1
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Ramirez A, Orcutt-Jahns BT, Pascoe S, Abraham A, Remigio B, Thomas N, Meyer AS. Integrative, high-resolution analysis of single cells across experimental conditions with PARAFAC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605698. [PMID: 39131377 PMCID: PMC11312543 DOI: 10.1101/2024.07.29.605698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Effective tools for exploration and analysis are needed to extract insights from large-scale single-cell measurement data. However, current techniques for handling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that the tensor decomposition method PARAFAC2 (Pf2) enables the dimensionality reduction of single-cell data across conditions. We demonstrate these benefits across two distinct contexts of single-cell RNA-sequencing (scRNA-seq) experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. By isolating relevant gene modules across cells and conditions, Pf2 enables straightforward associations of gene variation patterns across specific patients or perturbations while connecting each coordinated change to certain cells without pre-defining cell types. The theoretical grounding of Pf2 suggests a unified framework for many modeling tasks associated with single-cell data. Thus, Pf2 provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts.
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Affiliation(s)
- Andrew Ramirez
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
| | | | - Sean Pascoe
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Armaan Abraham
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
| | | | | | - Aaron S. Meyer
- Department of Bioengineering, University of California, Los Angeles (UCLA), CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, CA, USA
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2
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Glass DR, Mayer-Blackwell K, Ramchurren N, Parks KR, Duran GE, Wright AK, Bastidas Torres AN, Islas L, Kim YH, Fling SP, Khodadoust MS, Newell EW. Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma. Cell Rep Med 2024; 5:101527. [PMID: 38670099 PMCID: PMC11148639 DOI: 10.1016/j.xcrm.2024.101527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/17/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients have not been systematically characterized. We apply a suite of high-dimensional technologies to investigate the local, cellular, and systemic responses in CTCL patients receiving either mono- or combination anti-PD-1 plus interferon-gamma (IFN-γ) therapy. Neoplastic T cells display no evidence of activation after immunotherapy. IFN-γ induces muted endogenous immunological responses, while anti-PD-1 elicits broader changes, including increased abundance of CLA+CD39+ T cells. We develop an unbiased multi-omic profiling approach enabling discovery of immune modules stratifying patients. We identify an enrichment of activated regulatory CLA+CD39+ T cells in non-responders and activated cytotoxic CLA+CD39+ T cells in leukemic patients. Our results provide insights into the effects of immunotherapy in CTCL patients and a generalizable framework for multi-omic analysis of clinical trials.
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Affiliation(s)
- David R Glass
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - K Rachael Parks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - George E Duran
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Wright
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Laura Islas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Youn H Kim
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven P Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Cancer Immunotherapy Trials Network, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael S Khodadoust
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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3
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Zdybał K, Parente A, Sutherland JC. Improving reduced-order models through nonlinear decoding of projection-dependent outputs. PATTERNS (NEW YORK, N.Y.) 2023; 4:100859. [PMID: 38035196 PMCID: PMC10682754 DOI: 10.1016/j.patter.2023.100859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/12/2023] [Accepted: 09/14/2023] [Indexed: 12/02/2023]
Abstract
A fundamental hindrance to building data-driven reduced-order models (ROMs) is the poor topological quality of a low-dimensional data projection. This includes behavior such as overlapping, twisting, or large curvatures or uneven data density that can generate nonuniqueness and steep gradients in quantities of interest (QoIs). Here, we employ an encoder-decoder neural network architecture for dimensionality reduction. We find that nonlinear decoding of projection-dependent QoIs, when embedded in a dimensionality reduction technique, promotes improved low-dimensional representations of complex multiscale and multiphysics datasets. When data projection (encoding) is affected by forcing accurate nonlinear reconstruction of the QoIs (decoding), we minimize nonuniqueness and gradients in representing QoIs on a projection. This in turn leads to enhanced predictive accuracy of a ROM. Our findings are relevant to a variety of disciplines that develop data-driven ROMs of dynamical systems such as reacting flows, plasma physics, atmospheric physics, or computational neuroscience.
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Affiliation(s)
- Kamila Zdybał
- Université Libre de Bruxelles, École Polytechnique de Bruxelles, Aero-Thermo-Mechanics Laboratory, Brussels, Belgium
- BRITE: Brussels Institute for Thermal-Fluid Systems and Clean Energy, Brussels, Belgium
| | - Alessandro Parente
- Université Libre de Bruxelles, École Polytechnique de Bruxelles, Aero-Thermo-Mechanics Laboratory, Brussels, Belgium
- BRITE: Brussels Institute for Thermal-Fluid Systems and Clean Energy, Brussels, Belgium
| | - James C. Sutherland
- Department of Chemical Engineering, University of Utah, Salt Lake City, UT, USA
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4
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Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC. Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555623. [PMID: 37693547 PMCID: PMC10491219 DOI: 10.1101/2023.08.30.555623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.
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Affiliation(s)
- Patricia Favaro
- Department of Pathology, Stanford University
- These authors contributed equally
| | - David R. Glass
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Present address: Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Luciene Borges
- Department of Pathology, Stanford University
- Present address: Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
- These authors contributed equally
| | - Reema Baskar
- Department of Pathology, Stanford University
- Present address: Genome Institute of Singapore
| | | | - Daniel Ho
- Department of Pathology, Stanford University
| | | | | | - Vanessa M. Scanlon
- Department of Laboratory Medicine, Yale School of Medicine
- Present address: Center for Regenerative Medicine and Skeletal Biology, University of Connecticut Health
| | | | - Sean C. Bendall
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Lead author
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5
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Rao M, Amouzgar M, Harden JT, Lapasaran MG, Trickey A, Armstrong B, Odim J, Debnam T, Esquivel CO, Bendall SC, Martinez OM, Krams SM. High-dimensional profiling of pediatric immune responses to solid organ transplantation. Cell Rep Med 2023; 4:101147. [PMID: 37552988 PMCID: PMC10439249 DOI: 10.1016/j.xcrm.2023.101147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/05/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Solid organ transplant remains a life-saving therapy for children with end-stage heart, lung, liver, or kidney disease; however, ∼33% of allograft recipients experience acute rejection within the first year after transplant. Our ability to detect early rejection is hampered by an incomplete understanding of the immune changes associated with allograft health, particularly in the pediatric population. We performed detailed, multilineage, single-cell analysis of the peripheral blood immune composition in pediatric solid organ transplant recipients, with high-dimensional mass cytometry. Supervised and unsupervised analysis methods to study cell-type proportions indicate that the allograft type strongly influences the post-transplant immune profile. Further, when organ-specific differences are considered, graft health is associated with changes in the proportion of distinct T cell subpopulations. Together, these data form the basis for mechanistic studies into the pathobiology of rejection and allow for the development of new immunosuppressive agents with greater specificity.
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Affiliation(s)
- Mahil Rao
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Meelad Amouzgar
- Immunology Graduate Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - James T Harden
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Immunology Graduate Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - M Gay Lapasaran
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Amber Trickey
- Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | | | - Jonah Odim
- National Institutes of Health, Bethesda, MD, USA
| | | | - Carlos O Esquivel
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sean C Bendall
- Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Olivia M Martinez
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sheri M Krams
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
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6
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Campbell KM, Amouzgar M, Pfeiffer SM, Howes TR, Medina E, Travers M, Steiner G, Weber JS, Wolchok JD, Larkin J, Hodi FS, Boffo S, Salvador L, Tenney D, Tang T, Thompson MA, Spencer CN, Wells DK, Ribas A. Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma. Cancer Cell 2023; 41:791-806.e4. [PMID: 37037616 PMCID: PMC10187051 DOI: 10.1016/j.ccell.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
Immune checkpoint inhibitors (ICIs), including CTLA-4- and PD-1-blocking antibodies, can have profound effects on tumor immune cell infiltration that have not been consistent in biopsy series reported to date. Here, we analyze seven molecular datasets of samples from patients with advanced melanoma (N = 514) treated with ICI agents to investigate clinical, genomic, and transcriptomic features of anti-PD-1 response in cutaneous melanoma. We find that prior anti-CTLA-4 therapy is associated with differences in genomic, individual gene, and gene signatures in anti-PD-1 responders. Anti-CTLA-4-experienced melanoma tumors that respond to PD-1 blockade exhibit increased tumor mutational burden, inflammatory signatures, and altered cell cycle processes compared with anti-CTLA-4-naive tumors or anti-CTLA-4-experienced, anti-PD-1-nonresponsive melanoma tumors. We report a harmonized, aggregate resource and suggest that prior CTLA-4 blockade therapy is associated with marked differences in the tumor microenvironment that impact the predictive features of PD-1 blockade therapy response.
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Affiliation(s)
- Katie M Campbell
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Meelad Amouzgar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | | | - Timothy R Howes
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Egmidio Medina
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Travers
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Gabriela Steiner
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Jeffrey S Weber
- Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jedd D Wolchok
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medicine, New York, NY 10065, USA
| | - James Larkin
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Silvia Boffo
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | - Lisa Salvador
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | - Daniel Tenney
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | - Tracy Tang
- Bristol Myers Squibb Corp., Princeton, NJ 08540, USA
| | | | | | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Antoni Ribas
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90024, USA.
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7
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Robinson ML, Glass DR, Duran V, Agudelo Rojas OL, Sanz AM, Consuegra M, Sahoo MK, Hartmann FJ, Bosse M, Gelvez RM, Bueno N, Pinsky BA, Montoya JG, Maecker H, Estupiñan Cardenas MI, Villar Centeno LA, Garrido EMR, Rosso F, Bendall SC, Einav S. Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. SCIENCE ADVANCES 2023; 9:eade7702. [PMID: 36961888 PMCID: PMC10038348 DOI: 10.1126/sciadv.ade7702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/21/2023] [Indexed: 06/17/2023]
Abstract
Approximately 5 million dengue virus-infected patients progress to a potentially life-threatening severe dengue (SD) infection annually. To identify the immune features and temporal dynamics underlying SD progression, we performed deep immune profiling by mass cytometry of PBMCs collected longitudinally from SD progressors (SDp) and uncomplicated dengue (D) patients. While D is characterized by early activation of innate immune responses, in SDp there is rapid expansion and activation of IgG-secreting plasma cells and memory and regulatory T cells. Concurrently, SDp, particularly children, demonstrate increased proinflammatory NK cells, inadequate expansion of CD16+ monocytes, and high expression of the FcγR CD64 on myeloid cells, yet a signature of diminished antigen presentation. Syndrome-specific determinants include suppressed dendritic cell abundance in shock/hemorrhage versus enriched plasma cell expansion in organ impairment. This study reveals uncoordinated immune responses in SDp and provides insights into SD pathogenesis in humans with potential implications for prediction and treatment.
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Affiliation(s)
- Makeda L. Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David R. Glass
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Veronica Duran
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, 499 Illinois St., 4th Floor, San Francisco, CA 94158, USA
| | | | - Ana Maria Sanz
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Monika Consuegra
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Malaya Kumar Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Felix J. Hartmann
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosa Margarita Gelvez
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Nathalia Bueno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Benjamin A. Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jose G. Montoya
- Palo Alto Medical Foundation, Dr. Jack S. Remington Laboratory for Specialty Diagnostics, Palo Alto, CA, USA
| | - Holden Maecker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Luis Angel Villar Centeno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Elsa Marina Rojas Garrido
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Fernando Rosso
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
- Department of Internal Medicine, Division of Infectious Diseases, Fundación Valle del Lili, Cali, Colombia
| | - Sean C. Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, 499 Illinois St., 4th Floor, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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8
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Glass DR, Amouzgar M. Data science through the lens of systems immunology. PATTERNS (NEW YORK, N.Y.) 2022; 3:100574. [PMID: 36033601 PMCID: PMC9403400 DOI: 10.1016/j.patter.2022.100574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
Glass, a post-doctoral researcher, and Amouzgar, a PhD student, in Bendall lab proposed a supervised dimensionality reduction method to explore and analyze single-cell data. Their Patterns paper highlights the advantages of supervised learning in single-cell datasets with class labels. They talk about the essential role of data science in this project and in their lives.
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Affiliation(s)
- David R. Glass
- Department of Pathology, Stanford University, Stanford, CA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | - Meelad Amouzgar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
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9
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Rahimikollu J, Das J. A supervised take on dimensionality reduction via hybrid subset selection. PATTERNS (NEW YORK, N.Y.) 2022; 3:100563. [PMID: 36033587 PMCID: PMC9403371 DOI: 10.1016/j.patter.2022.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Amouzgar et al. present HSS-LDA, a supervised dimensionality reduction approach for single-cell data that outperforms existing unsupervised techniques. They couple hybrid subset selection to linear discriminant analysis and identify interpretable linear combinations of predictors that best separate predefined biological groups.
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Affiliation(s)
- Javad Rahimikollu
- CMU-Pitt Program in Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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