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Schmidt M, Avagyan S, Reiche K, Binder H, Loeffler-Wirth H. A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections. Curr Issues Mol Biol 2024; 46:4701-4720. [PMID: 38785552 PMCID: PMC11119626 DOI: 10.3390/cimb46050284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
A crucial feature of life is its spatial organization and compartmentalization on the molecular, cellular, and tissue levels. Spatial transcriptomics (ST) technology has opened a new chapter of the sequencing revolution, emerging rapidly with transformative effects across biology. This technique produces extensive and complex sequencing data, raising the need for computational methods for their comprehensive analysis and interpretation. We developed the ST browser web tool for the interactive discovery of ST images, focusing on different functional aspects such as single gene expression, the expression of functional gene sets, as well as the inspection of the spatial patterns of cell-cell interactions. As a unique feature, our tool applies self-organizing map (SOM) machine learning to the ST data. Our SOM data portrayal method generates individual gene expression landscapes for each spot in the ST image, enabling its downstream analysis with high resolution. The performance of the spatial browser is demonstrated by disentangling the intra-tumoral heterogeneity of melanoma and the microarchitecture of the mouse brain. The integration of machine-learning-based SOM portrayal into an interactive ST analysis environment opens novel perspectives for the comprehensive knowledge mining of the organization and interactions of cellular ecosystems.
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Affiliation(s)
- Maria Schmidt
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
| | - Susanna Avagyan
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan Str., Yerevan 0062, Armenia
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstrasse 1, 04103 Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, 04103 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan Str., Yerevan 0062, Armenia
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
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2
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Arakelyan A, Avagyan S, Kurnosov A, Mkrtchyan T, Mkrtchyan G, Zakharyan R, Mayilyan KR, Binder H. Temporal changes of gene expression in health, schizophrenia, bipolar disorder, and major depressive disorder. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2024; 10:19. [PMID: 38368435 PMCID: PMC10874418 DOI: 10.1038/s41537-024-00443-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/02/2024] [Indexed: 02/19/2024]
Abstract
The molecular events underlying the development, manifestation, and course of schizophrenia, bipolar disorder, and major depressive disorder span from embryonic life to advanced age. However, little is known about the early dynamics of gene expression in these disorders due to their relatively late manifestation. To address this, we conducted a secondary analysis of post-mortem prefrontal cortex datasets using bioinformatics and machine learning techniques to identify differentially expressed gene modules associated with aging and the diseases, determine their time-perturbation points, and assess enrichment with expression quantitative trait loci (eQTL) genes. Our findings revealed early, mid, and late deregulation of expression of functional gene modules involved in neurodevelopment, plasticity, homeostasis, and immune response. This supports the hypothesis that multiple hits throughout life contribute to disease manifestation rather than a single early-life event. Moreover, the time-perturbed functional gene modules were associated with genetic loci affecting gene expression, highlighting the role of genetic factors in gene expression dynamics and the development of disease phenotypes. Our findings emphasize the importance of investigating time-dependent perturbations in gene expression before the age of onset in elucidating the molecular mechanisms of psychiatric disorders.
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Affiliation(s)
- Arsen Arakelyan
- Institute of Molecular Biology NAS RA, Yerevan, Armenia.
- Armenian Bioinformatics Institute, Yerevan, Armenia.
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan, Armenia.
| | | | | | - Tigran Mkrtchyan
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan, Armenia
| | | | - Roksana Zakharyan
- Institute of Molecular Biology NAS RA, Yerevan, Armenia
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan, Armenia
| | - Karine R Mayilyan
- Institute of Molecular Biology NAS RA, Yerevan, Armenia
- Department of Therapeutics, Faculty of General Medicine, University of Traditional Medicine, Yerevan, Armenia
| | - Hans Binder
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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3
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Konecny T, Nikoghosyan M, Binder H. Machine learning extracts marks of thiamine's role in cold acclimation in the transcriptome of Vitis vinifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1303542. [PMID: 38126012 PMCID: PMC10731266 DOI: 10.3389/fpls.2023.1303542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Introduction The escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine. Methods We used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific "portraits" of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied. Results Our analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines. Discussion Application of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants.
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Affiliation(s)
- Tomas Konecny
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Maria Nikoghosyan
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Bioinformatics Group, Institute of Molecular Biology Institute of National Academy of Sciences RA, Yerevan, Armenia
| | - Hans Binder
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany
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Silva N, Rajado AT, Esteves F, Brito D, Apolónio J, Roberto VP, Binnie A, Araújo I, Nóbrega C, Bragança J, Castelo-Branco P. Measuring healthy ageing: current and future tools. Biogerontology 2023; 24:845-866. [PMID: 37439885 PMCID: PMC10615962 DOI: 10.1007/s10522-023-10041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023]
Abstract
Human ageing is a complex, multifactorial process characterised by physiological damage, increased risk of age-related diseases and inevitable functional deterioration. As the population of the world grows older, placing significant strain on social and healthcare resources, there is a growing need to identify reliable and easy-to-employ markers of healthy ageing for early detection of ageing trajectories and disease risk. Such markers would allow for the targeted implementation of strategies or treatments that can lessen suffering, disability, and dependence in old age. In this review, we summarise the healthy ageing scores reported in the literature, with a focus on the past 5 years, and compare and contrast the variables employed. The use of approaches to determine biological age, molecular biomarkers, ageing trajectories, and multi-omics ageing scores are reviewed. We conclude that the ideal healthy ageing score is multisystemic and able to encompass all of the potential alterations associated with ageing. It should also be longitudinal and able to accurately predict ageing complications at an early stage in order to maximize the chances of successful early intervention.
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Affiliation(s)
- Nádia Silva
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Ana Teresa Rajado
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Filipa Esteves
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - David Brito
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Joana Apolónio
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Vânia Palma Roberto
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
| | - Alexandra Binnie
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Department of Critical Care, William Osler Health System, Etobicoke, ON, Canada
| | - Inês Araújo
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Pedro Castelo-Branco
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal.
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal.
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal.
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal.
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Juigné C, Becker E, Gondret F. Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs. BMC Genomics 2023; 24:647. [PMID: 37891507 PMCID: PMC10605982 DOI: 10.1186/s12864-023-09751-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs. RESULTS The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly ([Formula: see text]) or tended to be ([Formula: see text]) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma. CONCLUSION These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits.
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Affiliation(s)
- Camille Juigné
- PEGASE, INRAE, Institut Agro, Saint-Gilles, F-35590, France
- University Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France
| | - Emmanuelle Becker
- University Rennes, Inria, CNRS, IRISA - UMR 6074, Rennes, F-35000, France
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Luna-Ramirez RI, Limesand SW, Goyal R, Pendleton AL, Rincón G, Zeng X, Luna-Nevárez G, Reyna-Granados JR, Luna-Nevárez P. Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress. Genes (Basel) 2023; 14:1590. [PMID: 37628641 PMCID: PMC10454332 DOI: 10.3390/genes14081590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes.
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Affiliation(s)
- Rosa I. Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sean W. Limesand
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Ravi Goyal
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Alexander L. Pendleton
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Xi Zeng
- Zoetis Inc., VMRD Genetics R&D, Kalamazoo, MI 49007, USA
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Javier R. Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
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Silva N, Rajado AT, Esteves F, Brito D, Apolónio J, Roberto VP, Binnie A, Araújo I, Nóbrega C, Bragança J, Castelo-Branco P, Andrade RP, Calado S, Faleiro ML, Matos C, Marques N, Marreiros A, Nzwalo H, Pais S, Palmeirim I, Simão S, Joaquim N, Miranda R, Pêgas A, Sardo A. Measuring healthy ageing: current and future tools. Biogerontology 2023. [DOI: https:/doi.org/10.1007/s10522-023-10041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 09/01/2023]
Abstract
AbstractHuman ageing is a complex, multifactorial process characterised by physiological damage, increased risk of age-related diseases and inevitable functional deterioration. As the population of the world grows older, placing significant strain on social and healthcare resources, there is a growing need to identify reliable and easy-to-employ markers of healthy ageing for early detection of ageing trajectories and disease risk. Such markers would allow for the targeted implementation of strategies or treatments that can lessen suffering, disability, and dependence in old age. In this review, we summarise the healthy ageing scores reported in the literature, with a focus on the past 5 years, and compare and contrast the variables employed. The use of approaches to determine biological age, molecular biomarkers, ageing trajectories, and multi-omics ageing scores are reviewed. We conclude that the ideal healthy ageing score is multisystemic and able to encompass all of the potential alterations associated with ageing. It should also be longitudinal and able to accurately predict ageing complications at an early stage in order to maximize the chances of successful early intervention.
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8
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Tran NQV, Le MK, Nguyen TA, Kondo T, Nakao A. Association of Circadian Clock Gene Expression with Pediatric/Adolescent Asthma and Its Comorbidities. Int J Mol Sci 2023; 24:ijms24087477. [PMID: 37108640 PMCID: PMC10138904 DOI: 10.3390/ijms24087477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The pathology of asthma is characterized by marked day-night variation, which is likely controlled by circadian clock activity. This study aimed to clarify the association of core circadian clock gene expression with clinical features of asthma. For this purpose, we accessed the National Center for Biotechnology Information database and analyzed transcriptomes of peripheral blood mononuclear cells and clinical characteristics of 134 pediatric/adolescent patients with asthma. Based on the expression patterns of seven core circadian clock genes (CLOCK, BMAL1, PER1-3, CRY1-2), we identified three circadian clusters (CCs) with distinct comorbidities and transcriptomic expressions. In the three CC subtypes, allergic rhinitis, and atopic dermatitis, both asthma comorbidities occurred in different proportions: CC1 had a high proportion of allergic rhinitis and atopic dermatitis; CC2 had a high proportion of atopic dermatitis but a low proportion of allergic rhinitis; and CC3 had a high proportion of allergic rhinitis but a low proportion of atopic dermatitis. This might be associated with the low activity of the FcεRI signaling pathway in CC2 and the cytokine-cytokine receptor interaction pathways in CC3. This is the first report to consider circadian clock gene expression in subcategories of patients with asthma and to explore their contribution to pathophysiology and comorbidity.
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Affiliation(s)
- Nguyen Quoc Vuong Tran
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Minh-Khang Le
- Department of Human Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Thuy-An Nguyen
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Tetsuo Kondo
- Department of Human Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Atsuhito Nakao
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
- Atopy Research Center, Juntendo University, School of Medicine, Tokyo 113-8421, Japan
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Gormally BMG, Lopes PC. The effect of infection risk on female blood transcriptomics. Gen Comp Endocrinol 2023; 330:114139. [PMID: 36209834 DOI: 10.1016/j.ygcen.2022.114139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
Abstract
Defenses against pathogens can take on many forms. For instance, behavioral avoidance of diseased conspecifics is widely documented. Interactions with these infectious conspecifics can also, however, lead to physiological changes in uninfected animals, an effect that is much less well understood. These changes in behavior and physiology are particularly important to study in a reproductive context, where they can impact reproductive decisions and offspring quality. Here, we studied how an acute (3 h) exposure to an immune-challenged male affected female blood transcriptomics and behavior. We predicted that females paired with immune-challenged males would reduce eating and drinking behaviors (as avoidance behaviors) and that their blood would show activation of immune and stress responses. We used female Japanese quail as a study system because they have been shown to respond to male traits, in terms of their own physiology and egg investment. Only two genes showed significant differential expression due to treatment, including an increase in the threonine dehydrogenase (TDH) transcript, an enzyme important for threonine breakdown. However, hundreds of genes in pathways related to activation of immune responses showed coordinated up-regulation in females exposed to immune-challenged males. Suppressed pathways revealed potential changes to metabolism and reduced responsiveness to glucocorticoids. Contrary to our prediction, we found that females paired with immune-challenged males increased food consumption. Water consumption was not changed by treatment. These findings suggest that even short exposure to diseased conspecifics can trigger both behavioral and physiological responses in healthy animals.
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Affiliation(s)
- Brenna M G Gormally
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Patricia C Lopes
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA.
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Kirsten T, Meineke FA, Loeffler-Wirth H, Beger C, Uciteli A, Stäubert S, Löbe M, Hänsel R, Rauscher FG, Schuster J, Peschel T, Herre H, Wagner J, Zachariae S, Engel C, Scholz M, Rahm E, Binder H, Loeffler M. The Leipzig Health Atlas-An Open Platform to Present, Archive, and Share Biomedical Data, Analyses, and Models Online. Methods Inf Med 2022; 61:e103-e115. [PMID: 35915977 PMCID: PMC9788914 DOI: 10.1055/a-1914-1985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Clinical trials, epidemiological studies, clinical registries, and other prospective research projects, together with patient care services, are main sources of data in the medical research domain. They serve often as a basis for secondary research in evidence-based medicine, prediction models for disease, and its progression. This data are often neither sufficiently described nor accessible. Related models are often not accessible as a functional program tool for interested users from the health care and biomedical domains. OBJECTIVE The interdisciplinary project Leipzig Health Atlas (LHA) was developed to close this gap. LHA is an online platform that serves as a sustainable archive providing medical data, metadata, models, and novel phenotypes from clinical trials, epidemiological studies, and other medical research projects. METHODS Data, models, and phenotypes are described by semantically rich metadata. The platform prefers to share data and models presented in original publications but is also open for nonpublished data. LHA provides and associates unique permanent identifiers for each dataset and model. Hence, the platform can be used to share prepared, quality-assured datasets and models while they are referenced in publications. All managed data, models, and phenotypes in LHA follow the FAIR principles, with public availability or restricted access for specific user groups. RESULTS The LHA platform is in productive mode (https://www.health-atlas.de/). It is already used by a variety of clinical trial and research groups and is becoming increasingly popular also in the biomedical community. LHA is an integral part of the forthcoming initiative building a national research data infrastructure for health in Germany.
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Affiliation(s)
- Toralf Kirsten
- Department of Medical Data Science, Leipzig University Medical Center, Leipzig, Germany,Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany,Address for correspondence Toralf Kirsten Department of Medical Data Science, Leipzig UniversityHärtelstraße 16-18, 04107 LeipzigGermany
| | - Frank A. Meineke
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Henry Loeffler-Wirth
- LIFE Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Christoph Beger
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Alexandr Uciteli
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Sebastian Stäubert
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Matthias Löbe
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - René Hänsel
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Franziska G. Rauscher
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Judith Schuster
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Thomas Peschel
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Heinrich Herre
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Jonas Wagner
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Silke Zachariae
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany
| | - Erhard Rahm
- Department of Computer Sciences, Leipzig University, Leipzig, Germany
| | - Hans Binder
- LIFE Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig University, Leipzig, Germany,Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany,LIFE Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
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11
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Loeffler-Wirth H, Rade M, Arakelyan A, Kreuz M, Loeffler M, Koehl U, Reiche K, Binder H. Transcriptional states of CAR-T infusion relate to neurotoxicity – lessons from high-resolution single-cell SOM expression portraying. Front Immunol 2022; 13:994885. [PMID: 36248848 PMCID: PMC9558919 DOI: 10.3389/fimmu.2022.994885] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/29/2022] [Indexed: 11/26/2022] Open
Abstract
Anti-CD19 CAR-T cell immunotherapy is a hopeful treatment option for patients with B cell lymphomas, however it copes with partly severe adverse effects like neurotoxicity. Single-cell resolved molecular data sets in combination with clinical parametrization allow for comprehensive characterization of cellular subpopulations, their transcriptomic states, and their relation to the adverse effects. We here present a re-analysis of single-cell RNA sequencing data of 24 patients comprising more than 130,000 cells with focus on cellular states and their association to immune cell related neurotoxicity. For this, we developed a single-cell data portraying workflow to disentangle the transcriptional state space with single-cell resolution and its analysis in terms of modularly-composed cellular programs. We demonstrated capabilities of single-cell data portraying to disentangle transcriptional states using intuitive visualization, functional mining, molecular cell stratification, and variability analyses. Our analysis revealed that the T cell composition of the patient’s infusion product as well as the spectrum of their transcriptional states of cells derived from patients with low ICANS grade do not markedly differ from those of cells from high ICANS patients, while the relative abundancies, particularly that of cycling cells, of LAG3-mediated exhaustion and of CAR positive cells, vary. Our study provides molecular details of the transcriptomic landscape with possible impact to overcome neurotoxicity.
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Affiliation(s)
- Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics (IZBI), Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
- *Correspondence: Henry Loeffler-Wirth,
| | - Michael Rade
- Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Arsen Arakelyan
- Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Markus Kreuz
- Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Markus Loeffler
- Interdisciplinary Centre for Bioinformatics (IZBI), Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Ulrike Koehl
- Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Kristin Reiche
- Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics (IZBI), Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
- Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
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12
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Oh SL, Zhou M, Chin EWM, Amarnath G, Cheah CH, Ng KP, Kandiah N, Goh ELK, Chiam KH. Alzheimer's Disease Blood Biomarkers Associated With Neuroinflammation as Therapeutic Targets for Early Personalized Intervention. Front Digit Health 2022; 4:875895. [PMID: 35899035 PMCID: PMC9309434 DOI: 10.3389/fdgth.2022.875895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The definitive diagnosis of Alzheimer's Disease (AD) without the need for neuropathological confirmation remains a challenge in AD research today, despite efforts to uncover the molecular and biological underpinnings of the disease process. Furthermore, the potential for therapeutic intervention is limited upon the onset of symptoms, providing motivation for studying and treating the AD precursor mild cognitive impairment (MCI), the prodromal stage of AD instead. Applying machine learning classification to transcriptomic data of MCI, AD, and cognitively normal (CN) control patients, we identified differentially expressed genes that serve as biomarkers for the characterization and classification of subjects into MCI or AD groups. Predictive models employing these biomarker genes exhibited good classification performances for CN, MCI, and AD, significantly above random chance. The PI3K-Akt, IL-17, JAK-STAT, TNF, and Ras signaling pathways were also enriched in these biomarker genes, indicating their diagnostic potential and pathophysiological roles in MCI and AD. These findings could aid in the recognition of MCI and AD risk in clinical settings, allow for the tracking of disease progression over time in individuals as part of a therapeutic approach, and provide possible personalized drug targets for early intervention of MCI and AD.
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Affiliation(s)
- Sher Li Oh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- IGP-Neuroscience, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Meikun Zhou
- Bioinformatics Institute, ASTAR, Singapore, Singapore
| | - Eunice W. M. Chin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Gautami Amarnath
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Chee Hoe Cheah
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Kok Pin Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Neurology, National Neuroscience Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nagaendran Kandiah
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Eyleen L. K. Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- *Correspondence: Eyleen L. K. Goh
| | - Keng-Hwee Chiam
- Bioinformatics Institute, ASTAR, Singapore, Singapore
- Keng-Hwee Chiam
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13
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Tong X, Li WX, Liang J, Zheng Y, Dai SX. Two different aging paths in human blood revealed by integrated analysis of gene Expression, mutation and alternative splicing. Gene 2022; 829:146501. [PMID: 35452709 DOI: 10.1016/j.gene.2022.146501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
Aging is a complex life process that human organs and tissues steadily and continuously decline. Aging has huge heterogeneity, which shows different aging rates among different individuals and in different tissues of the same individual. Many studies of aging are often contradictory and show little common signature. The integrated analysis of these transcriptome datasets will provide an unbiased global view of the aging process. Here, we integrated 8 transcriptome datasets including 757 samples from healthy human blood to study aging from three aspects of gene expression, mutations, and alternative splicing. Surprisingly, we found that transcriptome changes in blood are relatively independent of the chronological age. Further pseudotime analysis revealed two different aging paths (AgingPath1 and AgingPath2) in human blood. The differentially expressed genes (DEGs) along the two paths showed a limited overlap and are enriched in different biological processes. The mutations of DEGs in AgingPath1 are significantly increased in the aging process, while the opposite trend was observed in AgingPath2. Expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) analysis identified 304 important mutations that can affect both gene expression and alternative splicing during aging. Finally, by comparison between aging and Alzheimer's disease, we identified 37 common DEGs in AgingPath1, AgingPath2 and Alzheimer's disease. These genes may contribute to the shift from aging state to Alzheimer's disease. In summary, this study revealed the two aging paths and the related genes and mutations, which provides a new insight into aging and aging-related disease.
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Affiliation(s)
- Xin Tong
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jihao Liang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Yang Zheng
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Shao-Xing Dai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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14
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Kolobkov DS, Sviridova DA, Abilev SK, Kuzovlev AN, Salnikova LE. Genes and Diseases: Insights from Transcriptomics Studies. Genes (Basel) 2022; 13:genes13071168. [PMID: 35885950 PMCID: PMC9317567 DOI: 10.3390/genes13071168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 01/25/2023] Open
Abstract
Results of expression studies can be useful to clarify the genotype-phenotype relationship. However, according to data from recent literature, there is a large group of genes that are revealed as differentially expressed (DE) in many studies, regardless of the biological context. Additional analyses could shed more light on the relationships between genes, their differential expression, and diseases. We generated a set of 9972 disease genes from five gene-phenotype databases (OMIM, ORPHANET, DDG2P, DisGeNet and MalaCards) and a report of the International Union of Immunological Societies. To study transcriptomics of disease and non-disease genes in healthy tissues, we obtained data from the Human Protein Atlas (HPA) website. We analyzed the dependency between expression in healthy tissues and gene occurrence in Gene Expression Omnibus series using tools within the Enrichr libraries. The results of expression studies were annotated with Gene Ontology (GO) and Human Phenotype Ontology (HPO) terms. Using transcriptomics analysis of healthy tissues, we validated the previous findings of higher expression levels of disease genes in pathologically linked tissues compared to other tissues. Preferentially DE genes were generally highly expressed in one or multiple tissues and were enriched for disease genes. According to the results of GO enrichment analyses, both down- and up-regulated DE genes most often took part in immune response, translation and tissue-specific processes. A connection between DE-related pathology and the diversity of HPO terms was found. Investigating a link between expression and phenotype contributes to understanding the mode of development and progression of human diseases.
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Affiliation(s)
- Dmitry S. Kolobkov
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; (D.S.K.); (D.A.S.); (S.K.A.)
| | - Darya A. Sviridova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; (D.S.K.); (D.A.S.); (S.K.A.)
| | - Serikbai K. Abilev
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; (D.S.K.); (D.A.S.); (S.K.A.)
| | - Artem N. Kuzovlev
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 107031, Russia;
| | - Lyubov E. Salnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; (D.S.K.); (D.A.S.); (S.K.A.)
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow 107031, Russia;
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow 117997, Russia
- Correspondence:
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15
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Engel C, Wirkner K, Zeynalova S, Baber R, Binder H, Ceglarek U, Enzenbach C, Fuchs M, Hagendorff A, Henger S, Hinz A, Rauscher FG, Reusche M, Riedel-Heller SG, Röhr S, Sacher J, Sander C, Schroeter ML, Tarnok A, Treudler R, Villringer A, Wachter R, Witte AV, Thiery J, Scholz M, Loeffler M. Cohort Profile: The LIFE-Adult-Study. Int J Epidemiol 2022; 52:e66-e79. [PMID: 35640047 PMCID: PMC9908058 DOI: 10.1093/ije/dyac114] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 05/10/2022] [Indexed: 01/14/2023] Open
Affiliation(s)
- Christoph Engel
- Corresponding author. Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Haertelstrasse 16–18, 04107 Leipzig, Germany. E-mail:
| | | | | | - Ronny Baber
- Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig Medical Center, Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany,Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig Medical Center, Leipzig, Germany
| | - Cornelia Enzenbach
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany,Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Michael Fuchs
- Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany,Division Otolaryngology, Head and Neck Surgery, Phoniatrics and Audiology, University of Leipzig Medical Center, Leipzig, Germany
| | - Andreas Hagendorff
- Department of Cardiology, University of Leipzig Medical Center, Leipzig, Germany
| | - Sylvia Henger
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany,Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Andreas Hinz
- Department of Medical Psychology and Medical Sociology, Leipzig University, Leipzig, Germany
| | - Franziska G Rauscher
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany,Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Matthias Reusche
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany,Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Steffi G Riedel-Heller
- Institute of Social Medicine, Occupational Medicine and Public Health (ISAP), Leipzig University, Leipzig, Germany
| | - Susanne Röhr
- Institute of Social Medicine, Occupational Medicine and Public Health (ISAP), Leipzig University, Leipzig, Germany,Global Brain Health Institute (GBHI), Trinity College Dublin, Dublin, Ireland
| | - Julia Sacher
- Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany,Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Christian Sander
- Leipzig Research Centre for Civilization Diseases, Leipzig University, Leipzig, Germany,Department of Psychiatry and Psychotherapy, University of Leipzig Medical Center, Leipzig, Germany
| | - Matthias L Schroeter
- Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany,Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Attila Tarnok
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany,Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Regina Treudler
- Department of Dermatology, Venerology and Allergology, University of Leipzig Medical Center, Leipzig, Germany,Leipzig Interdisciplinary Allergy Center (LICA)—Comprehensive Allergy Center, University of Leipzig Medical Center, Leipzig, Germany
| | - Arno Villringer
- Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany,Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Rolf Wachter
- Clinic and Policlinic for Cardiology, University of Leipzig Medical Center, Leipzig, Germany
| | - A Veronica Witte
- Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany,Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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16
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The Transcriptome and Methylome of the Developing and Aging Brain and Their Relations to Gliomas and Psychological Disorders. Cells 2022; 11:cells11030362. [PMID: 35159171 PMCID: PMC8834030 DOI: 10.3390/cells11030362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 02/01/2023] Open
Abstract
Mutually linked expression and methylation dynamics in the brain govern genome regulation over the whole lifetime with an impact on cognition, psychological disorders, and cancer. We performed a joint study of gene expression and DNA methylation of brain tissue originating from the human prefrontal cortex of individuals across the lifespan to describe changes in cellular programs and their regulation by epigenetic mechanisms. The analysis considers previous knowledge in terms of functional gene signatures and chromatin states derived from independent studies, aging profiles of a battery of chromatin modifying enzymes, and data of gliomas and neuropsychological disorders for a holistic view on the development and aging of the brain. Expression and methylation changes from babies to elderly adults decompose into different modes associated with the serial activation of (brain) developmental, learning, metabolic and inflammatory functions, where methylation in gene promoters mostly represses transcription. Expression of genes encoding methylome modifying enzymes is very diverse reflecting complex regulations during lifetime which also associates with the marked remodeling of chromatin between permissive and restrictive states. Data of brain cancer and psychotic disorders reveal footprints of pathophysiologies related to brain development and aging. Comparison of aging brains with gliomas supports the view that glioblastoma-like and astrocytoma-like tumors exhibit higher cellular plasticity activated in the developing healthy brain while oligodendrogliomas have a more stable differentiation hierarchy more resembling the aged brain. The balance and specific shifts between volatile and stable and between more irreversible and more plastic epigenomic networks govern the development and aging of healthy and diseased brain.
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17
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Schmidt M, Arshad M, Bernhart SH, Hakobyan S, Arakelyan A, Loeffler-Wirth H, Binder H. The Evolving Faces of the SARS-CoV-2 Genome. Viruses 2021; 13:1764. [PMID: 34578345 PMCID: PMC8472651 DOI: 10.3390/v13091764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023] Open
Abstract
Surveillance of the evolving SARS-CoV-2 genome combined with epidemiological monitoring and emerging vaccination became paramount tasks to control the pandemic which is rapidly changing in time and space. Genomic surveillance must combine generation and sharing sequence data with appropriate bioinformatics monitoring and analysis methods. We applied molecular portrayal using self-organizing maps machine learning (SOM portrayal) to characterize the diversity of the virus genomes, their mutual relatedness and development since the beginning of the pandemic. The genetic landscape obtained visualizes the relevant mutations in a lineage-specific fashion and provides developmental paths in genetic state space from early lineages towards the variants of concern alpha, beta, gamma and delta. The different genes of the virus have specific footprints in the landscape reflecting their biological impact. SOM portrayal provides a novel option for 'bioinformatics surveillance' of the pandemic, with strong odds regarding visualization, intuitive perception and 'personalization' of the mutational patterns of the virus genomes.
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Affiliation(s)
- Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Mamoona Arshad
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Stephan H. Bernhart
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Siras Hakobyan
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia
| | - Arsen Arakelyan
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (M.A.); (S.H.B.); (H.L.-W.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
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18
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Willscher E, Hopp L, Kreuz M, Schmidt M, Hakobyan S, Arakelyan A, Hentschel B, Jones DTW, Pfister SM, Loeffler M, Loeffler-Wirth H, Binder H. High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers (Basel) 2021; 13:3198. [PMID: 34206856 PMCID: PMC8268631 DOI: 10.3390/cancers13133198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
Molecular mechanisms of lower-grade (II-III) diffuse gliomas (LGG) are still poorly understood, mainly because of their heterogeneity. They split into astrocytoma- (IDH-A) and oligodendroglioma-like (IDH-O) tumors both carrying mutations(s) at the isocitrate dehydrogenase (IDH) gene and into IDH wild type (IDH-wt) gliomas of glioblastoma resemblance. We generated detailed maps of the transcriptomes and DNA methylomes, revealing that cell functions divided into three major archetypic hallmarks: (i) increased proliferation in IDH-wt and, to a lesser degree, IDH-O; (ii) increased inflammation in IDH-A and IDH-wt; and (iii) the loss of synaptic transmission in all subtypes. Immunogenic properties of IDH-A are diverse, partly resembling signatures observed in grade IV mesenchymal glioblastomas or in grade I pilocytic astrocytomas. We analyzed details of coregulation between gene expression and DNA methylation and of the immunogenic micro-environment presumably driving tumor development and treatment resistance. Our transcriptome and methylome maps support personalized, case-by-case views to decipher the heterogeneity of glioma states in terms of data portraits. Thereby, molecular cartography provides a graphical coordinate system that links gene-level information with glioma subtypes, their phenotypes, and clinical context.
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Affiliation(s)
- Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Markus Kreuz
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Siras Hakobyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Bettina Hentschel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - David T. W. Jones
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Markus Loeffler
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
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19
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Huang D, Liu AYN, Leung KS, Tang NLS. Direct Measurement of B Lymphocyte Gene Expression Biomarkers in Peripheral Blood Transcriptomics Enables Early Prediction of Vaccine Seroconversion. Genes (Basel) 2021; 12:genes12070971. [PMID: 34202032 PMCID: PMC8304400 DOI: 10.3390/genes12070971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
Peripheral blood transcriptome is a highly promising area for biomarker development. However, transcript abundances (TA) in these cell mixture samples are confounded by proportions of the component leukocyte subpopulations. This poses a challenge to clinical applications, as the cell of origin of any change in TA is not known without prior cell separation procedure. We developed a framework to develop a cell-type informative TA biomarkers which enable determination of TA of a single cell-type (B lymphocytes) directly in cell mixture samples of peripheral blood (e.g., peripheral blood mononuclear cells, PBMC) without the need for subpopulation separation. It is applicable to a panel of genes called B cell informative genes. Then a ratio of two B cell informative genes (a target gene and a stably expressed reference gene) obtained in PBMC was used as a new biomarker to represent the target gene expression in purified B lymphocytes. This approach, which eliminates the tedious procedure of cell separation and directly determines TA of a leukocyte subpopulation in peripheral blood samples, is called the Direct LS-TA method. This method is applied to gene expression datasets collected in influenza vaccination trials as early predictive biomarkers of seroconversion. By using TNFRSF17 or TXNDC5 as the target genes and TNFRSF13C or FCRLA as the reference genes, the Direct LS-TA B cell biomarkers were determined directly in the PBMC transcriptome data and were highly correlated with TA of the corresponding target genes in purified B lymphocytes. Vaccination responders had almost a 2-fold higher Direct LS-TA biomarker level of TNFRSF17 (log 2 SMD = 0.84, 95% CI = 0.47–1.21) on day 7 after vaccination. The sensitivity of these Direct LS-TA biomarkers in the prediction of seroconversion was greater than 0.7 and area-under curves (AUC) were over 0.8 in many datasets. In this paper, we report a straightforward approach to directly estimate B lymphocyte gene expression in PBMC, which could be used in a routine clinical setting. Moreover, the method enables the practice of precision medicine in the prediction of vaccination response. More importantly, seroconversion could now be predicted as early as day 7. As the acquired immunology pathway is common to vaccination against influenza and COVID-19, these biomarkers could also be useful to predict seroconversion for the new COVID-19 vaccines.
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Affiliation(s)
- Dan Huang
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
| | - Alex Y. N. Liu
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
| | - Kwong-Sak Leung
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Nelson L. S. Tang
- Cytomics Limited, Hong Kong Science and Technology Park, Hong Kong, China; (D.H.); (A.Y.N.L.); (K.-S.L.)
- Department of Chemical Pathology and Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
- Correspondence:
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Wolf J, Willscher E, Loeffler-Wirth H, Schmidt M, Flemming G, Zurek M, Uhlig HH, Händel N, Binder H. Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies. Int J Mol Sci 2021; 22:ijms22052551. [PMID: 33806322 PMCID: PMC7961974 DOI: 10.3390/ijms22052551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Coeliac disease (CD) is a clinically heterogeneous autoimmune disease with variable presentation and progression triggered by gluten intake. Molecular or genetic factors contribute to disease heterogeneity, but the reasons for different outcomes are poorly understood. Transcriptome studies of tissue biopsies from CD patients are scarce. Here, we present a high-resolution analysis of the transcriptomes extracted from duodenal biopsies of 24 children and adolescents with active CD and 21 individuals without CD but with intestinal afflictions as controls. The transcriptomes of CD patients divide into three groups-a mixed group presenting the control cases, and CD-low and CD-high groups referring to lower and higher levels of CD severity. Persistence of symptoms was weakly associated with subgroup, but the highest marsh stages were present in subgroup CD-high, together with the highest cell cycle rates as an indicator of virtually complete villous atrophy. Considerable variation in inflammation-level between subgroups was further deciphered into immune cell types using cell type de-convolution. Self-organizing maps portrayal was applied to provide high-resolution landscapes of the CD-transcriptome. We find asymmetric patterns of miRNA and long non-coding RNA and discuss the effect of epigenetic regulation. Expression of genes involved in interferon gamma signaling represent suitable markers to distinguish CD from non-CD cases. Multiple pathways overlay in CD biopsies in different ways, giving rise to heterogeneous transcriptional patterns, which potentially provide information about etiology and the course of the disease.
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Affiliation(s)
- Johannes Wolf
- Department of Laboratory Medicine at Hospital “St. Georg” Leipzig, 04129 Leipzig, Germany;
- Immuno Deficiency Centre Leipzig (IDCL) at Hospital St. Georg Leipzig, Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiency Diseases, 04129 Leipzig, Germany
| | - Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Gunter Flemming
- Paediatric Gastroenterology Unit, University Hospital for Children and Adolescents, 04103 Leipzig, Germany;
| | - Marlen Zurek
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research Centre, Experimental Medicine, Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX4 2PG, UK;
| | - Norman Händel
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
- Correspondence:
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