression profiles compared to H-VT, which may indicate different clinical effects. In light of these findings, further mechanistic studies are warranted. In conclusion, we found no advantage of lower tidal volume use, which was in fact associated with a slightly unfavorable pattern of inflammatory gene expression.
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Affiliation(s)
- Michaël Sage
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Wendy See
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Stéphanie Nault
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christophe Morin
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christina Michalski
- BC Children’s Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
- Department of Experimental Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectiology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Sofia Marouan
- Department of Pathology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pascal M. Lavoie
- BC Children’s Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
- Department of Experimental Medicine, The University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - Philippe Micheau
- Department of Mechanical Engineering, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Paul Praud
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Pediatrics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Étienne Fortin-Pellerin
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Pediatrics, Université de Sherbrooke, Sherbrooke, QC, Canada
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11
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Su F, Wang G, Ji J, Zhang P, Wang F, Li Z. Real-time detection of mRNA splicing variants with specifically designed reverse-transcription loop-mediated isothermal amplification. RSC Adv 2020; 10:6271-6276. [PMID: 35495989 PMCID: PMC9049701 DOI: 10.1039/d0ra00591f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 01/31/2020] [Indexed: 01/22/2023] Open
Abstract
Alternative splicing is a ubiquitous and crucial process in cellular processes and has a specific linkage with diseases. To date, developing cost-effective methods with high sensitivity and specificity for detection of splicing variants has been needed. Herein, we report a novel splicing variant assay based on specifically designed reverse-transcription loop-mediated isothermal amplification. After reverse transcribing the splicing variant into cDNA, four DNA primers are specifically designed to recognize six distinct regions. The four DNA primers can hybridize with corresponding sequences for extension and strand displacement DNA synthesis to form stem-loop DNA and then LAMP amplification is started. The proposed method can detect as low as 100 aM splicing variants in real-time fashion with high specificity, showing great potential in biological function and clinical studies. A novel splicing variant assay is developed based on specifically designed reverse-transcription (RT) loop-mediated isothermal amplification.![]()
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Affiliation(s)
- Fengxia Su
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Guanhao Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Jianing Ji
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Pengbo Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Fangfang Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
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Toledo I, Zhao X, Lacasse P. Effects of milking frequency and domperidone injections on milk production and prolactin signaling in the mammary gland of dairy cows. J Dairy Sci 2020; 103:1969-1981. [DOI: 10.3168/jds.2019-17330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/29/2019] [Indexed: 11/19/2022]
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13
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A bioinformatics workflow for the evaluation of RT-qPCR primer specificity: Application for the assessment of gene expression data reliability in toxicological studies. Regul Toxicol Pharmacol 2020; 111:104575. [PMID: 31945455 DOI: 10.1016/j.yrtph.2020.104575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
The reliability of Reverse Transcription quantitative real-time PCR (RT-qPCR) gene expression data depends on proper primer design and RNA quality controls. Despite freely available genomic databases and bioinformatics tools, primer design deficiencies can be found across life science publications. In order to assess the prevalence of such deficiencies in the toxicological literature, 504 primer sets extracted from a random selection of 70 recent rat toxicological studies were evaluated. The specificity of each primer set was systematically analysed using a bioinformatics workflow developed from publicly available resources (NCBI Primer BLAST, in silico PCR in UCSC genome browser, Ensembl DNA database). Potential mismatches (9%), cross-matches (13.5%), co-amplification of multiple gene splice variants (9%) and sub-optimal amplicon sizes (25%) were identified for a significant proportion of the primer sets assessed in silico. Quality controls for gDNA contamination of RNA samples were infrequently reported in the surveyed manuscripts. Hence, the impacts of gDNA contamination on RT-qPCR data were further investigated, revealing that lowly expressed genes presented higher susceptibility to contaminating gDNA. In addition to the retrospective identification of potential primer design issues presented in this study, the described bioinformatics workflow can also be used prospectively to select candidate primer sets for experimental validation.
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Zhang P, Guo N, Gao K, Su F, Wang F, Li Z. Direct recognition and sensitive detection of circular RNA with ligation-based PCR. Org Biomol Chem 2020; 18:3269-3273. [DOI: 10.1039/d0ob00625d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A sensitive and specific method for circRNA detection is developed through the direct ligation of two ingeniously designed DNA probes.
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Affiliation(s)
- Pengbo Zhang
- School of Chemistry and Biology Engineering
- University of Science and Technology Beijing
- Beijing
- P. R. China
| | - Na Guo
- School of Chemistry and Biology Engineering
- University of Science and Technology Beijing
- Beijing
- P. R. China
| | - Kejian Gao
- School of Chemistry and Biology Engineering
- University of Science and Technology Beijing
- Beijing
- P. R. China
| | - Fengxia Su
- School of Chemistry and Biology Engineering
- University of Science and Technology Beijing
- Beijing
- P. R. China
| | - Fangfang Wang
- School of Chemistry and Biology Engineering
- University of Science and Technology Beijing
- Beijing
- P. R. China
| | - Zhengping Li
- School of Chemistry and Biology Engineering
- University of Science and Technology Beijing
- Beijing
- P. R. China
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15
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Dichotomic effects of clinically used drugs on tumor growth, bone remodeling and pain management. Sci Rep 2019; 9:20155. [PMID: 31882872 PMCID: PMC6934511 DOI: 10.1038/s41598-019-56622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 12/12/2019] [Indexed: 11/08/2022] Open
Abstract
Improvements in the survival of breast cancer patients have led to the emergence of bone health and pain management as key aspects of patient’s quality of life. Here, we used a female rat MRMT-1 model of breast cancer-induced bone pain to compare the effects of three drugs used clinically morphine, nabilone and zoledronate on tumor progression, bone remodeling and pain relief. We found that chronic morphine reduced the mechanical hypersensitivity induced by the proliferation of the luminal B aggressive breast cancer cells in the tumor-bearing femur and prevented spinal neuronal and astrocyte activation. Using MTT cell viability assay and MRI coupled to 18FDG PET imaging followed by ex vivo 3D µCT, we further demonstrated that morphine did not directly exert tumor growth promoting or inhibiting effects on MRMT-1 cancer cells but induced detrimental effects on bone healing by disturbing the balance between bone formation and breakdown. In sharp contrast, both the FDA-approved bisphosphonate zoledronate and the synthetic cannabinoid nabilone prescribed as antiemetics to patients receiving chemotherapy were effective in limiting the osteolytic bone destruction, thus preserving the bone architecture. The protective effect of nabilone on bone metabolism was further accompanied by a direct inhibition of tumor growth. As opposed to zoledronate, nabilone was however not able to manage bone tumor-induced pain and reactive gliosis. Altogether, our results revealed that morphine, nabilone and zoledronate exert disparate effects on tumor growth, bone metabolism and pain control. These findings also support the use of nabilone as an adjuvant therapy for bone metastases.
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16
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Jodoin R, Carrier JC, Rivard N, Bisaillon M, Perreault JP. G-quadruplex located in the 5'UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance. Nucleic Acids Res 2019; 47:10247-10266. [PMID: 31504805 PMCID: PMC6821271 DOI: 10.1093/nar/gkz777] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 12/19/2022] Open
Abstract
The anti-apoptotic BAG-1 protein isoforms are known to be overexpressed in colorectal tumors and are considered to be potential therapeutic targets. The isoforms are derived from alternative translation initiations occuring at four in-frame start codons of a single mRNA transcript. Its 5′UTR also contains an internal ribosome entry site (IRES) regulating the cap-independent translation of the transcript. An RNA G-quadruplex (rG4) is located at the 5′end of the BAG-1 5′UTR, upstream of the known cis-regulatory elements. Herein, we observed that the expression of BAG-1 isoforms is post-transcriptionally regulated in colorectal cancer cells and tumors, and that stabilisation of the rG4 by small molecules ligands reduces the expression of endogenous BAG-1 isoforms. We demonstrated a critical role for the rG4 in the control of both cap-dependent and independent translation of the BAG-1 mRNA in colorectal cancer cells. Additionally, we found an upstream ORF that also represses BAG-1 mRNA translation. The structural probing of the complete 5′UTR showed that the rG4 acts as a steric block which controls the initiation of translation at each start codon of the transcript and also maintains the global 5′UTR secondary structure required for IRES-dependent translation.
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Affiliation(s)
- Rachel Jodoin
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Julie C Carrier
- Service de Gastro-entérologie, Département de médecine, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Nathalie Rivard
- Département d'Anatomie et de Biologie Cellulaire, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Martin Bisaillon
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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Béliveau F, Tarkar A, Dion SP, Désilets A, Ghinet MG, Boudreault PL, St-Georges C, Marsault É, Paone D, Collins J, Macphee CH, Campobasso N, Groy A, Cottom J, Ouellette M, Pope AJ, Leduc R. Discovery and Development of TMPRSS6 Inhibitors Modulating Hepcidin Levels in Human Hepatocytes. Cell Chem Biol 2019; 26:1559-1572.e9. [DOI: 10.1016/j.chembiol.2019.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/06/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023]
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18
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Gillet V, Ouellet A, Stepanov Y, Rodosthenous RS, Croft EK, Brennan K, Abdelouahab N, Baccarelli A, Takser L. miRNA Profiles in Extracellular Vesicles From Serum Early in Pregnancies Complicated by Gestational Diabetes Mellitus. J Clin Endocrinol Metab 2019; 104:5157-5169. [PMID: 31058973 PMCID: PMC6760296 DOI: 10.1210/jc.2018-02693] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
CONTEXT Underlying mechanisms leading to gestational diabetes mellitus (GDM) are still under investigation, and it is unclear whether the placenta plays a role in triggering glucose intolerance or if its functions are modified in response to the hyperglycemia. Circulating miRNAs are involved in placental development and function and are encapsulated in extracellular vesicles (EVs). OBJECTIVE To compare differential expression of miRNAs in circulating EVs in pregnancies complicated by GDM vs controls. METHODS This was a case-control study nested in a prospective pregnancy cohort including 23 women with GDM and 46 matched controls. The presence of serum EVs in early pregnancy was validated by transmission electron microscopy. Placental dimensions were assessed at 11 to 13 weeks of gestation. Differential expression of 17 miRNAs encapsulated in EVs (miR‒122-5p, miR‒132-3p, miR-1323, miR‒182-3p, miR‒210-3p, miR‒29a-3p, miR‒29b-3p, miR‒342-3p, miR‒517-5p, miR‒517a-3p, miR‒518b, miR-520h, miR‒525-5p, miR‒136-5p, miR‒342-3p, miR‒376c-5p, and miR‒494-3p) was assessed using quantitative reverse transcription PCR. RESULTS EVs were present in the early phase of placentation (6 to 15 weeks of gestation) in both cases and controls. No differences were observed for placental dimensions and estimated placental volume between GDM and control groups. Ten miRNAs (miR‒122-5p; miR‒132-3p; miR‒1323; miR‒136-5p; miR‒182-3p; miR‒210-3p; miR‒29a-3p; miR‒29b-3p; miR‒342-3p, and miR-520h) showed significantly higher levels in GDM cases than in controls (P ≤ 0.05). Bioinformatics analysis showed that these miRNAs are involved in trophoblast proliferation/differentiation as well as in insulin secretion/regulation and glucose transport in pregnant women. CONCLUSION The miRNA content of blood EVs may be a promising avenue for studying the early effect of impaired glucose metabolism on placental development.
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Affiliation(s)
- Virginie Gillet
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Correspondence and Reprint Requests: Virginie Gillet, MSc, or Larissa Takser, MD, PhD, Faculté de Médecine et des Sciences de la Santé 3001, 12ème Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada. E-mail: or
| | - Annie Ouellet
- Département d’Obstétrique et de Gynécologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Yulia Stepanov
- Département d’Obstétrique et de Gynécologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Erika Kathe Croft
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Kasey Brennan
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Nadia Abdelouahab
- Département d’Obstétrique et de Gynécologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Andrea Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Larissa Takser
- Département de Pédiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Psychiatrie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Correspondence and Reprint Requests: Virginie Gillet, MSc, or Larissa Takser, MD, PhD, Faculté de Médecine et des Sciences de la Santé 3001, 12ème Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada. E-mail: or
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20
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Brodeur CM, Thibault P, Durand M, Perreault JP, Bisaillon M. Dissecting the expression landscape of cytochromes P450 in hepatocellular carcinoma: towards novel molecular biomarkers. Genes Cancer 2019; 10:97-108. [PMID: 31258835 PMCID: PMC6584210 DOI: 10.18632/genesandcancer.190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths around the world. Recent advances in genomic technologies have allowed the identification of various molecular signatures in HCC tissues. For instance, differential gene expression levels of various cytochrome P450 genes (CYP450) have been reported in studies performed on limited numbers of HCC tissue samples, or focused on a small subset on CYP450s. In the present study, we monitored the expression landscape of all the members of the CYP450 family (57 genes) in more than 200 HCC tissues using RNA-Seq data from The Cancer Genome Atlas. Using stringent statistical filters and data from paired tissues, we identified significantly dysregulated CYP450 genes in HCC. Moreover, the expression level of selected CYP450s was validated by qPCR on cDNA samples from an independent cohort. Threshold values (sensitivity and specificity) based on dysregulated gene expression were also determined to allow for confident identification of HCC tissues. Finally, a global look at expression levels of the 57 members of the CYP450 family across ten different cancer types revealed specific expression signatures. Overall, this study provides useful information on the transcriptomic landscape of CYP450 genes in HCC and on new potential HCC biomarkers.
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Affiliation(s)
- Camille Martenon Brodeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Philippe Thibault
- Laboratoire de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mathieu Durand
- Laboratoire de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jean-Pierre Perreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Martin Bisaillon
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Parenteau J, Maignon L, Berthoumieux M, Catala M, Gagnon V, Abou Elela S. Introns are mediators of cell response to starvation. Nature 2019; 565:612-617. [DOI: 10.1038/s41586-018-0859-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022]
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22
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Gagné-Sansfacon J, Langlois A, Langlois MJ, Coulombe G, Tremblay S, Vaillancourt-Lavigueur V, Qu CK, Menendez A, Rivard N. The tyrosine phosphatase Shp-2 confers resistance to colonic inflammation by driving goblet cell function and crypt regeneration. J Pathol 2018; 247:135-146. [PMID: 30376595 PMCID: PMC6519201 DOI: 10.1002/path.5177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/30/2018] [Accepted: 12/25/2018] [Indexed: 12/18/2022]
Abstract
The Src homology‐2 domain‐containing tyrosine phosphatase 2 (SHP‐2) regulates many cellular processes, including proliferation, differentiation and survival. Polymorphisms in the gene encoding SHP‐2 are associated with an increased susceptibility to develop ulcerative colitis. We recently reported that intestinal epithelial cell (IEC)‐specific deletion of Shp‐2 in mice (Shp‐2IEC‐KO) leads to chronic colitis and colitis‐associated cancer. This suggests that SHP‐2‐dependent signaling protects the colonic epithelium against inflammation and colitis‐associated cancer development. To verify this hypothesis, we generated mice expressing the Shp‐2 E76K activated form specifically in IEC. Our results showed that sustained Shp‐2 activation in IEC increased intestine and crypt length, correlating with increased cell proliferation and migration. Crypt regeneration capacity was also markedly enhanced, as revealed by ex vivo organoid culture. Shp‐2 activation alters the secretory cell lineage, as evidenced by increased goblet cell numbers and mucus secretion. Notably, these mice also demonstrated elevated ERK signaling in IEC and exhibited resistance against both chemical‐ and Citrobacter rodentium‐induced colitis. In contrast, mice with IEC‐specific Shp‐2 deletion displayed reduced ERK signaling and rapidly developed chronic colitis. Remarkably, expression of an activated form of Braf in Shp‐2‐deficient mice restored ERK activation, goblet cell production and prevented colitis. Altogether, our results indicate that chronic activation of Shp‐2/ERK signaling in the colonic epithelium confers resistance to mucosal erosion and colitis. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jessica Gagné-Sansfacon
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Ariane Langlois
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Marie-Josée Langlois
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Geneviève Coulombe
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Sarah Tremblay
- Department of Microbiology and Infectiology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Vanessa Vaillancourt-Lavigueur
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Cheng-Kui Qu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alfredo Menendez
- Department of Microbiology and Infectiology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Nathalie Rivard
- Department of Anatomy and Cell Biology, Cancer Research Pavilion, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
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23
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Chen Z, Mo J, Brosseau JP, Shipman T, Wang Y, Liao CP, Cooper JM, Allaway RJ, Gosline SJC, Guinney J, Carroll TJ, Le LQ. Spatiotemporal Loss of NF1 in Schwann Cell Lineage Leads to Different Types of Cutaneous Neurofibroma Susceptible to Modification by the Hippo Pathway. Cancer Discov 2018; 9:114-129. [PMID: 30348677 DOI: 10.1158/2159-8290.cd-18-0151] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/18/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a cancer predisposition disorder that results from inactivation of the tumor suppressor neurofibromin, a negative regulator of RAS signaling. Patients with NF1 present with a wide range of clinical manifestations, and the tumor with highest prevalence is cutaneous neurofibroma (cNF). Most patients harboring cNF suffer greatly from the burden of those tumors, which have no effective medical treatment. Ironically, none of the numerous NF1 mouse models developed so far recapitulate cNF. Here, we discovered that HOXB7 serves as a lineage marker to trace the developmental origin of cNF neoplastic cells. Ablating Nf1 in the HOXB7 lineage faithfully recapitulates both human cutaneous and plexiform neurofibroma. In addition, we discovered that modulation of the Hippo pathway acts as a "modifier" for neurofibroma tumorigenesis. This mouse model opens the doors for deciphering the evolution of cNF to identify effective therapies, where none exist today. SIGNIFICANCE: This study provides insights into the developmental origin of cNF, the most common tumor in NF1, and generates the first mouse model that faithfully recapitulates both human cutaneous and plexiform neurofibroma. The study also demonstrates that the Hippo pathway can modify neurofibromagenesis, suggesting that dampening the Hippo pathway could be an attractive therapeutic target.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Zhiguo Chen
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Juan Mo
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jean-Philippe Brosseau
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tracey Shipman
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yong Wang
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chung-Ping Liao
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jonathan M Cooper
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | | | | | | | - Thomas J Carroll
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, Texas.,Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lu Q Le
- Department of Dermatology, The University of Texas Southwestern Medical Center, Dallas, Texas. .,Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas.,Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas.,Neurofibromatosis Clinic, The University of Texas Southwestern Medical Center, Dallas, Texas
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24
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Boivin V, Deschamps-Francoeur G, Couture S, Nottingham RM, Bouchard-Bourelle P, Lambowitz AM, Scott MS, Abou-Elela S. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA (NEW YORK, N.Y.) 2018; 24:950-965. [PMID: 29703781 PMCID: PMC6004057 DOI: 10.1261/rna.064493.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/24/2018] [Indexed: 06/01/2023]
Abstract
Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. Structured noncoding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing.
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Affiliation(s)
- Vincent Boivin
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Philia Bouchard-Bourelle
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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25
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Dion SP, Béliveau F, Désilets A, Ghinet MG, Leduc R. Transcriptome analysis reveals TMPRSS6 isoforms with distinct functionalities. J Cell Mol Med 2018; 22:2498-2509. [PMID: 29441715 PMCID: PMC5867103 DOI: 10.1111/jcmm.13562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/10/2018] [Indexed: 11/30/2022] Open
Abstract
TMPRSS6 (matriptase-2) is a type II transmembrane serine protease involved in iron homoeostasis. At the cell surface of hepatocytes, TMPRSS6 cleaves haemojuvelin (HJV) and regulates the BMP/SMAD signalling pathway leading to production of hepcidin, a key regulator of iron absorption. Although four TMPRSS6 human isoforms and three mice Tmprss6 isoforms are annotated in databases (Ensembl and RefSeq), their relative expression or activity has not been studied. Analyses of RNA-seq data and RT-PCR from human tissues reveal that TMPRSS6 isoform 1 (TMPRSS6-1) and 3 are mostly expressed in human testis while TMPRSS6-2 and TMPRSS6-4 are the main transcripts expressed in human liver, testis and pituitary. Furthermore, we confirm the existence and analyse the relative expression of three annotated mice Tmprss6 isoforms. Using heterologous expression in HEK293 and Hep3B cells, we show that all human TMPRSS6 isoforms reach the cell surface but only TMPRSS6-1 undergoes internalization. Moreover, truncated TMPRSS6-3 or catalytically altered TMPRSS6-4 interact with HJV and prevent its cleavage by TMPRSS6-2, suggesting their potential role as dominant negative isoforms. Taken together, our results highlight the importance of understanding the precise function of each TMPRSS6 isoforms both in human and in mouse.
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Affiliation(s)
- Sébastien P. Dion
- Department of Pharmacology‐PhysiologyFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
- Institut de Pharmacologie de SherbrookeFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
| | - François Béliveau
- Department of Pharmacology‐PhysiologyFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
- Institut de Pharmacologie de SherbrookeFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
| | - Antoine Désilets
- Department of Pharmacology‐PhysiologyFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
- Institut de Pharmacologie de SherbrookeFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
| | - Mariana Gabriela Ghinet
- Department of Pharmacology‐PhysiologyFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
- Institut de Pharmacologie de SherbrookeFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
| | - Richard Leduc
- Department of Pharmacology‐PhysiologyFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
- Institut de Pharmacologie de SherbrookeFaculty of Medicine and Health SciencesUniversité de SherbrookeSherbrookeQCCanada
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26
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Tong J, Thompson I, Zhao X, Lacasse P. Effect of 17β-estradiol on milk production, hormone secretion, and mammary gland gene expression in dairy cows. J Dairy Sci 2018; 101:2588-2601. [DOI: 10.3168/jds.2017-13353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022]
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27
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Rouleau SG, Garant JM, Bolduc F, Bisaillon M, Perreault JP. G-Quadruplexes influence pri-microRNA processing. RNA Biol 2017; 15:198-206. [PMID: 29171334 DOI: 10.1080/15476286.2017.1405211] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA G-Quadruplexes (G4) have been shown to possess many biological functions, including the regulation of microRNA (miRNA) biogenesis and function. However, their impact on pri-miRNA processing remains unknown. We identified G4 located near the Drosha cleavage site in three distinct pri-miRNAs: pri-mir200c, pri-mir451a, and pri-mir497. The folding of the potential G4 motifs was determined in solution. Subsequently, mutations disrupting G4 folding led to important changes in the mature miRNAs levels in cells. Moreover, using small antisense oligonucleotides binding to the pri-miRNA, it was possible to modulate, either positively or negatively, the mature miRNA levels. Together, these data demonstrate that G4 motifs could contribute to the regulation of pri-mRNA processing, a novel role for G4. Considering that bio-informatics screening indicates that between 9% and 50% of all pri-miRNAs contain a putative G4, these structures possess interesting potential as future therapeutic targets.
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Affiliation(s)
- Samuel G Rouleau
- a Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer , Université de , Sherbrooke, 3201 Jean-Mignault, Sherbrooke , Québec , Canada
| | - Jean-Michel Garant
- a Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer , Université de , Sherbrooke, 3201 Jean-Mignault, Sherbrooke , Québec , Canada
| | - François Bolduc
- a Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer , Université de , Sherbrooke, 3201 Jean-Mignault, Sherbrooke , Québec , Canada
| | - Martin Bisaillon
- a Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer , Université de , Sherbrooke, 3201 Jean-Mignault, Sherbrooke , Québec , Canada
| | - Jean-Pierre Perreault
- a Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer , Université de , Sherbrooke, 3201 Jean-Mignault, Sherbrooke , Québec , Canada
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28
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Dapas M, Kandpal M, Bi Y, Davuluri RV. Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. Brief Bioinform 2017; 18:260-269. [PMID: 26944083 PMCID: PMC5444266 DOI: 10.1093/bib/bbw016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Indexed: 01/04/2023] Open
Abstract
Given that the majority of multi-exon genes generate diverse functional products, it is important to evaluate expression at the isoform level. Previous studies have demonstrated strong gene-level correlations between RNA sequencing (RNA-seq) and microarray platforms, but have not studied their concordance at the isoform level. We performed transcript abundance estimation on raw RNA-seq and exon-array expression profiles available for common glioblastoma multiforme samples from The Cancer Genome Atlas using different analysis pipelines, and compared both the isoform- and gene-level expression estimates between programs and platforms. The results showed better concordance between RNA-seq/exon-array and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) platforms for fold change estimates than for raw abundance estimates, suggesting that fold change normalization against a control is an important step for integrating expression data across platforms. Based on RT-qPCR validations, eXpress and Multi-Mapping Bayesian Gene eXpression (MMBGX) programs achieved the best performance for RNA-seq and exon-array platforms, respectively, for deriving the isoform-level fold change values. While eXpress achieved the highest correlation with the RT-qPCR and exon-array (MMBGX) results overall, RSEM was more highly correlated with MMBGX for the subset of transcripts that are highly variable across the samples. eXpress appears to be most successful in discriminating lowly expressed transcripts, but IsoformEx and RSEM correlate more strongly with MMBGX for highly expressed transcripts. The results also reinforce how potentially important isoform-level expression changes can be masked by gene-level estimates, and demonstrate that exon arrays yield comparable results to RNA-seq for evaluating isoform-level expression changes.
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Affiliation(s)
| | - Manoj Kandpal
- Department of Veterinary Surgery & Radiology, College of Veterinary & Animal Sciences, GBPUAT, Pantnagar - 263 145, Uttarakhand, India
| | - Yingtao Bi
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, 19104 Philadelphia, PA, USA
| | - Ramana V Davuluri
- Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, 19104 Philadelphia, PA, USA
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29
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Lanchec E, Désilets A, Béliveau F, Flamier A, Mahmoud S, Bernier G, Gris D, Leduc R, Lavoie C. The type II transmembrane serine protease matriptase cleaves the amyloid precursor protein and reduces its processing to β-amyloid peptide. J Biol Chem 2017; 292:20669-20682. [PMID: 29054928 DOI: 10.1074/jbc.m117.792911] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/16/2017] [Indexed: 11/06/2022] Open
Abstract
Recent studies have reported that many proteases, besides the canonical α-, β-, and γ-secretases, cleave the amyloid precursor protein (APP) and modulate β-amyloid (Aβ) peptide production. Moreover, specific APP isoforms contain Kunitz protease-inhibitory domains, which regulate the proteolytic activity of serine proteases. This prompted us to investigate the role of matriptase, a member of the type II transmembrane serine protease family, in APP processing. Using quantitative RT-PCR, we detected matriptase mRNA in several regions of the human brain with an enrichment in neurons. RNA sequencing data of human dorsolateral prefrontal cortex revealed relatively high levels of matriptase RNA in young individuals, whereas lower levels were detected in older individuals. We further demonstrate that matriptase and APP directly interact with each other and that matriptase cleaves APP at a specific arginine residue (Arg-102) both in vitro and in cells. Site-directed (Arg-to-Ala) mutagenesis of this cleavage site abolished matriptase-mediated APP processing. Moreover, we observed that a soluble, shed matriptase form cleaves endogenous APP in SH-SY5Y cells and that this cleavage significantly reduces APP processing to Aβ40. In summary, this study identifies matriptase as an APP-cleaving enzyme, an activity that could have important consequences for the abundance of Aβ and in Alzheimer's disease pathology.
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Affiliation(s)
- Erwan Lanchec
- From the Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada
| | - Antoine Désilets
- From the Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada
| | - François Béliveau
- From the Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada
| | - Anthony Flamier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boulevard de l'Assomption, Montréal, Quebec H1T 2M4, Canada
| | - Shaimaa Mahmoud
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada, and
| | - Gilbert Bernier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, 5415 Boulevard de l'Assomption, Montréal, Quebec H1T 2M4, Canada.,Department of Neurosciences, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Denis Gris
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada, and
| | - Richard Leduc
- From the Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada,
| | - Christine Lavoie
- From the Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada,
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30
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Shkreta L, Blanchette M, Toutant J, Wilhelm E, Bell B, Story BA, Balachandran A, Cochrane A, Cheung PK, Harrigan PR, Grierson DS, Chabot B. Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication. Nucleic Acids Res 2017; 45:4051-4067. [PMID: 27928057 PMCID: PMC5397194 DOI: 10.1093/nar/gkw1223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
We recently identified the 4-pyridinone-benzisothiazole carboxamide compound 1C8 as displaying strong anti-HIV-1 potency against a variety of clinical strains in vitro. Here we show that 1C8 decreases the expression of HIV-1 and alters splicing events involved in the production of HIV-1 mRNAs. Although 1C8 was designed to be a structural mimic of the fused tetracyclic indole compound IDC16 that targets SRSF1, it did not affect the splice site shifting activity of SRSF1. Instead, 1C8 altered splicing regulation mediated by SRSF10. Depleting SRSF10 by RNA interference affected viral splicing and, like 1C8, decreased expression of Tat, Gag and Env. Incubating cells with 1C8 promoted the dephosphorylation of SRSF10 and increased its interaction with hTra2β, a protein previously implicated in the control of HIV-1 RNA splicing. While 1C8 affects the alternative splicing of cellular transcripts controlled by SRSF10 and hTra2β, concentrations greater than those needed to inhibit HIV-1 replication were required to elicit significant alterations. Thus, the ability of 1C8 to alter the SRSF10-dependent splicing of HIV-1 transcripts, with minor effects on cellular splicing, supports the view that SRSF10 may be used as a target for the development of new anti-viral agents.
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Affiliation(s)
- Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Johanne Toutant
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Emmanuelle Wilhelm
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Brendan Bell
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Benjamin A Story
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Peter K Cheung
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, 608-1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David S Grierson
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
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31
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Rouleau S, Glouzon JPS, Brumwell A, Bisaillon M, Perreault JP. 3' UTR G-quadruplexes regulate miRNA binding. RNA (NEW YORK, N.Y.) 2017; 23:1172-1179. [PMID: 28473452 PMCID: PMC5513062 DOI: 10.1261/rna.060962.117] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/02/2017] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that repress the translation of their target genes. It has previously been shown that a target's availability to miRNA can be affected by its structure. G-quadruplexes (G4) are noncanonical structures adopted by G-rich nucleic acids that have been shown to have multiple biological functions. In this study, whether or not G4 structures' presence in the 3' UTRs of mRNAs can hinder miRNA binding was investigated. Putative G4 overlapping with predicted miRNAs' binding sites was searched for, and 44,294 hits were found in humans. The FADS2 mRNA/mir331-3p pair was selected as a model example. In-line probing and G4-specific fluorescent ligand experiments binding were performed and confirmed the presence of a G4 near the predicted miRNA binding site. Subsequent luciferase assays showed that the presence of the G4 prevents the binding of mir331-3p in cellulo. Together, these results served as proof of concept that a G4 structure present in a 3' UTR sequence should be taken into consideration when predicting miRNA binding sites.
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Affiliation(s)
- Samuel Rouleau
- Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke (Québec), Canada J1E 4K8
| | - Jean-Pierre Sehi Glouzon
- Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke (Québec), Canada J1E 4K8
| | - Andrea Brumwell
- Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke (Québec), Canada J1E 4K8
| | - Martin Bisaillon
- Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke (Québec), Canada J1E 4K8
| | - Jean-Pierre Perreault
- Département de Biochimie, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke (Québec), Canada J1E 4K8
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Wang H, Wang H, Duan X, Sun Y, Wang X, Li Z. Highly sensitive and multiplexed quantification of mRNA splice variants by the direct ligation of DNA probes at the exon junction and universal PCR amplification. Chem Sci 2017; 8:3635-3640. [PMID: 28580102 PMCID: PMC5437374 DOI: 10.1039/c7sc00094d] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/01/2017] [Indexed: 02/06/2023] Open
Abstract
Alternative messenger RNA (mRNA) splicing is a basic mechanism of gene regulation. In general, reverse transcription and polymerase based primer extension limit the sensitivity and selectivity of the current detection of mRNA splice variants, respectively. Here, we show that, using the ligation of two properly designed probes at the exon junction combined with universal PCR amplification, as little as a single copy of a mRNA splice variant per cell can be accurately determined, and the dynamic range covers six orders of magnitude. Three mRNA splice variants were measured from total RNA samples derived from different cell lines. Moreover, by encoding the ligation probes with different lengths, multiplexed mRNA splice variants can be simultaneously detected in one-tube PCR amplification using electrophoretic separation.
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Affiliation(s)
- Honghong Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Hui Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Yuanyuan Sun
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Xiangdong Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
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Lanctôt S, Fustier P, Taherian A, Bisakowski B, Zhao X, Lacasse P. Effect of intramammary infusion of chitosan hydrogels at drying-off on bovine mammary gland involution. J Dairy Sci 2017; 100:2269-2281. [DOI: 10.3168/jds.2016-12087] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/26/2016] [Indexed: 12/23/2022]
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Fei DL, Motowski H, Chatrikhi R, Prasad S, Yu J, Gao S, Kielkopf CL, Bradley RK, Varmus H. Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. PLoS Genet 2016; 12:e1006384. [PMID: 27776121 PMCID: PMC5077151 DOI: 10.1371/journal.pgen.1006384] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022] Open
Abstract
We have asked how the common S34F mutation in the splicing factor U2AF1 regulates alternative splicing in lung cancer, and why wild-type U2AF1 is retained in cancers with this mutation. A human lung epithelial cell line was genetically modified so that U2AF1S34F is expressed from one of the two endogenous U2AF1 loci. By altering levels of mutant or wild-type U2AF1 in this cell line and by analyzing published data on human lung adenocarcinomas, we show that S34F-associated changes in alternative splicing are proportional to the ratio of S34F:wild-type gene products and not to absolute levels of either the mutant or wild-type factor. Preferential recognition of specific 3' splice sites in S34F-expressing cells is largely explained by differential in vitro RNA-binding affinities of mutant versus wild-type U2AF1 for those same 3' splice sites. Finally, we show that lung adenocarcinoma cell lines bearing U2AF1 mutations do not require the mutant protein for growth in vitro or in vivo. In contrast, wild-type U2AF1 is required for survival, regardless of whether cells carry the U2AF1S34F allele. Our results provide mechanistic explanations of the magnitude of splicing changes observed in U2AF1-mutant cells and why tumors harboring U2AF1 mutations always retain an expressed copy of the wild-type allele.
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Affiliation(s)
- Dennis Liang Fei
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Hayley Motowski
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Rakesh Chatrikhi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, United States Of America
| | - Sameer Prasad
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Jovian Yu
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
| | - Shaojian Gao
- Genetics Branch, National Cancer Institute, Bethesda, United States Of America
| | - Clara L. Kielkopf
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Robert K. Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States Of America
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
| | - Harold Varmus
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States Of America
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, United States Of America
- * E-mail: (DLF); (CLK); (RKB); (HV)
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Bergeron J, Gerges N, Guiraut C, Grbic D, Allard MJ, Fortier LC, Vaillancourt C, Sébire G. Activation of the IL-1β/CXCL1/MMP-10 axis in chorioamnionitis induced by inactivated Group B Streptococcus. Placenta 2016; 47:116-123. [PMID: 27780533 DOI: 10.1016/j.placenta.2016.09.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/25/2016] [Indexed: 11/19/2022]
Abstract
Infection or inflammation during pregnancy is known to lead to maternal immune activation triggering a fetal inflammatory response syndrome associated with deleterious effects, such as brain injury and neurodevelopmental disabilities. Group B Streptococcus (GBS) - one of the most common bacterium colonizing pregnant women - can be responsible for chorioamnionitis. Given that interleukin (IL)-1β has a major role in anti-GBS host defense, we hypothesized that IL-1β-driven innate immune response is implicated in GBS-induced chorioamnionitis. Using a rat model of GBS-induced chorioamnionitis, this study showed that inflammatory response to this pathogen was associated with maternal and placental IL-1β hyper expression. Following placental chemokine (C-X-C motif) ligand 1 (CXCL1) production, polymorphonuclear leukocytes (PMN) placental infiltration started at 24 h post-GBS exposure, and MMP-10 was released within these placentas. At 72 h, PMN infiltration extended to membranes and to membranes' arteries. This was associated with IL-1β release within the fetus blood at 72 h. Such a GBS-associated inflammatory cascade might be deleterious for fetal organs. These results pave the way toward targeted placento-protective anti-inflammatory strategies against GBS-induced chorioamnionitis.
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Affiliation(s)
- Julie Bergeron
- Département de pédiatrie, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada.
| | - Noha Gerges
- Departments of Pediatrics and Neurology and Neurosurgery, McGill University, 1001, Décarie boulevard, room EM0.3211, Montreal, Québec, H4A 3J1, Canada.
| | - Clémence Guiraut
- Departments of Pediatrics and Neurology and Neurosurgery, McGill University, 1001, Décarie boulevard, room EM0.3211, Montreal, Québec, H4A 3J1, Canada.
| | - Djordje Grbic
- Département de pédiatrie, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada.
| | - Marie-Julie Allard
- Departments of Pediatrics and Neurology and Neurosurgery, McGill University, 1001, Décarie boulevard, room EM0.3211, Montreal, Québec, H4A 3J1, Canada
| | - Louis-Charles Fortier
- Département de Microbiologie, Université de Sherbrooke, 3201 rue Jean Mignault, Sherbrooke, Quebec, J1E 4K8, Canada.
| | - Cathy Vaillancourt
- INRS- Centre Institut Armand Frappier, 531 boulevard des Prairies, Laval, Quebec, H7V 1B7, Canada.
| | - Guillaume Sébire
- Département de pédiatrie, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada; Departments of Pediatrics and Neurology and Neurosurgery, McGill University, 1001, Décarie boulevard, room EM0.3211, Montreal, Québec, H4A 3J1, Canada.
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Laroche-Lefebvre C, Yousefi M, Daudelin JF, Charpentier T, Tarrab E, Klinck R, Lamarre A, Labrecque N, Stäger S, Duplay P. Dok-1 and Dok-2 Regulate the Formation of Memory CD8+ T Cells. THE JOURNAL OF IMMUNOLOGY 2016; 197:3618-3627. [PMID: 27664281 DOI: 10.4049/jimmunol.1600385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 09/06/2016] [Indexed: 11/19/2022]
Abstract
Diverse signals received by CD8+ T cells are integrated to achieve the required magnitude of cell expansion and the appropriate balance of effector/memory CD8+ T cell generation. Notably, the strength and nature of TCR signaling influence the differentiation and functional capacity of effector and memory CD8+ T cells. Dok-1 and Dok-2, the two members of the Dok family expressed in T cells, negatively regulate TCR signaling in vitro. However, the role of Dok proteins in modulating T cell function in vivo has not yet studied. We studied the function of Dok-1 and Dok-2 proteins in the regulation of the CD8+ T cell response to vaccinia virus infection. Comparison of responses to vaccinia virus expressing OVA peptide SIINFEKL by wild-type and Dok-1/2-/- CD8+ OT-I cells showed that the absence of Dok-1 and Dok-2 slightly reduced the magnitude of virus-specific effector CD8+ T cell expansion. This was not due to reduced proliferation or enhanced apoptosis of effector CD8+ T cells. Dok-1/2-deficient effector CD8+ T cells showed increased cell surface TCR expression following virus infection in vivo and increased expression of granzyme B and TNF upon stimulation with peptide Ag ex vivo. Finally, Dok-1/2-deficient effector CD8+ T had a severe defect in survival that resulted in impaired generation of memory CD8+ T cells. These results reveal the critical involvement of Dok-1 and Dok-2 in a negative-feedback loop that prevents overactivation of CD8+ T cells and promotes memory formation.
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Affiliation(s)
- Constance Laroche-Lefebvre
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada
| | - Mitra Yousefi
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada
| | - Jean-François Daudelin
- Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec H1T 2M4, Canada; and
| | - Tania Charpentier
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada
| | - Esther Tarrab
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada
| | - Roscoe Klinck
- Laboratoire de Génomique Fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Alain Lamarre
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada
| | - Nathalie Labrecque
- Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec H1T 2M4, Canada; and
| | - Simona Stäger
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada
| | - Pascale Duplay
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, Laval, Quebec H7V 1B7, Canada;
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Blondeau A, Lucier JF, Matteau D, Dumont L, Rodrigue S, Jacques PÉ, Blouin R. Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells. Neural Dev 2016; 11:13. [PMID: 27468987 PMCID: PMC4965899 DOI: 10.1186/s13064-016-0068-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background Recent genetic studies in model organisms, such as Drosophila, C. elegans and mice, have highlighted a critical role for dual leucine zipper kinase (DLK) in neural development and axonal responses to injury. However, exactly how DLK fulfills these functions remains to be determined. Using RNA-seq profiling, we evaluated the global changes in gene expression that are caused by shRNA-mediated knockdown of endogenous DLK in differentiated Neuro-2a neuroblastoma cells. Results Our analysis led to the identification of numerous up- and down-regulated genes, among which several were found to be associated with system development and axon guidance according to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, respectively. Because of their importance in axonal growth, pruning and regeneration during development and adult life, we then examined by quantitative RT-PCR the mRNA expression levels of the identified axon guidance genes in DLK-depleted cells. Consistent with the RNA-seq data, our results confirmed that loss of DLK altered expression of the genes encoding neuropilin 1 (Nrp1), plexin A4 (Plxna4), Eph receptor A7 (Epha7), Rho family GTPase 1 (Rnd1) and semaphorin 6B (Sema6b). Interestingly, this regulation of Nrp1 and Plxna4 mRNA expression by DLK in Neuro-2a cells was also reflected at the protein level, implicating DLK in the modulation of the function of these axon guidance molecules. Conclusions Collectively, these results provide the first evidence that axon guidance genes are downstream targets of the DLK signaling pathway, which through their regulation probably modulates neuronal cell development, structure and function. Electronic supplementary material The online version of this article (doi:10.1186/s13064-016-0068-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andréanne Blondeau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Jean-François Lucier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Dominick Matteau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Lauralyne Dumont
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Pierre-Étienne Jacques
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.,Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.,Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, Canada
| | - Richard Blouin
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
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Fackenthal JD, Yoshimatsu T, Zhang B, de Garibay GR, Colombo M, De Vecchi G, Ayoub SC, Lal K, Olopade OI, Vega A, Santamariña M, Blanco A, Wappenschmidt B, Becker A, Houdayer C, Walker LC, López-Perolio I, Thomassen M, Parsons M, Whiley P, Blok MJ, Brandão RD, Tserpelis D, Baralle D, Montalban G, Gutiérrez-Enríquez S, Díez O, Lazaro C, Spurdle AB, Radice P, de la Hoya M. Naturally occurring BRCA2 alternative mRNA splicing events in clinically relevant samples. J Med Genet 2016; 53:548-58. [PMID: 27060066 DOI: 10.1136/jmedgenet-2015-103570] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/10/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 are the two principal tumour suppressor genes associated with inherited high risk of breast and ovarian cancer. Genetic testing of BRCA1/2 will often reveal one or more sequence variants of uncertain clinical significance, some of which may affect normal splicing patterns and thereby disrupt gene function. mRNA analyses are therefore among the tests used to interpret the clinical significance of some genetic variants. However, these could be confounded by the appearance of naturally occurring alternative transcripts unrelated to germline sequence variation or defects in gene function. To understand which novel splicing events are associated with splicing mutations and which are part of the normal BRCA2 splicing repertoire, a study was undertaken by members of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium to characterise the spectrum of naturally occurring BRCA2 mRNA alternate-splicing events. METHODS mRNA was prepared from several blood and breast tissue-derived cells and cell lines by contributing ENIGMA laboratories. cDNA representing BRCA2 alternate splice sites was amplified and visualised using capillary or agarose gel electrophoresis, followed by sequencing. RESULTS We demonstrate the existence of 24 different BRCA2 mRNA alternate-splicing events in lymphoblastoid cell lines and both breast cancer and non-cancerous breast cell lines. CONCLUSIONS These naturally occurring alternate-splicing events contribute to the array of cDNA fragments that may be seen in assays for mutation-associated splicing defects. Caution must be observed in assigning alternate-splicing events to potential splicing mutations.
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Affiliation(s)
| | - Toshio Yoshimatsu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Bifeng Zhang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Samantha C Ayoub
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Kumar Lal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Barbara Wappenschmidt
- Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University of Cologne and University Hospital Cologne, Germany
| | - Alexandra Becker
- Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University of Cologne and University Hospital Cologne, Germany
| | - Claude Houdayer
- Service de Génétique and INSERM U830, Institut Curie and Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Irene López-Perolio
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Michael Parsons
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Phillip Whiley
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Rita D Brandão
- Maastricht Science Programme, Faculty of Humanities and Sciences, Maastricht University, Maastricht, The Netherlands
| | - Demis Tserpelis
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diana Baralle
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Sara Gutiérrez-Enríquez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain Clinical and Molecular Genetics Area, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | | | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Miguel de la Hoya
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
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Global transcriptional response of Clostridium difficile carrying the CD38 prophage. Appl Environ Microbiol 2016; 81:1364-74. [PMID: 25501487 DOI: 10.1128/aem.03656-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Clostridium difficile is one of the most dangerous pathogens in hospital settings. Most strains of C. difficile carry one or more prophages, and some of them, like CD38-2 and CD119, can influence the expression of toxin genes. However, little is known about the global host response in the presence of a given prophage. In order to fill this knowledge gap, we used high-throughput RNA sequencing (RNA-seq) to conduct a genome-wide transcriptomic analysis of the epidemic C. difficile strain R20291 carrying the CD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and phosphotransferase system (PTS) subunits involved in glucose, fructose, and glucitol/sorbitol uptake and metabolism. CD38-2 also upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was that encoding the conserved phase-variable cell wall protein CwpV, which was upregulated 20-fold in the lysogen. Quantitative PCR and immunofluorescence showed that the increased cwpV expression results from a greater proportion of cells actively transcribing the gene. Indeed, 95% of f lysogenic cells express cwpV, as opposed to only 5% of wild-type cells. Furthermore, the higher proportion of cells expressing cwpV results from a higher frequency of recombination of the genetic switch controlling phase variation, which we confirmed to be dependent on the host-encoded recombinase RecV. In summary, CD38-2 interferes with phase variation of the surface protein CwpV and the expression of metabolic genes.
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Abstract
Design of primers and probes is one of the most crucial factors affecting the success and quality of quantitative real-time PCR (qPCR) analyses, since an accurate and reliable quantification depends on using efficient primers and probes. Design of primers and probes should meet several criteria to find potential primers and probes for specific qPCR assays. The formation of primer-dimers and other non-specific products should be avoided or reduced. This factor is especially important when designing primers for SYBR(®) Green protocols but also in designing probes to ensure specificity of the developed qPCR protocol. To design primers and probes for qPCR, multiple software programs and websites are available being numerous of them free. These tools often consider the default requirements for primers and probes, although new research advances in primer and probe design should be progressively added to different algorithm programs. After a proper design, a precise validation of the primers and probes is necessary. Specific consideration should be taken into account when designing primers and probes for multiplex qPCR and reverse transcription qPCR (RT-qPCR). This chapter provides guidelines for the design of suitable primers and probes and their subsequent validation through the development of singlex qPCR, multiplex qPCR, and RT-qPCR protocols.
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41
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Lin JC. Impacts of Alternative Splicing Events on the Differentiation of Adipocytes. Int J Mol Sci 2015; 16:22169-89. [PMID: 26389882 PMCID: PMC4613302 DOI: 10.3390/ijms160922169] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/07/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing was found to be a common phenomenon after the advent of whole transcriptome analyses or next generation sequencing. Over 90% of human genes were demonstrated to undergo at least one alternative splicing event. Alternative splicing is an effective mechanism to spatiotemporally expand protein diversity, which influences the cell fate and tissue development. The first focus of this review is to highlight recent studies, which demonstrated effects of alternative splicing on the differentiation of adipocytes. Moreover, use of evolving high-throughput approaches, such as transcriptome analyses (RNA sequencing), to profile adipogenic transcriptomes, is also addressed.
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Affiliation(s)
- Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan.
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42
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Receptor for Advanced Glycation End-Products Signaling Interferes with the Vascular Smooth Muscle Cell Contractile Phenotype and Function. PLoS One 2015; 10:e0128881. [PMID: 26248341 PMCID: PMC4527751 DOI: 10.1371/journal.pone.0128881] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/02/2015] [Indexed: 11/27/2022] Open
Abstract
Increased blood glucose concentrations promote reactions between glucose and proteins to form advanced glycation end-products (AGE). Circulating AGE in the blood plasma can activate the receptor for advanced end-products (RAGE), which is present on both endothelial and vascular smooth muscle cells (VSMC). RAGE exhibits a complex signaling that involves small G-proteins and mitogen activated protein kinases (MAPK), which lead to increased nuclear factor kappa B (NF-κB) activity. While RAGE signaling has been previously addressed in endothelial cells, little is known regarding its impact on the function of VSMC. Therefore, we hypothesized that RAGE signaling leads to alterations in the mechanical and functional properties of VSMC, which could contribute to complications associated with diabetes. We demonstrated that RAGE is expressed and functional in the A7r5 VSMC model, and its activation by AGE significantly increased NF-κB activity, which is known to interfere with the contractile phenotype of VSMC. The protein levels of the contraction-related transcription factor myocardin were also decreased by RAGE activation with a concomitant decrease in the mRNA and protein levels of transgelin (SM-22α), a regulator of VSMC contraction. Interestingly, we demonstrated that RAGE activation increased the overall cell rigidity, an effect that can be related to an increase in myosin activity. Finally, although RAGE stimulation amplified calcium signaling and slightly myosin activity in VSMC challenged with vasopressin, their contractile capacity was negatively affected. Overall, RAGE activation in VSMC could represent a keystone in the development of vascular diseases associated with diabetes by interfering with the contractile phenotype of VSMC through the modification of their mechanical and functional properties.
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Matamala N, Martínez MT, Lara B, Pérez L, Vázquez I, Jimenez A, Barquín M, Ferrarotti I, Blanco I, Janciauskiene S, Martinez-Delgado B. Alternative transcripts of the SERPINA1 gene in alpha-1 antitrypsin deficiency. J Transl Med 2015; 13:211. [PMID: 26141700 PMCID: PMC4490674 DOI: 10.1186/s12967-015-0585-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/25/2015] [Indexed: 12/14/2022] Open
Abstract
Background SERPINA1 is the gene for alpha-1 antitrypsin (AAT), an acute phase protein with anti-protease and immunoregulatory activities. Mutations in SERPINA1 gene cause AAT deficiency and predispose individuals to early-onset emphysema and liver diseases. Expression of the SERPINA1 gene is regulated by different promoters and alternative splicing events among non-coding exons 1A, 1B and 1C. Methods We have developed three quantitative PCR (QT-PCR) assays (1A, 1B and 1C). These assays were applied for the analysis of SERPINA1 alternative transcripts in: (1) 16 human tissues and (2) peripheral blood leukocytes from 33 subjects with AAT mutations and 7 controls. Results Tissue-specific expression was found for the SERPINA1 transcripts. The 1A transcripts were mainly expressed in leukocytes and lung tissue while those detected with the 1B assay were highly restricted to leukocytes. Only 1B transcripts significantly correlated with serum AAT levels. The 1C transcripts were specifically found in lung, liver, kidney and pancreas. Furthermore, the expression of transcripts was related to AAT genotypes. While deficient variants of AAT had no pronounced effect on the transcript expression, null alleles were associated with significant reduction of different transcripts. Conclusions The possibility to discriminate between SERPINA1 alternative splicing products will help us to understand better the regulation of SERPINA1 gene and its association with SERPINA1 mutations-related diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0585-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nerea Matamala
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | | | - Beatriz Lara
- Respiratory Medicine Department, Royal Exeter and Devon Hospital, Exeter, Devon, UK.
| | - Laura Pérez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Irene Vázquez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Azucena Jimenez
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Miguel Barquín
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
| | - Ilaria Ferrarotti
- Section of Pneumology, Department of Molecular Medicine, Center for Diagnosis of Inherited Alpha-1 Antitrypsin Deficiency, IRCCS San Matteo Hospital Foundation, University of Pavia, Pavia, Italy.
| | - Ignacio Blanco
- Alpha1-Antitrypsin Deficiency Spanish Registry, Lung Foundation RESPIRA, Spanish Society of Pneumology (SEPAR), Barcelona, Spain.
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, Hannover Medical School, Hanover, Germany. .,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30626, Hanover, Germany.
| | - Beatriz Martinez-Delgado
- Molecular Genetics Unit, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Carretera Majadahonda-Pozuelo Km 2,200, 28220, Majadahonda, Madrid, Spain.
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Proportional upregulation of CD97 isoforms in glioblastoma and glioblastoma-derived brain tumor initiating cells. PLoS One 2015; 10:e0111532. [PMID: 25714433 PMCID: PMC4340952 DOI: 10.1371/journal.pone.0111532] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/03/2014] [Indexed: 01/09/2023] Open
Abstract
CD97 is a novel glioma antigen that confers an invasive phenotype and poor survival in patients with glioblastoma (GBM), the most aggressive primary malignant brain tumor. The short isoform of CD97, known as EGF(1,2,5), has been shown to promote invasion and metastasis, but its role in gliomas and GBM-derived brain tumor initiating cells (BTICs) has not been studied. We sought to characterize CD97 expression among gliomas and identify the specific isoforms expressed. The short isoform of CD97 was identified in GBM and GBM-derived BTICs, but not low grade or anaplastic astrocytomas. All samples expressing the EGF(1,2,5) isoform were also found to express the EGF(1,2,3,5) isoform. These isoforms are believed to possess similar ligand binding patterns and interact with chondroitin sulfate, a component of the extracellular matrix, and the integrin α5β1. Using data acquired from the Cancer Genome Atlas (TCGA), we show that CD97 is upregulated among the classical and mesenchymal subtypes of GBM and significantly decreased among IDH1 mutant GBMs. Given its proven roles in tumor invasion, expression among aggressive genetic subtypes of GBM, and association with overall survival, CD97 is an attractive therapeutic target for patients with GBM.
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Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile. J Bacteriol 2014; 197:819-32. [PMID: 25512308 DOI: 10.1128/jb.02340-14] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile is an anaerobic Gram-positive bacterium that causes intestinal infections with symptoms ranging from mild diarrhea to fulminant colitis. Cyclic diguanosine monophosphate (c-di-GMP) is a bacterial second messenger that typically regulates the switch from motile, free-living to sessile and multicellular behaviors in Gram-negative bacteria. Increased intracellular c-di-GMP concentration in C. difficile was recently shown to reduce flagellar motility and to increase cell aggregation. In this work, we investigated the role of the primary type IV pilus (T4P) locus in c-di-GMP-dependent cell aggregation. Inactivation of two T4P genes, pilA1 (CD3513) and pilB1 (CD3512), abolished pilus formation and significantly reduced cell aggregation under high c-di-GMP conditions. pilA1 is preceded by a putative c-di-GMP riboswitch, predicted to be transcriptionally active upon c-di-GMP binding. Consistent with our prediction, high intracellular c-di-GMP concentration increased transcript levels of T4P genes. In addition, single-round in vitro transcription assays confirmed that transcription downstream of the predicted transcription terminator was dose dependent and specific to c-di-GMP binding to the riboswitch aptamer. These results support a model in which T4P gene transcription is upregulated by c-di-GMP as a result of its binding to an upstream transcriptionally activating riboswitch, promoting cell aggregation in C. difficile.
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Rouleau SG, Beaudoin JD, Bisaillon M, Perreault JP. Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches. Nucleic Acids Res 2014; 43:595-606. [PMID: 25510493 PMCID: PMC4288198 DOI: 10.1093/nar/gku1311] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
G-quadruplexes (G4) are intricate RNA structures found throughout the transcriptome. Because they are associated with a variety of biological cellular mechanisms, these fascinating structural motifs are seen as potential therapeutic targets against many diseases. While screening of chemical compounds specific to G4 motifs has yielded interesting results, no single compound successfully discriminates between G4 motifs based on nucleotide sequences alone. This level of specificity is best attained using antisense oligonucleotides (ASO). Indeed, oligonucleotide-based strategies are already used to modulate DNA G4 folding in vitro. Here, we report that, in human cells, the use of short ASO to promote and inhibit RNA G4 folding affects the translation of specific mRNAs, including one from the 5'UTR of the H2AFY gene, a histone variant associated with cellular differentiation and cancer. These results suggest that the relatively high specificity of ASO-based strategies holds significant potential for applications aimed at modulating G4-motif folding.
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Affiliation(s)
- Samuel G Rouleau
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
| | - Martin Bisaillon
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Québec, J1E 4K8, Canada
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Béliveau É, Lessard V, Guillemette G. STIM1 positively regulates the Ca2+ release activity of the inositol 1,4,5-trisphosphate receptor in bovine aortic endothelial cells. PLoS One 2014; 9:e114718. [PMID: 25506690 PMCID: PMC4266619 DOI: 10.1371/journal.pone.0114718] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/12/2014] [Indexed: 11/19/2022] Open
Abstract
The endothelium is actively involved in many functions of the cardiovascular system, such as the modulation of arterial pressure and the maintenance of blood flow. These functions require a great versatility of the intracellular Ca2+ signaling that resides in the fact that different signals can be encoded by varying the frequency and the amplitude of the Ca2+ response. Cells use both extracellular and intracellular Ca2+ pools to modulate the intracellular Ca2+ concentration. In non-excitable cells, the inositol 1,4,5-trisphosphate receptor (IP3R), located on the endoplasmic reticulum (ER), is responsible for the release of Ca2+ from the intracellular store. The proteins STIM1 and STIM2 are also located on the ER and they are involved in the activation of a store-operated Ca2+ entry (SOCE). Due to their Ca2+ sensor property and their close proximity with IP3Rs on the ER, STIMs could modulate the activity of IP3R. In this study, we showed that STIM1 and STIM2 are expressed in bovine aortic endothelial cells and they both interact with IP3R. While STIM2 appears to play a minor role, STIM1 plays an important role in the regulation of agonist-induced Ca2+ mobilization in BAECs by a positive effect on both the SOCE and the IP3R-dependent Ca2+ release.
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Affiliation(s)
- Éric Béliveau
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada, J1H 5N4
| | - Vincent Lessard
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada, J1H 5N4
| | - Gaétan Guillemette
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada, J1H 5N4
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Carraro N, Matteau D, Luo P, Rodrigue S, Burrus V. The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination. PLoS Genet 2014; 10:e1004714. [PMID: 25340549 PMCID: PMC4207636 DOI: 10.1371/journal.pgen.1004714] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/27/2014] [Indexed: 01/22/2023] Open
Abstract
Dissemination of antibiotic resistance genes occurs mostly by conjugation, which mediates DNA transfer between cells in direct contact. Conjugative plasmids of the IncA/C incompatibility group have become a substantial threat due to their broad host-range, the extended spectrum of antimicrobial resistance they confer, their prevalence in enteric bacteria and their very efficient spread by conjugation. However, their biology remains largely unexplored. Using the IncA/C conjugative plasmid pVCR94ΔX as a prototype, we have investigated the regulatory circuitry that governs IncA/C plasmids dissemination and found that the transcriptional activator complex AcaCD is essential for the expression of plasmid transfer genes. Using chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) approaches, we have identified the sequences recognized by AcaCD and characterized the AcaCD regulon. Data mining using the DNA motif recognized by AcaCD revealed potential AcaCD-binding sites upstream of genes involved in the intracellular mobility functions (recombination directionality factor and mobilization genes) in two widespread classes of genomic islands (GIs) phylogenetically unrelated to IncA/C plasmids. The first class, SGI1, confers and propagates multidrug resistance in Salmonella enterica and Proteus mirabilis, whereas MGIVmi1 in Vibrio mimicus belongs to a previously uncharacterized class of GIs. We have demonstrated that through expression of AcaCD, IncA/C plasmids specifically trigger the excision and mobilization of the GIs at high frequencies. This study provides new evidence of the considerable impact of IncA/C plasmids on bacterial genome plasticity through their own mobility and the mobilization of genomic islands. Multidrug resistance is a major health concern that complicates treatments of even the most common infections caused by bacteria. In recent years, IncA/C plasmids have emerged and spread in bacteria infecting humans, food-producing animals and food products, driving at the same time the dissemination of a broad spectrum of antibiotic resistance genes in environmental and in clinical settings. In this study, we have characterized the regulatory pathway that governs IncA/C plasmid dissemination. We have found that AcaCD, the master activator complex encoded by these plasmids, is not only essential for the dissemination of IncA/C plasmids but also activates unrelated mobile genetic elements in bacterial genomes, thereby further promoting the interspecies propagation of multidrug resistance and other adaptive traits at a very high frequency.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of bacterial molecular genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Dominick Matteau
- Laboratory of microbial systems and synthetic biology, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Peng Luo
- Laboratory of bacterial molecular genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada; CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Sébastien Rodrigue
- Laboratory of microbial systems and synthetic biology, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Vincent Burrus
- Laboratory of bacterial molecular genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
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Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, Couture S, Barbe-Marcoux M, Abou-Elela S, Scott MS. Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Res 2014; 42:10073-85. [PMID: 25074380 PMCID: PMC4150776 DOI: 10.1093/nar/gku664] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and cancer cell lines independent of their functions. The results indicate that C/D snoRNAs are expressed as two distinct forms differing in their ends with respect to boxes C and D and in their terminal stem length. Both forms are overexpressed in cancer cell lines but display a conserved end distribution. Surprisingly, the long forms are more dependent than the short forms on the expression of the core snoRNP protein NOP58, thought to be essential for C/D snoRNA production. In contrast, a subset of short forms are dependent on the splicing factor RBFOX2. Analysis of the potential secondary structure of both forms indicates that the k-turn motif required for binding of NOP58 is less stable in short forms which are thus less likely to mature into a canonical snoRNP. Taken together the data suggest that C/D snoRNAs are divided into at least two groups with distinct maturation and functional preferences.
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Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Daniel Garneau
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Fabien Dupuis-Sandoval
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Audrey Roy
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marie Frappier
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Mathieu Catala
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Mélissa Barbe-Marcoux
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Québec J1E 4K8, Canada Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing. Sci Rep 2014; 4:5453. [PMID: 24965658 PMCID: PMC4071321 DOI: 10.1038/srep05453] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/09/2014] [Indexed: 12/22/2022] Open
Abstract
The state and development of the intestinal epithelium is vital for infant health, and increased understanding in this area has been limited by an inability to directly assess epithelial cell biology in the healthy newborn intestine. To that end, we have developed a novel, noninvasive, molecular approach that utilizes next generation RNA sequencing on stool samples containing intact epithelial cells for the purpose of quantifying intestinal gene expression. We then applied this technique to compare host gene expression in healthy term and extremely preterm infants. Bioinformatic analyses demonstrate repeatable detection of human mRNA expression, and network analysis shows immune cell function and inflammation pathways to be up-regulated in preterm infants. This study provides incontrovertible evidence that whole-genome sequencing of stool-derived RNA can be used to examine the neonatal host epithelial transcriptome in infants, which opens up opportunities for sequential monitoring of gut gene expression in response to dietary or therapeutic interventions.
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