1
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Buchacher T, Shetty A, Koskela SA, Smolander J, Kaukonen R, Sousa AGG, Junttila S, Laiho A, Rundquist O, Lönnberg T, Marson A, Rasool O, Elo LL, Lahesmaa R. PIM kinases regulate early human Th17 cell differentiation. Cell Rep 2023; 42:113469. [PMID: 38039135 PMCID: PMC10765319 DOI: 10.1016/j.celrep.2023.113469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/23/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
The serine/threonine-specific Moloney murine leukemia virus (PIM) kinase family (i.e., PIM1, PIM2, and PIM3) has been extensively studied in tumorigenesis. PIM kinases are downstream of several cytokine signaling pathways that drive immune-mediated diseases. Uncontrolled T helper 17 (Th17) cell activation has been associated with the pathogenesis of autoimmunity. However, the detailed molecular function of PIMs in human Th17 cell regulation has yet to be studied. In the present study, we comprehensively investigated how the three PIMs simultaneously alter transcriptional gene regulation during early human Th17 cell differentiation. By combining PIM triple knockdown with bulk and scRNA-seq approaches, we found that PIM deficiency promotes the early expression of key Th17-related genes while suppressing Th1-lineage genes. Further, PIMs modulate Th cell signaling, potentially via STAT1 and STAT3. Overall, our study highlights the inhibitory role of PIMs in human Th17 cell differentiation, thereby suggesting their association with autoimmune phenotypes.
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Affiliation(s)
- Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland.
| | - Ankitha Shetty
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Saara A Koskela
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland; Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Riina Kaukonen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - António G G Sousa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Olof Rundquist
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland; Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, 20520 Turku, Finland; Institute of Biomedicine, University of Turku, 20520 Turku, Finland.
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2
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Charkiewicz R, Sulewska A, Mroz R, Charkiewicz A, Naumnik W, Kraska M, Gyenesei A, Galik B, Junttila S, Miskiewicz B, Stec R, Karabowicz P, Zawada M, Miltyk W, Niklinski J. Serum Insights: Leveraging the Power of miRNA Profiling as an Early Diagnostic Tool for Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:4910. [PMID: 37894277 PMCID: PMC10605272 DOI: 10.3390/cancers15204910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Non-small cell lung cancer is the predominant form of lung cancer and is associated with a poor prognosis. MiRNAs implicated in cancer initiation and progression can be easily detected in liquid biopsy samples and have the potential to serve as non-invasive biomarkers. In this study, we employed next-generation sequencing to globally profile miRNAs in serum samples from 71 early-stage NSCLC patients and 47 non-cancerous pulmonary condition patients. Preliminary analysis of differentially expressed miRNAs revealed 28 upregulated miRNAs in NSCLC compared to the control group. Functional enrichment analyses unveiled their involvement in NSCLC signaling pathways. Subsequently, we developed a gradient-boosting decision tree classifier based on 2588 miRNAs, which demonstrated high accuracy (0.837), sensitivity (0.806), and specificity (0.859) in effectively distinguishing NSCLC from non-cancerous individuals. Shapley Additive exPlanations analysis improved the model metrics by identifying the top 15 miRNAs with the strongest discriminatory value, yielding an AUC of 0.96 ± 0.04, accuracy of 0.896, sensitivity of 0.884, and specificity of 0.903. Our study establishes the potential utility of a non-invasive serum miRNA signature as a supportive tool for early detection of NSCLC while also shedding light on dysregulated miRNAs in NSCLC biology. For enhanced credibility and understanding, further validation in an independent cohort of patients is warranted.
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Affiliation(s)
- Radoslaw Charkiewicz
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (M.K.)
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (M.K.)
| | - Robert Mroz
- 2nd Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland;
| | - Alicja Charkiewicz
- Department of Analysis and Bioanalysis of Medicines, Medical University of Bialystok, 15-089 Bialystok, Poland; (A.C.); (W.M.)
| | - Wojciech Naumnik
- 1st Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland;
| | - Marcin Kraska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (M.K.)
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Attila Gyenesei
- Szentagothai Research Center, Genomic and Bioinformatic Core Facility, H-7624 Pecs, Hungary; (A.G.); (B.G.)
| | - Bence Galik
- Szentagothai Research Center, Genomic and Bioinformatic Core Facility, H-7624 Pecs, Hungary; (A.G.); (B.G.)
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland;
| | - Borys Miskiewicz
- Department of Thoracic Surgery, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Rafal Stec
- Department of Oncology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Piotr Karabowicz
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland;
| | - Magdalena Zawada
- Department of Hematology Diagnostics and Genetics, The University Hospital, 30-688 Krakow, Poland;
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Medical University of Bialystok, 15-089 Bialystok, Poland; (A.C.); (W.M.)
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (M.K.)
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3
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Smolander J, Junttila S, Elo LL. Cell-connectivity-guided trajectory inference from single-cell data. Bioinformatics 2023; 39:btad515. [PMID: 37624916 PMCID: PMC10474950 DOI: 10.1093/bioinformatics/btad515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/24/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
MOTIVATION Single-cell RNA-sequencing enables cell-level investigation of cell differentiation, which can be modelled using trajectory inference methods. While tremendous effort has been put into designing these methods, inferring accurate trajectories automatically remains difficult. Therefore, the standard approach involves testing different trajectory inference methods and picking the trajectory giving the most biologically sensible model. As the default parameters are often suboptimal, their tuning requires methodological expertise. RESULTS We introduce Totem, an open-source, easy-to-use R package designed to facilitate inference of tree-shaped trajectories from single-cell data. Totem generates a large number of clustering results, estimates their topologies as minimum spanning trees, and uses them to measure the connectivity of the cells. Besides automatic selection of an appropriate trajectory, cell connectivity enables to visually pinpoint branching points and milestones relevant to the trajectory. Furthermore, testing different trajectories with Totem is fast, easy, and does not require in-depth methodological knowledge. AVAILABILITY AND IMPLEMENTATION Totem is available as an R package at https://github.com/elolab/Totem.
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Affiliation(s)
- Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Institute of Biomedicine, University of Turku, 20520 Turku, Finland
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4
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Jankowicz-Cieslak J, Hofinger BJ, Jarc L, Junttila S, Galik B, Gyenesei A, Ingelbrecht IL, Till BJ. Spectrum and Density of Gamma and X-ray Induced Mutations in a Non-Model Rice Cultivar. Plants (Basel) 2022; 11:3232. [PMID: 36501272 PMCID: PMC9741009 DOI: 10.3390/plants11233232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Physical mutagens are a powerful tool used for genetic research and breeding for over eight decades. Yet, when compared to chemical mutagens, data sets on the effect of different mutagens and dosages on the spectrum and density of induced mutations remain lacking. To address this, we investigated the landscape of mutations induced by gamma and X-ray radiation in the most widely cultivated crop species: rice. A mutant population of a tropical upland rice, Oryza sativa L., was generated and propagated via self-fertilization for seven generations. Five dosages ranging from 75 Gy to 600 Gy in both X-ray and gamma-irradiated material were applied. In the process of a forward genetic screens, 11 unique rice mutant lines showing phenotypic variation were selected for mutation analysis via whole-genome sequencing. Thousands of candidate mutations were recovered in each mutant with single base substitutions being the most common, followed by small indels and structural variants. Higher dosages resulted in a higher accumulation of mutations in gamma-irradiated material, but not in X-ray-treated plants. The in vivo role of all annotated rice genes is yet to be directly investigated. The ability to induce a high density of single nucleotide and structural variants through mutagenesis will likely remain an important approach for functional genomics and breeding.
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Affiliation(s)
- Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Bernhard J. Hofinger
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Luka Jarc
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Sini Junttila
- Bioinformatics and Scientific Computing Core, Vienna Biocenter Core Facilities GmbH, Dr-Bohr-Gasse 3, 1030 Vienna, Austria
- Medical Bioinformatics Centre, Turku Bioscience Centre, University of Turku, Tykistökatu 6, 20520 Turku, Finland
- Medical Bioinformatics Centre, Turku Bioscience Centre, Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Bence Galik
- Bioinformatics and Scientific Computing Core, Vienna Biocenter Core Facilities GmbH, Dr-Bohr-Gasse 3, 1030 Vienna, Austria
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility Szentágothai Research Centre, University of Pécs, H-7622 Pecs, Hungary
| | - Attila Gyenesei
- Bioinformatics and Scientific Computing Core, Vienna Biocenter Core Facilities GmbH, Dr-Bohr-Gasse 3, 1030 Vienna, Austria
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility Szentágothai Research Centre, University of Pécs, H-7622 Pecs, Hungary
| | - Ivan L. Ingelbrecht
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
| | - Bradley J. Till
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division, International Atomic Energy Agency (IAEA), 2444 Seibersdorf, Austria
- Veterinary Genetics Laboratory, University of California, Old Davis Road, Davis, CA 95616, USA
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5
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Junttila S, Smolander J, Elo LL. Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data. Brief Bioinform 2022; 23:6649780. [PMID: 35880426 PMCID: PMC9487674 DOI: 10.1093/bib/bbac286] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 12/13/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multisubject, multicondition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naïve single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudoreplicate bias. While several methods have already been introduced to carry out the statistical testing in multisubject scRNA-seq analysis, comparisons that include all these methods are currently lacking. Here, we performed a comprehensive comparison of 18 methods for the identification of DS changes between conditions from multisubject scRNA-seq data. Our results suggest that the pseudobulk methods performed generally best. Both pseudobulks and mixed models that model the subjects as a random effect were superior compared with the naïve single-cell methods that do not model the subjects in any way. While the naïve models achieved higher sensitivity than the pseudobulk methods and the mixed models, they were subject to a high number of false positives. In addition, accounting for subjects through latent variable modeling did not improve the performance of the naïve methods.
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Affiliation(s)
| | | | - Laura L Elo
- Corresponding author: Laura L. Elo, Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland. Tel.: +358504680795; E-mail:
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Välikangas T, Junttila S, Rytkönen KT, Kukkonen-Macchi A, Suomi T, Elo LL. COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts. Front Genet 2022; 13:929887. [PMID: 35991542 PMCID: PMC9388772 DOI: 10.3389/fgene.2022.929887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading across the world despite vast global vaccination efforts. Consequently, many studies have looked for potential human host factors and immune mechanisms associated with the disease. However, most studies have focused on comparing COVID-19 patients to healthy controls, while fewer have elucidated the specific host factors distinguishing COVID-19 from other infections. To discover genes specifically related to COVID-19, we reanalyzed transcriptome data from nine independent cohort studies, covering multiple infections, including COVID-19, influenza, seasonal coronaviruses, and bacterial pneumonia. The identified COVID-19-specific signature consisted of 149 genes, involving many signals previously associated with the disease, such as induction of a strong immunoglobulin response and hemostasis, as well as dysregulation of cell cycle-related processes. Additionally, potential new gene candidates related to COVID-19 were discovered. To facilitate exploration of the signature with respect to disease severity, disease progression, and different cell types, we also offer an online tool for easy visualization of the selected genes across multiple datasets at both bulk and single-cell levels.
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Affiliation(s)
- Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Kalle T. Rytkönen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anu Kukkonen-Macchi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- *Correspondence: Tomi Suomi, ; Laura L. Elo,
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Tomi Suomi, ; Laura L. Elo,
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7
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Khan MM, Khan MH, Kalim UU, Khan S, Junttila S, Paulin N, Kong L, Rasool O, Elo LL, Lahesmaa R. Long Intergenic Noncoding RNA MIAT as a Regulator of Human Th17 Cell Differentiation. Front Immunol 2022; 13:856762. [PMID: 35784351 PMCID: PMC9242727 DOI: 10.3389/fimmu.2022.856762] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
T helper 17 (Th17) cells protect against fungal and bacterial infections and are implicated in autoimmunity. Several long intergenic noncoding RNAs (lincRNA) are induced during Th17 differentiation, however, their contribution to Th17 differentiation is poorly understood. We aimed to characterize the function of the lincRNA Myocardial Infarction Associated Transcript (MIAT) during early human Th17 cell differentiation. We found MIAT to be upregulated early after induction of human Th17 cell differentiation along with an increase in the chromatin accessibility at the gene locus. STAT3, a key regulator of Th17 differentiation, directly bound to the MIAT promoter and induced its expression during the early stages of Th17 cell differentiation. MIAT resides in the nucleus and regulates the expression of several key Th17 genes, including IL17A, IL17F, CCR6 and CXCL13, possibly by altering the chromatin accessibility of key loci, including IL17A locus. Further, MIAT regulates the expression of protein kinase C alpha (PKCα), an upstream regulator of IL17A. A reanalysis of published single-cell RNA-seq data showed that MIAT was expressed in T cells from the synovium of RA patients. Our results demonstrate that MIAT contributes to human Th17 differentiation by upregulating several genes implicated in Th17 differentiation. High MIAT expression in T cells of RA patient synovia suggests a possible role of MIAT in Th17 mediated autoimmune pathologies.
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Affiliation(s)
- Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Sofia Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Niklas Paulin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Lingjia Kong
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center , University of Turku, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
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8
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Shetty A, Tripathi SK, Junttila S, Buchacher T, Biradar R, Bhosale S, Envall T, Laiho A, Moulder R, Rasool O, Galande S, Elo L, Lahesmaa R. A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation. Nucleic Acids Res 2022; 50:4938-4958. [PMID: 35511484 PMCID: PMC9122603 DOI: 10.1093/nar/gkac256] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using mouse models. However, species-specific differences underscore the need to validate these findings in human. Here, we characterized the human-specific roles of three AP-1 transcription factors, FOSL1, FOSL2 and BATF, during early stages of Th17 differentiation. Our results demonstrate that FOSL1 and FOSL2 co-repress Th17 fate-specification, whereas BATF promotes the Th17 lineage. Strikingly, FOSL1 was found to play different roles in human and mouse. Genome-wide binding analysis indicated that FOSL1, FOSL2 and BATF share occupancy over regulatory regions of genes involved in Th17 lineage commitment. These AP-1 factors also share their protein interacting partners, which suggests mechanisms for their functional interplay. Our study further reveals that the genomic binding sites of FOSL1, FOSL2 and BATF harbour hundreds of autoimmune disease-linked SNPs. We show that many of these SNPs alter the ability of these transcription factors to bind DNA. Our findings thus provide critical insights into AP-1-mediated regulation of human Th17-fate and associated pathologies.
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Affiliation(s)
| | | | | | | | - Rahul Biradar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Department of Biochemistry and Molecular Biology, Protein Research Group, University of Southern Denmark, Campusvej 55, Odense M, DK 5230, Denmark
| | - Tapio Envall
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
- Department of Life Sciences, Shiv Nadar University, Delhi-NCR
| | - Laura L Elo
- Correspondence may also be addressed to Laura Elo. Tel: +358 29 450 2090;
| | - Riitta Lahesmaa
- To whom correspondence should be addressed. Tel: +358 29 450 2415;
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9
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Starskaia I, Laajala E, Grönroos T, Härkönen T, Junttila S, Kattelus R, Kallionpää H, Laiho A, Suni V, Tillmann V, Lund R, Elo LL, Lähdesmäki H, Knip M, Kalim UU, Lahesmaa R. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia 2022; 65:844-860. [PMID: 35142878 PMCID: PMC8960578 DOI: 10.1007/s00125-022-05657-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
AIMS/HYPOTHESIS Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. METHODS Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4-CD8- cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. RESULTS We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4-CD8- cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. CONCLUSIONS/INTERPRETATION These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management.
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Affiliation(s)
- Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Essi Laajala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Taina Härkönen
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Roosa Kattelus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Veronika Suni
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vallo Tillmann
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
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10
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Smolander J, Junttila S, Venäläinen MS, Elo LL. scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data. Bioinformatics 2021; 38:1328-1335. [PMID: 34888622 PMCID: PMC8825760 DOI: 10.1093/bioinformatics/btab831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Computational models are needed to infer a representation of the cells, i.e. a trajectory, from single-cell RNA-sequencing data that model cell differentiation during a dynamic process. Although many trajectory inference methods exist, their performance varies greatly depending on the dataset and hence there is a need to establish more accurate, better generalizable methods. RESULTS We introduce scShaper, a new trajectory inference method that enables accurate linear trajectory inference. The ensemble approach of scShaper generates a continuous smooth pseudotime based on a set of discrete pseudotimes. We demonstrate that scShaper is able to infer accurate trajectories for a variety of trigonometric trajectories, including many for which the commonly used principal curves method fails. A comprehensive benchmarking with state-of-the-art methods revealed that scShaper achieved superior accuracy of the cell ordering and, in particular, the differentially expressed genes. Moreover, scShaper is a fast method with few hyperparameters, making it a promising alternative to the principal curves method for linear pseudotemporal ordering. AVAILABILITY AND IMPLEMENTATION scShaper is available as an R package at https://github.com/elolab/scshaper. The test data are available at https://doi.org/10.5281/zenodo.5734488. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Mikko S Venäläinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland,Institute of Biomedicine, University of Turku, 20520 Turku, Finland,To whom correspondence should be addressed.
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11
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Faux T, Rytkönen KT, Mahmoudian M, Paulin N, Junttila S, Laiho A, Elo LL. Differential ATAC-seq and ChIP-seq peak detection using ROTS. NAR Genom Bioinform 2021; 3:lqab059. [PMID: 34235431 PMCID: PMC8253552 DOI: 10.1093/nargab/lqab059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/12/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022] Open
Abstract
Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect differential chromatin states (ATAC-seq) or differential chromatin modification states (ChIP-seq) between conditions. We compare the performance of ROTS to existing and widely used methods for ATAC-seq and ChIP-seq data using both synthetic and real datasets. Our results show that ROTS outperformed other commonly used methods when analyzing ATAC-seq data. ROTS also displayed the most accurate detection of small differences when modeling with synthetic data. We observed that two-step methods that require the use of a separate peak caller often more accurately called enrichment borders, whereas one-step methods without a separate peak calling step were more versatile in calling sub-peaks. The top ranked differential regions detected by the methods had marked correlation with transcriptional differences of the closest genes. Overall, our study provides evidence that ROTS is a useful addition to the available differential peak detection methods to study chromatin and performs especially well when applied to study differential chromatin states in ATAC-seq data.
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Affiliation(s)
- Thomas Faux
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Kalle T Rytkönen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20014, Finland
| | - Mehrad Mahmoudian
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
- Department of Future Technologies, University of Turku, FI-20014 Turku, Finland
| | - Niklas Paulin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20014, Finland
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12
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Smolander J, Junttila S, Venäläinen MS, Elo LL. ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data. Bioinformatics 2021; 37:1107-1114. [PMID: 33151294 PMCID: PMC8150131 DOI: 10.1093/bioinformatics/btaa919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Single-cell RNA-seq allows researchers to identify cell populations based on unsupervised clustering of the transcriptome. However, subpopulations can have only subtle transcriptomic differences and the high dimensionality of the data makes their identification challenging. RESULTS We introduce ILoReg, an R package implementing a new cell population identification method that improves identification of cell populations with subtle differences through a probabilistic feature extraction step that is applied before clustering and visualization. The feature extraction is performed using a novel machine learning algorithm, called iterative clustering projection (ICP), that uses logistic regression and clustering similarity comparison to iteratively cluster data. Remarkably, ICP also manages to integrate feature selection with the clustering through L1-regularization, enabling the identification of genes that are differentially expressed between cell populations. By combining solutions of multiple ICP runs into a single consensus solution, ILoReg creates a representation that enables investigating cell populations with a high resolution. In particular, we show that the visualization of ILoReg allows segregation of immune and pancreatic cell populations in a more pronounced manner compared with current state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION ILoReg is available as an R package at https://bioconductor.org/packages/ILoReg. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Mikko S Venäläinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
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13
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Abstract
Aim: DNA methylation is a key epigenetic mechanism regulating gene expression. Identifying differentially methylated regions is integral to DNA methylation analysis and there is a need for robust tools reliably detecting regions with significant differences in their methylation status. Materials & methods: We present here a reproducibility-optimized test statistic (ROTS) for detection of differential DNA methylation from high-throughput sequencing or array-based data. Results: Using both simulated and real data, we demonstrate the ability of ROTS to identify differential methylation between sample groups. Conclusion: Compared with state-of-the-art methods, ROTS shows competitive sensitivity and specificity in detecting consistently differentially methylated regions.
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Affiliation(s)
- Veronika Suni
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland
| | - Fatemeh Seyednasrollah
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland
| | - Bishwa Ghimire
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku & Åbo Akademi University, FI-20520 Turku, Finland
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14
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Friston D, Junttila S, Lemes JBP, Laycock H, Torres-Perez JV, Want E, Gyenesei A, Nagy I. Leptin and fractalkine: novel subcutaneous cytokines in burn injury. Dis Model Mech 2020; 13:dmm042713. [PMID: 32127397 PMCID: PMC7197715 DOI: 10.1242/dmm.042713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
Burn injury is a pathology underpinned by progressive and aberrant inflammation. It is a major clinical challenge to survival and quality of life. Although the complex local and disseminating pathological processes of a burn injury ultimately stem from local tissue damage, to date relatively few studies have attempted to characterise the local inflammatory mediator profile. Here, cytokine content and associated transcriptional changes were measured in rat skin for three hours immediately following induction of a scald-type (60°C, 2 min) burn injury model. Leptin (P=0.0002) and fractalkine (P=0.0478) concentrations were significantly elevated post-burn above pre-burn and control site values, coinciding with the development of burn site oedema and differential expression of leptin mRNA (P=0.0004). Further, gene sequencing enrichment analysis indicated cytokine-cytokine receptor interaction (P=1.45×10-6). Subsequent behavioural studies demonstrated that, following subcutaneous injection into the dorsum of the paw, both leptin and fractalkine induced mechanical allodynia, heat hyperalgesia and the recruitment of macrophages. This is the first report of leptin elevation specifically at the burn site, and the first report of fractalkine elevation in any tissue post-burn which, together with the functional findings, calls for exploration of the influence of these cytokines on pain, inflammation and burn wound progression. In addition, targeting these signalling molecules represents a therapeutic potential as early formative mediators of these pathological processes.
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Affiliation(s)
- Dominic Friston
- Nociception Group, Section of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, Chelsea and Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK
| | - Sini Junttila
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Julia Borges Paes Lemes
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, Carl Von Linnaeus, Sao Paulo, 13083-864, Brazil
| | - Helen Laycock
- Nociception Group, Section of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, Chelsea and Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK
| | - Jose Vicente Torres-Perez
- Nociception Group, Section of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, Chelsea and Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK
| | - Elizabeth Want
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Attila Gyenesei
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Istvan Nagy
- Nociception Group, Section of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, Chelsea and Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK
- Department of Physiology, University of Debrecen, Debrecen, Nagyerdei krt 98, H-4012, Hungary
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15
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Paczkowska-Abdulsalam M, Niemira M, Bielska A, Szałkowska A, Raczkowska BA, Junttila S, Gyenesei A, Adamska-Patruno E, Maliszewska K, Citko A, Szczerbiński Ł, Krętowski A. Evaluation of Transcriptomic Regulations behind Metabolic Syndrome in Obese and Lean Subjects. Int J Mol Sci 2020; 21:ijms21041455. [PMID: 32093387 PMCID: PMC7073064 DOI: 10.3390/ijms21041455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 01/03/2023] Open
Abstract
Multiple mechanisms have been suggested to confer to the pathophysiology of metabolic syndrome (MetS), however despite great interest from the scientific community, the exact contribution of each of MetS risk factors still remains unclear. The present study aimed to investigate molecular signatures in peripheral blood of individuals affected by MetS and different degrees of obesity. Metabolic health of 1204 individuals from 1000PLUS cohort was assessed, and 32 subjects were recruited to four study groups: MetS lean, MetS obese, “healthy obese”, and healthy lean. Whole-blood transcriptome next generation sequencing with functional data analysis were carried out. MetS obese and MetS lean study participants showed the upregulation of genes involved in inflammation and coagulation processes: granulocyte adhesion and diapedesis (p < 0.0001, p = 0.0063), prothrombin activation pathway (p = 0.0032, p = 0.0091), coagulation system (p = 0.0010, p = 0.0155). The results for “healthy obese” indicate enrichment in molecules associated with protein synthesis (p < 0.0001), mitochondrial dysfunction (p < 0.0001), and oxidative phosphorylation (p < 0.0001). Our results suggest that MetS is related to the state of inflammation and vascular system changes independent of excess body weight. Furthermore, “healthy obese”, despite not fulfilling the criteria for MetS diagnosis, seems to display an intermediate state with a lower degree of metabolic abnormalities, before they proceed to a full blown MetS.
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Affiliation(s)
- Magdalena Paczkowska-Abdulsalam
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
- Correspondence: ; Tel.: +48-85-831-81-59
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Agnieszka Bielska
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Anna Szałkowska
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Sini Junttila
- Vienna Biocenter Core Facilities, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Attila Gyenesei
- Vienna Biocenter Core Facilities, Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Edyta Adamska-Patruno
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Katarzyna Maliszewska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Anna Citko
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Łukasz Szczerbiński
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Adam Krętowski
- Clinical Research Centre, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Białystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
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16
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Haider S, Gamperl M, Burkard TR, Kunihs V, Kaindl U, Junttila S, Fiala C, Schmidt K, Mendjan S, Knöfler M, Latos PA. Estrogen Signaling Drives Ciliogenesis in Human Endometrial Organoids. Endocrinology 2019; 160:2282-2297. [PMID: 31290979 DOI: 10.1210/en.2019-00314] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
The human endometrium is the inner lining of the uterus consisting of stromal and epithelial (secretory and ciliated) cells. It undergoes a hormonally regulated monthly cycle of growth, differentiation, and desquamation. However, how these cyclic changes control the balance between secretory and ciliated cells remains unclear. Here, we established endometrial organoids to investigate the estrogen (E2)-driven control of cell fate decisions in human endometrial epithelium. We demonstrate that they preserve the structure, expression patterns, secretory properties, and E2 responsiveness of their tissue of origin. Next, we show that the induction of ciliated cells is orchestrated by the coordinated action of E2 and NOTCH signaling. Although E2 is the primary driver, inhibition of NOTCH signaling provides a permissive environment. However, inhibition of NOTCH alone is not sufficient to trigger ciliogenesis. Overall, we provide insights into endometrial biology and propose endometrial organoids as a robust and powerful model for studying ciliogenesis in vitro.
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Affiliation(s)
- Sandra Haider
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Magdalena Gamperl
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Victoria Kunihs
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Ulrich Kaindl
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | | | | | - Katy Schmidt
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria
| | - Martin Knöfler
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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17
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Rosser J, Bachmann B, Jordan C, Ribitsch I, Haltmayer E, Gueltekin S, Junttila S, Galik B, Gyenesei A, Haddadi B, Harasek M, Egerbacher M, Ertl P, Jenner F. Microfluidic nutrient gradient-based three-dimensional chondrocyte culture-on-a-chip as an in vitro equine arthritis model. Mater Today Bio 2019; 4:100023. [PMID: 32159153 PMCID: PMC7061638 DOI: 10.1016/j.mtbio.2019.100023] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/27/2023] Open
Abstract
In this work, we describe a microfluidic three-dimensional (3D) chondrocyte culture mimicking in vivo articular chondrocyte morphology, cell distribution, metabolism, and gene expression. This has been accomplished by establishing a physiologic nutrient diffusion gradient across the simulated matrix, while geometric design constraints of the microchambers drive native-like cellular behavior. Primary equine chondrocytes remained viable for the extended culture time of 3 weeks and maintained the low metabolic activity and high Sox9, aggrecan, and Col2 expression typical of articular chondrocytes. Our microfluidic 3D chondrocyte microtissues were further exposed to inflammatory cytokines to establish an animal-free, in vitro osteoarthritis model. Results of our study indicate that our microtissue model emulates the basic characteristics of native cartilage and responds to biochemical injury, thus providing a new foundation for exploration of osteoarthritis pathophysiology in both human and veterinary patients.
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Affiliation(s)
- J Rosser
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - B Bachmann
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - C Jordan
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - I Ribitsch
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - E Haltmayer
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - S Gueltekin
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - S Junttila
- BIOCOMP, Bioinformatics & Scientific Computing VBCF, Vienna Biocenter Core Facilities GmbH, GmbH, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - B Galik
- BIOCOMP, Bioinformatics & Scientific Computing VBCF, Vienna Biocenter Core Facilities GmbH, GmbH, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - A Gyenesei
- BIOCOMP, Bioinformatics & Scientific Computing VBCF, Vienna Biocenter Core Facilities GmbH, GmbH, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - B Haddadi
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - M Harasek
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - M Egerbacher
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - P Ertl
- Faculty of Technical Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - F Jenner
- Department of Equine Surgery, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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18
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Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Z. Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. Front Mol Neurosci 2018; 11:219. [PMID: 29997476 PMCID: PMC6028693 DOI: 10.3389/fnmol.2018.00219] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/06/2018] [Indexed: 12/23/2022] Open
Abstract
Orofacial pain and headache disorders are among the most debilitating pain conditions. While the pathophysiological basis of these disorders may be diverse, it is generally accepted that a common mechanism behind the arising pain is the sensitization of extra- and intracranial trigeminal primary afferents. In the present study we investigated gene expression changes in the trigeminal ganglia (TRG), trigeminal nucleus caudalis (TNC) and peripheral blood mononuclear cells (PBMC) evoked by Complete Freund's Adjuvant (CFA)-induced orofacial inflammation in rats, as a model of trigeminal sensitization. Microarray analysis revealed 512 differentially expressed genes between the ipsi- and contralateral TRG samples 7 days after CFA injection. Time-dependent expression changes of G-protein coupled receptor 39 (Gpr39), kisspeptin-1 receptor (Kiss1r), kisspeptin (Kiss1), as well as synaptic plasticity-associated Lkaaear1 (Lkr) and Neurod2 mRNA were described on the basis of qPCR results. The greatest alterations were observed on day 3 ipsilaterally, when orofacial mechanical allodynia reached its maximum. This corresponded well with patterns of neuronal (Fosb), microglia (Iba1), and astrocyte (Gfap) activation markers in both TRG and TNC, and interestingly also in PBMCs. This is the first description of up- and downregulated genes both in primary and secondary sensory neurones of the trigeminovascular system that might play important roles in neuroinflammatory activation mechanisms. We are the first to show transcriptomic alterations in the PBMCs that are similar to the neuronal changes. These results open new perspectives and initiate further investigations in the research of trigeminal pain disorders.
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Affiliation(s)
- Timea Aczél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | - József Kun
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
| | - Éva Szőke
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
| | - Tibor Rauch
- Section of Molecular Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Sini Junttila
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Attila Gyenesei
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Kata Bölcskei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
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19
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Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F. Linear ubiquitination by LUBEL has a role in Drosophila heat stress response. EMBO Rep 2016; 17:1624-1640. [PMID: 27702987 PMCID: PMC5090701 DOI: 10.15252/embr.201642378] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/05/2016] [Indexed: 12/17/2022] Open
Abstract
The HOIP ubiquitin E3 ligase generates linear ubiquitin chains by forming a complex with HOIL‐1L and SHARPIN in mammals. Here, we provide the first evidence of linear ubiquitination induced by a HOIP orthologue in Drosophila. We identify Drosophila CG11321, which we named Linear Ubiquitin E3 ligase (LUBEL), and find that it catalyzes linear ubiquitination in vitro. We detect endogenous linear ubiquitin chain‐derived peptides by mass spectrometry in Drosophila Schneider 2 cells and adult flies. Furthermore, using CRISPR/Cas9 technology, we establish linear ubiquitination‐defective flies by mutating residues essential for the catalytic activity of LUBEL. Linear ubiquitination signals accumulate upon heat shock in flies. Interestingly, flies with LUBEL mutations display reduced survival and climbing defects upon heat shock, which is also observed upon specific LUBEL depletion in muscle. Thus, LUBEL is involved in the heat response by controlling linear ubiquitination in flies.
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Affiliation(s)
- Tomoko Asaoka
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Jorge Almagro
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Christine Ehrhardt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Isabella Tsai
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Luiza Deszcz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Sini Junttila
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Leonie Ringrose
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Humboldt-Universität zu Berlin IRI for the Life Sciences, Berlin, Germany
| | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Attila Gyenesei
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
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20
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Budzyńska PM, Niemelä M, Sarapulov AV, Kyläniemi MK, Nera KP, Junttila S, Laiho A, Mattila PK, Alinikula J, Lassila O. IRF4 Deficiency Leads to Altered BCR Signalling Revealed by Enhanced PI3K Pathway, Decreased SHIP Expression and Defected Cytoskeletal Responses. Scand J Immunol 2016; 82:418-28. [PMID: 26173778 DOI: 10.1111/sji.12343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/07/2015] [Indexed: 12/13/2022]
Abstract
The graded expression of transcription factor interferon regulatory factor 4 (IRF4) regulates B cell development and is critical for plasma cell differentiation. However, the mechanisms, by which IRF4 elicits its crucial tasks, are largely unknown. To characterize the molecular targets of IRF4 in B cells, we established an IRF4-deficient DT40 B cell line. We found that in the absence of IRF4, the expression of several molecules involved in BCR signalling was altered. For example, the expression of B cell adaptor for PI3K (BCAP) was upregulated, whereas the SHIP (SH2-containing Inositol 5?-Phosphatase) expression was downregulated. These molecular unbalances were accompanied by increased BCR-induced calcium signalling, attenuated B cell linker protein (BLNK) and ERK activity and enhanced activity of PI3K/protein kinase B (Akt) pathway. Further, the IRF4-deficient cells showed dramatically diminished cytoskeletal responses to anti-IgM cross-linking. Our results show that IRF4 has an important role in the regulation of BCR signalling and help to shed light on the molecular mechanisms of B cell development and germinal centre response.
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Affiliation(s)
- P M Budzyńska
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland.,Turku Doctoral Programme of Biomedical Sciences, University of Turku, Turku, Finland
| | - M Niemelä
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - A V Sarapulov
- Institute of Biomedicine, Department of Pathology, University of Turku, Turku, Finland
| | - M K Kyläniemi
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - K-P Nera
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - S Junttila
- The Finnish Microarray and Sequencing Center, Turku Centre for Biotechnology, Turku, Finland
| | - A Laiho
- The Finnish Microarray and Sequencing Center, Turku Centre for Biotechnology, Turku, Finland
| | - P K Mattila
- Institute of Biomedicine, Department of Pathology, University of Turku, Turku, Finland
| | - J Alinikula
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - O Lassila
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
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21
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Vehniäinen ER, Bremer K, Scott JA, Junttila S, Laiho A, Gyenesei A, Hodson PV, Oikari AOJ. Retene causes multifunctional transcriptomic changes in the heart of rainbow trout (Oncorhynchus mykiss) embryos. Environ Toxicol Pharmacol 2016; 41:95-102. [PMID: 26667672 DOI: 10.1016/j.etap.2015.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
Fish are particularly sensitive to aryl hydrocarbon receptor (AhR)-mediated developmental toxicity. The molecular mechanisms behind these adverse effects have remained largely unresolved in salmonids, and for AhR-agonistic polycyclic aromatic hydrocarbons (PAHs). This study explored the cardiac transcriptome of rainbow trout (Oncorhynchus mykiss) eleuteroembryos exposed to retene, an AhR-agonistic PAH. The embryos were exposed to retene (nominal concentration 32 μg/L) and control, their hearts were collected before, at and after the onset of the visible signs of developmental toxicity, and transcriptomic changes were studied by microarray analysis. Retene up- or down-regulated 122 genes. The largest Gene Ontology groups were signal transduction, transcription, apoptosis, cell growth, cytoskeleton, cell adhesion/mobility, cardiovascular development, xenobiotic metabolism, protein metabolism, lipid metabolism and transport, and amino acid metabolism. Together these findings suggest that retene affects multiple signaling cascades in the heart of rainbow trout embryos, and potentially disturbs processes related to cardiovascular development and function.
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Affiliation(s)
- Eeva-Riikka Vehniäinen
- University of Jyväskylä, Department of Biological and Environmental Science, P.O. Box 35, FI-40014 University of Jyväskylä, Finland.
| | - Katharina Bremer
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - Jason A Scott
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - Sini Junttila
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 A, FI-20520 Turku, Finland
| | - Asta Laiho
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 A, FI-20520 Turku, Finland
| | - Attila Gyenesei
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 A, FI-20520 Turku, Finland
| | - Peter V Hodson
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada; School of Environmental Studies, Queen's University, 116 Barrie Street, Kingston, Ontario K7L 3N6, Canada
| | - Aimo O J Oikari
- University of Jyväskylä, Department of Biological and Environmental Science, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
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22
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Babu M, Durga Devi T, Mäkinen P, Kaikkonen M, Lesch HP, Junttila S, Laiho A, Ghimire B, Gyenesei A, Ylä-Herttuala S. Differential Promoter Methylation of Macrophage Genes Is Associated With Impaired Vascular Growth in Ischemic Muscles of Hyperlipidemic and Type 2 Diabetic Mice: Genome-Wide Promoter Methylation Study. Circ Res 2015; 117:289-99. [PMID: 26085133 DOI: 10.1161/circresaha.115.306424] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/17/2015] [Indexed: 12/18/2022]
Abstract
RATIONALE Hyperlipidemia and type 2 diabetes mellitus (T2DM) severely impair adaptive vascular growth responses in ischemic muscles. This is largely attributed to dysregulated gene expression, although details of the changes are unknown. OBJECTIVE To define the role of promoter methylation in adaptive vascular growth in hyperlipidemia (LDLR(-/-)ApoB(100/100)) and T2DM (IGF-II/LDLR(-/-)ApoB(100/100)) mouse models of hindlimb ischemia. METHODS AND RESULTS Unilateral hindlimb ischemia was induced by ligating femoral artery. Perfusion was assessed using ultrasound, and capillary and arteriole parameters were assessed using immunohistochemistry. Genome-wide methylated DNA sequencing was performed with DNA isolated from ischemic muscle, tissue macrophages (Mϕs), and endothelial cells. Compared with the controls, hyperlipidemia and T2DM mice showed impaired perfusion recovery, which was associated with impaired angiogenesis and arteriogenesis. Genome-wide proximal promoter DNA methylation analysis suggested differential patterns of methylation in Mϕ genes in ischemic muscles. Classically activated M1-Mϕ gene promoters, including Cfb, Serping1, and Tnfsf15, were significantly hypomethylated, whereas alternatively activated M2-Mϕ gene promoters, including Nrp1, Cxcr4, Plxnd1, Arg1, Cdk18, and Fes, were significantly hypermethylated in Mϕs isolated from hyperlipidemia and T2DM ischemic muscles compared with controls. These results combined with mRNA expression and immunohistochemistry showed the predominance of proinflammatory M1-Mϕs, compared with anti-inflammatory and proangiogenic M2-Mϕs in hyperlipidemia and T2DM ischemic muscles. CONCLUSIONS We found significant promoter hypomethylation of genes typical for proinflammatory M1-Mϕs and hypermethylation of anti-inflammatory, proangiogenic M2-Mϕ genes in hyperlipidemia and T2DM ischemic muscles. Epigenetic alterations modify Mϕ phenotype toward proinflammatory M1 as opposed to anti-inflammatory, proangiogenic, and tissue repair M2 phenotype, which may contribute to the impaired adaptive vascular growth under these pathological conditions.
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Affiliation(s)
- Mohan Babu
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Thota Durga Devi
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Petri Mäkinen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Minna Kaikkonen
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Hanna P Lesch
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Sini Junttila
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Asta Laiho
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Bishwa Ghimire
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Attila Gyenesei
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.)
| | - Seppo Ylä-Herttuala
- From the Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland (M.B., T.D.D., P.M., M.K., H.P.L., S.Y.-H.); Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Turku, Finland (S.J., A.L., B.G., A.G.); and Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland (S.Y.-H.).
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23
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Junttila S, Laiho A, Gyenesei A, Rudd S. Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. BMC Genomics 2013; 14:870. [PMID: 24325588 PMCID: PMC3878897 DOI: 10.1186/1471-2164-14-870] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/14/2013] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Lichens are symbiotic organisms with a fungal and an algal or a cyanobacterial partner. Lichens inhabit some of the harshest climates on earth and most lichen species are desiccation-tolerant. Lichen desiccation-tolerance has been studied at the biochemical level and through proteomics, but the underlying molecular genetic mechanisms remain largely unexplored. The objective of our study was to examine the effects of dehydration and rehydration on the gene expression of Cladonia rangiferina. RESULTS Samples of C. rangiferina were collected at several time points during both the dehydration and rehydration process and the gene expression intensities were measured using a custom DNA microarray. Several genes, which were differentially expressed in one or more time points, were identified. The microarray results were validated using qRT-PCR analysis. Enrichment analysis of differentially expressed transcripts was also performed to identify the Gene Ontology terms most associated with the rehydration and dehydration process. CONCLUSIONS Our data identify differential expression patterns for hundreds of genes that are modulated during dehydration and rehydration in Cladonia rangiferina. These dehydration and rehydration events clearly differ from each other at the molecular level and the largest changes to gene expression are observed within minutes following rehydration. Distinct changes are observed during the earliest stage of rehydration and the mechanisms not appear to be shared with the later stages of wetting or with drying. Several of the most differentially expressed genes are similar to genes identified in previous studies that have investigated the molecular mechanisms of other desiccation-tolerant organisms. We present here the first microarray experiment for any lichen species and have for the first time studied the genetic mechanisms behind lichen desiccation-tolerance at the whole transcriptome level.
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Affiliation(s)
- Sini Junttila
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Attila Gyenesei
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Stephen Rudd
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
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24
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Hyytiäinen H, Juntunen P, Scott T, Kytömäki L, Venho R, Laiho A, Junttila S, Gyenesei A, Revez J, Hänninen ML. Effect of ciprofloxacin exposure on DNA repair mechanisms in Campylobacter jejuni. Microbiology (Reading) 2013; 159:2513-2523. [DOI: 10.1099/mic.0.069203-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Hyytiäinen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Pekka Juntunen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Thomas Scott
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Leena Kytömäki
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Reija Venho
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Asta Laiho
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Sini Junttila
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Attila Gyenesei
- Finnish Microarray and Sequencing Centre (FMSC), Turku Centre for Biotechnology (BTK), University of Turku and Åbo Akademi University, Tykistökatu 6 A, Turku 20521, Finland
| | - Joana Revez
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, P.O. Box 66, University of Helsinki 00014, Finland
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25
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Teittinen KJ, Grönroos T, Parikka M, Junttila S, Uusimäki A, Laiho A, Korkeamäki H, Kurppa K, Turpeinen H, Pesu M, Gyenesei A, Rämet M, Lohi O. SAP30L (Sin3A-associated protein 30-like) is involved in regulation of cardiac development and hematopoiesis in zebrafish embryos. J Cell Biochem 2013; 113:3843-52. [PMID: 22821512 DOI: 10.1002/jcb.24298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Sin3A-associated proteins SAP30 and SAP30L share 70% sequence identity and are part of the multiprotein Sin3A corepressor complex. They participate in gene repression events by linking members of the complex and stabilizing interactions among the protein members as well as between proteins and DNA. While most organisms have both SAP30 and SAP30L, the zebrafish is exceptional because it only has SAP30L. Here we demonstrate that SAP30L is expressed ubiquitously in embryonic and adult zebrafish tissues. Knockdown of SAP30L using morpholino-mediated technology resulted in a morphant phenotype manifesting as cardiac insufficiency and defective hemoglobinization of red blood cells. A microarray analysis of gene expression in SAP30L morphant embryos revealed changes in the expression of genes involved in regulation of transcription, TGF-beta signaling, Wnt-family transcription factors, and nuclear genes encoding mitochondrial proteins. The expression of the heart-specific nkx2.5 gene was markedly down-regulated in SAP30L morphants, and the cardiac phenotype could be partially rescued by nkx2.5 mRNA. In addition, changes were detected in the expression of genes known to be important in hemoglobin synthesis and erythropoiesis. Our results demonstrate that SAP30L regulates several transcriptional pathways in zebrafish embryos and is involved in the development of cardiac and hematopoietic systems.
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Affiliation(s)
- Kaisa J Teittinen
- Paediatric Research Centre, University of Tampere School of Medicine and Tampere University Hospital, 33520 Tampere, Finland.
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Junttila S, Rudd S. Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST sequence data. BMC Genomics 2012; 13:575. [PMID: 23110403 PMCID: PMC3534622 DOI: 10.1186/1471-2164-13-575] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 10/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lichens are symbiotic organisms that have a remarkable ability to survive in some of the most extreme terrestrial climates on earth. Lichens can endure frequent desiccation and wetting cycles and are able to survive in a dehydrated molecular dormant state for decades at a time. Genetic resources have been established in lichen species for the study of molecular systematics and their taxonomic classification. No lichen species have been characterised yet using genomics and the molecular mechanisms underlying the lichen symbiosis and the fundamentals of desiccation tolerance remain undescribed. We report the characterisation of a transcriptome of the grey reindeer lichen, Cladonia rangiferina, using high-throughput next-generation transcriptome sequencing and traditional Sanger EST sequencing data. RESULTS Altogether 243,729 high quality sequence reads were de novo assembled into 16,204 contigs and 49,587 singletons. The genome of origin for the sequences produced was predicted using Eclat with sequences derived from the axenically grown symbiotic partners used as training sequences for the classification model. 62.8% of the sequences were classified as being of fungal origin while the remaining 37.2% were predicted as being of algal origin. The assembled sequences were annotated by BLASTX comparison against a non-redundant protein sequence database with 34.4% of the sequences having a BLAST match. 29.3% of the sequences had a Gene Ontology term match and 27.9% of the sequences had a domain or structural match following an InterPro search. 60 KEGG pathways with more than 10 associated sequences were identified. CONCLUSIONS Our results present a first transcriptome sequencing and de novo assembly for a lichen species and describe the ongoing molecular processes and the most active pathways in C. rangiferina. This brings a meaningful contribution to publicly available lichen sequence information. These data provide a first glimpse into the molecular nature of the lichen symbiosis and characterise the transcriptional space of this remarkable organism. These data will also enable further studies aimed at deciphering the genetic mechanisms behind lichen desiccation tolerance.
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Affiliation(s)
- Sini Junttila
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - Stephen Rudd
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
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Alinikula J, Nera KP, Junttila S, Lassila O. Alternate pathways for Bcl6-mediated regulation of B cell to plasma cell differentiation. Eur J Immunol 2011; 41:2404-13. [PMID: 21674482 DOI: 10.1002/eji.201141553] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/29/2011] [Accepted: 05/20/2011] [Indexed: 11/08/2022]
Abstract
The transcription factor Bcl6 regulates germinal center formation and differentiation of B cells into high-affinity antibody-producing plasma cells. The direct double-negative regulatory circuit between Bcl6 and Blimp-1 is well established. We now reveal alternative mechanisms for Bcl6-mediated regulation of B-cell differentiation to plasma cells and show with DT40 cells that Bcl6 directly promotes the expression of Bach2, a known suppressor of Blimp-1. Moreover, Bcl6 suppresses Blimp-1 expression through direct binding to the IRF4 gene, as well as by promoting the expression of MITF, a known suppressor of IRF4. We also provide evidence that Bcl6 is needed for the expression of AID and UNG, the indispensable proteins for somatic hypermutation and class-switch recombination, and UNG appears to be a direct Bcl6 target. Our findings reveal a complex regulatory network in which Bcl6 acts as a key element dictating the transition of DT40 B cells to plasma cells.
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Affiliation(s)
- Jukka Alinikula
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland.
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Junttila S, Lim KJ, Rudd S. Optimization and comparison of different methods for RNA isolation for cDNA library construction from the reindeer lichen Cladonia rangiferina. BMC Res Notes 2009; 2:204. [PMID: 19804636 PMCID: PMC2762986 DOI: 10.1186/1756-0500-2-204] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/05/2009] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The reindeer lichen is the product of a mutualistic relationship between a fungus and an algae. Lichen demonstrate a remarkable capacity to tolerate dehydration. This tolerance is driven by a variety of biochemical processes and the accumulation of specific secondary metabolites that may be of relevance to the pharmaceutical, biotechnology and agriculture industries. These protective metabolites hinder in vitro enzymatic reactions required in cDNA synthesis. Along with the low concentrations of RNA present within lichen tissues, the process of creating a cDNA library is technically challenging. FINDINGS An evaluation of existing commercial and published protocols for RNA extraction from plant or fungal tissues has been performed and experimental conditions have been optimised to balance the need for the highest quality total ribonucleotides and the constraints of budget, time and human resources. CONCLUSION We present a protocol that balances inexpensive RNA extraction methods with commercial RNA clean-up kits to yield sufficient RNA for cDNA library construction. Evaluation of the protocol and the construction of, and sampling from, a cDNA library is used to demonstrate the suitability of the RNA extraction method for expressed sequence tag production.
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Affiliation(s)
- Sini Junttila
- Centre for Biotechnology, Tykistökatu 6 A, 20520 Turku, Finland
| | - Kean-Jin Lim
- Centre for Biotechnology, Tykistökatu 6 A, 20520 Turku, Finland
| | - Stephen Rudd
- Centre for Biotechnology, Tykistökatu 6 A, 20520 Turku, Finland
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Abstract
The culture medium of Streptomyces xanthochromogenes JH903 was found to show selective activity against DNA-repair-deficient Escherichia coli CM871 strain. In this report we describe a simple method to locate and isolate DNA binding compounds from the fermentation broth. The method is based on the retention of DNA-reacting compounds in cellulose complexed with DNA, and purification of these compounds with thin-layer chromatography. Screening of microbial metabolites from chloroform extracts of fermentation media resulted in detection of five genotoxic fractions.
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Affiliation(s)
- J Holmalahti
- Department of Pharmaceutical Chemistry, University of Kuopio, Finland
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Ihlebekk H, Eilertsen S, Junttila S, Grindal G, Moe R. CONTROL OF PLANT HEIGHT IN CAMPANULA ISOPHYLLA BY TEMPERATURE ALTERNATIONS; INVOLVEMENT OF GAS. ACTA ACUST UNITED AC 1995. [DOI: 10.17660/actahortic.1995.394.38] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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