Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation
Summary: Understanding the regulation of normal and malignant human hematopoiesis requires comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Here, we develop a tailored bioinformatic pipeline to integrate public and proprietary single-cell RNA sequencing (scR...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-05-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222004953 |
| _version_ | 1828340703408685056 |
|---|---|
| author | Jin Ye Isabel A. Calvo Itziar Cenzano Amaia Vilas Xabier Martinez-de-Morentin Miren Lasaga Diego Alignani Bruno Paiva Ana C. Viñado Patxi San Martin-Uriz Juan P. Romero Delia Quilez Agreda Marta Miñana Barrios Ignacio Sancho-González Gabriele Todisco Luca Malcovati Nuria Planell Borja Saez Jesper N. Tegner Felipe Prosper David Gomez-Cabrero |
| author_facet | Jin Ye Isabel A. Calvo Itziar Cenzano Amaia Vilas Xabier Martinez-de-Morentin Miren Lasaga Diego Alignani Bruno Paiva Ana C. Viñado Patxi San Martin-Uriz Juan P. Romero Delia Quilez Agreda Marta Miñana Barrios Ignacio Sancho-González Gabriele Todisco Luca Malcovati Nuria Planell Borja Saez Jesper N. Tegner Felipe Prosper David Gomez-Cabrero |
| author_sort | Jin Ye |
| collection | DOAJ |
| description | Summary: Understanding the regulation of normal and malignant human hematopoiesis requires comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Here, we develop a tailored bioinformatic pipeline to integrate public and proprietary single-cell RNA sequencing (scRNA-seq) datasets. As a result, we robustly identify for the first time 14 intermediate cell states and 11 stages of differentiation in the endothelial and mesenchymal BM compartments, respectively. Our data provide the most comprehensive description to date of the murine HSC-regulatory microenvironment and suggest a higher level of specialization of the cellular circuits than previously anticipated. Furthermore, this deep characterization allows inferring conserved features in human, suggesting that the layers of microenvironmental regulation of hematopoiesis may also be shared between species. Our resource and methodology is a stepping-stone toward a comprehensive cell atlas of the BM microenvironment. |
| first_indexed | 2024-04-13T23:00:10Z |
| format | Article |
| id | doaj.art-ccde1bb022e24ec1a1f2e788e69807b2 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-13T23:00:10Z |
| publishDate | 2022-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-ccde1bb022e24ec1a1f2e788e69807b22022-12-22T02:25:52ZengElsevieriScience2589-00422022-05-01255104225Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservationJin Ye0Isabel A. Calvo1Itziar Cenzano2Amaia Vilas3Xabier Martinez-de-Morentin4Miren Lasaga5Diego Alignani6Bruno Paiva7Ana C. Viñado8Patxi San Martin-Uriz9Juan P. Romero10Delia Quilez Agreda11Marta Miñana Barrios12Ignacio Sancho-González13Gabriele Todisco14Luca Malcovati15Nuria Planell16Borja Saez17Jesper N. Tegner18Felipe Prosper19David Gomez-Cabrero20Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi ArabiaUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, SpainNavarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, SpainNavarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, SpainHospital Reina Sofía de Tudela, 31500 Navarra, SpainHospital Reina Sofía de Tudela, 31500 Navarra, SpainHospital Reina Sofía de Tudela, 31500 Navarra, SpainDepartment of Molecular Medicine, University of Pavia & Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, 17177 Stockholm, SwedenDepartment of Molecular Medicine, University of Pavia & Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, ItalyNavarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, SpainUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain; Corresponding authorBioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia; Department of Medicine, Centre for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Stockholm, Sweden; Computer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia; Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia; Corresponding authorUniversidad de Navarra, CIMA, Hematology-Oncology Program, Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Navarra, Spain; Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Madrid, Spain; Service of Hematology and Cell Therapy, Clínica Universidad de Navarra; CCUN, Pamplona, Navarra, 31008; Spain; Corresponding authorBioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia; Navarrabiomed, ComplejoHospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, 31008 Navarra, Spain; Department of Medicine, Centre for Molecular Medicine, Karolinska Institutet, 17177 Stockholm, Stockholm, Sweden; Centre for Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College, London WC2R 2LS, UK; Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal 23955, Saudi Arabia; Corresponding authorSummary: Understanding the regulation of normal and malignant human hematopoiesis requires comprehensive cell atlas of the hematopoietic stem cell (HSC) regulatory microenvironment. Here, we develop a tailored bioinformatic pipeline to integrate public and proprietary single-cell RNA sequencing (scRNA-seq) datasets. As a result, we robustly identify for the first time 14 intermediate cell states and 11 stages of differentiation in the endothelial and mesenchymal BM compartments, respectively. Our data provide the most comprehensive description to date of the murine HSC-regulatory microenvironment and suggest a higher level of specialization of the cellular circuits than previously anticipated. Furthermore, this deep characterization allows inferring conserved features in human, suggesting that the layers of microenvironmental regulation of hematopoiesis may also be shared between species. Our resource and methodology is a stepping-stone toward a comprehensive cell atlas of the BM microenvironment.http://www.sciencedirect.com/science/article/pii/S2589004222004953Biological sciencesStem cells researchOmicsTranscriptomics |
| spellingShingle | Jin Ye Isabel A. Calvo Itziar Cenzano Amaia Vilas Xabier Martinez-de-Morentin Miren Lasaga Diego Alignani Bruno Paiva Ana C. Viñado Patxi San Martin-Uriz Juan P. Romero Delia Quilez Agreda Marta Miñana Barrios Ignacio Sancho-González Gabriele Todisco Luca Malcovati Nuria Planell Borja Saez Jesper N. Tegner Felipe Prosper David Gomez-Cabrero Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation iScience Biological sciences Stem cells research Omics Transcriptomics |
| title | Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation |
| title_full | Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation |
| title_fullStr | Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation |
| title_full_unstemmed | Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation |
| title_short | Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation |
| title_sort | deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation |
| topic | Biological sciences Stem cells research Omics Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222004953 |
| work_keys_str_mv | AT jinye deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT isabelacalvo deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT itziarcenzano deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT amaiavilas deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT xabiermartinezdemorentin deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT mirenlasaga deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT diegoalignani deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT brunopaiva deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT anacvinado deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT patxisanmartinuriz deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT juanpromero deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT deliaquilezagreda deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT martaminanabarrios deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT ignaciosanchogonzalez deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT gabrieletodisco deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT lucamalcovati deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT nuriaplanell deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT borjasaez deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT jesperntegner deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT felipeprosper deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation AT davidgomezcabrero deconvolutionofthehematopoieticstemcellmicroenvironmentrevealsahighdegreeofspecializationandconservation |