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Reichmann J, Sarrazin C, Schmale S, Blaurock C, Balkema-Buschmann A, Schmitzer B, Salditt T. 3D imaging of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography enables drug testing. Sci Rep 2024; 14:12348. [PMID: 38811688 PMCID: PMC11137149 DOI: 10.1038/s41598-024-61746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. To address these challenges, we here design and implement a novel integrated and high throughput XPCT imaging and analysis workflow for 3D histology, pathohistology and drug testing. Our approach uses semi-automated data acquisition, reconstruction and statistical quantification. We demonstrate its capability for the example of lung pathohistology in Covid-19. Using a small animal model, different Covid-19 drug candidates are administered after infection and tested in view of restoration of the physiological cytoarchitecture, specifically the alveolar morphology. To this end, we then use morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing quantitative insights into the pathological progression and partial recovery due to drug treatment. Finally, we stress that the XPCT image chain implemented here only used synchrotron radiation for validation, while the data used for analysis was recorded with laboratory μ CT radiation, more easily accessible for pre-clinical research.
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Affiliation(s)
- Jakob Reichmann
- Georg-August-University of Göttingen, Institute for X-Ray Physics, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Clement Sarrazin
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany
- Equipe RAPSODI, Centre INRIA de l'université de Lille, F-59000, Lille, France
| | - Sebastian Schmale
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Claudia Blaurock
- Friedrich-Loeffler-Institute, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | | | - Bernhard Schmitzer
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany.
| | - Tim Salditt
- Georg-August-University of Göttingen, Institute for X-Ray Physics, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.
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Zhou H, Xu M, Hu P, Li Y, Ren C, Li M, Pan Y, Wang S, Liu X. Identifying hub genes and common biological pathways between COVID-19 and benign prostatic hyperplasia by machine learning algorithms. Front Immunol 2023; 14:1172724. [PMID: 37426635 PMCID: PMC10328422 DOI: 10.3389/fimmu.2023.1172724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Background COVID-19, a serious respiratory disease that has the potential to affect numerous organs, is a serious threat to the health of people around the world. The objective of this article is to investigate the potential biological targets and mechanisms by which SARS-CoV-2 affects benign prostatic hyperplasia (BPH) and related symptoms. Methods We downloaded the COVID-19 datasets (GSE157103 and GSE166253) and the BPH datasets (GSE7307 and GSE132714) from the Gene Expression Omnibus (GEO) database. In GSE157103 and GSE7307, differentially expressed genes (DEGs) were found using the "Limma" package, and the intersection was utilized to obtain common DEGs. Further analyses followed, including those using Protein-Protein Interaction (PPI), Gene Ontology (GO) function enrichment analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Potential hub genes were screened using three machine learning methods, and they were later verified using GSE132714 and GSE166253. The CIBERSORT analysis and the identification of transcription factors, miRNAs, and drugs as candidates were among the subsequent analyses. Results We identified 97 common DEGs from GSE157103 and GSE7307. According to the GO and KEGG analyses, the primary gene enrichment pathways were immune-related pathways. Machine learning methods were used to identify five hub genes (BIRC5, DNAJC4, DTL, LILRB2, and NDC80). They had good diagnostic properties in the training sets and were validated in the validation sets. According to CIBERSORT analysis, hub genes were closely related to CD4 memory activated of T cells, T cells regulatory and NK cells activated. The top 10 drug candidates (lucanthone, phytoestrogens, etoposide, dasatinib, piroxicam, pyrvinium, rapamycin, niclosamide, genistein, and testosterone) will also be evaluated by the P value, which is expected to be helpful for the treatment of COVID-19-infected patients with BPH. Conclusion Our findings reveal common signaling pathways, possible biological targets, and promising small molecule drugs for BPH and COVID-19. This is crucial to understand the potential common pathogenic and susceptibility pathways between them.
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Affiliation(s)
- Hang Zhou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingming Xu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ping Hu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuezheng Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Congzhe Ren
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Muwei Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yang Pan
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
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Pinkert-Leetsch D, Frohn J, Ströbel P, Alves F, Salditt T, Missbach-Guentner J. Three-dimensional analysis of human pancreatic cancer specimens by phase-contrast based X-ray tomography - the next dimension of diagnosis. Cancer Imaging 2023; 23:43. [PMID: 37131262 PMCID: PMC10152799 DOI: 10.1186/s40644-023-00559-6] [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: 07/19/2022] [Accepted: 04/19/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The worldwide increase of pancreatic ductal adenocarcinoma (PDAC), which still has one of the lowest survival rates, requires novel imaging tools to improve early detection and to refine diagnosis. Therefore, the aim of this study was to assess the feasibility of propagation-based phase-contrast X-ray computed tomography of already paraffin-embedded and unlabeled human pancreatic tumor tissue to achieve a detailed three-dimensional (3D) view of the tumor sample in its entirety. METHODS Punch biopsies of areas of particular interest were taken from paraffin blocks after initial histological analysis of hematoxylin and eosin stained tumor sections. To cover the entire 3.5 mm diameter of the punch biopsy, nine individual tomograms with overlapping regions were acquired in a synchrotron parallel beam configuration and stitched together after data reconstruction. Due to the intrinsic contrast based on electron density differences of tissue components and a voxel size of 1.3 μm achieved PDAC and its precursors were clearly identified. RESULTS Characteristic tissue structures for PDAC and its precursors, such as dilated pancreatic ducts, altered ductal epithelium, diffuse immune cell infiltrations, increased occurrence of tumor stroma and perineural invasion were clearly identified. Certain structures of interest were visualized in three dimensions throughout the tissue punch. Pancreatic duct ectasia of different caliber and atypical shape as well as perineural infiltration could be contiguously traced by viewing serial tomographic slices and by applying semi-automatic segmentation. Histological validation of corresponding sections confirmed the former identified PDAC features. CONCLUSION In conclusion, virtual 3D histology via phase-contrast X-ray tomography visualizes diagnostically relevant tissue structures of PDAC in their entirety, preserving tissue integrity in label-free, paraffin embedded tissue biopsies. In the future, this will not only enable a more comprehensive diagnosis but also a possible identification of new 3D imaging tumor markers.
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Affiliation(s)
- Diana Pinkert-Leetsch
- Department of Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany.
| | - Jasper Frohn
- Institute for X-ray Physics, Georg-August-University, Goettingen, Germany
| | - Philipp Ströbel
- Department of Pathology, University Medical Center, Goettingen, Germany
| | - Frauke Alves
- Department of Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
- Department of Hematology and Medical Oncology, University Medical Center, Goettingen, Germany
- Translational Molecular Imaging, Max-Planck-Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, Georg-August-University, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
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Deep Survival Analysis With Clinical Variables for COVID-19. IEEE JOURNAL OF TRANSLATIONAL ENGINEERING IN HEALTH AND MEDICINE 2023; 11:223-231. [PMID: 36950264 PMCID: PMC10027076 DOI: 10.1109/jtehm.2023.3256966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 01/08/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
OBJECTIVE Millions of people have been affected by coronavirus disease 2019 (COVID-19), which has caused millions of deaths around the world. Artificial intelligence (AI) plays an increasing role in all areas of patient care, including prognostics. This paper proposes a novel predictive model based on one dimensional convolutional neural networks (1D CNN) to use clinical variables in predicting the survival outcome of COVID-19 patients. METHODS AND PROCEDURES We have considered two scenarios for survival analysis, 1) uni-variate analysis using the Log-rank test and Kaplan-Meier estimator and 2) combining all clinical variables ([Formula: see text]=44) for predicting the short-term from long-term survival. We considered the random forest (RF) model as a baseline model, comparing to our proposed 1D CNN in predicting survival groups. RESULTS Our experiments using the univariate analysis show that nine clinical variables are significantly associated with the survival outcome with corrected p < 0.05. Our approach of 1D CNN shows a significant improvement in performance metrics compared to the RF and the state-of-the-art techniques (i.e., 1D CNN) in predicting the survival group of patients with COVID-19. CONCLUSION Our model has been tested using clinical variables, where the performance is found promising. The 1D CNN model could be a useful tool for detecting the risk of mortality and developing treatment plans in a timely manner. CLINICAL IMPACT The findings indicate that using both Heparin and Exnox for treatment is typically the most useful factor in predicting a patient's chances of survival from COVID-19. Moreover, our predictive model shows that the combination of AI and clinical data can be applied to point-of-care services through fast-learning healthcare systems.
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Pierantoni M, Hammerman M, Silva Barreto I, Andersson L, Novak V, Isaksson H, Eliasson P. Heterotopic mineral deposits in intact rat Achilles tendons are characterized by a unique fiber-like structure. J Struct Biol X 2023; 7:100087. [PMID: 36938139 PMCID: PMC10018562 DOI: 10.1016/j.yjsbx.2023.100087] [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: 09/05/2022] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 02/26/2023] Open
Abstract
Heterotopic mineralization entails pathological mineral formation inside soft tissues. In human tendons mineralization is often associated with tendinopathies, tendon weakness and pain. In Achilles tendons, mineralization is considered to occur through heterotopic ossification (HO) primarily in response to tendon pathologies. However, refined details regarding HO deposition and microstructure are unknown. In this study, we characterize HO in intact rat Achilles tendons through high-resolution phase contrast enhanced synchrotron X-ray tomography. Furthermore, we test the potential of studying local tissue injury by needling intact Achilles tendons and the relation between tissue microdamage and HO. The results show that HO occurs in all intact Achilles tendons at 16 weeks of age. HO deposits are characterized by an elongated ellipsoidal shape and by a fiber-like internal structure which suggests that some collagen fibers have mineralized. The data indicates that deposition along fibers initiates in the pericellular area, and propagates into the intercellular area. Within HO deposits cells are larger and more rounded compared to tenocytes between unmineralized fibers, which are fewer and elongated. The results also indicate that multiple HO deposits may merge into bigger structures with time by accession along unmineralized fibers. Furthermore, the presence of unmineralized regions within the deposits may indicate that HOs are not only growing, but mineral resorption may also occur. Additionally, phase contrast synchrotron X-ray tomography allowed to distinguish microdamage at the fiber level in response to needling. The needle injury protocol could in the future enable to elucidate the relation between local inflammation, microdamage, and HO deposition.
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Affiliation(s)
- Maria Pierantoni
- Department of Biomedical Engineering, Lund University, Box 118, 221 00 Lund, Sweden
- Corresponding author.
| | - Malin Hammerman
- Department of Biomedical Engineering, Lund University, Box 118, 221 00 Lund, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | | | - Linnea Andersson
- Department of Biomedical Engineering, Lund University, Box 118, 221 00 Lund, Sweden
| | - Vladimir Novak
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Hanna Isaksson
- Department of Biomedical Engineering, Lund University, Box 118, 221 00 Lund, Sweden
| | - Pernilla Eliasson
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Department of Orthopaedics, Sahlgrenska University Hospital, Gothenburg, Sweden
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6
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Schroer CG, Wille HC, Seeck OH, Bagschik K, Schulte-Schrepping H, Tischer M, Graafsma H, Laasch W, Baev K, Klumpp S, Bartolini R, Reichert H, Leemans W, Weckert E. The synchrotron radiation source PETRA III and its future ultra-low-emittance upgrade PETRA IV. EUROPEAN PHYSICAL JOURNAL PLUS 2022; 137:1312. [PMID: 36532653 PMCID: PMC9734975 DOI: 10.1140/epjp/s13360-022-03517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
PETRA III at DESY is one of the brightest synchrotron radiation sources worldwide. It serves a broad international multidisciplinary user community from academia to industry at currently 25 specialised beamlines. With a storage-ring energy of 6 GeV, it provides mainly hard to high-energy X-rays for versatile experiments in a very broad range of scientific fields. It is ideally suited for an upgrade to the ultra-low emittance source PETRA IV, owing to its large circumference of 2304 m. With a targeted storage ring emittance of 20 × 5 pm 2 rad 2 , PETRA IV will reach spectral brightnesses two to three orders of magnitude higher than today. The unique beam parameters will make PETRA IV the ultimate in situ 3D microscope for biological, chemical, and physical processes helping to address key questions in health, energy, mobility, information technology, and earth and environment.
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Affiliation(s)
- Christian G. Schroer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Oliver H. Seeck
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Kai Bagschik
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Markus Tischer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Heinz Graafsma
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wiebke Laasch
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Karolin Baev
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Stephan Klumpp
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Riccardo Bartolini
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Harald Reichert
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wim Leemans
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Edgar Weckert
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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Wells G, Glasgow JN, Nargan K, Lumamba K, Madansein R, Maharaj K, Perumal LY, Matthew M, Hunter RL, Pacl H, Peabody Lever JE, Stanford DD, Singh SP, Bajpai P, Manne U, Benson PV, Rowe SM, le Roux S, Sigal A, Tshibalanganda M, Wells C, du Plessis A, Msimang M, Naidoo T, Steyn AJC. A high-resolution 3D atlas of the spectrum of tuberculous and COVID-19 lung lesions. EMBO Mol Med 2022; 14:e16283. [PMID: 36285507 PMCID: PMC9641421 DOI: 10.15252/emmm.202216283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 02/01/2023] Open
Abstract
Our current understanding of the spectrum of TB and COVID-19 lesions in the human lung is limited by a reliance on low-resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID-19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin-embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID-19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID-19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID-19 lesions within the framework of the entire lung.
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Affiliation(s)
- Gordon Wells
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Joel N Glasgow
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Kievershen Nargan
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Kapongo Lumamba
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Rajhmun Madansein
- Inkosi Albert Luthuli Central Hospital and University of KwaZulu‐NatalDurbanSouth Africa
| | - Kameel Maharaj
- Inkosi Albert Luthuli Central Hospital and University of KwaZulu‐NatalDurbanSouth Africa
| | - Leon Y Perumal
- Perumal & Partners RadiologistsAhmed Al‐Kadi Private HospitalDurbanSouth Africa
| | - Malcolm Matthew
- Perumal & Partners RadiologistsAhmed Al‐Kadi Private HospitalDurbanSouth Africa
| | - Robert L Hunter
- Department of Pathology and Laboratory MedicineUniversity of Texas Health Sciences Center at HoustonHoustonTXUSA
| | - Hayden Pacl
- Medical Scientist Training ProgramUniversity of Alabama at BirminghamBirminghamALUSA
| | | | - Denise D Stanford
- Department of MedicineUniversity of Alabama at BirminghamBirminghamALUSA
- Cystic Fibrosis Research CenterUniversity of Alabama at BirminghamBirminghamALUSA
| | - Satinder P Singh
- Department of MedicineUniversity of Alabama at BirminghamBirminghamALUSA
- Department of RadiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Prachi Bajpai
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Upender Manne
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Paul V Benson
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Steven M Rowe
- Department of MedicineUniversity of Alabama at BirminghamBirminghamALUSA
- Cystic Fibrosis Research CenterUniversity of Alabama at BirminghamBirminghamALUSA
| | | | - Alex Sigal
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Muofhe Tshibalanganda
- Research Group 3D Innovation, Physics DepartmentStellenbosch UniversityStellenboschSouth Africa
| | - Carlyn Wells
- CT Scanner Facility, Central Analytical FacilitiesStellenbosch UniversityStellenboschSouth Africa
| | - Anton du Plessis
- Research Group 3D Innovation, Physics DepartmentStellenbosch UniversityStellenboschSouth Africa
- Object Research SystemsMontrealQCCanada
| | - Mpumelelo Msimang
- Department of Anatomical Pathology, National Health Laboratory ServiceInkosi Albert Luthuli Central HospitalDurbanSouth Africa
| | - Threnesan Naidoo
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
- Department of Anatomical Pathology, National Health Laboratory ServiceInkosi Albert Luthuli Central HospitalDurbanSouth Africa
- Department of Laboratory Medicine & PathologyWalter Sisulu UniversityEastern CapeSouth Africa
| | - Adrie J C Steyn
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamALUSA
- Centers for AIDS Research and Free Radical BiologyUniversity of Alabama at BirminghamBirminghamALUSA
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Yan C, Niu Y, Wang X. Blood transcriptome analysis revealed the crosstalk between COVID-19 and HIV. Front Immunol 2022; 13:1008653. [PMID: 36389792 PMCID: PMC9650272 DOI: 10.3389/fimmu.2022.1008653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/29/2022] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND The severe coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has resulted in the most devastating pandemic in modern history. Human immunodeficiency virus (HIV) destroys immune system cells and weakens the body's ability to resist daily infections and diseases. Furthermore, HIV-infected individuals had double COVID-19 mortality risk and experienced worse COVID-related outcomes. However, the existing research still lacks the understanding of the molecular mechanism underlying crosstalk between COVID-19 and HIV. The aim of our work was to illustrate blood transcriptome crosstalk between COVID-19 and HIV and to provide potential drugs that might be useful for the treatment of HIV-infected COVID-19 patients. METHODS COVID-19 datasets (GSE171110 and GSE152418) were downloaded from Gene Expression Omnibus (GEO) database, including 54 whole-blood samples and 33 peripheral blood mononuclear cells samples, respectively. HIV dataset (GSE37250) was also obtained from GEO database, containing 537 whole-blood samples. Next, the "Deseq2" package was used to identify differentially expressed genes (DEGs) between COVID-19 datasets (GSE171110 and GSE152418) and the "limma" package was utilized to identify DEGs between HIV dataset (GSE37250). By intersecting these two DEG sets, we generated common DEGs for further analysis, containing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) functional enrichment analysis, protein-protein interaction (PPI) analysis, transcription factor (TF) candidate identification, microRNAs (miRNAs) candidate identification and drug candidate identification. RESULTS In this study, a total of 3213 DEGs were identified from the merged COVID-19 dataset (GSE171110 and GSE152418), and 1718 DEGs were obtained from GSE37250 dataset. Then, we identified 394 common DEGs from the intersection of the DEGs in COVID-19 and HIV datasets. GO and KEGG enrichment analysis indicated that common DEGs were mainly gathered in chromosome-related and cell cycle-related signal pathways. Top ten hub genes (CCNA2, CCNB1, CDC20, TOP2A, AURKB, PLK1, BUB1B, KIF11, DLGAP5, RRM2) were ranked according to their scores, which were screened out using degree algorithm on the basis of common DEGs. Moreover, top ten drug candidates (LUCANTHONE, Dasatinib, etoposide, Enterolactone, troglitazone, testosterone, estradiol, calcitriol, resveratrol, tetradioxin) ranked by their P values were screened out, which maybe be beneficial for the treatment of HIV-infected COVID-19 patients. CONCLUSION In this study, we provide potential molecular targets, signaling pathways, small molecular compounds, and promising biomarkers that contribute to worse COVID-19 prognosis in patients with HIV, which might contribute to precise diagnosis and treatment for HIV-infected COVID-19 patients.
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Affiliation(s)
- Cheng Yan
- *Correspondence: Cheng Yan, ; Xuannian Wang,
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9
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Huhn S, Lohse LM, Lucht J, Salditt T. Fast algorithms for nonlinear and constrained phase retrieval in near-field X-ray holography based on Tikhonov regularization. OPTICS EXPRESS 2022; 30:32871-32886. [PMID: 36242340 DOI: 10.1364/oe.462368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
Based on phase retrieval, lensless coherent imaging and in particular holography offers quantitative phase and amplitude images. This is of particular importance for spectral ranges where suitable lenses are challenging, such as for hard x-rays. Here, we propose a phase retrieval approach for inline x-ray holography based on Tikhonov regularization applied to the full nonlinear forward model of image formation. The approach can be seen as a nonlinear generalization of the well-established contrast transfer function (CTF) reconstruction method. While similar methods have been proposed before, the current work achieves nonlinear, constrained phase retrieval at competitive computation times. We thus enable high-throughput imaging of optically strong objects beyond the scope of CTF. Using different examples of inline holograms obtained from illumination by a x-ray waveguide-source, we demonstrate superior image quality even for samples which do not obey the assumption of a weakly varying phase. Since the presented approach does not rely on linearization, we expect it to be well suited also for other probes such as visible light or electrons, which often exhibit strong phase interaction.
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10
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Ackermann M. [On the way to the virtual microscope: synchrotron-radiation-based three-dimensional imaging in pathology]. PATHOLOGIE (HEIDELBERG, GERMANY) 2022; 43:15-20. [PMID: 36378286 PMCID: PMC9665030 DOI: 10.1007/s00292-022-01161-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Affiliation(s)
- Maximilian Ackermann
- Institut für Pathologie und Molekularpathologie, Helios Universitätsklinikum Wuppertal, Universität Witten-Herdecke, Heusnerstr. 40, 42283, Wuppertal, Deutschland. .,Institut für Funktionelle und Klinische Anatomie, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Deutschland.
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11
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Jonigk D, Werlein C, D. Lee P, Kauczor HU, Länger F, Ackermann M. Pulmonary and Systemic Pathology in COVID-19—Holistic Pathological Analyses. DEUTSCHES ARZTEBLATT INTERNATIONAL 2022; 119:429-435. [PMID: 35698804 PMCID: PMC9549895 DOI: 10.3238/arztebl.m2022.0231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 03/22/2022] [Accepted: 05/10/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND The COVID-19 pandemic is the third worldwide coronavirus-associated disease outbreak in the past 20 years. Lung involvement, with acute respiratory distress syndrome (ARDS) in severe cases, is the main clinical feature of this disease; the cardiovascular system, the central nervous system, and the gastrointestinal tract can also be affected. The pathophysiology of both pulmonary and extrapulmonary organ damage was almost completely unknown when the pandemic began. METHODS This review is based on pertinent publications retrieved by a selective search concerning the structural changes and pathophysiology of COVID-19, with a focus on imaging techniques. RESULTS Immunohistochemical, electron-microscopic and molecular pathological analyses of tissues obtained by autopsy have improved our understanding of COVID-19 pathophysiology, including molecular regulatory mechanisms. Intussusceptive angiogenesis (IA) has been found to be a prominent pattern of damage in the affected organs of COVID-19 patients. In IA, an existing vessel changes by invagination of the endothelium and formation of an intraluminal septum, ultimately giving rise to two new lumina. This alters hemodynamics within the vessel, leading to a loss of laminar flow and its replacement by turbulent, inhomogeneous flow. IA, which arises because of ischemia due to thrombosis, is itself a risk factor for the generation of further microthrombi; these have been detected in the lungs, heart, liver, kidneys, brain, and placenta of COVID-19 patients. CONCLUSION Studies of autopsy material from various tissues of COVID-19 patients have revealed ultrastructural evidence of altered microvascularity, IA, and multifocal thrombi. These changes may contribute to the pathophysiology of post-acute interstitial fibrotic organ changes as well as to the clinical picture of long COVID.
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Affiliation(s)
- Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover site, Hannover, Germany
- *Institut für Pathologie, Medizinische Hochschule Hannover Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | | | - Peter D. Lee
- Department of Mechanical Engineering, Faculty of Engineering Science, University College London, London, UK
| | - Hans-Ulrich Kauczor
- Department of Diagnostic and Interventional Radiology, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Länger
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover site, Hannover, Germany
| | - Maximilian Ackermann
- Institute of Pathology and Molecular Pathology, Helios University Hospital Wuppertal, University Hospital of Witten-Herdecke, Wuppertal, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center Mainz, Mainz, Germany
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12
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Jonigk D, Werlein C, Acker T, Aepfelbacher M, Amann KU, Baretton G, Barth P, Bohle RM, Büttner A, Büttner R, Dettmeyer R, Eichhorn P, Elezkurtaj S, Esposito I, Evert K, Evert M, Fend F, Gaßler N, Gattenlöhner S, Glatzel M, Göbel H, Gradhand E, Hansen T, Hartmann A, Heinemann A, Heppner FL, Hilsenbeck J, Horst D, Kamp JC, Mall G, Märkl B, Ondruschka B, Pablik J, Pfefferle S, Quaas A, Radbruch H, Röcken C, Rosenwald A, Roth W, Rudelius M, Schirmacher P, Slotta-Huspenina J, Smith K, Sommer L, Stock K, Ströbel P, Strobl S, Titze U, Weirich G, Weis J, Werner M, Wickenhauser C, Wiech T, Wild P, Welte T, von Stillfried S, Boor P. Organ manifestations of COVID-19: what have we learned so far (not only) from autopsies? Virchows Arch 2022; 481:139-159. [PMID: 35364700 PMCID: PMC8975445 DOI: 10.1007/s00428-022-03319-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
Abstract
The use of autopsies in medicine has been declining. The COVID-19 pandemic has documented and rejuvenated the importance of autopsies as a tool of modern medicine. In this review, we discuss the various autopsy techniques, the applicability of modern analytical methods to understand the pathophysiology of COVID-19, the major pathological organ findings, limitations or current studies, and open questions. This article summarizes published literature and the consented experience of the nationwide network of clinical, neuro-, and forensic pathologists from 27 German autopsy centers with more than 1200 COVID-19 autopsies. The autopsy tissues revealed that SARS-CoV-2 can be found in virtually all human organs and tissues, and the majority of cells. Autopsies have revealed the organ and tissue tropism of SARS-CoV-2, and the morphological features of COVID-19. This is characterized by diffuse alveolar damage, combined with angiocentric disease, which in turn is characterized by endothelial dysfunction, vascular inflammation, (micro-) thrombosis, vasoconstriction, and intussusceptive angiogenesis. These findings explained the increased pulmonary resistance in COVID-19 and supported the recommendations for antithrombotic treatment in COVID-19. In contrast, in extra-respiratory organs, pathological changes are often nonspecific and unclear to which extent these changes are due to direct infection vs. indirect/secondary mechanisms of organ injury, or a combination thereof. Ongoing research using autopsies aims at answering questions on disease mechanisms, e.g., focusing on variants of concern, and future challenges, such as post-COVID conditions. Autopsies are an invaluable tool in medicine and national and international interdisciplinary collaborative autopsy-based research initiatives are essential.
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Affiliation(s)
- Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany.
| | | | - Till Acker
- Institute of Neuropathology, University Hospital Giessen and Marburg, Giessen, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin U Amann
- Department of Nephropathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Gustavo Baretton
- Department of Pathology, University Hospital Dresden, Dresden, Germany
| | - Peter Barth
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Rainer M Bohle
- Department of Pathology, University Hospital Saarland Homburg, Homburg, Germany
| | - Andreas Büttner
- Institute of Forensic Medicine, University Medical Center Rostock, Rostock, Germany
| | - Reinhard Büttner
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - Reinhard Dettmeyer
- Department of Legal Medicine, University Hospital Giessen and Marburg, Giessen, Germany
| | - Philip Eichhorn
- Department of Pathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Sefer Elezkurtaj
- Department of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Irene Esposito
- Department of Pathology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Katja Evert
- Department of Pathology, University Hospital Regensburg, Regensburg, Germany
| | - Matthias Evert
- Department of Pathology, University Hospital Regensburg, Regensburg, Germany
| | - Falko Fend
- Department of Pathology, University Hospital Tübingen, Tübingen, Germany
| | - Nikolaus Gaßler
- Department of Pathology, University Hospital Jena, Jena, Germany
| | - Stefan Gattenlöhner
- Department of Pathology, University Hospital Giessen and Marburg, Giessen, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Heike Göbel
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - Elise Gradhand
- Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Torsten Hansen
- Department of Pathology, University Hospital OWL of the Bielefeld University, Campus Lippe, Detmold, Germany
| | - Arndt Hartmann
- Department of Pathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Axel Heinemann
- Department of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany.,Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Julia Hilsenbeck
- Department of Pathology, University Hospital Dresden, Dresden, Germany
| | - David Horst
- Department of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan C Kamp
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Gita Mall
- Department of Legal Medicine, University Hospital Jena, Jena, Germany
| | - Bruno Märkl
- General Pathology and Molecular Diagnostics, University Hospital Augsburg, Augsburg, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jessica Pablik
- Department of Pathology, University Hospital Dresden, Dresden, Germany
| | - Susanne Pfefferle
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Quaas
- Department of Pathology, University Hospital Cologne, Cologne, Germany
| | - Helena Radbruch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Wilfried Roth
- Department of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Martina Rudelius
- Institute of Pathology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Peter Schirmacher
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Slotta-Huspenina
- Department of Pathology, TUM School of Medicine of Technical University of Munich, Munich, Germany
| | - Kevin Smith
- Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Linna Sommer
- Department of Pathology, University Hospital Dresden, Dresden, Germany
| | - Konrad Stock
- Department of Nephrology, TUM School of Medicine of Technical University of Munich, Munich, Germany
| | - Philipp Ströbel
- Department of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Stephanie Strobl
- Department of Pathology, University Medical Center Mainz, Mainz, Germany
| | - Ulf Titze
- Department of Pathology, University Hospital OWL of the Bielefeld University, Campus Lippe, Detmold, Germany
| | - Gregor Weirich
- Department of Pathology, TUM School of Medicine of Technical University of Munich, Munich, Germany
| | - Joachim Weis
- Department of Neuropathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Claudia Wickenhauser
- Department of Pathology, University Hospital Halle (Saale), Halle (Saale), Germany
| | - Thorsten Wiech
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Wild
- Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | | | - Peter Boor
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany. .,Department of Nephrology and Immunology, University Hospital RWTH Aachen, Aachen, Germany.
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13
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Verleden SE, Braubach P, Werlein C, Plucinski E, Kuhnel MP, Snoeckx A, El Addouli H, Welte T, Haverich A, Laenger FP, Dettmer S, Pauwels P, Verplancke V, Van Schil PE, Lapperre T, Kwakkel-Van-Erp JM, Ackermann M, Hendriks JMH, Jonigk D. From Macroscopy to Ultrastructure: An Integrative Approach to Pulmonary Pathology. Front Med (Lausanne) 2022; 9:859337. [PMID: 35372395 PMCID: PMC8965844 DOI: 10.3389/fmed.2022.859337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Pathology and radiology are complimentary tools, and their joint application is often crucial in obtaining an accurate diagnosis in non-neoplastic pulmonary diseases. However, both come with significant limitations of their own: Computed Tomography (CT) can only visualize larger structures due to its inherent–relatively–poor resolution, while (histo) pathology is often limited due to small sample size and sampling error and only allows for a 2D investigation. An innovative approach of inflating whole lung specimens and subjecting these subsequently to CT and whole lung microCT allows for an accurate matching of CT-imaging and histopathology data of exactly the same areas. Systematic application of this approach allows for a more targeted assessment of localized disease extent and more specifically can be used to investigate early mechanisms of lung diseases on a morphological and molecular level. Therefore, this technique is suitable to selectively investigate changes in the large and small airways, as well as the pulmonary arteries, veins and capillaries in relation to the disease extent in the same lung specimen. In this perspective we provide an overview of the different strategies that are currently being used, as well as how this growing field could further evolve.
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Affiliation(s)
- Stijn E. Verleden
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Division of Pneumology, University Hospital Antwerp, Edegem, Belgium
- Department of Thoracic and Vascular Surgery, University Hospital Antwerp, Edegem, Belgium
| | - Peter Braubach
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | | | - Edith Plucinski
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Mark P. Kuhnel
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Annemiek Snoeckx
- Division of Radiology, University Hospital Antwerp and University of Antwerp, Edegem, Belgium
| | - Haroun El Addouli
- Division of Radiology, University Hospital Antwerp and University of Antwerp, Edegem, Belgium
| | - Tobias Welte
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Division of Pneumology, Hannover Medical School, Hannover, Germany
| | - Axel Haverich
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Division of Thoracic Surgery, Hannover Medical School, Hannover, Germany
| | - Florian P. Laenger
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Sabine Dettmer
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Department of Radiology, Hannover Medical School, Hannover, Germany
| | - Patrick Pauwels
- Division of Pathology, University Hospital Antwerp, Edegem, Belgium
| | | | - Paul E. Van Schil
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Department of Thoracic and Vascular Surgery, University Hospital Antwerp, Edegem, Belgium
| | - Therese Lapperre
- Division of Pneumology, University Hospital Antwerp, Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics (LEMP), Antwerp University, Antwerp, Belgium
| | - Johanna M. Kwakkel-Van-Erp
- Division of Pneumology, University Hospital Antwerp, Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics (LEMP), Antwerp University, Antwerp, Belgium
| | - Maximilian Ackermann
- Institute of Pathology and Department of Molecular Pathology, Helios University Clinic Wuppertal, University of Witten-Herdecke, Witten, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jeroen M. H. Hendriks
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), Antwerp University, Antwerp, Belgium
- Department of Thoracic and Vascular Surgery, University Hospital Antwerp, Edegem, Belgium
| | - Danny Jonigk
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute for Pathology, Hannover Medical School, Hannover, Germany
- *Correspondence: Danny Jonigk
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14
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Vogl C, Neef J, Wichmann C. Methods for multiscale structural and functional analysis of the mammalian cochlea. Mol Cell Neurosci 2022; 120:103720. [DOI: 10.1016/j.mcn.2022.103720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/13/2022] [Accepted: 03/08/2022] [Indexed: 01/11/2023] Open
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15
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Reichardt M, Moller Jensen P, Andersen Dahl V, Bjorholm Dahl A, Ackermann M, Shah H, Länger F, Werlein C, Kuehnel MP, Jonigk D, Salditt T. 3D virtual histopathology of cardiac tissue from Covid-19 patients based on phase-contrast X-ray tomography. eLife 2021; 10:e71359. [PMID: 34930527 PMCID: PMC8747495 DOI: 10.7554/elife.71359] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022] Open
Abstract
For the first time, we have used phase-contrast X-ray tomography to characterize the three-dimensional (3d) structure of cardiac tissue from patients who succumbed to Covid-19. By extending conventional histopathological examination by a third dimension, the delicate pathological changes of the vascular system of severe Covid-19 progressions can be analyzed, fully quantified and compared to other types of viral myocarditis and controls. To this end, cardiac samples with a cross-section of 3.5mm were scanned at a laboratory setup as well as at a parallel beam setup at a synchrotron radiation facility the synchrotron in a parallel beam configuration. The vascular network was segmented by a deep learning architecture suitable for 3d datasets (V-net), trained by sparse manual annotations. Pathological alterations of vessels, concerning the variation of diameters and the amount of small holes, were observed, indicative of elevated occurrence of intussusceptive angiogenesis, also confirmed by high-resolution cone beam X-ray tomography and scanning electron microscopy. Furthermore, we implemented a fully automated analysis of the tissue structure in the form of shape measures based on the structure tensor. The corresponding distributions show that the histopathology of Covid-19 differs from both influenza and typical coxsackie virus myocarditis.
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Affiliation(s)
- Marius Reichardt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-PlatzGöttingenGermany
| | | | | | | | - Maximilian Ackermann
- Institute of Anatomy and Cell Biology, University Medical Center of the Johannes Gutenberg-University MainzMainzGermany
| | - Harshit Shah
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL), Hannover (BREATH)HannoverGermany
| | - Florian Länger
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL), Hannover (BREATH)HannoverGermany
| | | | - Mark P Kuehnel
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL), Hannover (BREATH)HannoverGermany
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL), Hannover (BREATH)HannoverGermany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-PlatzGöttingenGermany
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16
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Walsh CL, Tafforeau P, Wagner WL, Jafree DJ, Bellier A, Werlein C, Kühnel MP, Boller E, Walker-Samuel S, Robertus JL, Long DA, Jacob J, Marussi S, Brown E, Holroyd N, Jonigk DD, Ackermann M, Lee PD. Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography. Nat Methods 2021; 18:1532-1541. [PMID: 34737453 PMCID: PMC8648561 DOI: 10.1038/s41592-021-01317-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)'s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- C L Walsh
- Department of Mechanical Engineering, University College London, London, UK.
- Centre for Advanced Biomedical Imaging, University College London, London, UK.
| | - P Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France.
| | - W L Wagner
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- German Lung Research Centre (DZL), Translational Lung Research Centre Heidelberg (TLRC), Heidelberg, Germany
| | - D J Jafree
- Developmental Biology and Cancer Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
- UCL MB/PhD Programme, Faculty of Medical Sciences, University College London, London, UK
| | - A Bellier
- French Alps Laboratory of Anatomy (LADAF), Grenoble Alpes University, Grenoble, France
| | - C Werlein
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - M P Kühnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - E Boller
- European Synchrotron Radiation Facility, Grenoble, France
| | - S Walker-Samuel
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - J L Robertus
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - D A Long
- Developmental Biology and Cancer Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - J Jacob
- Centre for Medical Image Computing, University College London, London, UK
- UCL Respiratory, University College London, London, UK
| | - S Marussi
- Department of Mechanical Engineering, University College London, London, UK
| | - E Brown
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - N Holroyd
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - D D Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany.
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
| | - M Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Pathology and Department of Molecular Pathology, Helios University Clinic Wuppertal, University of Witten-Herdecke, Wuppertal, Germany.
| | - P D Lee
- Department of Mechanical Engineering, University College London, London, UK.
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17
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Zhang L, Zhao H, Zhou Z, Jia M, Zhang L, Jiang J, Gao F. Improving spatial resolution with an edge-enhancement model for low-dose propagation-based X-ray phase-contrast computed tomography. OPTICS EXPRESS 2021; 29:37399-37417. [PMID: 34808812 DOI: 10.1364/oe.440664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Propagation-based X-ray phase-contrast computed tomography (PB-PCCT) has been increasingly popular for distinguishing low contrast tissues. Phase retrieval is an important step to quantitatively obtain the phase information before the tomographic reconstructions, while typical phase retrieval methods in PB-PCCT, such as homogenous transport of intensity equation (TIE-Hom), are essentially low-pass filters and thus improve the signal to noise ratio at the expense of the reduced spatial resolution of the reconstructed image. To improve the reconstructed spatial resolution, measured phase contrast projections with high edge enhancement and the phase projections retrieved by TIE-Hom were weighted summed and fed into an iterative tomographic algorithm within the framework of the adaptive steepest descent projections onto convex sets (ASD-POCS), which was employed for suppressing the image noise in low dose reconstructions because of the sparse-view scanning strategy or low exposure time for single phase contrast projection. The merging strategy decreases the accuracy of the linear model of PB-PCCT and would finally lead to the reconstruction failure in iterative reconstructions. Therefore, the additive median root prior is also introduced in the algorithm to partly increase the model accuracy. The reconstructed spatial resolution and noise performance can be flexibly balanced by a pair of antagonistic hyper-parameters. Validations were performed by the established phase-contrast Feldkamp-Davis-Kress, phase-retrieved Feldkamp-Davis-Kress, conventional ASD-POCS and the proposed enhanced ASD-POCS with a numerical phantom dataset and experimental biomaterial dataset. Simulation results show that the proposed algorithm outperforms the conventional ASD-POCS in spatial evaluation assessments such as root mean square error (a ratio of 9.78%), contrast to noise ratio (CNR) (a ratio of 7.46%), and also frequency evaluation assessments such as modulation transfer function (a ratio of 66.48% of MTF50% (50% MTF value)), noise power spectrum (a ratio of 35.25% of f50% (50% value of the Nyquist frequency)) and noise equivalent quanta (1-2 orders of magnitude at high frequencies). Experimental results again confirm the superiority of proposed strategy relative to the conventional one in terms of edge sharpness and CNR (an average increase of 67.35%).
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18
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Spier AB, Evans CE. Emerging and Established Histological Techniques for the Analysis of Thrombosis in COVID-19 Lungs. Front Cardiovasc Med 2021; 8:745906. [PMID: 34621804 PMCID: PMC8490625 DOI: 10.3389/fcvm.2021.745906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the potentially lethal disease that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients with COVID-19 have an increased risk of thrombosis, but the role of thrombosis in the pathogenesis and progression of severe COVID-19 remains unclear. A better understanding of the contribution of thrombosis to the development and progression of COVID-19 could lead to the development of novel COVID-19 treatments. For this reason, established and emerging histological techniques have recently been used to analyze COVID-19 lungs quantitatively and visually and in two and three dimensions. The gold standard and novel state-of the-art histological techniques that have been used to assess thrombosis in COVID-19 lungs are described in this Mini Review.
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Affiliation(s)
- Addie B Spier
- Department of Medicine, University of Illinois College of Medicine, Rockford, IL, United States
| | - Colin E Evans
- Department of Pediatrics, Lung and Vascular Biology Program, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States.,Department of Pediatrics, Division of Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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19
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Pierantoni M, Silva Barreto I, Hammerman M, Verhoeven L, Törnquist E, Novak V, Mokso R, Eliasson P, Isaksson H. A quality optimization approach to image Achilles tendon microstructure by phase-contrast enhanced synchrotron micro-tomography. Sci Rep 2021; 11:17313. [PMID: 34453067 PMCID: PMC8397765 DOI: 10.1038/s41598-021-96589-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022] Open
Abstract
Achilles tendons are mechanosensitive, and their complex hierarchical structure is in part the result of the mechanical stimulation conveyed by the muscles. To fully understand how their microstructure responds to mechanical loading a non-invasive approach for 3D high resolution imaging suitable for soft tissue is required. Here we propose a protocol that can capture the complex 3D organization of the Achilles tendon microstructure, using phase-contrast enhanced synchrotron micro-tomography (SR-PhC-μCT). We investigate the effects that sample preparation and imaging conditions have on the resulting image quality, by considering four types of sample preparations and two imaging setups (sub-micrometric and micrometric final pixel sizes). The image quality is assessed using four quantitative parameters. The results show that for studying tendon collagen fibers, conventional invasive sample preparations such as fixation and embedding are not necessary or advantageous. Instead, fresh frozen samples result in high-quality images that capture the complex 3D organization of tendon fibers in conditions as close as possible to natural. The comprehensive nature of this innovative study by SR-PhC-μCT breaks ground for future studies of soft complex biological tissue in 3D with high resolution in close to natural conditions, which could be further used for in situ characterization of how soft tissue responds to mechanical stimuli on a microscopic level.
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Affiliation(s)
- Maria Pierantoni
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden.
| | | | - Malin Hammerman
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Lissa Verhoeven
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
| | - Elin Törnquist
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
| | - Vladimir Novak
- Swiss Light Source, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Rajmund Mokso
- Swiss Light Source, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Division of Solid Mechanics, Lund University, Box 118, 221 00, Lund, Sweden
| | - Pernilla Eliasson
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Hanna Isaksson
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
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20
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Lung heterogeneity as a predictor for disease severity and response to therapy. CURRENT OPINION IN PHYSIOLOGY 2021. [DOI: 10.1016/j.cophys.2021.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Frequency and Significance of Pathologic Pulmonary Findings in Postmortem Examinations-A Single Center Experience before COVID-19. Diagnostics (Basel) 2021; 11:diagnostics11050894. [PMID: 34069794 PMCID: PMC8157293 DOI: 10.3390/diagnostics11050894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/15/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has shown the importance of postmortem investigation of deceased patients. For a correct interpretation of the pulmonary findings in this new era, it is, however, crucial to be familiar with pathologic pulmonary conditions observed in postmortem investigations in general. Adequate postmortem histopathological evaluation of the lungs may be affected by suboptimal gross work up, autolysis or poor fixation. Using a standardized preparation approach which consisted in instillation of 4% buffered formaldehyde through the large bronchi for proper fixation and preparing large frontal tissue sections of 1-2 cm thickness after at least 24 h fixation, we comprehensively analyzed postmortem pulmonary findings from consecutive adult autopsies of a two-year period before the occurrence of COVID-19 (2016-2017). In total, significant pathological findings were observed in 97/189 patients (51%), with 28 patients showing more than one pathologic condition. Acute pneumonia was diagnosed 33/128 times (26%), embolism 24 times (19%), primary pulmonary neoplasms 18 times (14%), organizing pneumonia and other fibrosing conditions 14 times (11%), pulmonary metastases 13 times (10%), diffuse alveolar damage 12 times (9%), severe emphysema 9 times (7%) and other pathologies, e.g., amyloidosis 5/128 times (4%). Pulmonary/cardiopulmonary disease was the cause of death in 60 patients (32%). Clinical and pathological diagnoses regarding lung findings correlated completely in 75 patients (40%). Autopsy led to confirmation of a clinically suspected pulmonary diagnosis in 57 patients (39%) and clarification of an unclear clinical lung finding in 16 patients (8%). Major discrepant findings regarding the lungs (N = 31; 16%) comprised cases with clinical suspicions that could not be confirmed or new findings not diagnosed intra vitam. A significant proportion of acute pneumonias (N = 8; 24% of all cases with this diagnosis; p = 0.011) was not diagnosed clinically. We confirmed the frequent occurrence of pulmonary pathologies in autopsies, including inflammatory and neoplastic lesions as the most frequent pathological findings. Acute pneumonia was an important cause for discrepancy between clinical and postmortem diagnostics.
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22
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Zaeck LM, Scheibner D, Sehl J, Müller M, Hoffmann D, Beer M, Abdelwhab EM, Mettenleiter TC, Breithaupt A, Finke S. Light Sheet Microscopy-Assisted 3D Analysis of SARS-CoV-2 Infection in the Respiratory Tract of the Ferret Model. Viruses 2021; 13:529. [PMID: 33807059 PMCID: PMC8004956 DOI: 10.3390/v13030529] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023] Open
Abstract
The visualization of viral pathogens in infected tissues is an invaluable tool to understand spatial virus distribution, localization, and cell tropism in vivo. Commonly, virus-infected tissues are analyzed using conventional immunohistochemistry in paraffin-embedded thin sections. Here, we demonstrate the utility of volumetric three-dimensional (3D) immunofluorescence imaging using tissue optical clearing and light sheet microscopy to investigate host-pathogen interactions of pandemic SARS-CoV-2 in ferrets at a mesoscopic scale. The superior spatial context of large, intact samples (>150 mm3) allowed detailed quantification of interrelated parameters like focus-to-focus distance or SARS-CoV-2-infected area, facilitating an in-depth description of SARS-CoV-2 infection foci. Accordingly, we could confirm a preferential infection of the ferret upper respiratory tract by SARS-CoV-2 and suggest clustering of infection foci in close proximity. Conclusively, we present a proof-of-concept study for investigating critically important respiratory pathogens in their spatial tissue morphology and demonstrate the first specific 3D visualization of SARS-CoV-2 infection.
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Affiliation(s)
- Luca M. Zaeck
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (L.M.Z.); (D.S.); (M.M.); (E.M.A.)
| | - David Scheibner
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (L.M.Z.); (D.S.); (M.M.); (E.M.A.)
| | - Julia Sehl
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (J.S.); (A.B.)
| | - Martin Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (L.M.Z.); (D.S.); (M.M.); (E.M.A.)
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (D.H.); (M.B.)
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (D.H.); (M.B.)
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (L.M.Z.); (D.S.); (M.M.); (E.M.A.)
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany;
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (J.S.); (A.B.)
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (L.M.Z.); (D.S.); (M.M.); (E.M.A.)
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23
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Boor P, Eichhorn P, Hartmann A, Lax SF, Märkl B, Menter T, Skok K, Slotta-Huspenina J, von Stillfried S, Tzankov A, Weirich G. [Practical aspects of COVID-19 autopsies]. DER PATHOLOGE 2021; 42:197-207. [PMID: 33625535 PMCID: PMC7903213 DOI: 10.1007/s00292-021-00925-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/28/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND The COVID-19 pandemic represents a so far unknown challenge for the medical community. Autopsies are important for studying this disease, but their safety was challenged at the beginning of the pandemic. OBJECTIVES To determine whether COVID-19 autopsies can be performed under existing legal conditions and which safety standards are required. MATERIALS AND METHODS The autopsy procedure undertaken in five institutions in Germany, Austria, and Switzerland is detailed with respect to legal and safety standards. RESULTS In all institutions the autopsies were performed in technically feasible rooms. The personal equipment consisted of functional clothing including a disposable gown and apron, a surgical cap, eye protection, FFP‑3 masks, and two pairs of gloves. In four institutions, complete autopsies were performed; in one institution the ultrasound-guided biopsy within the postmortal imaging and biopsy program. The latter does not allow the appreciation of gross organ pathology; however, it is able to retrieve standardized biopsies for diagnostic and research purposes. Several scientific articles in highly ranked journals resulted from these autopsies and allowed deep insights into organ damage and conclusions to better understand the pathomechanisms. Viral RNA was frequently detectable in the COVID-19 deceased, but the issue of infectivity remains unresolved and it is questionable if Ct values are greater than 30. CONCLUSIONS With appropriate safeguards, autopsies of people who have died from COVID-19 can be performed safely and are highly relevant to medical research.
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Affiliation(s)
- Peter Boor
- Institut für Pathologie, Universitätsklinikum Aachen, RTWH Aachen, Aachen, Deutschland
| | - Philip Eichhorn
- Institut für Pathologie, Universitätsklinikum Erlangen, Erlangen, Deutschland
| | - Arndt Hartmann
- Institut für Pathologie, Universitätsklinikum Erlangen, Erlangen, Deutschland
| | - Sigurd F Lax
- Institut für Pathologie, Landeskrankenhaus Graz II, Akademisches Lehrkrankenhaus der Medizinischen Universität Graz, Graz, Österreich
- Medizinische Fakultät, Johannes-Kepler-Universität Linz, Linz, Österreich
| | - Bruno Märkl
- Allgemeine und Spezielle Pathologie, Medizinische Fakultät, Universität Augsburg, Augsburg, Deutschland.
- Institut für Pathologie und Molekulare Diagnostik, Universitätsklinikum Augsburg, Stenglinstr. 2, 86156, Augsburg, Deutschland.
| | - Thomas Menter
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Universität Basel, Basel, Schweiz
| | - Kristijan Skok
- Institut für Pathologie, Landeskrankenhaus Graz II, Akademisches Lehrkrankenhaus der Medizinischen Universität Graz, Graz, Österreich
| | - Julia Slotta-Huspenina
- Institut für Pathologie und pathologische Anatomie, Technische Universität München, München, Deutschland
| | - Saskia von Stillfried
- Institut für Pathologie, Universitätsklinikum Aachen, RTWH Aachen, Aachen, Deutschland
| | - Alexandar Tzankov
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Universität Basel, Basel, Schweiz
| | - Gregor Weirich
- Institut für Pathologie und pathologische Anatomie, Technische Universität München, München, Deutschland
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24
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Walsh C, Tafforeau P, Wagner WL, Jafree DJ, Bellier A, Werlein C, Kühnel MP, Boller E, Walker-Samuel S, Robertus JL, Long DA, Jacob J, Marussi S, Brown E, Holroyd N, Jonigk DD, Ackermann M, Lee PD. Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429481. [PMID: 33564772 PMCID: PMC7872374 DOI: 10.1101/2021.02.03.429481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facility's Extremely Brilliant Source: the world's first high-energy 4 th generation X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organ's structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organ's individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.
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Affiliation(s)
- C Walsh
- Centre for Advanced Biomedical Imaging, University College London, U.K
| | - P Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France
| | - Willi L Wagner
- Dept of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany Translational Lung Research Centre Heidelberg (TLRC), German Lung Research Centre (DZL), Heidelberg, Germany
| | - D J Jafree
- Developmental Biology and Cancer Programme, Great Ormond Street Institute of Child Health, University College London, UK
- UCL MB/PhD Programme, Faculty of Medical Sciences, University College London, UK
| | - A Bellier
- French Alps Laboratory of Anatomy (LADAF), Grenoble Alpes University, Grenoble, France
| | - C Werlein
- Institute of Pathology, Hannover Medical School, Hannover, Germany (Carl-Neuberg-Straße 1, 30625 Hannover)
| | - M P Kühnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany (Carl-Neuberg-Straße 1, 30625 Hannover)
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH)
| | - E Boller
- European Synchrotron Radiation Facility, Grenoble, France
| | - S Walker-Samuel
- Centre for Advanced Biomedical Imaging, University College London, U.K
| | - J L Robertus
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - D A Long
- Developmental Biology and Cancer Programme, Great Ormond Street Institute of Child Health, University College London, UK
| | - J Jacob
- Centre for Medical Image Computing, University College London, London, UK
- Department of Radiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - S Marussi
- Department of Mechanical Engineering University College London, U.K
| | - E Brown
- Centre for Advanced Biomedical Imaging, University College London, U.K
| | - N Holroyd
- Centre for Advanced Biomedical Imaging, University College London, U.K
| | - D D Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany (Carl-Neuberg-Straße 1, 30625 Hannover)
- Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH)
| | - M Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz
| | - P D Lee
- Department of Mechanical Engineering University College London, U.K
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25
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New Look at RSV Infection: Tissue Clearing and 3D Imaging of the Entire Mouse Lung at Cellular Resolution. Viruses 2021; 13:v13020201. [PMID: 33525646 PMCID: PMC7912480 DOI: 10.3390/v13020201] [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: 12/18/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Respiratory Syncytial Virus (RSV) is the major cause of severe acute respiratory tract illness in young children worldwide and a main pathogen for the elderly and immune-compromised people. In the absence of vaccines or effective treatments, a better characterization of the pathogenesis of RSV infection is required. To date, the pathophysiology of the disease and its diagnosis has mostly relied on chest X-ray and genome detection in nasopharyngeal swabs. The development of new imaging approaches is instrumental to further the description of RSV spread, virus-host interactions and related acute respiratory disease, at the level of the entire lung. METHODS By combining tissue clearing, 3D microscopy and image processing, we developed a novel visualization tool of RSV infection in undissected mouse lungs. RESULTS Whole tissue analysis allowed the identification of infected cell subtypes, based on both morphological traits and position within the cellular network. Furthermore, 3D imaging was also valuable to detect the cytoplasmic viral factories, also called inclusion bodies, a hallmark of RSV infection. CONCLUSIONS Whole lung clearing and 3D deep imaging represents an unprecedented visualization method of infected lungs to allow insight into RSV pathophysiology and improve the 2D histology analyses.
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Eckermann M, Frohn J, Reichardt M, Osterhoff M, Sprung M, Westermeier F, Tzankov A, Werlein C, Kühnel M, Jonigk D, Salditt T. 3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography. eLife 2020; 9:e60408. [PMID: 32815517 PMCID: PMC7473770 DOI: 10.7554/elife.60408] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
| | - Jasper Frohn
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Marius Reichardt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | | | | | - Alexandar Tzankov
- Institut für Medizinische Genetik und Pathologie, Universitätsspital BaselBaselSwitzerland
| | - Christopher Werlein
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Mark Kühnel
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
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