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Kolabas ZI, Kuemmerle LB, Perneczky R, Förstera B, Ulukaya S, Ali M, Kapoor S, Bartos LM, Büttner M, Caliskan OS, Rong Z, Mai H, Höher L, Jeridi D, Molbay M, Khalin I, Deligiannis IK, Negwer M, Roberts K, Simats A, Carofiglio O, Todorov MI, Horvath I, Ozturk F, Hummel S, Biechele G, Zatcepin A, Unterrainer M, Gnörich J, Roodselaar J, Shrouder J, Khosravani P, Tast B, Richter L, Díaz-Marugán L, Kaltenecker D, Lux L, Chen Y, Zhao S, Rauchmann BS, Sterr M, Kunze I, Stanic K, Kan VWY, Besson-Girard S, Katzdobler S, Palleis C, Schädler J, Paetzold JC, Liebscher S, Hauser AE, Gokce O, Lickert H, Steinke H, Benakis C, Braun C, Martinez-Jimenez CP, Buerger K, Albert NL, Höglinger G, Levin J, Haass C, Kopczak A, Dichgans M, Havla J, Kümpfel T, Kerschensteiner M, Schifferer M, Simons M, Liesz A, Krahmer N, Bayraktar OA, Franzmeier N, Plesnila N, Erener S, Puelles VG, Delbridge C, Bhatia HS, Hellal F, Elsner M, Bechmann I, Ondruschka B, Brendel M, Theis FJ, Erturk A. Distinct molecular profiles of skull bone marrow in health and neurological disorders. Cell 2023; 186:3706-3725.e29. [PMID: 37562402 PMCID: PMC10443631 DOI: 10.1016/j.cell.2023.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/24/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
The bone marrow in the skull is important for shaping immune responses in the brain and meninges, but its molecular makeup among bones and relevance in human diseases remain unclear. Here, we show that the mouse skull has the most distinct transcriptomic profile compared with other bones in states of health and injury, characterized by a late-stage neutrophil phenotype. In humans, proteome analysis reveals that the skull marrow is the most distinct, with differentially expressed neutrophil-related pathways and a unique synaptic protein signature. 3D imaging demonstrates the structural and cellular details of human skull-meninges connections (SMCs) compared with veins. Last, using translocator protein positron emission tomography (TSPO-PET) imaging, we show that the skull bone marrow reflects inflammatory brain responses with a disease-specific spatial distribution in patients with various neurological disorders. The unique molecular profile and anatomical and functional connections of the skull show its potential as a site for diagnosing, monitoring, and treating brain diseases.
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Affiliation(s)
- Zeynep Ilgin Kolabas
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Graduate School of Systemic Neurosciences (GSN), Munich, Germany
| | - Louis B Kuemmerle
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Robert Perneczky
- Division of Mental Health in Older Adults and Alzheimer Therapy and Research Center, Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University Munich, 80336 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Benjamin Förstera
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Selin Ulukaya
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Mayar Ali
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Graduate School of Systemic Neurosciences (GSN), Munich, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Saketh Kapoor
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Laura M Bartos
- Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maren Büttner
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ozum Sehnaz Caliskan
- Institute for Diabetes and Obesity, Helmholtz Center Munich and German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Zhouyi Rong
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Hongcheng Mai
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Luciano Höher
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Denise Jeridi
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Muge Molbay
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Igor Khalin
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | | | - Moritz Negwer
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | | | - Alba Simats
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Olga Carofiglio
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Mihail I Todorov
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Izabela Horvath
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; School of Computation, Information and Technology (CIT), TUM, Boltzmannstr. 3, 85748 Garching, Germany
| | - Furkan Ozturk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Selina Hummel
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gloria Biechele
- Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Artem Zatcepin
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marcus Unterrainer
- Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Johannes Gnörich
- Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jay Roodselaar
- Charité - Universitätsmedizin Berlin, Department of Rheumatology and Clinical Immunology, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Joshua Shrouder
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Pardis Khosravani
- Biomedical Center (BMC), Core Facility Flow Cytometry, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Benjamin Tast
- Biomedical Center (BMC), Core Facility Flow Cytometry, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa Richter
- Biomedical Center (BMC), Core Facility Flow Cytometry, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laura Díaz-Marugán
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Doris Kaltenecker
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Diabetes and Cancer, Helmholtz Munich, Munich, Germany
| | - Laurin Lux
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Ying Chen
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Shan Zhao
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Boris-Stephan Rauchmann
- Division of Mental Health in Older Adults and Alzheimer Therapy and Research Center, Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University Munich, 80336 Munich, Germany; Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK; Institute of Neuroradiology, University Hospital LMU, Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ines Kunze
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karen Stanic
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Vanessa W Y Kan
- Institute of Clinical Neuroimmunology, University Hospital Munich, Ludwig-Maximilians University Munich, Munich, Germany
| | - Simon Besson-Girard
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Graduate School of Systemic Neurosciences (GSN), Munich, Germany
| | - Sabrina Katzdobler
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carla Palleis
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julia Schädler
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes C Paetzold
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Department of Computing, Imperial College London, London, UK
| | - Sabine Liebscher
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute of Clinical Neuroimmunology, University Hospital Munich, Ludwig-Maximilians University Munich, Munich, Germany; Biomedical Center (BMC), Medical Faculty, Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Anja E Hauser
- Charité - Universitätsmedizin Berlin, Department of Rheumatology and Clinical Immunology, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Ozgun Gokce
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Hanno Steinke
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Corinne Benakis
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Christian Braun
- Institute of Legal Medicine, Faculty of Medicine, LMU Munich, Germany
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Katharina Buerger
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Nathalie L Albert
- Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Günter Höglinger
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Levin
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna Kopczak
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Joachim Havla
- Institute of Clinical Neuroimmunology, University Hospital Munich, Ludwig-Maximilians University Munich, Munich, Germany; Biomedical Center (BMC), Medical Faculty, Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, University Hospital Munich, Ludwig-Maximilians University Munich, Munich, Germany; Biomedical Center (BMC), Medical Faculty, Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Martin Kerschensteiner
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Institute of Clinical Neuroimmunology, University Hospital Munich, Ludwig-Maximilians University Munich, Munich, Germany; Biomedical Center (BMC), Medical Faculty, Ludwig-Maximilians Universität Munich, Munich, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Mikael Simons
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Arthur Liesz
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Graduate School of Systemic Neurosciences (GSN), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Center Munich and German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | | | - Nicolai Franzmeier
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Nikolaus Plesnila
- Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Suheda Erener
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Claire Delbridge
- Institute of Pathology, Department of Neuropathology, Technical University Munich, TUM School of Medicine, Munich, Germany
| | - Harsharan Singh Bhatia
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Farida Hellal
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Markus Elsner
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Brendel
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Department of Nuclear Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Mathematics, Technische Universität München, Garching bei München, Germany
| | - Ali Erturk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany; Institute for Stroke and Dementia Research, LMU University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Graduate School of Systemic Neurosciences (GSN), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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Crawford LB. Hematopoietic stem cells and betaherpesvirus latency. Front Cell Infect Microbiol 2023; 13:1189805. [PMID: 37346032 PMCID: PMC10279960 DOI: 10.3389/fcimb.2023.1189805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023] Open
Abstract
The human betaherpesviruses including human cytomegalovirus (HCMV), human herpesvirus (HHV)-6a and HHV-6b, and HHV-7 infect and establish latency in CD34+ hematopoietic stem and progenitor cells (HPCs). The diverse repertoire of HPCs in humans and the complex interactions between these viruses and host HPCs regulate the viral lifecycle, including latency. Precise manipulation of host and viral factors contribute to preferential maintenance of the viral genome, increased host cell survival, and specific manipulation of the cellular environment including suppression of neighboring cells and immune control. The dynamic control of these processes by the virus regulate inter- and intra-host signals critical to the establishment of chronic infection. Regulation occurs through direct viral protein interactions and cellular signaling, miRNA regulation, and viral mimics of cellular receptors and ligands, all leading to control of cell proliferation, survival, and differentiation. Hematopoietic stem cells have unique biological properties and the tandem control of virus and host make this a unique environment for chronic herpesvirus infection in the bone marrow. This review highlights the elegant complexities of the betaherpesvirus latency and HPC virus-host interactions.
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Affiliation(s)
- Lindsey B Crawford
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, United States
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Duplex sequencing identifies genomic features that determine susceptibility to benzo(a)pyrene-induced in vivo mutations. BMC Genomics 2022; 23:542. [PMID: 35902794 PMCID: PMC9331077 DOI: 10.1186/s12864-022-08752-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Exposure to environmental mutagens increases the risk of cancer and genetic disorders. We used Duplex Sequencing (DS), a high-accuracy error-corrected sequencing technology, to analyze mutation induction across twenty 2.4 kb intergenic and genic targets in the bone marrow of MutaMouse males exposed to benzo(a)pyrene (BaP), a widespread environmental pollutant. DS revealed a linear dose-related induction of mutations across all targets with low intra-group variability. Heterochromatic and intergenic regions exhibited the highest mutation frequencies (MF). C:G > A:T transversions at CCA, CCC and GCC trinucleotides were enriched in BaP-exposed mice consistent with the known etiology of BaP mutagenesis. However, GC-content had no effect on mutation susceptibility. A positive correlation was observed between DS and the “gold-standard” transgenic rodent gene mutation assay. Overall, we demonstrate that DS is a promising approach to study in vivo mutagenesis and yields critical insight into the genomic features governing mutation susceptibility, spectrum, and variability across the genome.
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Wang D, Gu Y, Huo C, Zhao Y, Teng M, Li Y. MCEMP1 is a potential therapeutic biomarker associated with immune infiltration in advanced gastric cancer microenvironment. Gene 2022; 840:146760. [PMID: 35905854 DOI: 10.1016/j.gene.2022.146760] [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: 11/13/2021] [Revised: 07/03/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Over the last decade, breakthroughs have been made in cancer immunotherapy. However, for advanced gastric cancer (AGC), the complexity and heterogeneity of the tumor microenvironment (TME) has been the biggest challenge for immunotherapy. Therefore, an intensive study on TME of AGC is necessary. METHODS ESTIMATE and CIBERSORT algorithms were applied to analyze the transcriptome data of AGC using TCGA database systematically. We identified mast cell-expressed membrane protein 1 (MCEMP1) as a potential prognostic marker by protein-protein interaction (PPI) and Univariate Cox regression. The expression of MCEMP1 was evaluated by immunohistochemistry (IHC) and quantitative real time PCR. We assessed prognostic values of MCEMP1 with use of Kaplan-Meier and Multivariate Cox regression analysis. Gene set enrichment analysis (GSEA) was used to analyze the molecular mechanism of MCEMP1. The correlation between MCEMP1 expression and tumor immune infiltration was analyzed by the TIMER database and CIBERSORT algorithm, which was confirmed by IHC. RESULTS The mRNA and protein expression of MCEMP1 was up-regulated substantially and related to poor survival in AGC. GSEA analysis revealed that MCEMP1 was involved in the immune-related signaling pathways. We further demonstrated that the expression of MCEMP1 was correlated with multiple immune cells and immune checkpoints. The results of IHC indicated that there was a positive correlation between PD-L1 expression and MCEMP1, suggesting that MCEMP1 may affect the prognosis of AGC patients by regulating immune infiltration and the function of immune cells. CONCLUSION MCEMP1 may serve as a biomarker associated with immune infiltration in TME and could be a potential therapeutic target for AGC patients.
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Affiliation(s)
- Daijun Wang
- Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou 730030, Gansu, China
| | - Yanmei Gu
- Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou 730030, Gansu, China
| | - Chengdong Huo
- Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou 730030, Gansu, China
| | - Yang Zhao
- Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou 730030, Gansu, China; Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, Gansu, China
| | - Muzhou Teng
- Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou 730030, Gansu, China; Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, Gansu, China.
| | - Yumin Li
- Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou 730030, Gansu, China; Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou 730030, Gansu, China.
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Moysi E, Paris RM, Le Grand R, Koup RA, Petrovas C. Human lymph node immune dynamics as driver of vaccine efficacy: an understudied aspect of immune responses. Expert Rev Vaccines 2022; 21:633-644. [PMID: 35193447 DOI: 10.1080/14760584.2022.2045198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION During the last century, changes in hygiene, sanitation, and the advent of childhood vaccination have resulted in profound reductions in mortality from infectious diseases. Despite this success, infectious diseases remain an enigmatic public health threat, where effective vaccines for influenza, human immunodeficiency virus (HIV), tuberculosis, and malaria, among others remain elusive. AREA COVERED In addition to the immune evasion tactics employed by complex pathogens, our understanding of immunopathogenesis and the development of effective vaccines is also complexified by the inherent variability of human immune responses. Lymph nodes (LNs) are the anatomical sites where B cell responses develop. An important, but understudied component of immune response complexity is variation in LN immune dynamics and in particular variation in germinal center follicular helper T cells (Tfh) and B cells which can be impacted by genetic variation, aging, the microbiome and chronic infection. EXPERT OPINION This review describes the contribution of genetic variation, aging, microbiome and chronic infection on LN immune dynamics and associated Tfh responses and offers perspective on how inclusion of LN immune subset and cytoarchitecture analyses, along with peripheral blood biomarkers can supplement systems vaccinology or immunology approaches for the development of vaccines or other interventions to prevent infectious diseases.
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Affiliation(s)
- Eirini Moysi
- Tissue Analysis Core, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | | | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Constantinos Petrovas
- Tissue Analysis Core, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.,Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol 2022; 20:25. [PMID: 35073880 PMCID: PMC8788080 DOI: 10.1186/s12915-022-01229-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/07/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs. RESULTS An open-access pig expression map ( www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented. CONCLUSIONS Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource ( www.rnaatlas.org ), including a comparison to the expression of human orthologs.
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Affiliation(s)
- Max Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - María Bueno Álvez
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jiaying Yu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Tao Ma
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | | | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Lars Bolund
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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7
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Choi YS, Jeong E, Lee JS, Kim SK, Jo SH, Kim YG, Sung HJ, Cho SW, Jin Y. Immunomodulatory Scaffolds Derived from Lymph Node Extracellular Matrices. ACS APPLIED MATERIALS & INTERFACES 2021; 13:14037-14049. [PMID: 33745275 DOI: 10.1021/acsami.1c02542] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Immunomodulation in the local tissue microenvironment is pivotal for the determination of macrophage phenotypes and regulation of functions necessary for pro-healing effects. Herein, we demonstrate that a lymph node extracellular matrix (LNEM) prepared by the decellularization of lymph node tissues can mimic lymph node microenvironments for immunomodulation in two-dimensional (2D) and three-dimensional (3D) formats. The LNEM exhibits strengthened immunomodulatory effects in comparison to conventional collagen-based platforms. A 3D LNEM hydrogel is more effective than the 2D LNEM coating in inducing M2 macrophage polarization. The 3D LNEM induces macrophage elongation and enhances the M2-type marker expression and the secretion of anti-inflammatory cytokines. Additionally, the phagocytic function of macrophages is improved upon exposure to the intricate 3D LNEM environment. We demonstrate the reduced susceptibility of liver organoids to a hepatotoxic drug when co-cultured with macrophages in a 3D LNEM. This effect could be attributed to the enhanced anti-inflammatory functions and indicates its potential as a drug-testing platform that enables drug responses similar to those observed in vivo. Finally, the implantation of an LNEM hydrogel in a mouse volumetric muscle loss model facilitates the recruitment of host macrophages to the site of injury and enhances macrophage polarization toward the M2 phenotype for tissue healing in vivo. Therefore, 3D immune system-mimicking biomaterials could serve as useful platforms for tissue modeling and regenerative medicine development.
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Affiliation(s)
- Yi Sun Choi
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Eunseon Jeong
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung Seung Lee
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Su Kyeom Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea
| | - Hak-Joon Sung
- Department of Medical Engineering, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yoonhee Jin
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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8
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Díez P, Pérez-Andrés M, Bøgsted M, Azkargorta M, García-Valiente R, Dégano RM, Blanco E, Mateos-Gomez S, Bárcena P, Santa Cruz S, Góngora R, Elortza F, Landeira-Viñuela A, Juanes-Velasco P, Segura V, Manzano-Román R, Almeida J, Dybkaer K, Orfao A, Fuentes M. Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation. Front Immunol 2021; 12:637832. [PMID: 33859640 PMCID: PMC8043114 DOI: 10.3389/fimmu.2021.637832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/10/2021] [Indexed: 11/23/2022] Open
Abstract
Human B-cell differentiation has been extensively investigated on genomic and transcriptomic grounds; however, no studies have accomplished so far detailed analysis of antigen-dependent maturation-associated human B-cell populations from a proteomic perspective. Here, we investigate for the first time the quantitative proteomic profiles of B-cells undergoing antigen-dependent maturation using a label-free LC-MS/MS approach applied on 5 purified B-cell subpopulations (naive, centroblasts, centrocytes, memory and plasma B-cells) from human tonsils (data are available via ProteomeXchange with identifier PXD006191). Our results revealed that the actual differences among these B-cell subpopulations are a combination of expression of a few maturation stage-specific proteins within each B-cell subset and maturation-associated changes in relative protein expression levels, which are related with metabolic regulation. The considerable overlap of the proteome of the 5 studied B-cell subsets strengthens the key role of the regulation of the stoichiometry of molecules associated with metabolic regulation and programming, among other signaling cascades (such as antigen recognition and presentation and cell survival) crucial for the transition between each B-cell maturation stage.
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Affiliation(s)
- Paula Díez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martín Pérez-Andrés
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | | | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Elena Blanco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Sheila Mateos-Gomez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Paloma Bárcena
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Santiago Santa Cruz
- Service of Otolaryngology and Cervical Facial Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Victor Segura
- Division of Hepatology and Gene Therapy, Proteomics and BioInformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Karen Dybkaer
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alberto Orfao
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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9
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Digre A, Lindskog C. The Human Protein Atlas-Spatial localization of the human proteome in health and disease. Protein Sci 2021; 30:218-233. [PMID: 33146890 PMCID: PMC7737765 DOI: 10.1002/pro.3987] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022]
Abstract
For a complete understanding of a system's processes and each protein's role in health and disease, it is essential to study protein expression with a spatial resolution, as the exact location of proteins at tissue, cellular, or subcellular levels is tightly linked to protein function. The Human Protein Atlas (HPA) project is a large-scale initiative aiming at mapping the entire human proteome using antibody-based proteomics and integration of various other omics technologies. The publicly available knowledge resource www.proteinatlas.org is one of the world's most visited biological databases and has been extensively updated during the last few years. The current version is divided into six main sections, each focusing on particular aspects of the human proteome: (a) the Tissue Atlas showing the distribution of proteins across all major tissues and organs in the human body; (b) the Cell Atlas showing the subcellular localization of proteins in single cells; (c) the Pathology Atlas showing the impact of protein levels on survival of patients with cancer; (d) the Blood Atlas showing the expression profiles of blood cells and actively secreted proteins; (e) the Brain Atlas showing the distribution of proteins in human, mouse, and pig brain; and (f) the Metabolic Atlas showing the involvement of proteins in human metabolism. The HPA constitutes an important resource for further understanding of human biology, and the publicly available datasets hold much promise for integration with other emerging efforts focusing on single cell analyses, both at transcriptomic and proteomic level.
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Affiliation(s)
- Andreas Digre
- Department of Immunology, Genetics and PathologyRudbeck Laboratory, Uppsala UniversityUppsalaSweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and PathologyRudbeck Laboratory, Uppsala UniversityUppsalaSweden
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10
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Dowling P, Gargan S, Zweyer M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteome-wide Changes in the mdx-4cv Spleen due to Pathophysiological Cross Talk with Dystrophin-Deficient Skeletal Muscle. iScience 2020; 23:101500. [PMID: 32916630 PMCID: PMC7490529 DOI: 10.1016/j.isci.2020.101500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/30/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023] Open
Abstract
Duchenne muscular dystrophy is primarily characterized by progressive muscle wasting due to deficiency in the membrane cytoskeletal protein dystrophin but is also associated with body-wide cellular disturbances in a variety of non-muscle tissues. In this study, we have focused on the comparative proteomic analysis of the spleen and established considerable changes in this crucial secondary lymphoid organ from the genetic mdx-4cv mouse model of dystrophinopathy. An apparent short isoform of dystrophin and associated glycoproteins were identified in spleen by mass spectrometry but appear not be affected in muscular dystrophy. In contrast, the mdx-4cv spleen showed significant proteome-wide changes in other protein species that are involved in metabolism, signaling, and cellular architecture. Since the spleen plays a key role in the immune response, these proteomic alterations may reflect pathophysiological cross talk between the lymphoid system and dystrophic muscles, which are affected by both fiber degeneration and inflammation.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare W23F2H6, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23F2H6, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare W23F2H6, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23F2H6, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, 53113 Bonn, Germany
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare W23F2H6, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare W23F2H6, Ireland
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11
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Calciolari E, Donos N. Proteomic and Transcriptomic Approaches for Studying Bone Regeneration in Health and Systemically Compromised Conditions. Proteomics Clin Appl 2020; 14:e1900084. [PMID: 32131137 DOI: 10.1002/prca.201900084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/05/2020] [Indexed: 01/04/2023]
Abstract
Bone regeneration is a complex biological process, where the molecular mechanisms are only partially understood. In an ageing population, where the prevalence of chronic diseases with an impact on bone metabolism is increasing, it becomes crucial to identify new strategies that would improve regenerative outcomes also in medically compromised patients. In this context, omics are demonstrating a great potential, as they offer new insights on the molecular mechanisms regulating physiologic/pathologic bone healing and, at the same time, allow the identification of new diagnostic and therapeutic targets. This review provides an overview on the current evidence on the use of transcriptomic and proteomic approaches in bone regeneration research, particularly in relation to type 1 diabetes and osteoporosis, and discusses future scenarios and potential benefits and limitations on the integration of multi-omics. It is suggested that future research will leverage the synergy of omics with statistical modeling and bioinformatics to prompt the understanding of the biology underpinning bone formation in health and medically compromised conditions. With an eye toward personalized medicine, new strategies combining the mining of large datasets and bioinformatic data with a detailed characterization of relevant phenotypes will need to be pursued to further the understanding of disease mechanisms.
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Affiliation(s)
- Elena Calciolari
- Centre for Oral Immunobiology and Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, E1 2AD, UK.,Department of Medicine and Surgery, School of Dental Medicine, University of Parma, via Gramsci 14, Parma, 43126, Italy
| | - Nikolaos Donos
- Centre for Oral Immunobiology and Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, E1 2AD, UK
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12
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Abstract
Germinal centers are short-lived microanatomical compartments with essential roles in adaptive immunity. These lymphoid structures can be identified in secondary lymphoid organs using both flow cytometry and immunohistological analyses, but only the latter provides useful architectural and spatial information. Here we describe how to use immunofluorescence and immunohistochemistry with specific antibodies to precisely highlight the cellular and architectural features of germinal centers, both in human and mouse secondary lymphoid organs, and to study their normal development and disturbance in disease.
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Affiliation(s)
- David Dominguez-Sola
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, Box 1044A, New York, NY, 10029, USA.
- The Tisch Cancer Institute & Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Giorgio Cattoretti
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca (UNIMIB), Via Cadore 48, 20900, Monza, Italy.
- Anatomia Patologica, Azienda Ospedaliera San Gerardo, Via Pergolesi 33, 20900, Monza, Italy.
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13
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Raman K, O'Donnell MJ, Czlonkowska A, Duarte YC, Lopez-Jaramillo P, Peñaherrera E, Sharma M, Shoamanesh A, Skowronska M, Yusuf S, Paré G. Peripheral Blood MCEMP1 Gene Expression as a Biomarker for Stroke Prognosis. Stroke 2016; 47:652-8. [PMID: 26846866 DOI: 10.1161/strokeaha.115.011854] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/12/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND PURPOSE A limitation when making early decisions on stroke management is the lack of rapid diagnostic and prognostic testing. Our study sought to identify peripheral blood RNA biomarkers associated with stroke. The secondary aims were to assess the discriminative capacity of RNA biomarkers for primary stroke type and stroke prognosis at 1-month. METHODS Whole-blood gene expression profiling was conducted on the discovery cohort: 129 first-time stroke cases that had blood sampling within 5 days of symptom onset and 170 control participants with no history of stroke. RESULTS Through multiple regression analysis, we determined that expression of the gene MCEMP1 had the strongest association with stroke of 11 181 genes tested. MCEMP1 increased by 2.4-fold in stroke when compared with controls (95% confidence interval, 2.0-2.8; P=8.2×10(-22)). In addition, expression was elevated in intracerebral hemorrhage when compared with ischemic stroke cases (P=3.9×10(-4)). MCEMP1 was also highest soon after symptom onset and had no association with stroke risk factors. Furthermore, MCEMP1 expression independently improved discrimination of 1-month outcome. Indeed, discrimination models for disability and mortality that included MCEMP1 expression, baseline modified Rankin Scale score, and primary stroke type improved discrimination when compared with a model without MCEMP1 (disability Net Reclassification Index, 0.76; P=3.0×10(-6) and mortality Net Reclassification Index, 1.3; P=1.1×10(-9)). Significant associations with MCEMP1 were confirmed in an independent validation cohort of 28 stroke cases and 34 controls. CONCLUSIONS This study demonstrates that peripheral blood expression of MCEMP1 may have utility for stroke diagnosis and as a prognostic biomarker of stroke outcome at 1-month.
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Affiliation(s)
- Kripa Raman
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Martin J O'Donnell
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Anna Czlonkowska
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Yan Carlos Duarte
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Patricio Lopez-Jaramillo
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Ernesto Peñaherrera
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Mike Sharma
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Ashkan Shoamanesh
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Marta Skowronska
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Salim Yusuf
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.)
| | - Guillaume Paré
- From the Population Health Research Institute and Hamilton Health Sciences (K.R., M.O., M. Sharma, A.S., S.Y., G.P.), and Department of Medical Science (K.R.), Medicine (M.O.), Neurology (M. Sharma, A.S.), Clinical Epidemiology and Biostatistics (S.Y.), Pathology and Molecular Medicine (G.P.), McMaster University, Hamilton, Ontario, Canada; HRB-Clinical Research Facility, National University of Ireland, Galway, Ireland (M.O.); Second Department of Neurology, Institute of Psychiatry and Neurology, Warsaw Medical University, Warsaw, Poland (A.C., M. Skowronska); Luis Vernaza Hospital, Guayaquil, Ecuador (Y.C.D., E.P.); Ophthalmological Foundation of Santander, Floridablanca, Santander, Colombia (P.L.-J.); and Instituto MASIRA, School of Health Sciences, University of Santander (UDES), Bucaramanga, Santander, Colombia (P.L.-J.).
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