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Lewis SA, Ruttenberg A, Iyiyol T, Kong N, Jin SC, Kruer MC. Potential clinical applications of advanced genomic analysis in cerebral palsy. EBioMedicine 2024; 106:105229. [PMID: 38970919 PMCID: PMC11282942 DOI: 10.1016/j.ebiom.2024.105229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have been the primary methods for establishing new CP-gene relationships and providing a genetic etiology for individual patients, the cause of their condition remains unknown for many patients with CP. Recent advancements in genomic technologies offer additional opportunities to uncover variations in human genomes, transcriptomes, and epigenomes that have previously escaped detection. In this review, we outline the use of these state-of-the-art technologies to address the molecular diagnostic challenges experienced by individuals with CP. We also explore the importance of identifying a molecular etiology whenever possible, given the potential for genomic medicine to provide opportunities to treat patients with CP in new and more precise ways.
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Affiliation(s)
- Sara A Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States
| | - Andrew Ruttenberg
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tuğçe Iyiyol
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Nahyun Kong
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States; Programs in Neuroscience and Molecular & Cellular Biology, School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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Imbach KJ, Treadway NJ, Prahalad V, Kosters A, Arafat D, Duan M, Gergely T, Ponder LA, Chandrakasan S, Ghosn EEB, Prahalad S, Gibson G. Profiling the peripheral immune response to ex vivo TNF stimulation in untreated juvenile idiopathic arthritis using single cell RNA sequencing. Pediatr Rheumatol Online J 2023; 21:17. [PMID: 36793127 PMCID: PMC9929251 DOI: 10.1186/s12969-023-00787-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/08/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Juvenile Idiopathic Arthritis (JIA) is an autoimmune disease with a heterogenous clinical presentation and unpredictable response to available therapies. This personalized transcriptomics study sought proof-of-concept for single-cell RNA sequencing to characterize patient-specific immune profiles. METHODS Whole blood samples from six untreated children, newly diagnosed with JIA, and two healthy controls were cultured for 24 h with or without ex vivo TNF stimulation and subjected to scRNAseq to examine cellular populations and transcript expression in PBMCs. A novel analytical pipeline, scPool, was developed wherein cells are first pooled into pseudocells prior to expression analysis, facilitating variance partitioning of the effects of TNF stimulus, JIA disease status, and individual donor. RESULTS Seventeen robust immune cell-types were identified, the abundance of which was significantly affected by TNF stimulus, which resulted in notable elevation of memory CD8 + T-cells and NK56 cells, but down-regulation of naïve B-cell proportions. Memory CD8 + and CD4 + T-cells were also both reduced in the JIA cases relative to two controls. Significant differential expression responses to TNF stimulus were also characterized, with monocytes showing more transcriptional shifts than T-lymphocyte subsets, while the B-cell response was more limited. We also show that donor variability exceeds the small degree of possible intrinsic differentiation between JIA and control profiles. An incidental finding of interest was association of HLA-DQA2 and HLA-DRB5 expression with JIA status. CONCLUSIONS These results support the development of personalized immune-profiling combined with ex-vivo immune stimulation for evaluation of patient-specific modes of immune cell activity in autoimmune rheumatic disease.
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Affiliation(s)
- Kathleen J. Imbach
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Nicole J. Treadway
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Vaishali Prahalad
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Astrid Kosters
- grid.189967.80000 0001 0941 6502Lowance Center for Human Immunology, Division of Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Dalia Arafat
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Meixue Duan
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Talia Gergely
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Lori A. Ponder
- grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA
| | - Shanmuganathan Chandrakasan
- grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA ,grid.189967.80000 0001 0941 6502Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30223 USA
| | - Eliver E. B. Ghosn
- grid.189967.80000 0001 0941 6502Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30223 USA ,grid.189967.80000 0001 0941 6502Lowance Center for Human Immunology, Division of Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30223 USA ,grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA
| | - Sampath Prahalad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30223, USA. .,Center for Immunity and Applied Genomics, Children's Healthcare of Atlanta, Atlanta, GA, 30223, USA. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30223, USA.
| | - Greg Gibson
- grid.213917.f0000 0001 2097 4943Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA ,grid.428158.20000 0004 0371 6071Center for Immunity and Applied Genomics, Children’s Healthcare of Atlanta, Atlanta, GA 30223 USA
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Mueller K, Saha K. Single Cell Technologies to Dissect Heterogenous Immune Cell Therapy Products. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100343. [PMID: 34957355 PMCID: PMC8693636 DOI: 10.1016/j.cobme.2021.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Single cell tools have dramatically transformed the life sciences; concurrently, autologous and allogeneic immune cell therapies have recently entered the clinic. Here we discuss methods, applications, and considerations for single cell technologies in the context of immune cell manufacturing. Molecular heterogeneity can be profiled at the level of the genome, epigenome, transcriptome, proteome, metabolome, and antigen receptor repertoire, in isolation or in tandem through multi-omic approaches. Such data inform heterogeneity within cell products and can be linked to potency readouts and clinical data, with the ultimate goal of identifying Critical Quality Attributes to predict patient outcomes. Non-destructive approaches hold promise for monitoring cell state and analyzing the impacts of gene edits within engineered products. Destructive omics approaches could be combined with non-destructive technologies to predict therapeutic potency. These technologies are poised to redefine cell manufacturing toward rapid, cost-effective, and high-throughput methods to detect and respond to dynamic cell states.
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Affiliation(s)
- Katherine Mueller
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
- Grainger Institute for Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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Yuan X, Wang J, Huang Y, Shangguan D, Zhang P. Single-Cell Profiling to Explore Immunological Heterogeneity of Tumor Microenvironment in Breast Cancer. Front Immunol 2021; 12:643692. [PMID: 33717201 PMCID: PMC7947360 DOI: 10.3389/fimmu.2021.643692] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/05/2021] [Indexed: 01/23/2023] Open
Abstract
Immune infiltrates in the tumor microenvironment (TME) of breast cancer (BRCA) have been shown to play a critical role in tumorigenesis, progression, invasion, and therapy resistance, and thereby will affect the clinical outcomes of BRCA patients. However, a wide range of intratumoral heterogeneity shaped by the tumor cells and immune cells in the surrounding microenvironment is a major obstacle in understanding and treating BRCA. Recent progress in single-cell technologies such as single-cell RNA sequencing (scRNA-seq), mass cytometry, and digital spatial profiling has enabled the detailed characterization of intratumoral immune cells and vastly improved our understanding of less-defined cell subsets in the tumor immune environment. By measuring transcriptomes or proteomics at the single-cell level, it provides an unprecedented view of the cellular architecture consist of phenotypical and functional diversities of tumor-infiltrating immune cells. In this review, we focus on landmark studies of single-cell profiling of immunological heterogeneity in the TME, and discuss its clinical applications, translational outlook, and limitations in breast cancer studies.
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Affiliation(s)
- Xiao Yuan
- Changsha KingMed Center for Clinical Laboratory Co., Ltd, Changsha, China
| | - Jinxi Wang
- First Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, China
| | - Yixuan Huang
- Division of Immunotherapy, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Peng Zhang
- Division of Immunotherapy, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
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Rampias T. Exploring the Eco-Evolutionary Dynamics of Tumor Subclones. Cancers (Basel) 2020; 12:cancers12113436. [PMID: 33228073 PMCID: PMC7699358 DOI: 10.3390/cancers12113436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022] Open
Abstract
Mutational processes constantly shape the cancer genome and defects in DNA repair pathways of tumor cells facilitate the accumulation of genomic alterations [...].
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Affiliation(s)
- Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, Basic Research Center, 11527 Athens, Greece
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Zhang J, Wang W, Huang J, Wang X, Zeng Y. How far is single-cell sequencing from clinical application? Clin Transl Med 2020; 10:e117. [PMID: 32623809 PMCID: PMC7418798 DOI: 10.1002/ctm2.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jiaqiang Zhang
- Department of Anesthesiology and Perioperative Medicine, Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - William Wang
- Center for Tumor Diagnosis and Therapy, Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jianan Huang
- Center for Tumor Diagnosis and Therapy, Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xiangdong Wang
- Center for Tumor Diagnosis and Therapy, Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Jinshan Hospital, Fudan University, Shanghai, China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
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