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Lymphangioleiomyomatosis (LAM) Cell Atlas
  1. Yina Du1,
  2. Minzhe Guo1,
  3. Yixin Wu1,
  4. Andrew Wagner1,
  5. Anne Karina Perl1,
  6. Kathryn Wikenheiser-Brokamp1,
  7. Jane Yu2,
  8. Nishant Gupta3,
  9. Elizabeth Kopras2,
  10. Vera Krymskaya4,
  11. Kseniya Obraztsova5,
  12. Yan Tang6,
  13. David Kwiatkowski6,
  14. Elizabeth P Henske7,
  15. Francis McCormack2,
  16. Yan Xu1
  1. 1The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
  2. 2Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
  3. 3University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
  4. 4Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
  5. 5Division of Pulmonary, Allergy, and Critical Care Medicine, Lung Biology Institute, Perelman School of Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
  6. 6Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Massachusetts, USA
  7. 7Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
  1. Correspondence to Dr Yan Xu, The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Yan.Xu{at}cchmc.org

Abstract

Lymphangioleiomyomatosis (LAM) is a rare lung disease of women, causing cystic remodelling of the lung and progressive respiratory failure. The cellular composition, microenvironment and cellular interactions within the LAM lesion remain unclear. To facilitate data sharing and collaborative LAM research, we performed an integrative analysis of single-cell data compiled from lung, uterus and kidney of patients with LAM from three research centres and developed an LAM Cell Atlas (LCA) Web-Portal. The LCA offers a variety of interactive options for investigators to search, visualise and reanalyse comprehensive single-cell multiomics data sets to reveal dysregulated genetic programmes at transcriptomic, epigenomic and cell–cell connectome levels.

  • rare lung diseases
  • idiopathic pulmonary fibrosis
  • lung cancer
  • cystic fibrosis
  • pulmonary lymphoma

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Footnotes

  • Twitter @Captkope, @Yanxu_Cincy

  • Contributors FM and YX conceived and designed the experiments. EK coordinated tissue collection and organisation of fresh tissue. KW-B processed, evaluated and selected human lung tissues for single-cell RNA-seq/ATAC-seq and provided LAM tissue images. AKP and JY provided LAM research related images. MG, YW, AW and YX designed and performed lymphangioleiomyomatosis (LAM) single-cell RNA/ATAC analysis and ligand-receptor interactome analyses for UC/CCHMC data cohort and three-cohort data integration. YT, DK and EPH contributed LAM lung single-cell RNA-seq from BWH data cohort. KO and VK contributed LAM lung single-cell RNA-seq of UPenn data cohort. YD, MG and YX designed web portal; YD developed web application. NG and FM coordinated tissue collection and regulatory issues; and provided feedback on LCA construction. YX, YD and FM wrote the manuscript. All authors contributed to the manuscript writing and editing. All the authors read and approved the final manuscript.

  • Funding Supported by the LAM Foundation (LAM0141E01-20 to JY, and YX; LAM0138E01-19 to AKP and YX; LAM0142C01-20 to YT; LAM0131PB07-18 to FM and AKP) and the NHLBI (R01HL153045 to YX, and JY; R01HL141462, R01HL158737, and R01HL151647 to VK; U01HL148856 to YX; LungMAP2 pilot award to MG; U54HL127672 and U01HL131755-03 to FM; U01HL131022 to EPH, FM, VK).

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.

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