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Görtler F, Mensching-Buhr M, Skaar Ø, Schrod S, Sterr T, Schäfer A, Beißbarth T, Joshi A, Zacharias HU, Grellscheid SN, Altenbuchinger M. Adaptive digital tissue deconvolution. Bioinformatics 2024; 40:i100-i109. [PMID: 38940181 PMCID: PMC11256946 DOI: 10.1093/bioinformatics/btae263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION The inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systematically improve estimates. Such approaches allow to infer additional, less abundant cell types. However, they rely on training data which do not capture the full biological diversity encountered in transcriptomics analyses; data can contain cellular contributions not seen in the training data and as such, analyses can be biased or blurred. Thus, computational approaches have to deal with unknown, hidden contributions. Moreover, most methods are based on cellular archetypes which serve as a reference; e.g. a generic T-cell profile is used to infer the proportion of T-cells. It is well known that cells adapt their molecular phenotype to the environment and that pre-specified cell archetypes can distort the inference of cellular compositions. RESULTS We propose Adaptive Digital Tissue Deconvolution (ADTD) to estimate cellular proportions of pre-selected cell types together with possibly unknown and hidden background contributions. Moreover, ADTD adapts prototypic reference profiles to the molecular environment of the cells, which further resolves cell-type specific gene regulation from bulk transcriptomics data. We verify this in simulation studies and demonstrate that ADTD improves existing approaches in estimating cellular compositions. In an application to bulk transcriptomics data from breast cancer patients, we demonstrate that ADTD provides insights into cell-type specific molecular differences between breast cancer subtypes. AVAILABILITY AND IMPLEMENTATION A python implementation of ADTD and a tutorial are available at Gitlab and zenodo (doi:10.5281/zenodo.7548362).
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Affiliation(s)
- Franziska Görtler
- Computational Biology Unit, Department of Biological Sciences, University of Bergen, N-5008 Bergen, Norway
- Department of Oncology and Medical Physics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Malte Mensching-Buhr
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Ørjan Skaar
- Department of Informatics, Computational Biology Unit, University of Bergen, N-5008 Bergen, Norway
| | - Stefan Schrod
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Thomas Sterr
- Institute of Theoretical Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Schäfer
- Institute of Theoretical Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Tim Beißbarth
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Anagha Joshi
- Department of Clinical Science, Computational Biology Unit, University of Bergen, N-5008 Bergen, Norway
| | - Helena U Zacharias
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School, 30625 Hannover, Germany
| | | | - Michael Altenbuchinger
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37075 Göttingen, Germany
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Siska PJ, Decking SM, Babl N, Matos C, Bruss C, Singer K, Klitzke J, Schön M, Simeth J, Köstler J, Siegmund H, Ugele I, Paulus M, Dietl A, Kolodova K, Steines L, Freitag K, Peuker A, Schönhammer G, Raithel J, Graf B, Geismann F, Lubnow M, Mack M, Hau P, Bohr C, Burkhardt R, Gessner A, Salzberger B, Wagner R, Hanses F, Hitzenbichler F, Heudobler D, Lüke F, Pukrop T, Herr W, Wolff D, Spang R, Poeck H, Hoffmann P, Jantsch J, Brochhausen C, Lunz D, Rehli M, Kreutz M, Renner K. Metabolic imbalance of T cells in COVID-19 is hallmarked by basigin and mitigated by dexamethasone. J Clin Invest 2021; 131:148225. [PMID: 34779418 DOI: 10.1172/jci148225] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022] Open
Abstract
Metabolic pathways regulate immune responses and disrupted metabolism leads to immune dysfunction and disease. Coronavirus disease 2019 (COVID-19) is driven by imbalanced immune responses, yet the role of immunometabolism in COVID-19 pathogenesis remains unclear. By investigating 87 patients with confirmed SARS-CoV-2 infection, 6 critically ill non-COVID-19 patients, and 47 uninfected controls, we found an immunometabolic dysregulation in patients with progressed COVID-19. Specifically, T cells, monocytes, and granulocytes exhibited increased mitochondrial mass, yet only T cells accumulated intracellular reactive oxygen species (ROS), were metabolically quiescent, and showed a disrupted mitochondrial architecture. During recovery, T cell ROS decreased to match the uninfected controls. Transcriptionally, T cells from severe/critical COVID-19 patients showed an induction of ROS-responsive genes as well as genes related to mitochondrial function and the basigin network. Basigin (CD147) ligands cyclophilin A and the SARS-CoV-2 spike protein triggered ROS production in T cells in vitro. In line with this, only PCR-positive patients showed increased ROS levels. Dexamethasone treatment resulted in a downregulation of ROS in vitro and T cells from dexamethasone-treated patients exhibited low ROS and basigin levels. This was reflected by changes in the transcriptional landscape. Our findings provide evidence of an immunometabolic dysregulation in COVID-19 that can be mitigated by dexamethasone treatment.
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Affiliation(s)
- Peter J Siska
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sonja-Maria Decking
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | - Nathalie Babl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Carina Matos
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Christina Bruss
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Katrin Singer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg
| | - Jana Klitzke
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Marian Schön
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Jakob Simeth
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Josef Köstler
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Heiko Siegmund
- Institute of Pathology, University of Regensburg, Regensburg, Germany.,Central Biobank Regensburg, University Hospital and University of Regensburg, Regensburg, Germany
| | - Ines Ugele
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg
| | | | | | - Kristina Kolodova
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | | | - Katharina Freitag
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Alice Peuker
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Gabriele Schönhammer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Raithel
- Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | | | | | | | | | - Peter Hau
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology
| | - Christopher Bohr
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg
| | | | - Andre Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | | | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Frank Hanses
- Department of Infection Prevention and Infectious Diseases, and.,Emergency Department, University Hospital Regensburg, Regensburg, Germany
| | | | - Daniel Heudobler
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Bavarian Cancer Research Center, Regensburg, Germany
| | - Florian Lüke
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Tobias Pukrop
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Bavarian Cancer Research Center, Regensburg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Petra Hoffmann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Christoph Brochhausen
- Institute of Pathology, University of Regensburg, Regensburg, Germany.,Central Biobank Regensburg, University Hospital and University of Regensburg, Regensburg, Germany
| | | | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | - Marina Kreutz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
| | - Kathrin Renner
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology, University of Regensburg, Regensburg, Germany
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Schön M, Simeth J, Heinrich P, Görtler F, Solbrig S, Wettig T, Oefner PJ, Altenbuchinger M, Spang R. DTD: An R Package for Digital Tissue Deconvolution. J Comput Biol 2020; 27:386-389. [PMID: 31995409 PMCID: PMC7074920 DOI: 10.1089/cmb.2019.0469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Digital tissue deconvolution (DTD) estimates the cellular composition of a tissue from its bulk gene-expression profile. For this, DTD approximates the bulk as a mixture of cell-specific expression profiles. Different tissues have different cellular compositions, with cells in different activation states, and embedded in different environments. Consequently, DTD can profit from tailoring the deconvolution model to a specific tissue context. Loss-function learning adapts DTD to a specific tissue context, such as the deconvolution of blood, or a specific type of tumor tissue. We provide software for loss-function learning, for its validation and visualization, and for applying the DTD models to new data.
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Affiliation(s)
- Marian Schön
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Jakob Simeth
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Paul Heinrich
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Franziska Görtler
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Stefan Solbrig
- Department of Physics, University of Regensburg, Regensburg, Germany
| | - Tilo Wettig
- Department of Physics, University of Regensburg, Regensburg, Germany
| | - Peter J. Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Michael Altenbuchinger
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Rainer Spang
- Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
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