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Arreola-Ramírez JL, Vargas MH, Carbajal V, Alquicira-Mireles J, Montaño M, Ramos-Abraham C, Ortiz-Quintero B, Torres-Machorro AL, Rodríguez-Velasco A, Esquivel-Campos AL, Vásquez-Vásquez JA, Segura-Medina P. Mesenchymal stem cells attenuate the proinflammatory cytokine pattern in a guinea pig model of chronic cigarette smoke exposure. Cytokine 2023; 162:156104. [PMID: 36493630 DOI: 10.1016/j.cyto.2022.156104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/16/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022]
Abstract
AIMS Cigarette smoke often induces pulmonary and systemic inflammation. In animal models, mesenchymal stem cells (MSC) tend to ameliorate these effects. We aimed to explore the local and systemic expression of cytokines in guinea pigs chronically exposed to cigarette smoke, and their modifications by MSC. MAIN METHODS Concentrations of IL-1β, IL-6, IL-8, IL-12, TNF-α, INF-ɣ, TSG-6, MMP-9, TIMP-1, and/or TIMP-2 in serum and bronchoalveolar lavage (BALF) from animals exposed to tobacco smoke (20 cigarettes/day, 5 days/week for 10 weeks) were determined, and mRNA expression of some of them was measured in lung tissue. Intratracheal instillation of allogeneic bone marrow MSC (5x106 cells in 1 ml) was done at week 2. KEY FINDINGS After cigarette smoke, IL-6 and IFN-γ increased in serum and BALF, while IL-1β and IL-12 decreased in serum, and TSG-6 and TIMP-2 increased in BALF. IL-1β had a paradoxical increase in BALF. MSC had an almost null effect in unexposed animals. The intratracheal administration of MSC in guinea pigs exposed to cigarette smoke was associated with a statistically significant decrease of IL-12 and TSG-6 in serum, as well as a decrease of IL-1β and IFN-γ and an increase in TIMP-1 in BALF. Concerning mRNA expression in lung tissue, cigarette smoke did not modify the relative amount of the studied transcripts, but even so, MSC decreased the IL-12 mRNA and increased the TIMP-1 mRNA. SIGNIFICANCE A single intratracheal instillation of MSC reduces the pulmonary and systemic proinflammatory pattern induced by chronic exposure to cigarette smoke in guinea pigs. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- José Luis Arreola-Ramírez
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico.
| | - Mario H Vargas
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Verónica Carbajal
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Jesús Alquicira-Mireles
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Martha Montaño
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Carlos Ramos-Abraham
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Blanca Ortiz-Quintero
- Departamento de Investigación en Bioquímica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Ana Lilia Torres-Machorro
- Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Alicia Rodríguez-Velasco
- Servicio de Anatomía Patológica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, CP 06720, Mexico City, Mexico
| | - Ana Laura Esquivel-Campos
- Laboratorio de Investigación en Biología Experimental, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | | | - Patricia Segura-Medina
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, CP 14080, Mexico City, Mexico; Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Mexico City, Mexico
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2
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Pulito-Cueto V, Remuzgo-Martínez S, Genre F, Atienza-Mateo B, Mora-Cuesta VM, Iturbe-Fernández D, Lera-Gómez L, Sebastián Mora-Gil M, Prieto-Peña D, Portilla V, Blanco R, Corrales A, Ocejo-Vinyals JG, Gualillo O, Ferraz-Amaro I, Cifrián JM, López-Mejías R, González-Gay MA. Elevated VCAM-1, MCP-1 and ADMA serum levels related to pulmonary fibrosis of interstitial lung disease associated with rheumatoid arthritis. Front Mol Biosci 2022; 9:1056121. [PMID: 36601584 PMCID: PMC9806218 DOI: 10.3389/fmolb.2022.1056121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction: Early diagnosis of interstitial lung disease (ILD) associated with rheumatoid arthritis (RA) constitutes a challenge for the clinicians. Pulmonary vasculopathy is relevant in the development of interstitial lung disease. Accordingly, we aimed to explore the role of vascular cell adhesion molecule-1 (VCAM-1), monocyte chemoattractant protein-1 (MCP-1) and asymmetric dimethylarginine (ADMA), key molecules in the vasculopathy, as potential biomarkers of pulmonary fibrosis in RA-ILD+. Methods: We included 21 RA-ILD+ patients and two comparative groups: 25 RA-ILD- patients and 21 idiopathic pulmonary fibrosis (IPF) patients. Serum levels of the molecules were determined by ELISA, and mRNA expression was quantified by qPCR. Results: VCAM-1, MCP-1 and ADMA serum levels were increased in RA-ILD+ patients in relation to RA-ILD- and IPF patients. Additionally, RA-ILD+ patients exhibited increased CCL2 (gene encoding MCP-1) and decreased PRMT1 (gene related to ADMA synthesis) mRNA expression in relation to RA-ILD- patients. A lower expression of VCAM1, CCL2, and PRMT1 was observed in RA-ILD+ patients when compared with those with IPF. Furthermore, MCP-1 serum levels and PRMT1 mRNA expression were positively correlated with RA duration, and ADMA serum levels were positively associated with C-reactive protein in RA-ILD+ patients. Conclusion: Our study suggests that VCAM-1, MCP-1 and ADMA could be considered as useful biomarkers to identify ILD in RA patients, as well as to discriminate RA-ILD+ from IPF, contributing to the early diagnosis of RA-ILD+.
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Affiliation(s)
- Verónica Pulito-Cueto
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,*Correspondence: Verónica Pulito-Cueto,
| | - Sara Remuzgo-Martínez
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain
| | - Fernanda Genre
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain
| | - Belén Atienza-Mateo
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Víctor M. Mora-Cuesta
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Pneumology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - David Iturbe-Fernández
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Pneumology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Leticia Lera-Gómez
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain
| | - María Sebastián Mora-Gil
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain
| | - Diana Prieto-Peña
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Virginia Portilla
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Ricardo Blanco
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Alfonso Corrales
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - J. Gonzalo Ocejo-Vinyals
- Department of Immunology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Oreste Gualillo
- SERGAS (Servizo Galego de Saude) and IDIS (Instituto de Investigación Sanitaria de Santiago), NEIRID Lab. (Neuroendocrine Interactions in rheumatology and inflammatory diseases), Research laboratory 9, Santiago University Clinical Hospital, Santiago de Compostela, Spain
| | - Iván Ferraz-Amaro
- Department of Rheumatology, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - José M. Cifrián
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain,Department of Pneumology, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain,School of Medicine, Universidad de Cantabria, Santander, Cantabria, Spain
| | - Raquel López-Mejías
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Cantabria, Spain
| | - Miguel A. González-Gay
- Department of medicine and psychiatry, Universidad de Cantabria; Rheumatology division, Hospital Universitario Marqués de Valdecilla; Research group on genetic epidemiology and atherosclerosis in systemic diseases and in metabolic diseases of the musculoskeletal system, IDIVAL, Santander, Cantabria, Spain,Cardiovascular Pathophysiology and Genomics Research Unit, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021; 17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022] Open
Abstract
Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.
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Affiliation(s)
- Bikash K. Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniela M. Remus
- Callaghan Innovation Protein Science and Engineering, University of Canterbury, Christchurch, New Zealand
| | - Augustine Chen
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Craig van Dolleweerd
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
| | - Paul P. Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
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4
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Konina D, Sparber P, Viakhireva I, Filatova A, Skoblov M. Investigation of LINC00493/SMIM26 Gene Suggests Its Dual Functioning at mRNA and Protein Level. Int J Mol Sci 2021; 22:ijms22168477. [PMID: 34445188 PMCID: PMC8395196 DOI: 10.3390/ijms22168477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
The amount of human long noncoding RNA (lncRNA) genes is comparable to protein-coding; however, only a small number of lncRNAs are functionally annotated. Previously, it was shown that lncRNAs can participate in many key cellular processes, including regulation of gene expression at transcriptional and post-transcriptional levels. The lncRNA genes can contain small open reading frames (sORFs), and recent studies demonstrated that some of the resulting short proteins could play an important biological role. In the present study, we investigate the widely expressed lncRNA LINC00493. We determine the structure of the LINC00493 transcript, its cell localization and influence on cell physiology. Our data demonstrate that LINC00493 has an influence on cell viability in a cell-type-specific manner. Furthermore, it was recently shown that LINC00493 has a sORF that is translated into small protein SMIM26. The results of our knockdown and overexpression experiments suggest that both LINC00493/SMIM26 transcript and protein affect cell viability, but in the opposite manner.
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Affiliation(s)
- Daria Konina
- Moscow Institute of Physics and Technology, Phystech School of Biological and Medical Physics, 141701 Dolgoprudny, Russia
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
- Correspondence: (D.K.); (A.F.)
| | - Peter Sparber
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
| | - Iuliia Viakhireva
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
| | - Alexandra Filatova
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
- Correspondence: (D.K.); (A.F.)
| | - Mikhail Skoblov
- Research Centre of Medical Genetics, Laboratory of Functional Genomics, 115478 Moscow, Russia; (P.S.); (I.V.); (M.S.)
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5
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Veenstra TD. Omics in Systems Biology: Current Progress and Future Outlook. Proteomics 2021; 21:e2000235. [PMID: 33320441 DOI: 10.1002/pmic.202000235] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Biological research has undergone tremendous changes over the past three decades. Research used to almost exclusively focus on a single aspect of a single molecule per experiment. Modern technologies have enabled thousands of molecules to be simultaneously analyzed and the way that these molecules influence each other to be discerned. The change is so dramatic that it has given rise to a whole new descriptive suffix (i.e., omics) to describe these fields of study. While genomics was arguably the initial driver of this new trend, it quickly spread to other biological entities resulting in the creation of transcriptomics, proteomics, metabolomics, etc. The development of these "big four omics" created a wave of other omic fields, such as epigenomics, glycomics, lipidomics, microbiomics, and even foodomics; all with the purpose of comprehensively studying all the molecular entities or processes within their respective domain. The large number of omic fields that are invented even led to the term "panomics" as a way to classify them all under one category. Ultimately, all of these omic fields are setting the foundation for developing systems biology; in which the focus will be on determining the complex interactions that occur within biological systems.
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Booth KT, Azaiez H, Jahan I, Smith RJH, Fritzsch B. Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective. Front Genet 2018; 9:156. [PMID: 29868110 PMCID: PMC5951964 DOI: 10.3389/fgene.2018.00156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
The mammalian hearing organ is a regular array of two types of hair cells (HCs) surrounded by six types of supporting cells. Along the tonotopic axis, this conserved radial array of cell types shows longitudinal variations to enhance the tuning properties of basilar membrane. We present the current evidence supporting the hypothesis that quantitative local variations in gene expression profiles are responsible for local cell responses to global gene manipulations. With the advent of next generation sequencing and the unprecedented array of technologies offering high throughput analyses at the single cell level, transcriptomics will become a common tool to enhance our understanding of the inner ear. We provide an overview of the approaches and landmark studies undertaken to date to analyze single cell variations in the organ of Corti and discuss the current limitations. We next provide an overview of the complexity of known regulatory mechanisms in the inner ear. These mechanisms are tightly regulated temporally and spatially at the transcription, RNA-splicing, mRNA-regulation, and translation levels. Understanding the intricacies of regulatory mechanisms at play in the inner ear will require the use of complementary approaches, and most probably, a combinatorial strategy coupling transcriptomics, proteomics, and epigenomics technologies. We highlight how these data, in conjunction with recent insights into molecular cell transformation, can advance attempts to restore lost hair cells.
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Affiliation(s)
- Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Israt Jahan
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Bernd Fritzsch
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Department of Biology, University of Iowa, Iowa City, IA, United States
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Fishilevich S, Zimmerman S, Kohn A, Iny Stein T, Olender T, Kolker E, Safran M, Lancet D. Genic insights from integrated human proteomics in GeneCards. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw030. [PMID: 27048349 PMCID: PMC4820835 DOI: 10.1093/database/baw030] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/23/2016] [Indexed: 11/15/2022]
Abstract
GeneCards is a one-stop shop for searchable human gene annotations (http://www.genecards.org/). Data are automatically mined from ∼120 sources and presented in an integrated web card for every human gene. We report the application of recent advances in proteomics to enhance gene annotation and classification in GeneCards. First, we constructed the Human Integrated Protein Expression Database (HIPED), a unified database of protein abundance in human tissues, based on the publically available mass spectrometry (MS)-based proteomics sources ProteomicsDB, Multi-Omics Profiling Expression Database, Protein Abundance Across Organisms and The MaxQuant DataBase. The integrated database, residing within GeneCards, compares favourably with its individual sources, covering nearly 90% of human protein-coding genes. For gene annotation and comparisons, we first defined a protein expression vector for each gene, based on normalized abundances in 69 normal human tissues. This vector is portrayed in the GeneCards expression section as a bar graph, allowing visual inspection and comparison. These data are juxtaposed with transcriptome bar graphs. Using the protein expression vectors, we further defined a pairwise metric that helps assess expression-based pairwise proximity. This new metric for finding functional partners complements eight others, including sharing of pathways, gene ontology (GO) terms and domains, implemented in the GeneCards Suite. In parallel, we calculated proteome-based differential expression, highlighting a subset of tissues that overexpress a gene and subserving gene classification. This textual annotation allows users of VarElect, the suite’s next-generation phenotyper, to more effectively discover causative disease variants. Finally, we define the protein–RNA expression ratio and correlation as yet another attribute of every gene in each tissue, adding further annotative information. The results constitute a significant enhancement of several GeneCards sections and help promote and organize the genome-wide structural and functional knowledge of the human proteome. Database URL: http://www.genecards.org/
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Affiliation(s)
- Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shahar Zimmerman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Asher Kohn
- LifeMap Sciences Ltd., Tel Aviv 69710, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eugene Kolker
- CDO Analytics, Seattle Children's Hospital, Seattle, WA 98101 USA Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, WA 98101 USA Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington, 98101, USA Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington School of Medicine, Seattle, WA 98109, USA Department of Chemistry and Chemical Biology, Northeastern University College of Science, Boston, MA 02115 USA
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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Valdés-López O, Batek J, Gomez-Hernandez N, Nguyen CT, Isidra-Arellano MC, Zhang N, Joshi T, Xu D, Hixson KK, Weitz KK, Aldrich JT, Paša-Tolić L, Stacey G. Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles. FRONTIERS IN PLANT SCIENCE 2016; 7:517. [PMID: 27200004 PMCID: PMC4843095 DOI: 10.3389/fpls.2016.00517] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/01/2016] [Indexed: 05/19/2023]
Abstract
Heat stress is likely to be a key factor in the negative impact of climate change on crop production. Heat stress significantly influences the functions of roots, which provide support, water, and nutrients to other plant organs. Likewise, roots play an important role in the establishment of symbiotic associations with different microorganisms. Despite the physiological relevance of roots, few studies have examined their response to heat stress. In this study, we performed genome-wide transcriptomic and proteomic analyses on isolated root hairs, which are a single, epidermal cell type, and compared their response to stripped roots. On average, we identified 1849 and 3091 genes differentially regulated in root hairs and stripped roots, respectively, in response to heat stress. Our gene regulatory module analysis identified 10 key modules that might control the majority of the transcriptional response to heat stress. We also conducted proteomic analysis on membrane fractions isolated from root hairs and compared these responses to stripped roots. These experiments identified a variety of proteins whose expression changed within 3 h of application of heat stress. Most of these proteins were predicted to play a significant role in thermo-tolerance, as well as in chromatin remodeling and post-transcriptional regulation. The data presented represent an in-depth analysis of the heat stress response of a single cell type in soybean.
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Affiliation(s)
- Oswaldo Valdés-López
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
- Laboratorio de Genómica Funcional de Leguminosas, FES Iztacala Universidad Nacional Autónoma de MéxicoMéxico, Mexico
| | - Josef Batek
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Nicolas Gomez-Hernandez
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Cuong T. Nguyen
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, FES Iztacala Universidad Nacional Autónoma de MéxicoMéxico, Mexico
| | - Ning Zhang
- C.S. Bond Life Sciences Center, Informatics Institute, University of MissouriColumbia, MO, USA
| | - Trupti Joshi
- C.S. Bond Life Sciences Center, Informatics Institute, University of MissouriColumbia, MO, USA
- Department of Computer Science, University of MissouriColumbia, MO, USA
- Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of MissouriColumbia, MO, USA
| | - Dong Xu
- C.S. Bond Life Sciences Center, Informatics Institute, University of MissouriColumbia, MO, USA
- Department of Computer Science, University of MissouriColumbia, MO, USA
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Karl K. Weitz
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Joshua T. Aldrich
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Gary Stacey
- Division of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of MissouriColumbia, MO, USA
- *Correspondence: Gary Stacey
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Dassi E, Greco V, Sidarovich V, Zuccotti P, Arseni N, Scaruffi P, Tonini GP, Quattrone A. Translational compensation of genomic instability in neuroblastoma. Sci Rep 2015; 5:14364. [PMID: 26399178 PMCID: PMC4585852 DOI: 10.1038/srep14364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/25/2015] [Indexed: 11/23/2022] Open
Abstract
Cancer-associated gene expression imbalances are conventionally studied at the genomic, epigenomic and transcriptomic levels. Given the relevance of translational control in determining cell phenotypes, we evaluated the translatome, i.e., the transcriptome engaged in translation, as a descriptor of the effects of genetic instability in cancer. We performed this evaluation in high-risk neuroblastomas, which are characterized by a low frequency of point mutations or known cancer-driving genes and by the presence of several segmental chromosomal aberrations that produce gene-copy imbalances that guide aggressiveness. We thus integrated genome, transcriptome, translatome and miRome profiles in a representative panel of high-risk neuroblastoma cell lines. We identified a number of genes whose genomic imbalance was corrected by compensatory adaptations in translational efficiency. The transcriptomic level of these genes was predictive of poor prognosis in more than half of cases, and the genomic imbalances found in their loci were shared by 27 other tumor types. This homeostatic process is also not limited to copy number-altered genes, as we showed the translational stoichiometric rebalance of histone genes. We suggest that the translational buffering of fluctuations in these dose-sensitive transcripts is a potential driving process of neuroblastoma evolution.
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Affiliation(s)
- Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
| | - Valentina Greco
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
| | - Viktoryia Sidarovich
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
| | - Paola Zuccotti
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
| | - Natalia Arseni
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
| | - Paola Scaruffi
- Center of Physiopathology of Human Reproduction, Unit of Obstetrics and Gynecology, IRCSS A.O.U. San Martino IST, Genova, Italy
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Pediatric Research Institute, Fondazione Città della Speranza, Padova, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
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Rotavirus NSP3 Is a Translational Surrogate of the Poly(A) Binding Protein-Poly(A) Complex. J Virol 2015; 89:8773-82. [PMID: 26063427 DOI: 10.1128/jvi.01402-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED Through its interaction with the 5' translation initiation factor eIF4G, poly(A) binding protein (PABP) facilitates the translation of 5'-capped and 3'-poly(A)-tailed mRNAs. Rotavirus mRNAs are capped but not polyadenylated, instead terminating in a 3' GACC motif that is recognized by the viral protein NSP3, which competes with PABP for eIF4G binding. Upon rotavirus infection, viral, GACC-tailed mRNAs are efficiently translated, while host poly(A)-tailed mRNA translation is, in contrast, severely impaired. To explore the roles of NSP3 in these two opposing events, the translational capabilities of three capped mRNAs, distinguished by either a GACC, a poly(A), or a non-GACC and nonpoly(A) 3' end, have been monitored after electroporation of cells expressing all rotavirus proteins (infected cells) or only NSP3 (stably or transiently transfected cells). In infected cells, we found that the magnitudes of translation induction (GACC-tailed mRNA) and translation reduction [poly(A)-tailed mRNA] both depended on the rotavirus strain used but that translation reduction not genetically linked to NSP3. In transfected cells, even a small amount of NSP3 was sufficient to dramatically enhance GACC-tailed mRNA translation and, surprisingly, to slightly favor the translation of both poly(A)- and nonpoly(A)-tailed mRNAs, likely by stabilizing the eIF4E-eIF4G interaction. These data suggest that NSP3 is a translational surrogate of the PABP-poly(A) complex; therefore, it cannot by itself be responsible for inhibiting the translation of host poly(A)-tailed mRNAs upon rotavirus infection. IMPORTANCE To control host cell physiology and to circumvent innate immunity, many viruses have evolved powerful mechanisms aimed at inhibiting host mRNA translation while stimulating translation of their own mRNAs. How rotavirus tackles this challenge is still a matter of debate. Using rotavirus-infected cells, we show that the magnitude of cellular poly(A) mRNA translation differs with respect to rotavirus strains but is not genetically linked to NSP3. Using cells expressing rotavirus NSP3, we show that NSP3 alone not only dramatically enhances rotavirus-like mRNA translation but also enhances poly(A) mRNA translation rather than inhibiting it, likely by stabilizing the eIF4E-eIF4G complex. Thus, the inhibition of cellular polyadenylated mRNA translation during rotavirus infection cannot be attributed solely to NSP3 and is more likely the result of global competition between viral and host mRNAs for the cellular translation machinery.
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Plasmodium vivax trophozoite-stage proteomes. J Proteomics 2014; 115:157-76. [PMID: 25545414 DOI: 10.1016/j.jprot.2014.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 11/17/2014] [Accepted: 12/21/2014] [Indexed: 02/06/2023]
Abstract
UNLABELLED Plasmodium vivax is the causative infectious agent of 80-300 million annual cases of malaria. Many aspects of this parasite's biology remain unknown. To further elucidate the interaction of P. vivax with its Saimiri boliviensis host, we obtained detailed proteomes of infected red blood cells, representing the trophozoite-enriched stage of development. Data from two of three biological replicate proteomes, emphasized here, were analyzed using five search engines, which enhanced identifications and resulted in the most comprehensive P. vivax proteomes to date, with 1375 P. vivax and 3209 S. boliviensis identified proteins. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with P. vivax's known reticulocyte host-cell specificity. A majority of the host and pathogen proteins identified belong to specific functional categories, and several parasite gene families, while 33% of the P. vivax proteins have no reported function. Hemoglobin was significantly oxidized in both proteomes, and additional protein oxidation and nitration was detected in one of the two proteomes. Detailed analyses of these post-translational modifications are presented. The proteins identified here significantly expand the known P. vivax proteome and complexity of available host protein functionality underlying the host-parasite interactive biology, and reveal unsuspected oxidative modifications that may impact protein function. BIOLOGICAL SIGNIFICANCE Plasmodium vivax malaria is a serious neglected disease, causing an estimated 80 to 300 million cases annually in 95 countries. Infection can result in significant morbidity and possible death. P. vivax, unlike the much better-studied Plasmodium falciparum species, cannot be grown in long-term culture, has a dormant form in the liver called the hypnozoite stage, has a reticulocyte host-cell preference in the blood, and creates caveolae vesicle complexes at the surface of the infected reticulocyte membranes. Studies of stage-specific P. vivax expressed proteomes have been limited in scope and focused mainly on pathogen proteins, thus limiting understanding of the biology of this pathogen and its host interactions. Here three P. vivax proteomes are reported from biological replicates based on purified trophozoite-infected reticulocytes from different Saimiri boliviensis infections (the main non-human primate experimental model for P. vivax biology and pathogenesis). An in-depth analysis of two of the proteomes using 2D LC/MS/MS and multiple search engines identified 1375 pathogen proteins and 3209 host proteins. Numerous functional categories of both host and pathogen proteins were identified, including several known P. vivax protein family members (e.g., PHIST, eTRAMP and VIR), and 33% of protein identifications were classified as hypothetical. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with this parasite species' known reticulocyte host-cell specificity. In two biological replicates analyzed for post-translational modifications, hemoglobin was extensively oxidized, and various other proteins were also oxidized or nitrated in one of the two replicates. The cause of such protein modification remains to be determined but could include oxidized heme and oxygen radicals released from the infected red blood cell's parasite-induced acidic digestive vacuoles. In any case, the data suggests the presence of distinct infection-specific conditions whereby both the pathogen and host infected red blood cell proteins may be subject to significant oxidative stress.
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Dassi E, Quattrone A. Fingerprints of a message: integrating positional information on the transcriptome. Front Cell Dev Biol 2014; 2:39. [PMID: 25364746 PMCID: PMC4207014 DOI: 10.3389/fcell.2014.00039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/30/2014] [Indexed: 12/24/2022] Open
Abstract
The recent explosion of high-throughput sequencing methods applied to RNA molecules is allowing us to go beyond the description of sequence variants and their relative abundances, as measured by RNA-seq. We can now probe for RNA engagement in polysomes, for ribosomes, RNA binding proteins and microRNAs binding sites, for RNA secondary structure and for RNA methylation. These descriptors produce a steadily growing multidimensional array of positional information on RNA sequences, whose effective integration only would bring to decipher the regulatory interplay occurring between proteins, RNAs and their modifications on the transcriptome. This interplay ultimately dictates the degree of mRNA availability to translation, and thus the occurrence of cell phenotypes. However, several issues in data presentation are slowing down effective integration. A standardization effort for new dataset types produced should be urgently undertaken to solve these issues. Providing uniformed experimental details along with datasets processed to be directly usable and employing shared formats would greatly simplify integration efforts, strengthening hypotheses stemming from correlative observations and eventually bringing to mechanistic understanding.
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Affiliation(s)
- Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento Trento, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento Trento, Italy
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13
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Biswas A, Brown CM. Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3' untranslated regions (3' UTRs) of mRNAs. BMC Bioinformatics 2014; 15:174. [PMID: 24909639 PMCID: PMC4067372 DOI: 10.1186/1471-2105-15-174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/16/2014] [Indexed: 11/21/2022] Open
Abstract
Background Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly the 3′UTRs. Results Scan for Motifs (SFM) simplifies the process of identifying a wide range of regulatory elements on alignments of vertebrate 3′UTRs. SFM includes identification of both RNA Binding Protein (RBP) sites and targets of miRNAs. In addition to searching pre-computed alignments, the tool provides users the flexibility to search their own sequences or alignments. The regulatory elements may be filtered by expected value cutoffs and are cross-referenced back to their respective sources and literature. The output is an interactive graphical representation, highlighting potential regulatory elements and overlaps between them. The output also provides simple statistics and links to related resources for complementary analyses. The overall process is intuitive and fast. As SFM is a free web-application, the user does not need to install any software or databases. Conclusions Visualisation of the binding sites of different classes of effectors that bind to 3′UTRs will facilitate the study of regulatory elements in 3′ UTRs.
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Affiliation(s)
| | - Chris M Brown
- Department of Biochemistry, Genetics Otago, University of Otago, Dunedin, New Zealand.
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14
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Ponnala L, Wang Y, Sun Q, van Wijk KJ. Correlation of mRNA and protein abundance in the developing maize leaf. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:424-40. [PMID: 24547885 DOI: 10.1111/tpj.12482] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/30/2014] [Accepted: 02/11/2014] [Indexed: 05/24/2023]
Abstract
To help understand regulation of maize leaf blade development, including sink-source transitions and induction of C4 photosynthesis, we compared large-scale quantitative proteome and transcriptomes collected at specific stages along the developmental maize leaf blade gradient. Proteome data were based on label-free shotgun proteomics (spectral counting) and transcript data were based on RNA-seq using the same source materials, and had been published previously (Nat Genet, 42, 2010, 1060-1067; The Plant Cell, 22, 2010, 3509-3542). Transcript and protein abundance followed near normal distributions, in contrast with several studies with other organisms. Protein observability correlated with transcript abundance following a 'lazy step function' similar to that in bacteria and yeast. mRNA and protein abundance showed significant positive correlations (up to 0.8) for log-transformed length-weighted normalized spectral abundance factor (NSAF) and reads per kilobase of exon model per million mapped reads (RPKM) and non-weighted abundances (NadjSPC and COV) in dependence of function and development. Correlations were much weaker in the leaf 'sink-source' transition zone, i.e. the zone with massive investments in leaf chloroplast biogenesis and build-up of photosynthetic capacity. Clustering analyses of gene-specific protein-mRNA ratios revealed co-ordinated shifts in control points in gene expression along the leaf blade developmental gradient. The highest protein-mRNA ratio for each gene generally corresponded to leaf developmental stages in which the protein function was most important, with the exception of the 80S ribosome. Specific examples are discussed in the context of C4 photosynthesis, leaf development and sink-source transitions. This large-scale mRNA-protein correlation analysis in plants (maize) using label-free spectral counting for protein quantification and RNA-seq for mRNA abundance will provide a template for future mRNA-protein correlation studies.
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Affiliation(s)
- Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca, NY, 14853, USA
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15
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Aneichyk T, Bindreither D, Mantinger C, Grazio D, Goetsch K, Kofler R, Rainer J. Translational profiling in childhood acute lymphoblastic leukemia: no evidence for glucocorticoid regulation of mRNA translation. BMC Genomics 2013; 14:844. [PMID: 24289529 PMCID: PMC4046653 DOI: 10.1186/1471-2164-14-844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 11/25/2013] [Indexed: 11/24/2022] Open
Abstract
Background Glucocorticoids (GCs) are natural stress induced steroid hormones causing cell cycle arrest and cell death in lymphoid tissues. Therefore they are the central component in the treatment of lymphoid malignancies, in particular childhood acute lymphoblastic leukemia (chALL). GCs act mainly via regulating gene transcription, which has been intensively studied by us and others. GC control of mRNA translation has also been reported but has never been assessed systematically. In this study we investigate the effect of GCs on mRNA translation on a genome-wide scale. Results Childhood T- (CCRF-CEM) and precursor B-ALL (NALM6) cells were exposed to GCs and subjected to “translational profiling”, a technique combining sucrose-gradient fractionation followed by Affymetrix Exon microarray analysis of mRNA from different fractions, to assess the translational efficiency of the expressed genes. Analysis of GC regulation in ribosome-bound fractions versus transcriptional regulation revealed no significant differences, i.e., GC did not entail a significant shift between ribosomal bound and unbound mRNAs. Conclusions In the present study we analyzed for the first time possible effects of GC on the translational efficiency of expressed genes in two chALL model systems employing whole genome polysome profiling. Our results did not reveal significant differences in translational efficiency of expressed genes thereby arguing against a potential widespread regulatory effect of GCs on translation at least in the investigated in vitro systems. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-844) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tatsiana Aneichyk
- Division of Molecular Pathophysiology, Biocenter, Innsbruck Medical University, Innsbruck 6020, Austria.
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Tebaldi T, Dassi E, Kostoska G, Viero G, Quattrone A. tRanslatome: an R/Bioconductor package to portray translational control. ACTA ACUST UNITED AC 2013; 30:289-91. [PMID: 24222209 PMCID: PMC3892686 DOI: 10.1093/bioinformatics/btt634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Summary: High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different ‘-omics’. It has been recently demonstrated that translational control is a widespread phenomenon, with profound and still underestimated regulation capabilities. Although detecting changes in the levels of total messenger RNAs (mRNAs; the transcriptome), of polysomally loaded mRNAs (the translatome) and of proteins (the proteome) is experimentally feasible in a high-throughput way, the integration of these levels is still far from being robustly approached. Here we introduce tRanslatome, a new R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data. The package includes most of the available statistical methods developed for the analysis of high-throughput data, allowing the parallel comparison of differentially expressed genes and the corresponding differentially enriched biological themes. Notably, it also enables the prediction of translational regulatory elements on mRNA sequences. The utility of this tool is demonstrated with two case studies. Availability and implementation: tRanslatome is available in Bioconductor. Contact: t.tebaldi@unitn.it Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics - Centre for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Mattarello (TN) and Institute of Biophysics CNR - Via alla Cascata 56/C, 38123 Povo (TN), Italy
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Spangenberg L, Correa A, Dallagiovanna B, Naya H. Role of alternative polyadenylation during adipogenic differentiation: an in silico approach. PLoS One 2013; 8:e75578. [PMID: 24143171 PMCID: PMC3797115 DOI: 10.1371/journal.pone.0075578] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/14/2013] [Indexed: 01/22/2023] Open
Abstract
Post-transcriptional regulation of stem cell differentiation is far from being completely understood. Changes in protein levels are not fully correlated with corresponding changes in mRNAs; the observed differences might be partially explained by post-transcriptional regulation mechanisms, such as alternative polyadenylation. This would involve changes in protein binding, transcript usage, miRNAs and other non-coding RNAs. In the present work we analyzed the distribution of alternative transcripts during adipogenic differentiation and the potential role of miRNAs in post-transcriptional regulation. Our in silico analysis suggests a modest, consistent, bias in 3'UTR lengths during differentiation enabling a fine-tuned transcript regulation via small non-coding RNAs. Including these effects in the analyses partially accounts for the observed discrepancies in relative abundance of protein and mRNA.
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Affiliation(s)
- Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Alejandro Correa
- Instituto Carlos Chagas, Fiocruz-Paraná, Curitiba, Paraná, Brazil
| | | | - Hugo Naya
- Bioinformatics Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República
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