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MarrowQuant Across Aging and Aplasia: A Digital Pathology Workflow for Quantification of Bone Marrow Compartments in Histological Sections

  • Tratwal, Josefine1
  • Bekri, David1
  • Boussema, Chiheb1
  • Sarkis, Rita1
  • Kunz, Nicolas2
  • Koliqi, Tereza1
  • Rojas-Sutterlin, Shanti1
  • Schyrr, Frédérica1
  • Tavakol, Daniel Naveed1
  • Campos, Vasco1
  • Scheller, Erica L.3
  • Sarro, Rossella4
  • Bárcena, Carmen5
  • Bisig, Bettina4
  • Nardi, Valentina6
  • de Leval, Laurence4
  • Burri, Olivier7
  • Naveiras, Olaia1, 8
  • 1 Laboratory of Regenerative Hematopoiesis, Institute of Bioengineering and Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne , (Switzerland)
  • 2 Animal Imaging and Technology Core, Center for Biomedical Imaging, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne , (Switzerland)
  • 3 Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University, Saint Louis, MO , (United States)
  • 4 Institute of Pathology, Lausanne University Hospital (CHUV), Lausanne University (UNIL), Lausanne , (Switzerland)
  • 5 Department of Pathology, University Hospital 12 de Octubre, Madrid , (Spain)
  • 6 Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA , (United States)
  • 7 Bioimaging and Optics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne , (Switzerland)
  • 8 Department of Oncology, Hematology Service, Lausanne University Hospital (CHUV), Lausanne , (Switzerland)
Published Article
Frontiers in Endocrinology
Frontiers Media SA
Publication Date
Sep 24, 2020
DOI: 10.3389/fendo.2020.00480
PMID: 33071956
PMCID: PMC7542184
PubMed Central


The bone marrow (BM) exists heterogeneously as hematopoietic/red or adipocytic/yellow marrow depending on skeletal location, age, and physiological condition. Mouse models and patients undergoing radio/chemotherapy or suffering acute BM failure endure rapid adipocytic conversion of the marrow microenvironment, the so-called “red-to-yellow” transition. Following hematopoietic recovery, such as upon BM transplantation, a “yellow-to-red” transition occurs and functional hematopoiesis is restored. Gold Standards to estimate BM cellular composition are pathologists' assessment of hematopoietic cellularity in hematoxylin and eosin (H&E) stained histological sections as well as volumetric measurements of marrow adiposity with contrast-enhanced micro-computerized tomography (CE-μCT) upon osmium-tetroxide lipid staining. Due to user-dependent variables, reproducibility in longitudinal studies is a challenge for both methods. Here we report the development of a semi-automated image analysis plug-in, MarrowQuant , which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells, and the interstitial/microvascular compartment. A separate feature, AdipoQuant , fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with MarrowQuant lies within the range of scoring by four independent pathologists, while quantification of the total adipocyte area in whole bone sections compares with volumetric measurements. Employing our tool, we were able to develop a standardized map of BM hematopoietic cellularity and adiposity in mid-sections of murine C57BL/6 bones in homeostatic conditions, including quantification of the highly predictable red-to-yellow transitions in the proximal section of the caudal tail and in the proximal-to-distal tibia. Additionally, we present a comparative skeletal map induced by lethal irradiation, with longitudinal quantification of the “red-to-yellow-to-red” transition over 2 months in C57BL/6 femurs and tibiae. We find that, following BM transplantation, BM adiposity inversely correlates with kinetics of hematopoietic recovery and that a proximal to distal gradient is conserved. Analysis of in vivo recovery through magnetic resonance imaging (MRI) reveals comparable kinetics. On human trephine biopsies MarrowQuant successfully recognizes the BM compartments, opening avenues for its application in experimental, or clinical contexts that require standardized human BM evaluation.

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