Multiscale visualisation and analysis of innate immune cell migration at sites of hypoxic inflammation in vivo

Principal investigators: Friedemann Kiefer, Benjamin Risse
Project number: CRC 1450 B04
Project term: 01/2021–12/2024

Graphical abstract
© CRC inSight

Hypoxia is an efficient inducer of inflammation, resulting in immune cell invasion into the oxygen-deprived tissue. Accumulation of metabolically highly active immune cells increases oxygen consumption, aggravating hypoxia and tissue damage. The aim of this project is to generate new hypoxia reporters (1) and reporter mouse lines (2) based on the oxygen-independent fluorescent protein UnaG, as well as metabolic reporters (3), which will be functionally tested and applied in preclinical models of myocardial infarction (4), kidney ischemia and intestinal infection.

Using probabilistic machine learning on the imaging data generated, we will attempt to analyse quantitatively tissue hypoxia across multiple imaging scales (5) with a particular focus on the explainability of our deep learning models (6) to ensure trustworthy predictions. These insights will feed back into the sensor design and reporter mouse generation to further optimise our multi-scale analysis of hypoxia, metabolism and cell migration.

Blood vessels from the brain tissue of a mouse. This visualisation is based on images which were taken using lightsheet microscopy and show layers of a tissue sample (here a section of about 100 layers on 550 x 550 x 300 µm). To contrast the blood vessels, an adhesion molecule in their endothelial cells was stained. We merged the microscopy data into a 3D image on the computer and used the hysteresis thresholding method to segment the blood vessels, i.e. to digitally delineate them from other tissue regions. The image serves as a reference for new image processing methods utilising machine learning to improve segmentation.
© Daniel Beckmann/Benjamin Risse's research group, microscopy data by Nadine Bauer/Friedemann Kiefer's research group

Team

Principal investigators

Project members

Publications

The names of the principal investigators in our network have been bolded. Publications released prior to 2021, when funding for our network commenced, represent previous project-related work.

Accepted for publication

Kockwelp J, Thiele S, Kockwelp P, Bartsch J, Schliemann C, Angenendt L, Risse B. Cell Selection-based Data Reduction Pipeline for Whole Slide Image Analysis of Acute Myeloid Leukemia. IEEE/CVF Conference on Computer Vision and Pattern Recognition: accepted for publication.

2022

Eliat F, Sohn R, Renner H, Kagermeier T, Volkery S, Brinkmann H, Kirschnick N, Kiefer F, Grabos M, Becker K, Bedzhov I, Scholer HR, Bruder JM. Tissue clearing may alter emission and absorption properties of common fluorophores. Sci Rep 2022;12: 5551. Abstract
Peil J, Bock F, Kiefer F, Schmidt R, Heindl LM, Cursiefen C, Schlereth SL. New Therapeutic Approaches for Conjunctival Melanoma-What We Know So Far and Where Therapy Is Potentially Heading: Focus on Lymphatic Vessels and Dendritic Cells. Int J Mol Sci 2022;23Abstract

2021

Arasa J, Collado-Diaz V, Kritikos I, Medina-Sanchez JD, Friess MC, Sigmund EC, Schineis P, Hunter MC, Tacconi C, Paterson N, Nagasawa T, Kiefer F, Makinen T, Detmar M, Moser M, Lammermann T, Halin C. Upregulation of VCAM-1 in lymphatic collectors supports dendritic cell entry and rapid migration to lymph nodes in inflammation. J Exp Med 2021;218Abstract
Bian A, Jiang X, Berh D, Risse B. Resolving Colliding Larvae by Fitting ASM to Random Walker-Based Pre-Segmentations. IEEE/ACM Trans Comput Biol Bioinform 2021;18: 1184-1194. Abstract
Drees D, Scherzinger A, Hagerling R, Kiefer F, Jiang X. Scalable robust graph and feature extraction for arbitrary vessel networks in large volumetric datasets. BMC Bioinformatics 2021;22: 346. Abstract
Kirschnick N, Drees D, Redder E, Erapaneedi R, Pereira da Graca A, Schafers M, Jiang X, Kiefer F. Rapid methods for the evaluation of fluorescent reporters in tissue clearing and the segmentation of large vascular structures. iScience 2021;24: 102650. Abstract
Kong C, Bobe S, Pilger C, Lachetta M, Oie CI, Kirschnick N, Monkemoller V, Hubner W, Forster C, Schuttpelz M, Kiefer F, Huser T, Schulte Am Esch J. Multiscale and Multimodal Optical Imaging of the Ultrastructure of Human Liver Biopsies. Front Physiol 2021;12: 637136. Abstract
Redder E, Kirschnick N, Bobe S, Hagerling R, Hansmeier NR, Kiefer F. Vegfr3-tdTomato, a reporter mouse for microscopic visualization of lymphatic vessel by multiple modalities. PLoS One 2021;16: e0249256. Abstract
Sadras T, Martin M, Kume K, Robinson ME, Saravanakumar S, Lenz G, Chen Z, Song JY, Siddiqi T, Oksa L, Knapp AM, Cutler J, Cosgun KN, Klemm L, Ecker V, Winchester J, Ghergus D, Soulas-Sprauel P, Kiefer F, Heisterkamp N, Pandey A, Ngo V, Wang L, Jumaa H, Buchner M, Ruland J, Chan W-C, Meffre E, Martin T, Muschen M. Developmental partitioning of SYK and ZAP70 prevents autoimmunity and cancer. Mol Cell 2021;81: 2094-2111.e9. Abstract

2018

Hägerling R, Hoppe E, Dierkes C, Stehling M, Makinen T, Butz S, Vestweber D, Kiefer F. Distinct roles of VE‐cadherin for development and maintenance of specific lymph vessel beds. EMBO J 2018: e98271. Abstract
Klemm S, Jiang X, Risse B. Deep distance transform to segment visually indistinguishable merged objects. In: Proc. of 40th German Conference on Pattern Recognition (GCPR), Stuttgart 2018: 422-433.
Orlich M, Kiefer F. A qualitative comparison of ten tissue clearing techniques. Histol Histopathol 2018;33: 181-199. Abstract

2017

Hagerling R, Drees D, Scherzinger A, Dierkes C, Martin-Almedina S, Butz S, Gordon K, Schafers M, Hinrichs K, Ostergaard P, Vestweber D, Goerge T, Mansour S, Jiang X, Mortimer PS, Kiefer F. VIPAR, a quantitative approach to 3D histopathology applied to lymphatic malformations. JCI Insight 2017;2: e93424. Abstract

2016

Erapaneedi R, Belousov VV, Schafers M, Kiefer F. A novel family of fluorescent hypoxia sensors reveal strong heterogeneity in tumor hypoxia at the cellular level. Embo J 2016;35: 102-113. Abstract

2014

Lammel U, Bechtold M, Risse B, Berh D, Fleige A, Bunse I, Jiang X, Klambt C, Bogdan S. The Drosophila FHOD1-like formin Knittrig acts through Rok to promote stress fiber formation and directed macrophage migration during the cellular immune response. Development 2014;141: 1366-1380. Abstract

2013

Hägerling R, Pollmann C, Andreas M, Schmidt C, Nurmi H, Adams RH, Alitalo K, Andresen V, Schulte-Merker S, Kiefer F. A novel multistep mechanism for initial lymphangiogenesis in mouse embryos based on ultramicroscopy. EMBO J 2013;32: 629-644. Abstract
Risse B, Thomas S, Otto N, Lopmeier T, Valkov D, Jiang X, Klambt C. FIM, a novel FTIR-based imaging method for high throughput locomotion analysis. PLoS One 2013;8: e53963. Abstract
Sander M, Squarr AJ, Risse B, Jiang X, Bogdan S. Drosophila pupal macrophages--a versatile tool for combined ex vivo and in vivo imaging of actin dynamics at high resolution. Eur J Cell Biol 2013;92: 349-354. Abstract