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Francis DV, Charles AS, Jacob TM, Ruban A, Premkumar PS, Rabi S. Virtual microscopy as a teaching-learning tool for histology in a competency-based medical curriculum. Med J Armed Forces India 2023; 79:S156-S164. [PMID: 38144628 PMCID: PMC10746824 DOI: 10.1016/j.mjafi.2022.02.002] [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: 12/06/2021] [Accepted: 02/03/2022] [Indexed: 11/15/2022] Open
Abstract
Background Histology forms an important component of first-year medical education. Unfortunately, it is limited to the practical laboratory due to the need for a microscope and good quality slides. Virtual microscopy is a recent advancement, which uses computers as an alternative to microscopes. The aim of the study was to compare virtual microscopy (VM)-based practical classes with traditional microscopy (TM)-based practical classes for two cohorts of first-year medical students, by comparing learning achieved using two different test scores as well as a qualitative assessment of student and faculty perspectives regarding the feasibility and usefulness of VM. Methods Each cohort of students was divided into two equal batches and each batch underwent eight histology modules of which, four utilised traditional microscopes and four utilised virtual microscopes. Quantitative analysis was performed using a theory test (which assessed preparation, theory knowledge and understanding) as well as a spotter test (which assessed identification skills, reasoning, and recall). Qualitative analysis was performed using a structured questionnaire and focus group discussions. Results Modules using VM were better when compared with those using TM, showing statistically significant and better grades. Qualitative analysis performed, yielded important information as to how this technology can serve as a good adjunct to traditional histology classes in the competency-based curriculum by increasing student interest, enabling self-study, and reducing students dependence on the tutor. Conclusions VM forms a good adjunct as well as a standalone modality of learning to TM, as it improves accessibility to slides and promotes self-learning.
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Affiliation(s)
| | - Aby S. Charles
- Assistant Professor (Anatomy), Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Anand Ruban
- Associate Professor (Biochemistry), Christian Medical College, Vellore, Tamil Nadu, India
| | - Prasanna S. Premkumar
- Associate Professor (Biostatistics), Christian Medical College, Vellore, Tamil Nadu, India
| | - Suganthy Rabi
- Professor (Anatomy), Christian Medical College, Vellore, Tamil Nadu, India
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2
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Poger D, Yen L, Braet F. Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management. Histochem Cell Biol 2023; 160:169-192. [PMID: 37052655 PMCID: PMC10492738 DOI: 10.1007/s00418-023-02191-8] [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] [Accepted: 03/21/2023] [Indexed: 04/14/2023]
Abstract
The second decade of the twenty-first century witnessed a new challenge in the handling of microscopy data. Big data, data deluge, large data, data compliance, data analytics, data integrity, data interoperability, data retention and data lifecycle are terms that have introduced themselves to the electron microscopy sciences. This is largely attributed to the booming development of new microscopy hardware tools. As a result, large digital image files with an average size of one terabyte within one single acquisition session is not uncommon nowadays, especially in the field of cryogenic electron microscopy. This brings along numerous challenges in data transfer, compute and management. In this review, we will discuss in detail the current state of international knowledge on big data in contemporary electron microscopy and how big data can be transferred, computed and managed efficiently and sustainably. Workflows, solutions, approaches and suggestions will be provided, with the example of the latest experiences in Australia. Finally, important principles such as data integrity, data lifetime and the FAIR and CARE principles will be considered.
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Affiliation(s)
- David Poger
- Microscopy Australia, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Lisa Yen
- Microscopy Australia, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Filip Braet
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Medical Sciences (Molecular and Cellular Biomedicine), The University of Sydney, Sydney, NSW, 2006, Australia
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3
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Scheele CLGJ, Herrmann D, Yamashita E, Celso CL, Jenne CN, Oktay MH, Entenberg D, Friedl P, Weigert R, Meijboom FLB, Ishii M, Timpson P, van Rheenen J. Multiphoton intravital microscopy of rodents. NATURE REVIEWS. METHODS PRIMERS 2022; 2:89. [PMID: 37621948 PMCID: PMC10449057 DOI: 10.1038/s43586-022-00168-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/12/2022] [Indexed: 08/26/2023]
Abstract
Tissues are heterogeneous with respect to cellular and non-cellular components and in the dynamic interactions between these elements. To study the behaviour and fate of individual cells in these complex tissues, intravital microscopy (IVM) techniques such as multiphoton microscopy have been developed to visualize intact and live tissues at cellular and subcellular resolution. IVM experiments have revealed unique insights into the dynamic interplay between different cell types and their local environment, and how this drives morphogenesis and homeostasis of tissues, inflammation and immune responses, and the development of various diseases. This Primer introduces researchers to IVM technologies, with a focus on multiphoton microscopy of rodents, and discusses challenges, solutions and practical tips on how to perform IVM. To illustrate the unique potential of IVM, several examples of results are highlighted. Finally, we discuss data reproducibility and how to handle big imaging data sets.
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Affiliation(s)
- Colinda L. G. J. Scheele
- Laboratory for Intravital Imaging and Dynamics of Tumor Progression, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - David Herrmann
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Department, Sydney, New South Wales, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Erika Yamashita
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Cristina Lo Celso
- Department of Life Sciences and Centre for Hematology, Imperial College London, London, UK
- Sir Francis Crick Institute, London, UK
| | - Craig N. Jenne
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Maja H. Oktay
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
- Integrated Imaging Program, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
| | - David Entenberg
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
- Integrated Imaging Program, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
- David H. Koch Center for Applied Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roberto Weigert
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Franck L. B. Meijboom
- Department of Population Health Sciences, Sustainable Animal Stewardship, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Faculty of Humanities, Ethics Institute, Utrecht University, Utrecht, Netherlands
| | - Masaru Ishii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Paul Timpson
- Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Department, Sydney, New South Wales, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jacco van Rheenen
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
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4
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Schaefer IM, Hemming ML, Lundberg MZ, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi SP, George S, Morgan JA, Bertagnolli MM, Sicinska ET, Chu C, Zheng S, Mariño-Enríquez A, Hornick JL, Raut CP, Ou WB, Demetri GD, Saka SK, Fletcher JA. Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST. Br J Cancer 2022; 127:2072-2085. [PMID: 36175617 PMCID: PMC9681737 DOI: 10.1038/s41416-022-01990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Advanced gastrointestinal stromal tumour (GIST) is characterised by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximising response to therapeutic CDK4/6 inhibition. METHODS Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples. The impact of inhibitors of CDK2, CDK4 and CDK2/4/6 was determined through cell proliferation and protein detection assays. CDK-inhibitor resistance mechanisms were characterised in GIST cell lines after long-term exposure. RESULTS We identify recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways in clinical GIST samples. Therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation. Moreover, RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) are mechanisms of acquired CDK-inhibitor resistance in GIST. CONCLUSIONS These studies establish the biological rationale for CDK2 and CDK4/6 co-inhibition as a therapeutic strategy in patients with advanced GIST, including metastatic GIST progressing on tyrosine kinase inhibitors.
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Affiliation(s)
- Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Meijun Z Lundberg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew P Serrata
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ninning Liu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Suzanne George
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Jeffrey A Morgan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Monica M Bertagnolli
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ewa T Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shanshan Zheng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Adrian Mariño-Enríquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Chandrajit P Raut
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wen-Bin Ou
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - George D Demetri
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jonathan A Fletcher
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
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5
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Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. Nat Methods 2022; 19:1393-1402. [PMID: 36216958 PMCID: PMC9636025 DOI: 10.1038/s41592-022-01604-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/10/2022] [Indexed: 11/21/2022]
Abstract
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing. Light-Seq uses light-directed DNA barcoding in fixed cells and tissues for multiplexed spatial indexing and subsequent next generation sequencing. This approach blends spatial and omics information to enable analysis of rare cell types in complex tissues.
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6
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Schmidt C, Hanne J, Moore J, Meesters C, Ferrando-May E, Weidtkamp-Peters S. Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey. F1000Res 2022; 11:638. [PMID: 36405555 PMCID: PMC9641114 DOI: 10.12688/f1000research.121714.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods: An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results: The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusion: The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.
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Affiliation(s)
- Christian Schmidt
- Enabling Technology, German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany,Bioimaging Center, University of Konstanz, Konstanz, Germany,
| | - Janina Hanne
- German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany,
| | - Josh Moore
- German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany,Open Microscopy Environment Consortium, University of Dundee, Dundee, UK
| | - Christian Meesters
- High Performance Computing, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Elisa Ferrando-May
- Enabling Technology, German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany,Bioimaging Center, University of Konstanz, Konstanz, Germany,German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany
| | - Stefanie Weidtkamp-Peters
- German BioImaging - Society for Microscopy and Image Analysis e.V., Konstanz, Germany,Center for Advanced Imaging, Heinrich Heine University Dusseldorf, Dusseldorf, Germany
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7
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Westerling-Bui AD, Fast EM, Soare TW, Venkatachalan S, DeRan M, Fanelli AB, Kyrychenko S, Hoang H, Corriea GM, Zhang W, Yu M, Daniels M, Malojcic G, Pan-Zhou XR, Ledeboer MW, Harmange JC, Emani M, Tibbitts TT, Reilly JF, Mundel P. Transplanted organoids empower human preclinical assessment of drug candidate for the clinic. SCIENCE ADVANCES 2022; 8:eabj5633. [PMID: 35857479 PMCID: PMC9258952 DOI: 10.1126/sciadv.abj5633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pharmacodynamic (PD) studies are an essential component of preclinical drug discovery. Current approaches for PD studies, including the analysis of novel kidney disease targeting therapeutic agents, are limited to animal models with unclear translatability to the human condition. To address this challenge, we developed a novel approach for PD studies using transplanted, perfused human kidney organoids. We performed pharmacokinetic (PK) studies with GFB-887, an investigational new drug now in phase 2 trials. Orally dosed GFB-887 to athymic rats that had undergone organoid transplantation resulted in measurable drug exposure in transplanted organoids. We established the efficacy of orally dosed GFB-887 in PD studies, where quantitative analysis showed significant protection of kidney filter cells in human organoids and endogenous rat host kidneys. This widely applicable approach demonstrates feasibility of using transplanted human organoids in preclinical PD studies with an investigational new drug, empowering organoids to revolutionize drug discovery.
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Affiliation(s)
- Amy D. Westerling-Bui
- Goldfinch Bio Inc., Cambridge, MA 02142, USA
- Corresponding author. (A.D.W.-B.); (P.M.)
| | | | | | | | | | | | | | - Hien Hoang
- Goldfinch Bio Inc., Cambridge, MA 02142, USA
| | | | - Wei Zhang
- Goldfinch Bio Inc., Cambridge, MA 02142, USA
| | - Maolin Yu
- Goldfinch Bio Inc., Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | | | | - Peter Mundel
- Goldfinch Bio Inc., Cambridge, MA 02142, USA
- Corresponding author. (A.D.W.-B.); (P.M.)
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8
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Guo H, Stamper EL, Sato-Carlton A, Shimazoe MA, Li X, Zhang L, Stevens L, Tam KCJ, Dernburg AF, Carlton PM. Phosphoregulation of DSB-1 mediates control of meiotic double-strand break activity. eLife 2022; 11:77956. [PMID: 35758641 PMCID: PMC9278955 DOI: 10.7554/elife.77956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/23/2022] [Indexed: 12/28/2022] Open
Abstract
In the first meiotic cell division, proper segregation of chromosomes in most organisms depends on chiasmata, exchanges of continuity between homologous chromosomes that originate from the repair of programmed double-strand breaks (DSBs) catalyzed by the Spo11 endonuclease. Since DSBs can lead to irreparable damage in germ cells, while chromosomes lacking DSBs also lack chiasmata, the number of DSBs must be carefully regulated to be neither too high nor too low. Here, we show that in Caenorhabditis elegans, meiotic DSB levels are controlled by the phosphoregulation of DSB-1, a homolog of the yeast Spo11 cofactor Rec114, by the opposing activities of PP4PPH-4.1 phosphatase and ATRATL-1 kinase. Increased DSB-1 phosphorylation in pph-4.1 mutants correlates with reduction in DSB formation, while prevention of DSB-1 phosphorylation drastically increases the number of meiotic DSBs both in pph-4.1 mutants and in the wild-type background. C. elegans and its close relatives also possess a diverged paralog of DSB-1, called DSB-2, and loss of dsb-2 is known to reduce DSB formation in oocytes with increasing age. We show that the proportion of the phosphorylated, and thus inactivated, form of DSB-1 increases with age and upon loss of DSB-2, while non-phosphorylatable DSB-1 rescues the age-dependent decrease in DSBs in dsb-2 mutants. These results suggest that DSB-2 evolved in part to compensate for the inactivation of DSB-1 through phosphorylation, to maintain levels of DSBs in older animals. Our work shows that PP4PPH-4.1, ATRATL-1, and DSB-2 act in concert with DSB-1 to promote optimal DSB levels throughout the reproductive lifespan.
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Affiliation(s)
- Heyun Guo
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Ericca L Stamper
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Aya Sato-Carlton
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Masa A Shimazoe
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan.,Department of Science, Kyoto University, Kyoto, Japan
| | - Xuan Li
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Liangyu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - K C Jacky Tam
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan
| | - Abby F Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,California Institute for Quantitative Biosciences, Berkeley, United States.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Peter M Carlton
- Graduate School of Biostudies, Kyoto University, Yoshidakonoe, Sakyo, Kyoto, Japan.,Radiation Biology Center, Kyoto University, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
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9
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Adult mouse and human organoids derived from thyroid follicular cells and modeling of Graves' hyperthyroidism. Proc Natl Acad Sci U S A 2021; 118:2117017118. [PMID: 34916298 PMCID: PMC8713972 DOI: 10.1073/pnas.2117017118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 12/16/2022] Open
Abstract
The thyroid is essential for maintaining systemic homeostasis by regulating thyroid hormone concentrations in the bloodstream. This study describes an organoid-based model system to study mouse and human thyroid biology. Moreover, the study explores the potential of human organoids for modeling autoimmune disease, the anti-TSH receptor (TSHR) antibody-driven Graves’ hyperthyroidism. The thyroid maintains systemic homeostasis by regulating serum thyroid hormone concentrations. Here we report the establishment of three-dimensional (3D) organoids from adult thyroid tissue representing murine and human thyroid follicular cells (TFCs). The TFC organoids (TFCOs) harbor the complete machinery of hormone production as visualized by the presence of colloid in the lumen and by the presence of essential transporters and enzymes in the polarized epithelial cells that surround a central lumen. Both the established murine as human thyroid organoids express canonical thyroid markers PAX8 and NKX2.1, while the thyroid hormone precursor thyroglobulin is expressed at comparable levels to tissue. Single-cell RNA sequencing and transmission electron microscopy confirm that TFCOs phenocopy primary thyroid tissue. Thyroid hormones are readily detectable in conditioned medium of human TFCOs. We show clinically relevant responses (increased proliferation and hormone secretion) of human TFCOs toward a panel of Graves’ disease patient sera, demonstrating that organoids can model human autoimmune disease.
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10
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Badmos H, Cobbe N, Campbell A, Jackson R, Bennett D. Drosophila USP22/nonstop polarizes the actin cytoskeleton during collective border cell migration. J Cell Biol 2021; 220:212101. [PMID: 33988679 PMCID: PMC8129793 DOI: 10.1083/jcb.202007005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 02/06/2021] [Accepted: 04/23/2021] [Indexed: 01/04/2023] Open
Abstract
Polarization of the actin cytoskeleton is vital for the collective migration of cells in vivo. During invasive border cell migration in Drosophila, actin polarization is directly controlled by the Hippo signaling complex, which resides at contacts between border cells in the cluster. Here, we identify, in a genetic screen for deubiquitinating enzymes involved in border cell migration, an essential role for nonstop/USP22 in the expression of Hippo pathway components expanded and merlin. Loss of nonstop function consequently leads to a redistribution of F-actin and the polarity determinant Crumbs, loss of polarized actin protrusions, and tumbling of the border cell cluster. Nonstop is a component of the Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional coactivator complex, but SAGA’s histone acetyltransferase module, which does not bind to expanded or merlin, is dispensable for migration. Taken together, our results uncover novel roles for SAGA-independent nonstop/USP22 in collective cell migration, which may help guide studies in other systems where USP22 is necessary for cell motility and invasion.
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Affiliation(s)
- Hammed Badmos
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Neville Cobbe
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Amy Campbell
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Richard Jackson
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Daimark Bennett
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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11
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Chen J, Lippo L, Labella R, Tan SL, Marsden BD, Dustin ML, Ramasamy SK, Kusumbe AP. Decreased blood vessel density and endothelial cell subset dynamics during ageing of the endocrine system. EMBO J 2021; 40:e105242. [PMID: 33215738 PMCID: PMC7780152 DOI: 10.15252/embj.2020105242] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
Age-associated alterations of the hormone-secreting endocrine system cause organ dysfunction and disease states. However, the cell biology of endocrine tissue ageing remains poorly understood. Here, we perform comparative 3D imaging to understand age-related perturbations of the endothelial cell (EC) compartment in endocrine glands. Datasets of a wide range of markers highlight a decline in capillary and artery numbers, but not of perivascular cells in pancreas, testis and thyroid gland, with age in mice and humans. Further, angiogenesis and β-cell expansion in the pancreas are coupled by a distinct age-dependent subset of ECs. While this EC subpopulation supports pancreatic β cells, it declines during ageing concomitant with increased expression of the gap junction protein Gja1. EC-specific ablation of Gja1 restores β-cell expansion in the aged pancreas. These results provide a proof of concept for understanding age-related vascular changes and imply that therapeutic targeting of blood vessels may restore aged endocrine tissue function. This comprehensive data atlas offers over > 1,000 multicolour volumes for exploration and research in endocrinology, ageing, matrix and vascular biology.
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Affiliation(s)
- Junyu Chen
- Tissue and Tumor Microenvironments GroupThe Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
- Department of ProsthodonticsState Key Laboratory of Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Luciana Lippo
- Tissue and Tumor Microenvironments GroupThe Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Rossella Labella
- Tissue and Tumor Microenvironments GroupThe Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Sin Lih Tan
- Tissue and Tumor Microenvironments GroupThe Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Brian D Marsden
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
- Structural Genomics ConsortiumNDMUniversity of OxfordOxfordUK
| | - Michael L Dustin
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Saravana K Ramasamy
- Institute of Clinical SciencesImperial College LondonLondonUK
- MRC London Institute of Medical SciencesImperial College LondonLondonUK
| | - Anjali P Kusumbe
- Tissue and Tumor Microenvironments GroupThe Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
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12
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Saunders DC, Messmer J, Kusmartseva I, Beery ML, Yang M, Atkinson MA, Powers AC, Cartailler JP, Brissova M. Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease. PATTERNS 2020; 1:100120. [PMID: 33294866 PMCID: PMC7691395 DOI: 10.1016/j.patter.2020.100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/31/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022]
Abstract
Human tissue phenotyping generates complex spatial information from numerous imaging modalities, yet images typically become static figures for publication, and original data and metadata are rarely available. While comprehensive image maps exist for some organs, most resources have limited support for multiplexed imaging or have non-intuitive user interfaces. Therefore, we built a Pancreatlas resource that integrates several technologies into a unique interface, allowing users to access richly annotated web pages, drill down to individual images, and deeply explore data online. The current version of Pancreatlas contains over 800 unique images acquired by whole-slide scanning, confocal microscopy, and imaging mass cytometry, and is available at https://www.pancreatlas.org. To create this human pancreas-specific biological imaging resource, we developed a React-based web application and Python-based application programming interface, collectively called Flexible Framework for Integrating and Navigating Data (FFIND), which can be adapted beyond Pancreatlas to meet countless imaging or other structured data-management needs. Human organ phenotyping databases benefit from intuitive user interfaces Pancreatlas resource enables exploration of bioimaging data from human pancreas The front-end framework of Pancreatlas, FFIND, is modular and easily adaptable FFIND provides structured data-exploration capabilities across countless domains
Scientists need cost-effective yet fully featured database solutions that facilitate large dataset sharing in a structured and easily digestible manner. Flexible Framework for Integrating and Navigating Data (FFIND) is a data-agnostic web application that is designed to easily connect existing databases with data-browsing clients. We used FFIND to build Pancreatlas, an online imaging resource containing datasets linking imaging data with clinical data to facilitate advances in the understanding of diabetes, pancreatitis, and pancreatic cancer. FFIND architecture, which is available as open-source software, can be easily adapted to meet other field- or project-specific needs; we hope it will help data scientists reach a broader audience by reducing the development life cycle and providing familiar interactivity in communicating data and underlying stories.
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Affiliation(s)
- Diane C Saunders
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James Messmer
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Irina Kusmartseva
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, USA
| | - Maria L Beery
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, USA
| | - Mingder Yang
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, USA.,Department of Pediatrics, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,VA Tennessee Valley Healthcare System, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Jean-Philippe Cartailler
- Creative Data Solutions Shared Resource, Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Marcela Brissova
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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13
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Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ, van Donselaar E, Riesebosch S, Kuijpers HJH, Schipper D, van de Wetering WJ, de Graaf M, Koopmans M, Cuppen E, Peters PJ, Haagmans BL, Clevers H. SARS-CoV-2 productively infects human gut enterocytes. Science 2020; 369:50-54. [PMID: 32358202 DOI: 10.1101/2020.04.25.060350] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 05/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.
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Affiliation(s)
- Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Jelte van der Vaart
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - J Paul van Schayck
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Q Duimel
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Elly van Donselaar
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Helma J H Kuijpers
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Willine J van de Wetering
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marion Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Utrecht, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands.
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14
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Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ, van Donselaar E, Riesebosch S, Kuijpers HJH, Schipper D, van de Wetering WJ, de Graaf M, Koopmans M, Cuppen E, Peters PJ, Haagmans BL, Clevers H. SARS-CoV-2 productively infects human gut enterocytes. Science 2020; 369:50-54. [PMID: 32358202 PMCID: PMC7199907 DOI: 10.1126/science.abc1669] [Citation(s) in RCA: 1199] [Impact Index Per Article: 299.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.
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Affiliation(s)
- Mart M Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Jelte van der Vaart
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Jens Puschhof
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - J Paul van Schayck
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Q Duimel
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Elly van Donselaar
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Helma J H Kuijpers
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Willine J van de Wetering
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marion Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Utrecht, Netherlands
- Hartwig Medical Foundation, Amsterdam, Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Netherlands.
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15
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González G, Evans CL. Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets. Bioessays 2019; 41:e1900004. [PMID: 31094000 PMCID: PMC6538271 DOI: 10.1002/bies.201900004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/18/2019] [Indexed: 12/13/2022]
Abstract
Here, a streamlined, scalable, laboratory approach is discussed that enables medium-to-large dataset analysis. The presented approach combines data management, artificial intelligence, containerization, cluster orchestration, and quality control in a unified analytic pipeline. The unique combination of these individual building blocks creates a new and powerful analysis approach that can readily be applied to medium-to-large datasets by researchers to accelerate the pace of research. The proposed framework is applied to a project that counts the number of plasmonic nanoparticles bound to peripheral blood mononuclear cells in dark-field microscopy images. By using the techniques presented in this article, the images are automatically processed overnight, without user interaction, streamlining the path from experiment to conclusions.
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Affiliation(s)
- Germán González
- PNP Research Corporation, Drury, MA. 01343
- Sierra Research S.L.U. Avda Costa Blanca 132. Alicante. Spain. 03540
| | - Conor L. Evans
- Wellman Center for Photomedicine, Harvard Medical School, Massachusetts General Hospital, CNY149-3, 13th St, Charlestown, MA 02129
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
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16
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Besson S, Leigh R, Linkert M, Allan C, Burel JM, Carroll M, Gault D, Gozim R, Li S, Lindner D, Moore J, Moore W, Walczysko P, Wong F, Swedlow JR. Bringing Open Data to Whole Slide Imaging. DIGITAL PATHOLOGY : 15TH EUROPEAN CONGRESS, ECDP 2019, WARWICK, UK, APRIL 10-13, 2019 : PROCEEDINGS. EUROPEAN CONGRESS ON DIGITAL PATHOLOGY (15TH : 2019 : WARWICK, ENGLAND) 2019; 2019:3-10. [PMID: 31579322 DOI: 10.1007/978-3-030-23937-4_1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Faced with the need to support a growing number of whole slide imaging (WSI) file formats, our team has extended a long-standing community file format (OME-TIFF) for use in digital pathology. The format makes use of the core TIFF specification to store multi-resolution (or "pyramidal") representations of a single slide in a flexible, performant manner. Here we describe the structure of this format, its performance characteristics, as well as an open-source library support for reading and writing pyramidal OME-TIFFs.
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Affiliation(s)
- Sébastien Besson
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Roger Leigh
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Melissa Linkert
- Glencoe Software, Inc, 800 5th Ave, #101-259, Seattle, WA 98104, USA
| | - Chris Allan
- Glencoe Software, Inc, 800 5th Ave, #101-259, Seattle, WA 98104, USA
| | - Jean-Marie Burel
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Mark Carroll
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - David Gault
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Riad Gozim
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Simon Li
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Dominik Lindner
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Josh Moore
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Will Moore
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Petr Walczysko
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Frances Wong
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Jason R Swedlow
- Dept of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.,Glencoe Software, Inc, 800 5th Ave, #101-259, Seattle, WA 98104, USA
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17
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Tonsfeldt KJ, Schoeller EL, Brusman LE, Cui LJ, Lee J, Mellon PL. The Contribution of the Circadian Gene Bmal1 to Female Fertility and the Generation of the Preovulatory Luteinizing Hormone Surge. J Endocr Soc 2019; 3:716-733. [PMID: 30906911 PMCID: PMC6425515 DOI: 10.1210/js.2018-00228] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/08/2019] [Indexed: 12/19/2022] Open
Abstract
In rodents, the preovulatory LH surge is temporally gated, but the timing cue is unknown. Estrogen primes neurons in the anteroventral periventricular nucleus (AVPV) to secrete kisspeptin, which potently activates GnRH neurons to release GnRH, eliciting a surge of LH to induce ovulation. Deletion of the circadian clock gene Bmal1 results in infertility. Previous studies have found that Bmal1 knockout (KO) females do not display an LH surge at any time of day. We sought to determine whether neuroendocrine disruption contributes to the absence of the LH surge. Because Kiss1 expression in the AVPV is critical for regulating ovulation, we hypothesized that this population is disrupted in Bmal1 KO females. However, we found an appropriate rise in AVPV Kiss1 and Fos mRNA at the time of lights out in ovariectomized estrogen-treated animals, despite the absence of a measureable increase in LH. Furthermore, Bmal1 KO females have significantly increased LH response to kiss-10 administration, although the LH response to GnRH was unchanged. We then created Kiss1- and GnRH-specific Bmal1 KO mice to examine whether Bmal1 expression is necessary within either kisspeptin or GnRH neurons. We detected no significant differences in any measured reproductive parameter. Our results indicate that disruption of the hypothalamic regulation of fertility in the Bmal1 KO females is not dependent on endogenous clocks within either the GnRH or kisspeptin neurons.
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Affiliation(s)
- Karen J Tonsfeldt
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, California
| | - Erica L Schoeller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, California
| | - Liza E Brusman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, California
| | - Laura J Cui
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, California
| | - Jinkwon Lee
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, California
| | - Pamela L Mellon
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California San Diego, La Jolla, California
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18
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Abstract
Data science can be incorporated into every stage of a scientific study. Here we describe how data science can be used to generate hypotheses, to design experiments, to perform experiments, and to analyse data. We also present our vision for how data science techniques will be an integral part of the laboratory of the future.
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Affiliation(s)
- Daphne Ezer
- Alan Turing InstituteLondonUnited Kingdom
- Department of StatisticsUniversity of WarwickCoventryUnited Kingdom
| | - Kirstie Whitaker
- Alan Turing InstituteLondonUnited Kingdom
- Department of PsychiatryUniversity of CambridgeCambridgeUnited Kingdom
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19
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O'Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore WJ, Stenau E, Swedlow JR, Vuong J, Procter JB. Visualization of Biomedical Data. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013424] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.
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Affiliation(s)
- Seán I. O'Donoghue
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Benedetta Frida Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Susan J. Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Aaron E. Darling
- The ithree Institute, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - James M. Hogan
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane QLD, 4000, Australia
| | - Sandeep Kaur
- School of Computer Science and Engineering, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Lena Maier-Hein
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Davis J. McCarthy
- European Bioinformatics Institute (EBI), European Molecular Biology Laboratory (EMBL), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- St. Vincent's Institute of Medical Research, Fitzroy VIC 3065, Australia
| | - William J. Moore
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Esther Stenau
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jason R. Swedlow
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Jenny Vuong
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
| | - James B. Procter
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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20
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Nakhod KV, Rusanov AL, Luzgina ED, Druzhilovskiy DS, Luzgina NG, Lisitsa AV. [Quality control study of engineered skin tissue]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:10-15. [PMID: 29460829 DOI: 10.18097/pbmc20186401010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OMERO service was used to annotate the cell line HaCaT microscope images by two independent expert groups. The images were obtained in the course of developing tissue-engineered epithelium which consisted of several layers of the keratinocytes. Evaluation of expert opinions was performed by calculation of specificity, sensitivity and accuracy. The best convergence of opinions (91%) was achieved for the confluence of the cell monolayers. Accuracy 70% was observed in determining the extent of cell differentiation after 10 days of incubation. The paper illustrates the usefulness of OMERO service for dynamic cross-validation of quality in the development and standardization of cell preparations.
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Affiliation(s)
- K V Nakhod
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A L Rusanov
- Research and Manufacturing Association "Perspectiva", Novosibirsk, Russia
| | - E D Luzgina
- Research and Manufacturing Association "Perspectiva", Novosibirsk, Russia
| | | | - N G Luzgina
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
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Sato-Carlton A, Nakamura-Tabuchi C, Chartrand SK, Uchino T, Carlton PM. Phosphorylation of the synaptonemal complex protein SYP-1 promotes meiotic chromosome segregation. J Cell Biol 2017; 217:555-570. [PMID: 29222184 PMCID: PMC5800814 DOI: 10.1083/jcb.201707161] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/12/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022] Open
Abstract
Chromosomes that have undergone crossing over in meiotic prophase must maintain sister chromatid cohesion somewhere along their length between the first and second meiotic divisions. Although many eukaryotes use the centromere as a site to maintain cohesion, the holocentric organism Caenorhabditis elegans instead creates two chromosome domains of unequal length termed the short arm and long arm, which become the first and second site of cohesion loss at meiosis I and II. The mechanisms that confer distinct functions to the short and long arm domains remain poorly understood. Here, we show that phosphorylation of the synaptonemal complex protein SYP-1 is required to create these domains. Once crossover sites are designated, phosphorylated SYP-1 and PLK-2 become cooperatively confined to short arms and guide phosphorylated histone H3 and the chromosomal passenger complex to the site of meiosis I cohesion loss. Our results show that PLK-2 and phosphorylated SYP-1 ensure creation of the short arm subdomain, promoting disjunction of chromosomes in meiosis I.
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Affiliation(s)
| | | | | | - Tomoki Uchino
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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22
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Titlow JS, Yang L, Parton RM, Palanca A, Davis I. Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction. Methods Mol Biol 2017; 1649:163-175. [PMID: 29130196 PMCID: PMC6128253 DOI: 10.1007/978-1-4939-7213-5_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The lack of an effective, simple, and highly sensitive protocol for fluorescent in situ hybridization (FISH) at the Drosophila larval neuromuscular junction (NMJ) has hampered the study of mRNA biology. Here, we describe our modified single molecule FISH (smFISH) methods that work well in whole mount Drosophila NMJ preparations to quantify primary transcription and count individual cytoplasmic mRNA molecules in specimens while maintaining ultrastructural preservation. The smFISH method is suitable for high-throughput sample processing and 3D image acquisition using any conventional microscopy imaging modality and is compatible with the use of antibody colabeling and transgenic fluorescent protein tags in axons, glia, synapses, and muscle cells. These attributes make the method particularly amenable to super-resolution imaging. With 3D Structured Illumination Microscopy (3D-SIM), which increases spatial resolution by a factor of 2 in X, Y, and Z, we acquire super-resolution information about the distribution of single molecules of mRNA in relation to covisualized synaptic and cellular structures. Finally, we demonstrate the use of commercial and open source software for the quality control of single transcript expression analysis, 3D-SIM data acquisition and reconstruction as well as image archiving management and presentation. Our methods now allow the detailed mechanistic and functional analysis of sparse as well as abundant mRNAs at the NMJ in their appropriate cellular context.
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Affiliation(s)
- Joshua S. Titlow
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Lu Yang
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Richard M. Parton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ana Palanca
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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23
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Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR. Metadata management for high content screening in OMERO. Methods 2016; 96:27-32. [PMID: 26476368 PMCID: PMC4773399 DOI: 10.1016/j.ymeth.2015.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 01/18/2023] Open
Abstract
High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org.
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Affiliation(s)
- Simon Li
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Sébastien Besson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Colin Blackburn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Mark Carroll
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Richard K Ferguson
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Helen Flynn
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Kenneth Gillen
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Roger Leigh
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Dominik Lindner
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - William J Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Balaji Ramalingam
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Gabriella Rustici
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Aleksandra Tarkowska
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Petr Walczysko
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Eleanor Williams
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | | | - Jean-Marie Burel
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK
| | - Josh Moore
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA.
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