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Andreatta M, Hérault L, Gueguen P, Gfeller D, Berenstein AJ, Carmona SJ. Semi-supervised integration of single-cell transcriptomics data. Nat Commun 2024; 15:872. [PMID: 38287014 PMCID: PMC10825117 DOI: 10.1038/s41467-024-45240-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Batch effects in single-cell RNA-seq data pose a significant challenge for comparative analyses across samples, individuals, and conditions. Although batch effect correction methods are routinely applied, data integration often leads to overcorrection and can result in the loss of biological variability. In this work we present STACAS, a batch correction method for scRNA-seq that leverages prior knowledge on cell types to preserve biological variability upon integration. Through an open-source benchmark, we show that semi-supervised STACAS outperforms state-of-the-art unsupervised methods, as well as supervised methods such as scANVI and scGen. STACAS scales well to large datasets and is robust to incomplete and imprecise input cell type labels, which are commonly encountered in real-life integration tasks. We argue that the incorporation of prior cell type information should be a common practice in single-cell data integration, and we provide a flexible framework for semi-supervised batch effect correction.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Paul Gueguen
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ariel J Berenstein
- Laboratorio de Biología Molecular, División Patología, Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Buenos Aires, C1425EFD, Argentina
| | - Santiago J Carmona
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland.
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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Poplineau M, Platet N, Mazuel A, Hérault L, N’Guyen L, Koide S, Nakajima-Takagi Y, Kuribayashi W, Carbuccia N, Haboub L, Vernerey J, Oshima M, Birnbaum D, Iwama A, Duprez E. Noncanonical EZH2 drives retinoic acid resistance of variant acute promyelocytic leukemias. Blood 2022; 140:2358-2370. [PMID: 35984905 PMCID: PMC10653050 DOI: 10.1182/blood.2022015668] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open
Abstract
Cancer cell heterogeneity is a major driver of therapy resistance. To characterize resistant cells and their vulnerabilities, we studied the PLZF-RARA variant of acute promyelocytic leukemia, resistant to retinoic acid (RA), using single-cell multiomics. We uncovered transcriptional and chromatin heterogeneity in leukemia cells. We identified a subset of cells resistant to RA with proliferation, DNA replication, and repair signatures that depend on a fine-tuned E2F transcriptional network targeting the epigenetic regulator enhancer of zeste homolog 2 (EZH2). Epigenomic and functional analyses validated the driver role of EZH2 in RA resistance. Targeting pan-EZH2 activities (canonical/noncanonical) was necessary to eliminate leukemia relapse-initiating cells, which underlies a dependency of resistant cells on an EZH2 noncanonical activity and the necessity to degrade EZH2 to overcome resistance. Our study provides critical insights into the mechanisms of RA resistance that allow us to eliminate treatment-resistant leukemia cells by targeting EZH2, thus highlighting a potential targeted therapy approach. Beyond RA resistance and acute promyelocytic leukemia context, our study also demonstrates the power of single-cell multiomics to identify, characterize, and clear therapy-resistant cells.
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Affiliation(s)
- Mathilde Poplineau
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Nadine Platet
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Adrien Mazuel
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Léonard Hérault
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer
- MABioS, I2M, Aix Marseille University,CNRS UMR7373, Marseille, France
| | - Lia N’Guyen
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Shuhei Koide
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yaeko Nakajima-Takagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Wakako Kuribayashi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Nadine Carbuccia
- Predictive Oncology Laboratory, CRCM, Aix Marseille University, CNRS UMR7258, INSERM 1068, Institut Paoli-Calmettes, Marseille, France
| | - Loreen Haboub
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Julien Vernerey
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
| | - Motohiko Oshima
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, CRCM, Aix Marseille University, CNRS UMR7258, INSERM 1068, Institut Paoli-Calmettes, Marseille, France
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Estelle Duprez
- Epigenetic Control of Normal and Malignant Hematopoiesis, CRCM, Aix Marseille University, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer
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Hérault L, Poplineau M, Duprez E, Remy É. A novel Boolean network inference strategy to model early hematopoiesis aging. Comput Struct Biotechnol J 2022; 21:21-33. [PMID: 36514338 PMCID: PMC9719905 DOI: 10.1016/j.csbj.2022.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022] Open
Abstract
Hematopoietic stem cell (HSC) aging is a multifactorial event leading to changes in HSC properties and functions, which are intrinsically coordinated and affect the early hematopoiesis. To better understand the mechanisms and factors controlling these changes, we developed an original strategy to construct a Boolean model of HSC differentiation. Based on our previous scRNA-seq data, we exhaustively characterized active transcription modules or regulons along the differentiation trajectory and constructed an influence graph between 15 selected components involved in the dynamics of the process. Then we defined dynamical constraints between observed cellular states along the trajectory and using answer set programming with in silico perturbation analysis, we obtained a Boolean model explaining the early priming of HSCs. Finally, perturbations of the model based on age-related changes revealed important deregulations, such as the overactivation of Egr1 and Junb or the loss of Cebpa activation by Gata2. These new regulatory mechanisms were found to be relevant for the myeloid bias of aged HSC and explain the decreased transcriptional priming of HSCs to all mature cell types except megakaryocytes.
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Affiliation(s)
- Léonard Hérault
- Aix Marseille Université, CNRS, Marseille I2M, France,Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Élisabeth Remy
- Aix Marseille Université, CNRS, Marseille I2M, France,Corresponding author.
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Hérault L, Poplineau M, Remy E, Duprez E. Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon Aging. Cells 2022; 11:cells11193125. [PMID: 36231086 PMCID: PMC9563410 DOI: 10.3390/cells11193125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Single-cell transcriptomic technologies enable the uncovering and characterization of cellular heterogeneity and pave the way for studies aiming at understanding the origin and consequences of it. The hematopoietic system is in essence a very well adapted model system to benefit from this technological advance because it is characterized by different cellular states. Each cellular state, and its interconnection, may be defined by a specific location in the global transcriptional landscape sustained by a complex regulatory network. This transcriptomic signature is not fixed and evolved over time to give rise to less efficient hematopoietic stem cells (HSC), leading to a well-documented hematopoietic aging. Here, we review the advance of single-cell transcriptomic approaches for the understanding of HSC heterogeneity to grasp HSC deregulations upon aging. We also discuss the new bioinformatics tools developed for the analysis of the resulting large and complex datasets. Finally, since hematopoiesis is driven by fine-tuned and complex networks that must be interconnected to each other, we highlight how mathematical modeling is beneficial for doing such interconnection between multilayered information and to predict how HSC behave while aging.
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Affiliation(s)
- Léonard Hérault
- I2M, CNRS, Aix Marseille University, 13009 Marseille, France
- Epigenetic Factors in Normal and Malignant Hematopoiesis Lab., CRCM, CNRS, INSERM, Institut Paoli Calmettes, Aix Marseille University, 13009 Marseille, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis Lab., CRCM, CNRS, INSERM, Institut Paoli Calmettes, Aix Marseille University, 13009 Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Elisabeth Remy
- I2M, CNRS, Aix Marseille University, 13009 Marseille, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis Lab., CRCM, CNRS, INSERM, Institut Paoli Calmettes, Aix Marseille University, 13009 Marseille, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France
- Correspondence:
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Hérault L, Poplineau M, Mazuel A, Platet N, Remy É, Duprez E. Author Correction to: Single-cell RNA-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells. BMC Biol 2021; 19:80. [PMID: 33863333 PMCID: PMC8052674 DOI: 10.1186/s12915-021-01005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Léonard Hérault
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.,Aix Marseille Université, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Adrien Mazuel
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nadine Platet
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Élisabeth Remy
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.
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Hérault L, Poplineau M, Mazuel A, Platet N, Remy É, Duprez E. Single-cell RNA-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells. BMC Biol 2021; 19:19. [PMID: 33526011 PMCID: PMC7851934 DOI: 10.1186/s12915-021-00955-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/08/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hematopoietic stem cells (HSCs) are the guarantor of the proper functioning of hematopoiesis due to their incredible diversity of potential. During aging, heterogeneity of HSCs changes, contributing to the deterioration of the immune system. In this study, we revisited mouse HSC compartment and its transcriptional plasticity during aging at unicellular scale. RESULTS Through the analysis of 15,000 young and aged transcriptomes, we identified 15 groups of HSCs revealing rare and new specific HSC abilities that change with age. The implantation of new trajectories complemented with the analysis of transcription factor activities pointed consecutive states of HSC differentiation that were delayed by aging and explained the bias in differentiation of older HSCs. Moreover, reassigning cell cycle phases for each HSC clearly highlighted an imbalance of the cell cycle regulators of very immature aged HSCs that may contribute to their accumulation in an undifferentiated state. CONCLUSIONS Our results establish a new reference map of HSC differentiation in young and aged mice and reveal a potential mechanism that delays the differentiation of aged HSCs and could promote the emergence of age-related hematologic diseases.
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Affiliation(s)
- Léonard Hérault
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Adrien Mazuel
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nadine Platet
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Élisabeth Remy
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis Team, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.
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Poplineau M, Vernerey J, Platet N, N'guyen L, Hérault L, Esposito M, Saurin AJ, Guilouf C, Iwama A, Duprez E. PLZF limits enhancer activity during hematopoietic progenitor aging. Nucleic Acids Res 2019; 47:4509-4520. [PMID: 30892634 PMCID: PMC6511862 DOI: 10.1093/nar/gkz174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 12/19/2022] Open
Abstract
PLZF (promyelocytic leukemia zinc finger) is a transcription factor acting as a global regulator of hematopoietic commitment. PLZF displays an epigenetic specificity by recruiting chromatin-modifying factors but little is known about its role in remodeling chromatin of cells committed toward a given specific hematopoietic lineage. In murine myeloid progenitors, we decipher a new role for PLZF in restraining active genes and enhancers by targeting acetylated lysine 27 of Histone H3 (H3K27ac). Functional analyses reveal that active enhancers bound by PLZF are involved in biological processes related to metabolism and associated with hematopoietic aging. Comparing the epigenome of young and old myeloid progenitors, we reveal that H3K27ac variation at active enhancers is a hallmark of hematopoietic aging. Taken together, these data suggest that PLZF, associated with active enhancers, appears to restrain their activity as an epigenetic gatekeeper of hematopoietic aging.
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Affiliation(s)
- Mathilde Poplineau
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.,Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Julien Vernerey
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nadine Platet
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Lia N'guyen
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Léonard Hérault
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Michela Esposito
- Gustave Roussy, Université Paris-Saclay, Inserm U1170, CNRS Villejuif, France
| | | | - Christel Guilouf
- Gustave Roussy, Université Paris-Saclay, Inserm U1170, CNRS Villejuif, France
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Estelle Duprez
- Epigenetic Factors in Normal and Malignant Hematopoiesis, Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
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Balzano M, De Grandis M, Vu Manh TP, Chasson L, Bardin F, Farina A, Sergé A, Bidaut G, Charbord P, Hérault L, Bailly AL, Cartier-Michaud A, Boned A, Dalod M, Duprez E, Genever P, Coles M, Bajenoff M, Xerri L, Aurrand-Lions M, Schiff C, Mancini SJ. Nidogen-1 Contributes to the Interaction Network Involved in Pro-B Cell Retention in the Peri-sinusoidal Hematopoietic Stem Cell Niche. Cell Rep 2019; 26:3257-3271.e8. [DOI: 10.1016/j.celrep.2019.02.065] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/24/2018] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
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