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Otto DJ, Jordan C, Dury B, Dien C, Setty M. Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon. Nat Methods 2024; 21:1185-1195. [PMID: 38890426 DOI: 10.1038/s41592-024-02302-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Cell-state density characterizes the distribution of cells along phenotypic landscapes and is crucial for unraveling the mechanisms that drive diverse biological processes. Here, we present Mellon, an algorithm for estimation of cell-state densities from high-dimensional representations of single-cell data. We demonstrate Mellon's efficacy by dissecting the density landscape of differentiating systems, revealing a consistent pattern of high-density regions corresponding to major cell types intertwined with low-density, rare transitory states. We present evidence implicating enhancer priming and the activation of master regulators in emergence of these transitory states. Mellon offers the flexibility to perform temporal interpolation of time-series data, providing a detailed view of cell-state dynamics during developmental processes. Mellon facilitates density estimation across various single-cell data modalities, scaling linearly with the number of cells. Our work underscores the importance of cell-state density in understanding the differentiation processes, and the potential of Mellon to provide insights into mechanisms guiding biological trajectories.
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Affiliation(s)
- Dominik J Otto
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cailin Jordan
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Brennan Dury
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christine Dien
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Manu Setty
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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Otto D, Jordan C, Dury B, Dien C, Setty M. Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.548272. [PMID: 37502954 PMCID: PMC10369887 DOI: 10.1101/2023.07.09.548272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cell-state density characterizes the distribution of cells along phenotypic landscapes and is crucial for unraveling the mechanisms that drive cellular differentiation, regeneration, and disease. Here, we present Mellon, a novel computational algorithm for high-resolution estimation of cell-state densities from single-cell data. We demonstrate Mellon's efficacy by dissecting the density landscape of various differentiating systems, revealing a consistent pattern of high-density regions corresponding to major cell types intertwined with low-density, rare transitory states. Utilizing hematopoietic stem cell fate specification to B-cells as a case study, we present evidence implicating enhancer priming and the activation of master regulators in the emergence of these transitory states. Mellon offers the flexibility to perform temporal interpolation of time-series data, providing a detailed view of cell-state dynamics during the inherently continuous developmental processes. Scalable and adaptable, Mellon facilitates density estimation across various single-cell data modalities, scaling linearly with the number of cells. Our work underscores the importance of cell-state density in understanding the differentiation processes, and the potential of Mellon to provide new insights into the regulatory mechanisms guiding cellular fate decisions.
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Affiliation(s)
- Dominik Otto
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | - Cailin Jordan
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
- Molecular and Cellular Biology Program, University of Washington, Seattle WA
| | - Brennan Dury
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | - Christine Dien
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
| | - Manu Setty
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle WA
- Computational Biology Program, Public Health Sciences Division, Seattle WA
- Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle WA
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Jang JY, Hwang I, Pan H, Yao J, Alinari L, Imada E, Zanettini C, Kluk MJ, Wang Y, Lee Y, Lin HV, Huang X, Di Liberto M, Chen Z, Ballman KV, Cantley LC, Marchionni L, Inghirami G, Elemento O, Baiocchi RA, Chen-Kiang S, Belvedere S, Zheng H, Paik J. A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. J Clin Invest 2022; 132:160767. [PMID: 36282572 PMCID: PMC9753996 DOI: 10.1172/jci160767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022] Open
Abstract
Targeting lineage-defined transcriptional dependencies has emerged as an effective therapeutic strategy in cancer treatment. Through screening for molecular vulnerabilities of mantle cell lymphoma (MCL), we identified a set of transcription factors (TFs) including FOXO1, EBF1, PAX5, and IRF4 that are essential for MCL propagation. Integrated chromatin immunoprecipitation and sequencing (ChIP-Seq) with transcriptional network reconstruction analysis revealed FOXO1 as a master regulator that acts upstream in the regulatory TF hierarchy. FOXO1 is both necessary and sufficient to drive MCL lineage commitment through supporting the lineage-specific transcription programs. We further show that FOXO1, but not its close paralog FOXO3, can reprogram myeloid leukemia cells and induce B-lineage gene expression. Finally, we demonstrate that cpd10, a small molecule identified from an enriched FOXO1 inhibitor library, induces a robust cytotoxic response in MCL cells in vitro and suppresses MCL progression in vivo. Our findings establish FOXO1 inhibition as a therapeutic strategy targeting lineage-driven transcriptional addiction in MCL.
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Affiliation(s)
| | - Inah Hwang
- Department of Pathology and Laboratory Medicine and
| | - Heng Pan
- Caryl and Israel Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Eddie Imada
- Department of Pathology and Laboratory Medicine and
| | | | - Michael J. Kluk
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Yizhe Wang
- Department of Pathology and Laboratory Medicine and
| | - Yunkyoung Lee
- Forkhead BioTherapeutics Inc., New York, New York, USA
| | - Hua V. Lin
- Forkhead BioTherapeutics Inc., New York, New York, USA
| | | | - Maurizio Di Liberto
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Zhengming Chen
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Division of Biostatistics, Department of Population Health Sciences, and
| | - Karla V. Ballman
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Division of Biostatistics, Department of Population Health Sciences, and
| | - Lewis C. Cantley
- Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
| | | | - Hongwu Zheng
- Department of Pathology and Laboratory Medicine and
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine and,Sandra and Edward Meyer Cancer Center, Weill Medical College of Cornell University, New York, New York, USA
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Cord-Blood-Derived Professional Antigen-Presenting Cells: Functions and Applications in Current and Prospective Cell Therapies. Int J Mol Sci 2021; 22:ijms22115923. [PMID: 34072923 PMCID: PMC8199409 DOI: 10.3390/ijms22115923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 11/21/2022] Open
Abstract
Human umbilical cord blood (UCB) represents a valuable source of hematopoietic stem cells, particularly for patients lacking a matching donor. UCB provides practical advantages, including a lower risk of graft-versus-host-disease and permissive human leukocyte antigen mismatching. These advantageous properties have so far been applied for stem cell, mesenchymal stromal cell, and chimeric antigen receptor T cell therapies. However, UCB-derived professional antigen-presenting cells are increasingly being utilized in the context of immune tolerance and regenerative therapy. Here, we review the cell-specific characteristics as well as recent advancements in UCB-based cell therapies focusing on dendritic cells, monocytes, B lymphocytes, innate lymphoid cells, and macrophages.
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Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
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Affiliation(s)
| | | | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas –Universidad Autónoma de Madrid), Madrid, Spain
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