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Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity

View ORCID ProfileDaniyal J Jafree, View ORCID ProfileBenjamin Stewart, View ORCID ProfileMaria Kolatsi-Joannou, Benjamin Davis, Hannah Mitchell, Lauren G Russell, Lucía Marinas del Rey, William J Mason, Byung Il Lee, Lauren Heptinstall, Gideon Pomeranz, View ORCID ProfileDale Moulding, Laura Wilson, Tahmina Wickenden, Saif Malik, Natalie Holroyd, View ORCID ProfileClaire Walsh, View ORCID ProfileJennifer C Chandler, Kevin X Cao, View ORCID ProfilePaul JD Winyard, View ORCID ProfileKaren L Price, View ORCID ProfileAdrian S Woolf, View ORCID ProfileMarc Aurel Busche, View ORCID ProfileSimon Walker-Samuel, View ORCID ProfilePeter J Scambler, View ORCID ProfileReza Motallebzadeh, View ORCID ProfileMenna R Clatworthy, View ORCID ProfileDavid A Long
doi: https://doi.org/10.1101/2022.10.28.514222
Daniyal J Jafree
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
2UCL MB/PhD Programme, UCL, London, UK
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  • ORCID record for Daniyal J Jafree
Benjamin Stewart
3Molecular Immunity Unit, University of Cambridge, Cambridge, UK
4Cellular Genetics, Wellcome Sanger Institute, Hinxton UK
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Maria Kolatsi-Joannou
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Benjamin Davis
5Central Laser Facility, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, UK
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Hannah Mitchell
6Mathematical Sciences Research Centre, Queen’s University Belfast, Belfast, UK
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Lauren G Russell
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Lucía Marinas del Rey
7Research Department of Surgical Biotechnology, Division of Surgery and Interventional Science, UCL, London, UK
8UCL Institute of Immunity and Transplantation, UCL, London, UK
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William J Mason
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Byung Il Lee
9UK Dementia Research Institute, UCL, London, UK
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Lauren Heptinstall
10UCL Department of Pathology, Royal Free Hospital, London, UK
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Gideon Pomeranz
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Dale Moulding
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Laura Wilson
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Tahmina Wickenden
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Saif Malik
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Natalie Holroyd
11UCL Centre for Advanced Biomedical Imaging, London, UK
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Claire Walsh
11UCL Centre for Advanced Biomedical Imaging, London, UK
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Jennifer C Chandler
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Kevin X Cao
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Paul JD Winyard
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Karen L Price
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Adrian S Woolf
12School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, United Kingdom
13Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
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Marc Aurel Busche
9UK Dementia Research Institute, UCL, London, UK
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Simon Walker-Samuel
11UCL Centre for Advanced Biomedical Imaging, London, UK
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Peter J Scambler
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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Reza Motallebzadeh
7Research Department of Surgical Biotechnology, Division of Surgery and Interventional Science, UCL, London, UK
8UCL Institute of Immunity and Transplantation, UCL, London, UK
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Menna R Clatworthy
3Molecular Immunity Unit, University of Cambridge, Cambridge, UK
4Cellular Genetics, Wellcome Sanger Institute, Hinxton UK
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  • For correspondence: d.long@ucl.ac.uk mrc38@cam.ac.uk
David A Long
1Developmental Biology & Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, UK
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  • For correspondence: d.long@ucl.ac.uk mrc38@cam.ac.uk
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ABSTRACT

Studies of the structural and molecular features of the lymphatic vasculature, which clears fluid, macromolecules and leukocytes from the tissue microenvironment, have largely relied on animal models, with limited information in human organs beyond traditional immunohistochemical assessment. Here, we use three-dimensional imaging and single-cell RNA-sequencing to study lymphatics in the human kidney. We found a hierarchical arrangement of lymphatic vessels within human kidneys, initiating along specialised nephron epithelium in the renal cortex and displaying a distinct, kidney-specific transcriptional profile. In chronic transplant rejection we found kidney allograft lymphatic expansion alongside a loss of structural hierarchy, with human leukocyte antigen-expressing lymphatic vessels infiltrating the medulla, presenting a putative target for alloreactive antibodies. This occurred concurrently with lymphatic vessels invading and interconnecting tertiary lymphoid structures at early stages of lymphocyte colonisation. Analysis of intercellular signalling revealed upregulation of co-inhibitory molecule-mediated CD4+ T cell-lymphatic crosstalk in rejecting kidneys, potentially acting to limit local alloimmune responses. Overall, we delineate novel structural and molecular features of human kidney lymphatics and reveal perturbations to their phenotype and transcriptome in the context of alloimmunity.

SUMMARY Lymphatics regulate fluid balance and immune cell accumulation but are under-studied in human organs such as the kidney. Jafree and colleagues profiled human kidney lymphatics using three-dimensional imaging and single-cell RNA-sequencing, revealing structural and transcriptional perturbations in rejecting kidney transplants.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • A co-author was added

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 29, 2022.
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Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity
Daniyal J Jafree, Benjamin Stewart, Maria Kolatsi-Joannou, Benjamin Davis, Hannah Mitchell, Lauren G Russell, Lucía Marinas del Rey, William J Mason, Byung Il Lee, Lauren Heptinstall, Gideon Pomeranz, Dale Moulding, Laura Wilson, Tahmina Wickenden, Saif Malik, Natalie Holroyd, Claire Walsh, Jennifer C Chandler, Kevin X Cao, Paul JD Winyard, Karen L Price, Adrian S Woolf, Marc Aurel Busche, Simon Walker-Samuel, Peter J Scambler, Reza Motallebzadeh, Menna R Clatworthy, David A Long
bioRxiv 2022.10.28.514222; doi: https://doi.org/10.1101/2022.10.28.514222
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Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity
Daniyal J Jafree, Benjamin Stewart, Maria Kolatsi-Joannou, Benjamin Davis, Hannah Mitchell, Lauren G Russell, Lucía Marinas del Rey, William J Mason, Byung Il Lee, Lauren Heptinstall, Gideon Pomeranz, Dale Moulding, Laura Wilson, Tahmina Wickenden, Saif Malik, Natalie Holroyd, Claire Walsh, Jennifer C Chandler, Kevin X Cao, Paul JD Winyard, Karen L Price, Adrian S Woolf, Marc Aurel Busche, Simon Walker-Samuel, Peter J Scambler, Reza Motallebzadeh, Menna R Clatworthy, David A Long
bioRxiv 2022.10.28.514222; doi: https://doi.org/10.1101/2022.10.28.514222

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