1
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Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Maguire JA, Weidekamp MA, Hodge KM, Boehm K, Lu S, Chesi A, Bradfield JP, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SFA. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. CELL GENOMICS 2024; 4:100556. [PMID: 38697123 PMCID: PMC11099382 DOI: 10.1016/j.xgen.2024.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 05/04/2024]
Abstract
The ch12q13 locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via cis-regulation. We implicated rs7132908 as a putative causal variant by leveraging our in-house 3D genomic data and public domain datasets. Using a luciferase reporter assay, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. We generated isogenic human embryonic stem cell lines homozygous for either rs7132908 allele to assess changes in gene expression and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. The rs7132908 obesity risk allele influenced expression of FAIM2 and other genes and decreased the proportion of neurons produced by differentiation. We have functionally validated rs7132908 as a causal obesity variant that temporally regulates nearby effector genes and influences neurodevelopment and survival.
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Affiliation(s)
- Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B Trang
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M Volpe
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan P Bradfield
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Quantinuum Research LLC, San Diego, CA 92101, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A Anderson
- Department of Child and Adolescent Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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2
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Weber LM, Divecha HR, Tran MN, Kwon SH, Spangler A, Montgomery KD, Tippani M, Bharadwaj R, Kleinman JE, Page SC, Hyde TM, Collado-Torres L, Maynard KR, Martinowich K, Hicks SC. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife 2024; 12:RP84628. [PMID: 38266073 PMCID: PMC10945708 DOI: 10.7554/elife.84628] [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] [Indexed: 01/26/2024] Open
Abstract
Norepinephrine (NE) neurons in the locus coeruleus (LC) make long-range projections throughout the central nervous system, playing critical roles in arousal and mood, as well as various components of cognition including attention, learning, and memory. The LC-NE system is also implicated in multiple neurological and neuropsychiatric disorders. Importantly, LC-NE neurons are highly sensitive to degeneration in both Alzheimer's and Parkinson's disease. Despite the clinical importance of the brain region and the prominent role of LC-NE neurons in a variety of brain and behavioral functions, a detailed molecular characterization of the LC is lacking. Here, we used a combination of spatially-resolved transcriptomics and single-nucleus RNA-sequencing to characterize the molecular landscape of the LC region and the transcriptomic profile of LC-NE neurons in the human brain. We provide a freely accessible resource of these data in web-accessible and downloadable formats.
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Affiliation(s)
- Lukas M Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Abby Spangler
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
- Department of Neurology, Johns Hopkins School of MedicineBaltimoreUnited States
| | | | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
- The Kavli Neuroscience Discovery Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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3
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Benkafadar N, Sato MP, Ling AH, Janesick A, Scheibinger M, Jan TA, Heller S. An essential signaling cascade for avian auditory hair cell regeneration. Dev Cell 2024; 59:280-291.e5. [PMID: 38128539 DOI: 10.1016/j.devcel.2023.11.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/27/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Hearing loss is a chronic disease affecting millions of people worldwide, yet no restorative treatment options are available. Although non-mammalian species can regenerate their auditory sensory hair cells, mammals cannot. Birds retain facultative stem cells known as supporting cells that engage in proliferative regeneration when surrounding hair cells die. Here, we investigated gene expression changes in chicken supporting cells during auditory hair cell death. This identified a pathway involving the receptor F2RL1, HBEGF, EGFR, and ERK signaling. We propose a cascade starting with the proteolytic activation of F2RL1, followed by matrix-metalloprotease-mediated HBEGF shedding, and culminating in EGFR-mediated ERK signaling. Each component of this cascade is essential for supporting cell S-phase entry in vivo and is integral for hair cell regeneration. Furthermore, STAT3-phosphorylation converges with this signaling toward upregulation of transcription factors ATF3, FOSL2, and CREM. Our findings could provide a basis for designing treatments for hearing and balance disorders.
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Affiliation(s)
- Nesrine Benkafadar
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Mitsuo P Sato
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Angela H Ling
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Amanda Janesick
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mirko Scheibinger
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taha A Jan
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Stefan Heller
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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4
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Murphy AE, Fancy N, Skene N. Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset. eLife 2023; 12:RP90214. [PMID: 38047913 PMCID: PMC10695556 DOI: 10.7554/elife.90214] [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] [Indexed: 12/05/2023] Open
Abstract
Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer's disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues and use best-practice approaches to snRNA-seq differential expression, resulting in 549 times fewer DEGs at a false discovery rate of 0.05. Thus, this study highlights the impact of quality control and differential analysis methods on the discovery of disease-associated genes and aims to refocus the AD research field away from spuriously identified genes.
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Affiliation(s)
- Alan E Murphy
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nurun Fancy
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nathan Skene
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
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5
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Copertino DC, Holmberg CS, Weiler J, Ward AR, Howard JN, Levinger C, Pang AP, Corley MJ, Dündar F, Zumbo P, Betel D, Gandhi RT, McMahon DK, Bosch RJ, Linden N, Macatangay BJ, Cyktor JC, Eron JJ, Mellors JW, Kovacs C, Benko E, Bosque A, Jones RB. The latency-reversing agent HODHBt synergizes with IL-15 to enhance cytotoxic function of HIV-specific T cells. JCI Insight 2023; 8:e169028. [PMID: 37581929 PMCID: PMC10561764 DOI: 10.1172/jci.insight.169028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
IL-15 is under clinical investigation toward the goal of curing HIV infection because of its abilities to reverse HIV latency and enhance immune effector function. However, increased potency through combination with other agents may be needed. 3-Hydroxy-1,2,3-benzotriazin-4(3H)-one (HODHBt) enhances IL-15-mediated latency reversal and NK cell function by increasing STAT5 activation. We hypothesized that HODHBt would also synergize with IL-15, via STAT5, to directly enhance HIV-specific cytotoxic T cell responses. We showed that ex vivo IL-15 + HODHBt treatment markedly enhanced HIV-specific granzyme B-releasing T cell responses in PBMCs from antiretroviral therapy-suppressed (ART-suppressed) donors. We also observed upregulation of antigen processing and presentation in CD4+ T cells and increased surface MHC-I. In ex vivo PBMCs, IL-15 + HODHBt was sufficient to reduce intact proviruses in 1 of 3 ART-suppressed donors. Our findings reveal the potential for second-generation IL-15 studies incorporating HODHBt-like therapeutics. Iterative studies layering on additional latency reversal or other agents are needed to achieve consistent ex vivo reservoir reductions.
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Affiliation(s)
- Dennis C. Copertino
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Carissa S. Holmberg
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Jared Weiler
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Adam R. Ward
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - J. Natalie Howard
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Callie Levinger
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Alina P.S. Pang
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michael J. Corley
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Friederike Dündar
- Applied Bioinformatics Core and
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Catenion GmbH, Berlin, Germany
| | | | - Doron Betel
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Applied Bioinformatics Core and
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Rajesh T. Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Deborah K. McMahon
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Noemi Linden
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bernard J. Macatangay
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joshua C. Cyktor
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Alberto Bosque
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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6
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Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Ann Maguire J, Ann Weidekamp M, Boehm K, Chesi A, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SF. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.553157. [PMID: 37662342 PMCID: PMC10473629 DOI: 10.1101/2023.08.21.553157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival.
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Affiliation(s)
- Sheridan H. Littleton
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B. Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M. Volpe
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A. Anderson
- Department of Child and Adolescent Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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7
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Wei KH, Lin IT, Chowdhury K, Lim KL, Liu KT, Ko TM, Chang YM, Yang KC, Lai SL(B. Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration. eLife 2023; 12:e84679. [PMID: 37498060 PMCID: PMC10411971 DOI: 10.7554/elife.84679] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
Zebrafish exhibit a robust ability to regenerate their hearts following injury, and the immune system plays a key role in this process. We previously showed that delaying macrophage recruitment by clodronate liposome (-1d_CL, macrophage-delayed model) impairs neutrophil resolution and heart regeneration, even when the infiltrating macrophage number was restored within the first week post injury (Lai et al., 2017). It is thus intriguing to learn the regenerative macrophage property by comparing these late macrophages vs. control macrophages during cardiac repair. Here, we further investigate the mechanistic insights of heart regeneration by comparing the non-regenerative macrophage-delayed model with regenerative controls. Temporal RNAseq analyses revealed that -1d_CL treatment led to disrupted inflammatory resolution, reactive oxygen species homeostasis, and energy metabolism during cardiac repair. Comparative single-cell RNAseq profiling of inflammatory cells from regenerative vs. non-regenerative hearts further identified heterogeneous macrophages and neutrophils, showing alternative activation and cellular crosstalk leading to neutrophil retention and chronic inflammation. Among macrophages, two residential subpopulations (hbaa+ Mac and timp4.3+ Mac 3) were enriched only in regenerative hearts and barely recovered after +1d_CL treatment. To deplete the resident macrophage without delaying the circulating macrophage recruitment, we established the resident macrophage-deficient model by administrating CL earlier at 8 d (-8d_CL) before cryoinjury. Strikingly, resident macrophage-deficient zebrafish still exhibited defects in revascularization, cardiomyocyte survival, debris clearance, and extracellular matrix remodeling/scar resolution without functional compensation from the circulating/monocyte-derived macrophages. Our results characterized the diverse function and interaction between inflammatory cells and identified unique resident macrophages prerequisite for zebrafish heart regeneration.
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Affiliation(s)
- Ke-Hsuan Wei
- Graduate Institute of Life Sciences, National Defense Medical CenterTaipeiTaiwan
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - I-Ting Lin
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Kaushik Chowdhury
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Khai Lone Lim
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Kuan-Ting Liu
- Department of Biological Science & Technology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Tai-Ming Ko
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Department of Biological Science & Technology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Kai-Chien Yang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Department and Graduate Institute of Pharmacology, National Taiwan University College of MedicineTaipeiTaiwan
| | - Shih-Lei (Ben) Lai
- Graduate Institute of Life Sciences, National Defense Medical CenterTaipeiTaiwan
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
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8
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Goekeri C, Pennitz P, Groenewald W, Behrendt U, Kirsten H, Zobel CM, Berger S, Heinz GA, Mashreghi MF, Wienhold SM, Dietert K, Dorhoi A, Gruber AD, Scholz M, Rohde G, Suttorp N, Witzenrath M, Nouailles G. MicroRNA-223 Dampens Pulmonary Inflammation during Pneumococcal Pneumonia. Cells 2023; 12:cells12060959. [PMID: 36980300 PMCID: PMC10047070 DOI: 10.3390/cells12060959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Community-acquired pneumonia remains a major contributor to global communicable disease-mediated mortality. Neutrophils play a leading role in trying to contain bacterial lung infection, but they also drive detrimental pulmonary inflammation, when dysregulated. Here we aimed at understanding the role of microRNA-223 in orchestrating pulmonary inflammation during pneumococcal pneumonia. Serum microRNA-223 was measured in patients with pneumococcal pneumonia and in healthy subjects. Pulmonary inflammation in wild-type and microRNA-223-knockout mice was assessed in terms of disease course, histopathology, cellular recruitment and evaluation of inflammatory protein and gene signatures following pneumococcal infection. Low levels of serum microRNA-223 correlated with increased disease severity in pneumococcal pneumonia patients. Prolonged neutrophilic influx into the lungs and alveolar spaces was detected in pneumococci-infected microRNA-223-knockout mice, possibly accounting for aggravated histopathology and acute lung injury. Expression of microRNA-223 in wild-type mice was induced by pneumococcal infection in a time-dependent manner in whole lungs and lung neutrophils. Single-cell transcriptome analyses of murine lungs revealed a unique profile of antimicrobial and cellular maturation genes that are dysregulated in neutrophils lacking microRNA-223. Taken together, low levels of microRNA-223 in human pneumonia patient serum were associated with increased disease severity, whilst its absence provoked dysregulation of the neutrophil transcriptome in murine pneumococcal pneumonia.
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Affiliation(s)
- Cengiz Goekeri
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Faculty of Medicine, Cyprus International University, 99040 Nicosia, Cyprus
- Correspondence: (C.G.); (G.N.)
| | - Peter Pennitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Wibke Groenewald
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Ulrike Behrendt
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics, and Epidemiology, Universität Leipzig, 04107 Leipzig, Germany
| | - Christian M. Zobel
- Department of Internal Medicine, Bundeswehrkrankenhaus Berlin, 10115 Berlin, Germany
| | - Sarah Berger
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Gitta A. Heinz
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Institut der Leibniz-Gemeinschaft, 10117 Berlin, Germany
| | - Mir-Farzin Mashreghi
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Institut der Leibniz-Gemeinschaft, 10117 Berlin, Germany
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Sandra-Maria Wienhold
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Kristina Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Anca Dorhoi
- Institute of Immunology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- Faculty of Mathematics and Natural Sciences, University of Greifswald, 17489 Greifswald, Germany
| | - Achim D. Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology, Universität Leipzig, 04107 Leipzig, Germany
| | - Gernot Rohde
- Department of Respiratory Medicine, Medical Clinic I, Goethe-Universität Frankfurt am Main, 60596 Frankfurt am Main, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
- German Center for Lung Research (DZL), 10117 Berlin, Germany
| | | | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- CAPNETZ STIFTUNG, 30625 Hannover, Germany
- German Center for Lung Research (DZL), 10117 Berlin, Germany
| | - Geraldine Nouailles
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Correspondence: (C.G.); (G.N.)
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9
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Benkafadar N, Janesick A, Scheibinger M, Ling AH, Jan TA, Heller S. Transcriptomic characterization of dying hair cells in the avian cochlea. Cell Rep 2021; 34:108902. [PMID: 33761357 DOI: 10.1016/j.celrep.2021.108902] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/11/2021] [Accepted: 03/03/2021] [Indexed: 12/28/2022] Open
Abstract
Sensory hair cells are prone to apoptosis caused by various drugs including aminoglycoside antibiotics. In mammals, this vulnerability results in permanent hearing loss because lost hair cells are not regenerated. Conversely, hair cells regenerate in birds, making the avian inner ear an exquisite model for studying ototoxicity and regeneration. Here, we use single-cell RNA sequencing and trajectory analysis on control and dying hair cells after aminoglycoside treatment. Interestingly, the two major subtypes of avian cochlear hair cells, tall and short hair cells, respond differently. Dying short hair cells show a noticeable transient upregulation of many more genes than tall hair cells. The most prominent gene group identified is associated with potassium ion conductances, suggesting distinct physiological differences. Moreover, the dynamic characterization of >15,000 genes expressed in tall and short avian hair cells during their apoptotic demise comprises a resource for further investigations toward mammalian hair cell protection and hair cell regeneration.
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Affiliation(s)
- Nesrine Benkafadar
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Amanda Janesick
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mirko Scheibinger
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Angela H Ling
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Taha A Jan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stefan Heller
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Vicidomini R, Nguyen TH, Choudhury SD, Brody T, Serpe M. Assembly and Exploration of a Single Cell Atlas of the Drosophila Larval Ventral Cord. Identification of Rare Cell Types. Curr Protoc 2021; 1:e37. [PMID: 33600085 PMCID: PMC7899083 DOI: 10.1002/cpz1.37] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-cell RNA sequencing provides a new approach to an old problem: how to study cellular diversity in complex biological systems. This powerful tool has been instrumental in profiling different cell types and investigating, at the single-cell level, cell states, functions, and responses. However, mining these data requires new analytical and statistical methods for high-dimensional analyses that must be customized and adapted to specific goals. Here we present a custom multistage analysis pipeline which integrates modules contained in different R packages to ensure flexible, high-quality RNA-seq data analysis. We describe this workflow step by step, providing the codes, explaining the rationale for each function, and discussing the results and the limitations. We apply this pipeline to analyze different datasets of Drosophila larval ventral cords, identifying and describing rare cell types, such as astrocytes and neuroendocrine cells. This multistage analysis pipeline can be easily implemented by both novice and experienced scientists interested in neuronal and/or cellular diversity beyond the Drosophila model system. © 2021 US Government.
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Affiliation(s)
- Rosario Vicidomini
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Tho Huu Nguyen
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Saumitra Dey Choudhury
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Thomas Brody
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
| | - Mihaela Serpe
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland
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11
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Annapragada A, Sikora A, Bollard C, Conejo-Garcia J, Cruz CR, Demehri S, Demetriou M, Demirdjian L, Fong L, Horowitz M, Hutson A, Kadash-Edmondson K, Kufe D, Lipkin S, Liu S, McCarthy C, Morgan M, Morris Z, Pan Y, Pasquini M, Schoenberger S, Van Allen E, Vilar E, Xing Y, Zha W, Odunsi A. Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. J Immunother Cancer 2020; 8:e000796. [PMID: 32554617 PMCID: PMC7304845 DOI: 10.1136/jitc-2020-000796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Despite regulatory approval of several immune-based treatments for cancer in the past decade, a number of barriers remain to be addressed in order to fully harness the therapeutic potential of the immune system and provide benefits for patients with cancer. As part of the Cancer Moonshot initiative, the Immuno-Oncology Translational Network (IOTN) was established to accelerate the translation of basic discoveries to improve immunotherapy outcomes across the spectrum of adult cancers and to develop immune-based approaches that prevent cancers before they occur. The IOTN currently consists of 32 academic institutions in the USA. By leveraging cutting-edge preclinical research in immunotherapy and immunoprevention, open data and resource sharing, and fostering highly collaborative team science across the immuno-oncology ecosystem, the IOTN is designed to accelerate the generation of novel mechanism-driven immune-based cancer prevention and therapies, and the development of safe and effective personalized immuno-oncology approaches.
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Affiliation(s)
- Ananth Annapragada
- Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, Texas, USA
| | - Andrew Sikora
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Catherine Bollard
- Center for Cancer and Immunology Research, Children’s National Medical Center, Washington, District of Columbia, USA
| | - Jose Conejo-Garcia
- Department of Immunology, H Lee Moffitt Cancer Center and Research Center, Tampa, Florida, USA
| | - Conrad Russell Cruz
- Center for Cancer and Immunology Research, Children’s National Medical Center, Washington, District of Columbia, USA
| | - Shadmehr Demehri
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael Demetriou
- Department of Neurology, University of California Irvine, Irvine, California, USA
| | - Levon Demirdjian
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lawrence Fong
- Department of Hematology and Oncology, University of California San Francisco, San Francisco, California, USA
| | - Mary Horowitz
- Department of Medicine, Medical College of Wisconsin and Center for International Blood and Marrow Transplant Research, Milwaukee, Wisconsin, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Kathryn Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Donald Kufe
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Steven Lipkin
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Claire McCarthy
- Division of Cancer Biology, National Cancer Institute, Rockville, Maryland, USA
| | - Martin Morgan
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Zachary Morris
- Department of Human Oncology, University of Wisconsin Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Yang Pan
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marcelo Pasquini
- Department of Medicine, Medical College of Wisconsin and Center for International Blood and Marrow Transplant Research, Milwaukee, Wisconsin, USA
| | - Stephen Schoenberger
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wenjuan Zha
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | | | - Adekunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
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