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Yang K, Musio F, Ma Y, Juchler N, Paetzold JC, Al-Maskari R, Höher L, Li HB, Hamamci IE, Sekuboyina A, Shit S, Huang H, Prabhakar C, de la Rosa E, Waldmannstetter D, Kofler F, Navarro F, Menten M, Ezhov I, Rueckert D, Vos I, Ruigrok Y, Velthuis B, Kuijf H, Hämmerli J, Wurster C, Bijlenga P, Westphal L, Bisschop J, Colombo E, Baazaoui H, Makmur A, Hallinan J, Wiestler B, Kirschke JS, Wiest R, Montagnon E, Letourneau-Guillon L, Galdran A, Galati F, Falcetta D, Zuluaga MA, Lin C, Zhao H, Zhang Z, Ra S, Hwang J, Park H, Chen J, Wodzinski M, Müller H, Shi P, Liu W, Ma T, Yalçin C, Hamadache RE, Salvi J, Llado X, Estrada UMLT, Abramova V, Giancardo L, Oliver A, Liu J, Huang H, Cui Y, Lin Z, Liu Y, Zhu S, Patel TR, Tutino VM, Orouskhani M, Wang H, Mossa-Basha M, Zhu C, Rokuss MR, Kirchhoff Y, Disch N, Holzschuh J, Isensee F, Maier-Hein K, Sato Y, Hirsch S, Wegener S, Menze B. Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA. ArXiv 2024:arXiv:2312.17670v3. [PMID: 38235066 PMCID: PMC10793481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset. The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology. It was also the first large dataset with paired MRA and CTA from the same patients. TopCoW challenge formalized the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. We invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically.
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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: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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