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Laseca N, Molina A, Perdomo-González D, Ziadi C, Azor PJ, Valera M. Exploring the Genetic Landscape of Vitiligo in the Pura Raza Español Horse: A Genomic Perspective. Animals (Basel) 2024; 14:2420. [PMID: 39199954 PMCID: PMC11350783 DOI: 10.3390/ani14162420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Vitiligo is a depigmentation autoimmune disorder characterized by the progressive loss of melanocytes leading to the appearance of patchy depigmentation of the skin. The presence of vitiligo in horses is greater in those with grey coats. The aim of this study was therefore to perform a genome-wide association study (GWAS) to identify genomic regions and putative candidate loci associated with vitiligo depigmentation and susceptibility in the Pura Raza Español population. For this purpose, we performed a wssGBLUP (weighted single step genomic best linear unbiased prediction) using data from a total of 2359 animals genotyped with Affymetrix Axiom™ Equine 670 K and 1346 with Equine GeneSeek Genomic Profiler™ (GGP) Array V5. A total of 60,136 SNPs (single nucleotide polymorphisms) present on the 32 chromosomes from the consensus dataset after quality control were employed for the analysis. Vitiligo-like depigmentation was phenotyped by visual inspection of the different affected areas (eyes, mouth, nostrils) and was classified into nine categories with three degrees of severity (absent, slight, and severe). We identified one significant genomic region for vitiligo around the eyes, eight significant genomic regions for vitiligo around the mouth, and seven significant genomic regions for vitiligo around the nostrils, which explained the highest percentage of variance. These significant genomic regions contained candidate genes related to melanocytes, skin, immune system, tumour suppression, metastasis, and cutaneous carcinoma. These findings enable us to implement selective breeding strategies to decrease the incidence of vitiligo and to elucidate the genetic architecture underlying vitiligo in horses as well as the molecular mechanisms involved in the disease's development. However, further studies are needed to better understand this skin disorder in horses.
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Affiliation(s)
- Nora Laseca
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Ctra. Utrera Km 1, 41013 Sevilla, Spain; (N.L.); (D.P.-G.)
- Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Cortijo de Cuarto (Viejo), 41014 Sevilla, Spain;
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Ctra. Madrid Km 396, 44014 Córdoba, Spain; (A.M.); (C.Z.)
| | - Davinia Perdomo-González
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Ctra. Utrera Km 1, 41013 Sevilla, Spain; (N.L.); (D.P.-G.)
| | - Chiraz Ziadi
- Departamento de Genética, Universidad de Córdoba, Ctra. Madrid Km 396, 44014 Córdoba, Spain; (A.M.); (C.Z.)
| | - Pedro J. Azor
- Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Cortijo de Cuarto (Viejo), 41014 Sevilla, Spain;
| | - Mercedes Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Ctra. Utrera Km 1, 41013 Sevilla, Spain; (N.L.); (D.P.-G.)
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Miyahara K, Hino M, Yu Z, Ono C, Nagaoka A, Hatano M, Shishido R, Yabe H, Tomita H, Kunii Y. The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain. Front Psychiatry 2023; 14:1156524. [PMID: 37520228 PMCID: PMC10379646 DOI: 10.3389/fpsyt.2023.1156524] [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: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Evaluating and controlling confounders are necessary when investigating molecular pathogenesis using human postmortem brain tissue. Particularly, tissue pH and RNA integrity number (RIN) are valuable indicators for controlling confounders. However, the influences of these indicators on the expression of each gene in postmortem brain have not been fully investigated. Therefore, we aimed to assess these effects on gene expressions of human brain samples. Methods We isolated total RNA from occipital lobes of 13 patients with schizophrenia and measured the RIN and tissue pH. Gene expression was analyzed and gene sets affected by tissue pH and RIN were identified. Moreover, we examined the functions of these genes by enrichment analysis and upstream regulator analysis. Results We identified 2,043 genes (24.7%) whose expressions were highly correlated with pH; 3,004 genes (36.3%) whose expressions were highly correlated with RIN; and 1,293 genes (15.6%) whose expressions were highly correlated with both pH and RIN. Genes commonly affected by tissue pH and RIN were highly associated with energy production and the immune system. In addition, genes uniquely affected by tissue pH were highly associated with the cell cycle, whereas those uniquely affected by RIN were highly associated with RNA processing. Conclusion The current study elucidated the influence of pH and RIN on gene expression profiling and identified gene sets whose expressions were affected by tissue pH or RIN. These findings would be helpful in the control of confounders for future postmortem brain studies.
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Affiliation(s)
- Kazusa Miyahara
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Mizuki Hino
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Chiaki Ono
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Masataka Hatano
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Risa Shishido
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Psychiatry, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
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3
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Singh SP, Parween F, Edara N, Zhang HH, Chen J, Otaizo-Carrasquero F, Cheng D, Oppenheim NA, Ransier A, Zhu W, Shamsaddini A, Gardina PJ, Darko SW, Singh TP, Douek DC, Myers TG, Farber JM. Human CCR6+ Th Cells Show Both an Extended Stable Gradient of Th17 Activity and Imprinted Plasticity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1700-1716. [PMID: 37093875 PMCID: PMC10463241 DOI: 10.4049/jimmunol.2200874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Th17 cells have been investigated in mice primarily for their contributions to autoimmune diseases. However, the pathways of differentiation of Th17 and related Th cells (type 17 cells) and the structure of the type 17 memory population in humans are not well understood; such understanding is critical for manipulating these cells in vivo. By exploiting differences in levels of surface CCR6, we found that human type 17 memory cells, including individual T cell clonotypes, form an elongated continuum of type 17 character along which cells can be driven by increasing RORγt. This continuum includes cells preserved within the memory pool with potentials that reflect the early preferential activation of multiple over single lineages. The phenotypes and epigenomes of CCR6+ cells are stable across cell divisions under noninflammatory conditions. Nonetheless, activation in polarizing and nonpolarizing conditions can yield additional functionalities, revealing, respectively, both environmentally induced and imprinted mechanisms that contribute differentially across the type 17 continuum to yield the unusual plasticity ascribed to type 17 cells.
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Affiliation(s)
- Satya P. Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Farhat Parween
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Nithin Edara
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Hongwei H. Zhang
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Jinguo Chen
- Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Francisco Otaizo-Carrasquero
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Debby Cheng
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Nicole A. Oppenheim
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Amy Ransier
- Genome Analysis Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Wenjun Zhu
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Amirhossein Shamsaddini
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Paul J. Gardina
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Samuel W. Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tej Pratap Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Timothy G. Myers
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
| | - Joshua M. Farber
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD
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Rindler K, Krausgruber T, Thaler FM, Alkon N, Bangert C, Kurz H, Fortelny N, Rojahn TB, Jonak C, Griss J, Bock C, Brunner PM. Spontaneously Resolved Atopic Dermatitis Shows Melanocyte and Immune Cell Activation Distinct From Healthy Control Skin. Front Immunol 2021; 12:630892. [PMID: 33717163 PMCID: PMC7943477 DOI: 10.3389/fimmu.2021.630892] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/01/2021] [Indexed: 01/11/2023] Open
Abstract
Atopic dermatitis (AD) typically starts in infancy or early childhood, showing spontaneous remission in a subset of patients, while others develop lifelong disease. Despite an increased understanding of AD, factors guiding its natural course are only insufficiently elucidated. We thus performed suction blistering in skin of adult patients with stable, spontaneous remission from previous moderate-to-severe AD during childhood. Samples were compared to healthy controls without personal or familial history of atopy, and to chronic, active AD lesions. Skin cells and tissue fluid obtained were used for single-cell RNA sequencing and proteomic multiplex assays, respectively. We found overall cell composition and proteomic profiles of spontaneously healed AD to be comparable to healthy control skin, without upregulation of typical AD activity markers (e.g., IL13, S100As, and KRT16). Among all cell types in spontaneously healed AD, melanocytes harbored the largest numbers of differentially expressed genes in comparison to healthy controls, with upregulation of potentially anti-inflammatory markers such as PLA2G7. Conventional T-cells also showed increases in regulatory markers, and a general skewing toward a more Th1-like phenotype. By contrast, gene expression of regulatory T-cells and keratinocytes was essentially indistinguishable from healthy skin. Melanocytes and conventional T-cells might thus contribute a specific regulatory milieu in spontaneously healed AD skin.
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Affiliation(s)
- Katharina Rindler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix M. Thaler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Natalia Alkon
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christine Bangert
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Harald Kurz
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas B. Rojahn
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Constanze Jonak
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Griss
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Medical Statistics, Informatics, and Intelligent Systems, Institute of Artificial Intelligence and Decision Support, Medical University of Vienna, Vienna, Austria
| | - Patrick M. Brunner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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5
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Blanco G, Puiggros A, Sherry B, Nonell L, Calvo X, Puigdecanet E, Chiu PY, Kieso Y, Ferrer G, Palacios F, Arnal M, Rodríguez-Rivera M, Gimeno E, Abella E, Rai KR, Abrisqueta P, Bosch F, Calon A, Ferrer A, Chiorazzi N, Espinet B. Chronic lymphocytic leukemia-like monoclonal B-cell lymphocytosis exhibits an increased inflammatory signature that is reduced in early-stage chronic lymphocytic leukemia. Exp Hematol 2021; 95:68-80. [PMID: 33421548 DOI: 10.1016/j.exphem.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022]
Abstract
Several studies in chronic lymphocytic leukemia (CLL) patients have reported impaired immune cell functions, which contribute to tumor evasion and disease progression. However, studies on CLL-like monoclonal B-cell lymphocytosis (MBL) are scarce. In the study described here, we characterized the immune environment in 62 individuals with clinical MBL, 56 patients with early-stage CLL, and 31 healthy controls. Gene expression arrays and quantitative reverse transcription polymerase chain reaction were performed on RNA from CD4+ peripheral blood cells; serum cytokines were measured with immunoassays; and HLA-DR expression on circulating monocytes, as well as the percentages of Th1, cytotoxic, exhausted, and effector CD4+ T cells, were evaluated by flow cytometry. In addition, cell cultures of clonal B cells and CD14-enriched or -depleted cell fractions were performed. Strikingly, MBL and early-stage CLL differed in pro-inflammatory signatures. An increased inflammatory drive orchestrated mainly by monocytes was identified in MBL, which exhibited enhanced phagocytosis, pattern recognition receptors, interleukin-8 (IL8), HMGB1, and acute response signaling pathways and increased pro-inflammatory cytokines (in particular IL8, interferon γ [IFNγ], and tumor necrosis factor α). This inflammatory signature was diminished in early-stage CLL (reduced IL8 and IFNγ levels, IL8 signaling pathway, and monocytic HLA-DR expression compared with MBL), especially in those patients with mutations in IGHV genes. Additionally, CD4+ T cells of MBL and early-stage CLL exhibited a similar upregulation of Th1 and cytotoxic genes and expanded CXCR3+ and perforin+ CD4+ T cells, as well as PD1+ CD4+ T cells, compared with controls. Cell culture assays disclosed tumor-supporting effects of monocytes similarly observed in MBL and early-stage CLL. These novel findings reveal differences in the inflammatory environment between MBL and CLL, highlighting an active role for antigen stimulation in the very early stages of the disease, potentially related to malignant B-cell transformation.
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Affiliation(s)
- Gonzalo Blanco
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Anna Puiggros
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Barbara Sherry
- Center for Immunology and Inflammation, The Feinstein Institute for Medical Research, Manhasset, NY; Department of Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Department of Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY
| | | | - Xavier Calvo
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | | | - Pui Yan Chiu
- Center for Immunology and Inflammation, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Yasmine Kieso
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Gerardo Ferrer
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Florencia Palacios
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | | | - María Rodríguez-Rivera
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Eva Gimeno
- Servei d'Hematologia, Hospital del Mar-IMIM, Barcelona, Spain; Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Eugènia Abella
- Servei d'Hematologia, Hospital del Mar-IMIM, Barcelona, Spain; Grup de Recerca Clínica Aplicada en Neoplàsies Hematològiques, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Kanti R Rai
- Department of Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Pau Abrisqueta
- Servei d'Hematologia, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Francesc Bosch
- Servei d'Hematologia, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Alexandre Calon
- Laboratori de Recerca Translacional en Microambient Tumoral, Cancer Research Program, IMIM, Barcelona, Spain
| | - Ana Ferrer
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Nicholas Chiorazzi
- Department of Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Department of Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY; Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Manhasset, NY
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular, Laboratori de Citologia Hematològica, Servei de Patologia, Hospital del Mar, Barcelona, Spain; Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
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Jackson K, Milner RJ, Doty A, Hutchison S, Cortes-Hinojosa G, Riva A, Sahay B, Lejeune A, Bechtel S. Analysis of canine myeloid-derived suppressor cells (MDSCs) utilizing fluorescence-activated cell sorting, RNA protection mediums to yield quality RNA for single-cell RNA sequencing. Vet Immunol Immunopathol 2020; 231:110144. [PMID: 33278779 DOI: 10.1016/j.vetimm.2020.110144] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 10/15/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022]
Abstract
Fluorescence-activated cell sorting (FACS) is a branch of flow cytometry that allows for the isolation of specific cell populations that can then be further analyzed by single-cell RNA sequencing (scRNA-seq). When utilizing FACS for population isolation prior to sequencing, it is essential to consider the protection of RNA from RNase activity, environmental conditions, and the sorting efficiency to ensure optimum sample quality. This study aimed to optimize a previously published MDSC flow cytometry strategy to FACS sort canine Myeloid-Derived Suppressor Cells (MDSC) with various permutations of RNAlater ™ and RiboLock™ before and after FACS sorting. Concentrations of RNAlater™ greater than 2 % applied before flow analysis affected cell survival and fluorescence, whereas concentrations ≤ 2 % and time ≤ 4 h had little to no effect on cells. To shorten the procedural time and to enhance the sorting of rare populations, we used a primary PE-conjugated CD11b antibody and magnetic column. The combination of RiboLock™ pre- and post-sorting for FACS provided the best quality RNA as determined by the RNA integrity number (RIN ≥ 7) for scRNA-seq in a normal and dog and a dog with untreated oral melanoma dog. As proof of principle, we sequenced two samples, one from a normal dog another from a dog with untreated oral melanoma. Applying scRNA-Seq analysis using the 10X Genomic platform, we identified 6 clusters in the Seurat paired analysis of MDSC sorted samples. Two clusters, with the majority of the cells coming from the melanoma sample, had genes that were upregulated (> log2); these included MMP9, MMP1, HPGD, CPA3, and GATA3 and CYBB, CSTB, COX2, ATP6, and COX 17 for cluster 5 and 6 respectively. All genes have known associations with MDSCs. Further characterization using pathway analysis tools was not attempted due to the lower number of cells sequenced in the normal sample. The benefit deriving from the results of the study helped to gain data consistency when working with cells prone to RNase activity, and the scRNA-seq provided data showing transcriptional heterogeneity in MDSC populations and potentially identifying previously unreported or rare cell populations.
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Affiliation(s)
- K Jackson
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, United States
| | - R J Milner
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, United States.
| | - A Doty
- Flow Cytometry and Imaging Core Lab, Interdisciplinary Center for Biotechnology Research, University of Florida, United States
| | - S Hutchison
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, United States
| | - G Cortes-Hinojosa
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, United States
| | - A Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, United States
| | - B Sahay
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, United States
| | - A Lejeune
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, United States
| | - S Bechtel
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, United States
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7
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Camarillo JM, Swaminathan S, Abshiru NA, Sikora JW, Thomas PM, Kelleher NL. Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2526-2534. [PMID: 31286445 PMCID: PMC6917871 DOI: 10.1007/s13361-019-02255-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 05/24/2023]
Abstract
Histone posttranslational modifications (PTMs) are essential for regulating chromatin and maintaining gene expression throughout cell differentiation. Despite the deep level of understanding of immunophenotypic differentiation pathways in hematopoietic cells, few studies have investigated global levels of histone PTMs required for differentiation and maintenance of these distinct cell types. Here, we describe an approach to couple fluorescence-activated cell sorting (FACS) with targeted mass spectrometry to define global "epi-proteomic" signatures for primary leukocytes. FACS was used to sort closely and distantly related leukocytes from normal human peripheral blood for quantitation of histone PTMs with a multiple reaction monitoring LC-MS/MS method measuring histone PTMs on histones H3 and H4. We validate cell sorting directly into H2SO4 for immediate histone extraction to decrease time and number of steps after FACS to analyze histone PTMs. Relative histone PTM levels vary in T cells across healthy donors, and the majority of PTMs remain stable up to 2 days following initial blood draw. Large differences in the levels of histone PTMs are observed across the mature lymphoid and myeloid lineages, as well as between different types within the same lineage, though no differences are observed in closely related T cell subtypes. The results show a streamlined approach for quantifying global changes in histone PTMs in cell types separated by FACS that is poised for clinical deployment.
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Affiliation(s)
- Jeannie M Camarillo
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Suchitra Swaminathan
- Department of Medicine, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nebiyu A Abshiru
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Jacek W Sikora
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Paul M Thomas
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA.
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA.
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8
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Mastelic-Gavillet B, Vono M, Gonzalez-Dias P, Ferreira FM, Cardozo L, Lambert PH, Nakaya HI, Siegrist CA. Neonatal T Follicular Helper Cells Are Lodged in a Pre-T Follicular Helper Stage Favoring Innate Over Adaptive Germinal Center Responses. Front Immunol 2019; 10:1845. [PMID: 31456798 PMCID: PMC6700230 DOI: 10.3389/fimmu.2019.01845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/22/2019] [Indexed: 11/24/2022] Open
Abstract
T follicular helper (Tfh) cells have emerged as a critical limiting factor for controlling the magnitude of neonatal germinal center (GC) reactions and primary vaccine antibody responses. We compared the functional attributes of neonatal and adult Tfh cells at the transcriptomic level and demonstrated that the Tfh cell program is well-initiated in neonates although the Tfh gene-expression pattern (i.e., CXCR5, IL-21, BCL6, TBK1, STAT4, ASCL2, and c-MAF) is largely underrepresented as compared to adult Tfh cells. Importantly, we identified a TH2-bias of neonatal Tfh cells, with preferential differentiation toward short-lived pre-Tfh effector cells. Remarkably, adjuvantation with CpG-ODNs redirect neonatal pre-Tfh cells toward committed GC-Tfh cells, as illustrated by increased expression of Tfh signature genes and reduced expression of TH2-related genes.
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Affiliation(s)
- Beatris Mastelic-Gavillet
- Departments of Pathology-Immunology and Pediatrics, World Health Organization Collaborating Center for Vaccine Immunology, University of Geneva, Geneva, Switzerland
| | - Maria Vono
- Departments of Pathology-Immunology and Pediatrics, World Health Organization Collaborating Center for Vaccine Immunology, University of Geneva, Geneva, Switzerland
| | - Patrícia Gonzalez-Dias
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Frederico Moraes Ferreira
- Laboratory of Immunology, School of Medicine, Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Lucas Cardozo
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paul-Henri Lambert
- Departments of Pathology-Immunology and Pediatrics, World Health Organization Collaborating Center for Vaccine Immunology, University of Geneva, Geneva, Switzerland
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claire-Anne Siegrist
- Departments of Pathology-Immunology and Pediatrics, World Health Organization Collaborating Center for Vaccine Immunology, University of Geneva, Geneva, Switzerland
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9
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Carpentier S, Romagné F, Vivier E. A comprehensive approach to gene expression profiling in immune cells. Methods Enzymol 2019; 636:1-47. [PMID: 32178815 DOI: 10.1016/bs.mie.2019.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With the advent of whole-transcriptome studies and the growing need for public repositories, it has become essential to combine multiple heterogeneous datasets for immune cells. In this chapter, we describe the implementation of a compendium of 10,833 genes for 975 samples, corresponding to 52 resting immune cell types. We begin by describing the datasets, and their selection, in particular. We then explain the methodology implemented to create a qualified compendium: the processing of each array (quality control, normalization and bias correction), integration (merging rules, global normalization and batch removal) and validation. Finally some examples of use will be detailed. The utility and limitations of the compendium are also discussed, as an introduction to the next version.
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Affiliation(s)
| | | | - Eric Vivier
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France; Aix-Marseille Univ, APHM, CNRS, INSERM, CIML, Hôpital de la Timone, Marseille-Immunopole, Marseille, France.
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10
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Morou A, Brunet-Ratnasingham E, Dubé M, Charlebois R, Mercier E, Darko S, Brassard N, Nganou-Makamdop K, Arumugam S, Gendron-Lepage G, Yang L, Niessl J, Baxter AE, Billingsley JM, Rajakumar PA, Lefebvre F, Johnson RP, Tremblay C, Routy JP, Wyatt RT, Finzi A, Douek DC, Kaufmann DE. Altered differentiation is central to HIV-specific CD4 + T cell dysfunction in progressive disease. Nat Immunol 2019; 20:1059-1070. [PMID: 31308541 PMCID: PMC6642691 DOI: 10.1038/s41590-019-0418-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
Dysfunction of virus-specific CD4+ T cells in chronic human infections is poorly understood. We performed genome-wide transcriptional analyses and functional assays of CD4+ T cells specific for human immunodeficiency virus (HIV) from HIV-infected people before and after initiation of antiretroviral therapy (ART). A follicular helper T cell (TFH cell)-like profile characterized HIV-specific CD4+ T cells in viremic infection. HIV-specific CD4+ T cells from people spontaneously controlling the virus (elite controllers) robustly expressed genes associated with the TH1, TH17 and TH22 subsets of helper T cells. Viral suppression by ART resulted in a distinct transcriptional landscape, with a reduction in the expression of genes associated with TFH cells, but persistently low expression of genes associated with TH1, TH17 and TH22 cells compared to the elite controller profile. Thus, altered differentiation is central to the impairment of HIV-specific CD4+ T cells and involves both gain of function and loss of function.
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Affiliation(s)
- Antigoni Morou
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Elsa Brunet-Ratnasingham
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, La Jolla, CA, USA
| | - Roxanne Charlebois
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Eloi Mercier
- Canadian Centre for Computational Genomics-Montréal Node, Montreal, Quebec, Canada
| | - Sam Darko
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | | | - Sahaana Arumugam
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Gabrielle Gendron-Lepage
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Lifei Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia Niessl
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, La Jolla, CA, USA
| | - Amy E Baxter
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, La Jolla, CA, USA
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - James M Billingsley
- Yerkes National Primate Research Center and Emory University, Atlanta, GA, USA
| | | | - François Lefebvre
- Canadian Centre for Computational Genomics-Montréal Node, Montreal, Quebec, Canada
| | - R Paul Johnson
- Yerkes National Primate Research Center and Emory University, Atlanta, GA, USA
| | - Cécile Tremblay
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Richard T Wyatt
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrés Finzi
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.
- Université de Montréal, Montreal, Quebec, Canada.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, La Jolla, CA, USA.
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11
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Hoeppli RE, MacDonald KN, Leclair P, Fung VCW, Mojibian M, Gillies J, Rahavi SMR, Campbell AIM, Gandhi SK, Pesenacker AM, Reid G, Lim CJ, Levings MK. Tailoring the homing capacity of human Tregs for directed migration to sites of Th1-inflammation or intestinal regions. Am J Transplant 2019; 19:62-76. [PMID: 29766641 DOI: 10.1111/ajt.14936] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/17/2018] [Accepted: 05/06/2018] [Indexed: 01/25/2023]
Abstract
Cell-based therapy with CD4+ FOXP3+ regulatory T cells (Tregs) is a promising strategy to limit organ rejection and graft-vs-host disease. Ongoing clinical applications have yet to consider how human Tregs could be modified to direct their migration to specific inflammation sites and/or tissues for more targeted immunosuppression. We show here that stable, homing-receptor-tailored human Tregs can be generated from thymic Tregs isolated from pediatric thymus or adult blood. To direct migration to Th1-inflammatory sites, addition of interferon-γ and IL-12 during Treg expansion produced suppressive, epigenetically stable CXCR3+ TBET+ FOXP3+ T helper (Th)1-Tregs. CXCR3 remained expressed after injection in vivo and Th1-Tregs migrated efficiently towards CXCL10 in vitro. To induce tissue-specific migration, addition of retinoic acid (RA) during Treg expansion induced expression of the gut-homing receptors α4β7-integrin and CCR9. FOXP3+ RA-Tregs had elevated expression of the functional markers latency-associated peptide and glycoprotein A repetitions predominant, increased suppressive capacity in vitro and migrated efficiently to healthy and inflamed intestine after injection into mice. Homing-receptor-tailored Tregs were epigenetically stable even after long-term exposure to inflammatory conditions, suppressive in vivo and characterized by Th1- or gut-homing-specific transcriptomes. Tailoring human thymic Treg homing during in vitro expansion offers a new and clinically applicable approach to improving the potency and specificity of Treg therapy.
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Affiliation(s)
- R E Hoeppli
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - K N MacDonald
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - P Leclair
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - V C W Fung
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - M Mojibian
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - J Gillies
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - S M R Rahavi
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - A I M Campbell
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - S K Gandhi
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - A M Pesenacker
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - G Reid
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - C J Lim
- Department of Pediatrics, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - M K Levings
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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12
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Ren H, Han L, Liu H, Wang L, Liu X, Gao Y. Decreased Lymphocyte-to-Monocyte Ratio Predicts Poor Prognosis of Acute Ischemic Stroke Treated with Thrombolysis. Med Sci Monit 2017; 23:5826-5833. [PMID: 29220346 PMCID: PMC5731214 DOI: 10.12659/msm.907919] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Our previous study found that lower lymphocyte-to-monocyte ratio (LMR) is an independent risk factor of clinical outcome of acute ischemic stroke (AIS). However, whether lower LMR is independently associated with adverse prognosis of AIS treated with thrombolysis has not been determined. In this study, we explored the relationship between LMR and prognosis of AIS treated with thrombolysis. Material/Methods We retrospectively enrolled 108 patients treated with thrombolysis. LMR was calculated according to lymphocyte count and monocyte count on admission. Patients were classified into 3 groups according to LMR values on admission (group 1 LMR >4.34, group 2 LMR 2.79 to 4.34, group 3 LMR <2.79). Neurologic impairment was estimated by use of the National Institute of Health Stroke Scale. Clinical prognosis at 3 months was assessed by modified Rankin Scale. The relationship between LMR and neurologic impairment was analyzed by Spearman rank correlation. Receiver operating characteristic curve (ROC) was used to evaluate the ability of LMR to predict outcome. Results Patients in group 3 had lower lymphocyte counts and LMR values and higher monocyte counts (P<0.001). LMR value was negatively correlated with the degree of neurologic impairment (r=−0.372, P<0.001). The ROC suggested a moderate sensitivity (71.6%) and specificity (80.5%) of LMR for predicting prognosis with an optimal cut-off point at 3.48. Higher LMR value was an independent protective factor against adverse prognosis (odds ratio 0.683, 95% confidence interval 0.490−0.952, P=0.024). Conclusions A lower LMR value is an independent predictor of poor prognosis of AIS treated with thrombolytic therapy.
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Affiliation(s)
- Hao Ren
- Department of Neurology, The Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Lin Han
- Department of Neurology, Hengshui Hospital of Traditional Chinese Medicine, Hengshui, Hebei, China (mainland)
| | - Hongbin Liu
- Department of Neurology, Shijiazhuang Hospital of Traditional Chinese Medicine, Shijiazhuang, Hebei, China (mainland)
| | - Lin Wang
- Department of Neurology, The Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Xiao Liu
- Department of Neurology, The Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
| | - Yanjun Gao
- Department of Neurology, The Affiliated Hospital of Chengde Medical University, Chengde, Hebei, China (mainland)
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13
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Felts SJ, Van Keulen VP, Scheid AD, Allen KS, Bradshaw RK, Jen J, Peikert T, Middha S, Zhang Y, Block MS, Markovic SN, Pease LR. Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients. Cancer Immunol Immunother 2015; 64:1437-47. [PMID: 26245876 DOI: 10.1007/s00262-015-1745-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/18/2015] [Indexed: 01/09/2023]
Abstract
Melanoma patients exhibit changes in immune responsiveness in the local tumor environment, draining lymph nodes, and peripheral blood. Immune-targeting therapies are revolutionizing melanoma patient care increasingly, and studies show that patients derive clinical benefit from these newer agents. Nonetheless, predicting which patients will benefit from these costly therapies remains a challenge. In an effort to capture individual differences in immune responsiveness, we are analyzing patterns of gene expression in human peripheral blood cells using RNAseq. Focusing on CD4+ peripheral blood cells, we describe multiple categories of immune regulating genes, which are expressed in highly ordered patterns shared by cohorts of healthy subjects and stage IV melanoma patients. Despite displaying conservation in overall transcriptome structure, CD4+ peripheral blood cells from melanoma patients differ quantitatively from healthy subjects in the expression of more than 2000 genes. Moreover, 1300 differentially expressed genes are found in transcript response patterns following activation of CD4+ cells ex vivo, suggesting that widespread functional discrepancies differentiate the immune systems of healthy subjects and melanoma patients. While our analysis reveals that the transcriptome architecture characteristic of healthy subjects is maintained in cancer patients, the genes expressed differentially among individuals and across cohorts provide opportunities for understanding variable immune states as well as response potentials, thus establishing a foundation for predicting individual responses to stimuli such as immunotherapeutic agents.
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Affiliation(s)
- Sara J Felts
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Virginia P Van Keulen
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Adam D Scheid
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kathleen S Allen
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Renee K Bradshaw
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jin Jen
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Tobias Peikert
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Sumit Middha
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuji Zhang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew S Block
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Svetomir N Markovic
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Division of Hematology, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Larry R Pease
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA.
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