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Satpathy S, Thomas BE, Pilcher WJ, Bakhtiari M, Ponder LA, Pacholczyk R, Prahalad S, Bhasin SS, Munn DH, Bhasin MK. The Simple prEservatioN of Single cElls method for cryopreservation enables the generation of single-cell immune profiles from whole blood. Front Immunol 2023; 14:1271800. [PMID: 38090590 PMCID: PMC10713715 DOI: 10.3389/fimmu.2023.1271800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Current multistep methods utilized for preparing and cryopreserving single-cell suspensions from blood samples for single-cell RNA sequencing (scRNA-seq) are time-consuming, requiring trained personnel and special equipment, so limiting their clinical adoption. We developed a method, Simple prEservatioN of Single cElls (SENSE), for single-step cryopreservation of whole blood (WB) along with granulocyte depletion during single-cell assay, to generate high quality single-cell profiles (SCP). Methods WB was cryopreserved using the SENSE method and peripheral blood mononuclear cells (PBMCs) were isolated and cryopreserved using the traditional density-gradient method (PBMC method) from the same blood sample (n=6). The SCPs obtained from both methods were processed using a similar pipeline and quality control parameters. Further, entropy calculation, differential gene expression, and cellular communication analysis were performed to compare cell types and subtypes from both methods. Results Highly viable (86.3 ± 1.51%) single-cell suspensions (22,353 cells) were obtained from the six WB samples cryopreserved using the SENSE method. In-depth characterization of the scRNA-seq datasets from the samples processed with the SENSE method yielded high-quality profiles of lymphoid and myeloid cell types which were in concordance with the profiles obtained with classical multistep PBMC method processed samples. Additionally, the SENSE method cryopreserved samples exhibited significantly higher T-cell enrichment, enabling deeper characterization of T-cell subtypes. Overall, the SENSE and PBMC methods processed samples exhibited transcriptional, and cellular communication network level similarities across cell types with no batch effect except in myeloid lineage cells. Discussion Comparative analysis of scRNA-seq datasets obtained with the two cryopreservation methods i.e., SENSE and PBMC methods, yielded similar cellular and molecular profiles, confirming the suitability of the former method's incorporation in clinics/labs for cryopreserving and obtaining high-quality single-cells for conducting critical translational research.
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Affiliation(s)
- Sarthak Satpathy
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
| | - Beena E. Thomas
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - William J. Pilcher
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
| | - Mojtaba Bakhtiari
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - Lori A. Ponder
- Division of Rheumatology, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Rafal Pacholczyk
- Georgia Cancer Center, Augusta University, Augusta, GA, United States
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA, United States
| | - Sampath Prahalad
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Division of Rheumatology, Children’s Healthcare of Atlanta, Atlanta, GA, United States
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Swati S. Bhasin
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - David H. Munn
- Georgia Cancer Center, Augusta University, Augusta, GA, United States
- Department of Pediatrics, Augusta University, Augusta, GA, United States
| | - Manoj K. Bhasin
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
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Abdul-Aziz A, Devine RD, Lyberger JM, Chang H, Kovacs A, Lerma JR, Rogers AM, Byrd JC, Hertlein E, Behbehani GK. Mass Cytometry as a Tool for Investigating Senescence in Multiple Model Systems. Cells 2023; 12:2045. [PMID: 37626855 PMCID: PMC10453346 DOI: 10.3390/cells12162045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Cellular senescence is a durable cell cycle arrest as a result of the finite proliferative capacity of cells. Senescence responds to both intrinsic and extrinsic cellular stresses, such as aging, mitochondrial dysfunction, irradiation, and chemotherapy. Here, we report on the use of mass cytometry (MC) to analyze multiple model systems and demonstrate MC as a platform for senescence analysis at the single-cell level. We demonstrate changes to p16 expression, cell cycling fraction, and histone tail modifications in several established senescent model systems and using isolated human T cells. In bone marrow mesenchymal stromal cells (BMSCs), we show increased p16 expression with subsequent passage as well as a reduction in cycling cells and open chromatin marks. In WI-38 cells, we demonstrate increased p16 expression with both culture-induced senescence and oxidative stress-induced senescence (OSIS). We also use Wanderlust, a trajectory analysis tool, to demonstrate how p16 expression changes with histone tail modifications and cell cycle proteins. Finally, we demonstrate that repetitive stimulation of human T cells with CD3/CD28 beads induces an exhausted phenotype with increased p16 expression. This p16-expressing population exhibited higher expression of exhaustion markers such as EOMES and TOX. This work demonstrates that MC is a useful platform for studying senescence at a single-cell protein level, and is capable of measuring multiple markers of senescence at once with high confidence, thereby improving our understanding of senescent pathways.
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Affiliation(s)
- Amina Abdul-Aziz
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Raymond D. Devine
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Justin M. Lyberger
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Hsiaochi Chang
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Amy Kovacs
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - James R. Lerma
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Andrew M. Rogers
- Maine Medical Center, Portland, ME 04102, USA
- Tufts University School of Medicine, Boston, MA 02111, USA
| | - John C. Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Erin Hertlein
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45221, USA; (A.A.-A.)
| | - Gregory K. Behbehani
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Rochigneux P, Lisberg A, Garcia A, Granjeaud S, Madroszyk A, Fattori S, Gonçalves A, Devillier R, Maby P, Salem N, Gorvel L, Chanez B, Gukasyan J, Carroll J, Goldman J, Chretien AS, Olive D, Garon EB. Mass Cytometry Reveals Classical Monocytes, NK Cells, and ICOS+ CD4+ T Cells Associated with Pembrolizumab Efficacy in Patients with Lung Cancer. Clin Cancer Res 2022; 28:5136-5148. [PMID: 36166003 PMCID: PMC10085054 DOI: 10.1158/1078-0432.ccr-22-1386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/04/2022] [Accepted: 09/21/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Immune checkpoint inhibitors (ICI) have revolutionized the treatment of non-small cell lung cancer (NSCLC), but predictive biomarkers of their efficacy are imperfect. The primary objective is to evaluate circulating immune predictors of pembrolizumab efficacy in patients with advanced NSCLC. EXPERIMENTAL DESIGN We used high-dimensional mass cytometry (CyTOF) in baseline blood samples of patients with advanced NSCLC treated with pembrolizumab. CyTOF data were analyzed by machine-learning algorithms (Citrus, tSNE) and confirmed by manual gating followed by principal component analysis (between-group analysis). RESULTS We analyzed 27 patients from the seminal KEYNOTE-001 study (median follow-up of 60.6 months). We demonstrate that blood baseline frequencies of classical monocytes, natural killer (NK) cells, and ICOS+ CD4+ T cells are significantly associated with improved objective response rates, progression-free survival, and overall survival (OS). In addition, we report that a baseline immune peripheral score combining these three populations strongly predicts pembrolizumab efficacy (OS: HR = 0.25; 95% confidence interval = 0.12-0.51; P < 0.0001). CONCLUSIONS As this immune monitoring is easy in routine practice, we anticipate our findings may improve prediction of ICI benefit in patients with advanced NSCLC.
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Affiliation(s)
- Philippe Rochigneux
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
- Department of Medical Oncology, Paoli-Calmettes Institute, Marseille, France
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Aaron Lisberg
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Alejandro Garcia
- Cytometry Core Laboratory, David Geffen School of Medicine at the University of California, Los Angeles 90095, United States
| | - Samuel Granjeaud
- Integrative Bioinformatics Platform, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS, UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Anne Madroszyk
- Department of Medical Oncology, Paoli-Calmettes Institute, Marseille, France
| | - Stephane Fattori
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Anthony Gonçalves
- Department of Medical Oncology, Paoli-Calmettes Institute, Marseille, France
| | - Raynier Devillier
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Pauline Maby
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Nassim Salem
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Laurent Gorvel
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Brice Chanez
- Department of Medical Oncology, Paoli-Calmettes Institute, Marseille, France
| | - Jaklin Gukasyan
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - James Carroll
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Jonathan Goldman
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
| | - Anne Sophie Chretien
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Daniel Olive
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University UM105 and Paoli-Calmettes Institute, Marseille, France
| | - Edward B. Garon
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine at the University of California, Los Angeles, CA, United States
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Tomás RMF, Bissoyi A, Congdon TR, Gibson MI. Assay-ready Cryopreserved Cell Monolayers Enabled by Macromolecular Cryoprotectants. Biomacromolecules 2022; 23:3948-3959. [PMID: 35972897 PMCID: PMC9472225 DOI: 10.1021/acs.biomac.2c00791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Cell monolayers underpin the discovery and screening
of new drugs
and allow for fundamental studies of cell biology and disease. However,
current cryopreservation technologies do not allow cells to be stored
frozen while attached to tissue culture plastic. Hence, cells must
be thawed from suspension, cultured for several days or weeks, and
finally transferred into multiwell plates for the desired application.
This inefficient process consumes significant time handling cells,
rather than conducting biomedical research or other value-adding activities.
Here, we demonstrate that a synthetic macromolecular cryoprotectant
enables the routine, reproducible, and robust cryopreservation of
biomedically important cell monolayers, within industry-standard tissue
culture multiwell plates. The cells are simply thawed with media and
placed in an incubator ready to use within 24 h. Post-thaw cell recovery
values were >80% across three cell lines with low well-to-well
variance.
The cryopreserved cells retained healthy morphology, membrane integrity,
proliferative capacity, and metabolic activity; showed marginal increases
in apoptotic cells; and responded well to a toxicological challenge
using doxorubicin. These discoveries confirm that the cells are “assay-ready”
24 h after thaw. Overall, we show that macromolecular cryoprotectants
can address a long-standing cryobiological challenge and offers the
potential to transform routine cell culture for biomedical discovery.
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Affiliation(s)
- Ruben M F Tomás
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Akalabya Bissoyi
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | | | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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5
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Abstract
Cell cycle involves a series of changes that lead to cell growth and division. Cell cycle analysis is crucial to understand cellular responses to changing environmental conditions. Since its inception, flow cytometry has been particularly useful for cell cycle analysis at single cell level due to its speed and precision. Previously, flow cytometric cell cycle analysis relied solely on the measurement of cellular DNA content. Later, methods were developed for multiparametric analysis. This review explains the journey of flow cytometry to understand different molecular and cellular events underlying cell cycle using various protocols. Recent advances in the field that overcome the shortcomings of traditional flow cytometry and expand its scope for cell cycle studies are also discussed.
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6
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Deep and Durable Response to Nivolumab and Temozolomide in Small-Cell Lung Cancer Associated With an Early Decrease in Myeloid-Derived Suppressor Cells. Clin Lung Cancer 2020; 22:e487-e497. [PMID: 33234490 DOI: 10.1016/j.cllc.2020.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 11/20/2022]
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Snyder KJ, Zitzer NC, Gao Y, Choe HK, Sell NE, Neidemire-Colley L, Ignaci A, Kale C, Devine RD, Abad MG, Pietrzak M, Wang M, Lin H, Zhang YW, Behbehani GK, Jackman JE, Garzon R, Vaddi K, Baiocchi RA, Ranganathan P. PRMT5 regulates T cell interferon response and is a target for acute graft-versus-host disease. JCI Insight 2020; 5:131099. [PMID: 32191634 DOI: 10.1172/jci.insight.131099] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 03/16/2020] [Indexed: 01/09/2023] Open
Abstract
Acute graft-versus-host disease (aGVHD) is a T cell-mediated immunological disorder and the leading cause of nonrelapse mortality in patients who receive allogeneic hematopoietic cell transplants. Based on recent observations that protein arginine methyltransferase 5 (PRMT5) and arginine methylation are upregulated in activated memory T cells, we hypothesized that PRMT5 is involved in the pathogenesis of aGVHD. Here, we show that PRMT5 expression and enzymatic activity were upregulated in activated T cells in vitro and in T cells from mice developing aGVHD after allogeneic transplant. PRMT5 expression was also upregulated in T cells of patients who developed aGVHD after allogeneic hematopoietic cell transplant compared with those who did not develop aGVHD. PRMT5 inhibition using a selective small-molecule inhibitor (C220) substantially reduced mouse and human allogeneic T cell proliferation and inflammatory IFN-γ and IL-17 cytokine production. Administration of PRMT5 small-molecule inhibitors substantially improves survival, reducing disease incidence and clinical severity in mouse models of aGVHD without adversely affecting engraftment. Importantly, we show that PRMT5 inhibition retained the beneficial graft-versus-leukemia effect by maintaining cytotoxic CD8+ T cell responses. Mechanistically, we show that PRMT5 inhibition potently reduced STAT1 phosphorylation as well as transcription of proinflammatory genes, including interferon-stimulated genes and IL-17. Additionally, PRMT5 inhibition deregulates the cell cycle in activated T cells and disrupts signaling by affecting ERK1/2 phosphorylation. Thus, we have identified PRMT5 as a regulator of T cell responses and as a therapeutic target in aGVHD.
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Affiliation(s)
- Katiri J Snyder
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Nina C Zitzer
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Yandi Gao
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Hannah K Choe
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Natalie E Sell
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | | | - Anora Ignaci
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Charuta Kale
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Raymond D Devine
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | | | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Min Wang
- Prelude Therapeutics, Wilmington, Delaware, USA
| | - Hong Lin
- Prelude Therapeutics, Wilmington, Delaware, USA
| | | | - Gregory K Behbehani
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | | | - Ramiro Garzon
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Kris Vaddi
- Prelude Therapeutics, Wilmington, Delaware, USA
| | - Robert A Baiocchi
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
| | - Parvathi Ranganathan
- Division of Hematology, Department of Internal Medicine, Comprehensive Cancer Center
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Abstract
The regulated proliferation of cells is a critical factor in tumor progression, antineoplastic therapies, immune system regulation, and the cellular developmental of multicellular organisms. While measurement of cell cycle state by fluorescent flow cytometry is well established, mass cytometry allows the cell cycle to be measured along with large numbers of other antigens enabling characterization of the complex interactions between the cell cycle and wide variety of cellular processes. This method describes the use of mass cytometry for the analysis of cell cycle state for cells from three different sources: in vitro cultured cell lines, ex vivo human blood or bone marrow, and in vivo labeling of murine tissues. The method utilizes incorporation of 5-Iodo-2'-deoxyuridine (IdU), combined with measurement of phosphorylated retinoblastoma protein (pRb), Cyclin B1, and phosphorylated Histone H3 (pHH3). These measurements can be integrated into a gating strategy that enables clear separation of all five phases of the cell cycle.
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Affiliation(s)
- Gregory K Behbehani
- Division of Hematology, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.
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