1
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Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. Nat Commun 2024; 15:5888. [PMID: 39003254 DOI: 10.1038/s41467-024-50046-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 06/27/2024] [Indexed: 07/15/2024] Open
Abstract
Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.
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Affiliation(s)
- Yang Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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2
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Unger Avila P, Padvitski T, Leote AC, Chen H, Saez-Rodriguez J, Kann M, Beyer A. Gene regulatory networks in disease and ageing. Nat Rev Nephrol 2024:10.1038/s41581-024-00849-7. [PMID: 38867109 DOI: 10.1038/s41581-024-00849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/14/2024]
Abstract
The precise control of gene expression is required for the maintenance of cellular homeostasis and proper cellular function, and the declining control of gene expression with age is considered a major contributor to age-associated changes in cellular physiology and disease. The coordination of gene expression can be represented through models of the molecular interactions that govern gene expression levels, so-called gene regulatory networks. Gene regulatory networks can represent interactions that occur through signal transduction, those that involve regulatory transcription factors, or statistical models of gene-gene relationships based on the premise that certain sets of genes tend to be coexpressed across a range of conditions and cell types. Advances in experimental and computational technologies have enabled the inference of these networks on an unprecedented scale and at unprecedented precision. Here, we delineate different types of gene regulatory networks and their cell-biological interpretation. We describe methods for inferring such networks from large-scale, multi-omics datasets and present applications that have aided our understanding of cellular ageing and disease mechanisms.
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Affiliation(s)
- Paula Unger Avila
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tsimafei Padvitski
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ana Carolina Leote
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - He Chen
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Martin Kann
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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3
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Thirman HL, Hayes MJ, Brown LE, Porco JA, Irish JM. Single Cell Profiling Distinguishes Leukemia-Selective Chemotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.591362. [PMID: 38826485 PMCID: PMC11142275 DOI: 10.1101/2024.05.01.591362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
A central challenge in chemical biology is to distinguish molecular families in which small structural changes trigger large changes in cell biology. Such families might be ideal scaffolds for developing cell-selective chemical effectors - for example, molecules that activate DNA damage responses in malignant cells while sparing healthy cells. Across closely related structural variants, subtle structural changes have the potential to result in contrasting bioactivity patterns across different cell types. Here, we tested a 600-compound Diversity Set of screening molecules from the Boston University Center for Molecular Discovery (BU-CMD) in a novel phospho-flow assay that tracked fundamental cell biological processes, including DNA damage response, apoptosis, M-phase cell cycle, and protein synthesis in MV411 leukemia cells. Among the chemotypes screened, synthetic congeners of the rocaglate family were especially bioactive. In follow-up studies, 37 rocaglates were selected and deeply characterized using 12 million additional cellular measurements across MV411 leukemia cells and healthy peripheral blood mononuclear cells. Of the selected rocaglates, 92% displayed significant bioactivity in human cells, and 65% selectively induced DNA damage responses in leukemia and not healthy human blood cells. Furthermore, the signaling and cell-type selectivity were connected to structural features of rocaglate subfamilies. In particular, three rocaglates from the rocaglate pyrimidinone (RP) structural subclass were the only molecules that activated exceptional DNA damage responses in leukemia cells without activating a detectable DNA damage response in healthy cells. These results indicate that the RP subset should be extensively characterized for anticancer therapeutic potential as it relates to the DNA damage response. This single cell profiling approach advances a chemical biology platform to dissect how systematic variations in chemical structure can profoundly and differentially impact basic functions of healthy and diseased cells.
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Affiliation(s)
- Hannah L. Thirman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN, USA
| | - Madeline J. Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren E. Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
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4
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Bewersdorf JP, Shallis RM, Sharon E, Park S, Ramaswamy R, Roe CE, Irish JM, Caldwell A, Wei W, Yacoub A, Madanat YF, Zeidner JF, Altman JK, Odenike O, Yerrabothala S, Kovacsovics T, Podoltsev NA, Halene S, Little RF, Piekarz R, Gore SD, Kim TK, Zeidan AM. A multicenter phase Ib trial of the histone deacetylase inhibitor entinostat in combination with pembrolizumab in patients with myelodysplastic syndromes/neoplasms or acute myeloid leukemia refractory to hypomethylating agents. Ann Hematol 2024; 103:105-116. [PMID: 38036712 DOI: 10.1007/s00277-023-05552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Patients with myelodysplastic syndromes/neoplasms (MDS) or acute myeloid leukemia (AML) with hypomethylating agent failure have a poor prognosis. Myeloid-derived suppressor cells (MDSCs) can contribute to MDS progression and mediate resistance to anti-PD1 therapy. As histone deacetylase inhibitors (HDACi) decrease MDSCs in preclinical models, we conducted an investigator-initiated, NCI-Cancer Therapy Evaluation Program-sponsored, multicenter, dose escalation, and expansion phase Ib trial (NCT02936752) of the HDACi entinostat and the anti-PD1 antibody pembrolizumab. Twenty-eight patients (25 MDS and 3 AML) were enrolled. During dose escalation (n=13 patients), there was one dose-limiting toxicity (DLT) on dose level (DL) 1 (G5 pneumonia/bronchoalveolar hemorrhage) and two DLTs at DL 2 (G3 pharyngeal mucositis and G3 anorexia). Per the 3 + 3 dose escalation design, DL 1 (entinostat 8 mg PO days 1 and 15 + pembrolizumab 200 mg IV day 1 every 21 days) was expanded and another 15 patients were enrolled. Hematologic adverse events (AEs) were common. The most common non-hematologic ≥G3 AEs were infection (32%), hypoxia/respiratory failure (11%), and dyspnea (11%). There were no protocol-defined responses among the 28 patients enrolled. Two patients achieved a marrow complete remission (mCR). Using a systems immunology approach with mass cytometry and machine learning analysis, mCR patients had increased classical monocytes and macrophages but there was no significant change of MDSCs. In conclusion, combining entinostat with pembrolizumab in patients with advanced MDS and AML was associated with limited clinical efficacy and substantial toxicity. Absence of an effect on MDSCs could be a potential explanation for the limited efficacy of this combination. ClinicalTrial.gov Identifier: NCT02936752.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Rory M Shallis
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Elad Sharon
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Silvia Park
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rahul Ramaswamy
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA
| | - Anne Caldwell
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Wei Wei
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Abdulraheem Yacoub
- The Division of Hematologic Malignancies and Cellular Therapeutics (HMCT), The University of Kansas Cancer Center, Westwood, KS, USA
| | - Yazan F Madanat
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua F Zeidner
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jessica K Altman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | | | | | | | - Nikolai A Podoltsev
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Richard F Little
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Richard Piekarz
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Steven D Gore
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Tae Kon Kim
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA.
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Hematology Section, Department of Internal Medicine, Yale School of Medicine, Yale University, 333 Cedar Street, PO Box 208028, New Haven, CT, 06520-8028, USA.
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5
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Khanolkar A, Liu G, Simpson Schneider BM. Defining the Basal and Immunomodulatory Mediator-Induced Phosphoprotein Signature in Pediatric B Cell Acute Lymphoblastic Leukemia (B-ALL) Diagnostic Samples. Int J Mol Sci 2023; 24:13937. [PMID: 37762241 PMCID: PMC10531382 DOI: 10.3390/ijms241813937] [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: 06/29/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
It is theorized that dysregulated immune responses to infectious insults contribute to the development of pediatric B-ALL. In this context, our understanding of the immunomodulatory-mediator-induced signaling responses of leukemic blasts in pediatric B-ALL diagnostic samples is rather limited. Hence, in this study, we defined the signaling landscape of leukemic blasts, as well as normal mature B cells and T cells residing in diagnostic samples from 63 pediatric B-ALL patients. These samples were interrogated with a range of immunomodulatory-mediators within 24 h of collection, and phosflow analyses of downstream proximal signaling nodes were performed. Our data reveal evidence of basal hyperphosphorylation across a broad swath of these signaling nodes in leukemic blasts in contrast to normal mature B cells and T cells in the same sample. We also detected similarities in the phosphoprotein signature between blasts and mature B cells in response to IFNγ and IL-2 treatment, but significant divergence in the phosphoprotein signature was observed between blasts and mature B cells in response to IL-4, IL-7, IL-10, IL-21 and CD40 ligand treatment. Our results demonstrate the existence of both symmetry and asymmetry in the phosphoprotein signature between leukemic and non-leukemic cells in pediatric B-ALL diagnostic samples.
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Affiliation(s)
- Aaruni Khanolkar
- Department of Pathology, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pathology, Northwestern University, Chicago, IL 60611, USA
| | - Guorong Liu
- Department of Pathology, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
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6
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Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556277. [PMID: 37732260 PMCID: PMC10508777 DOI: 10.1101/2023.09.04.556277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
To further realize proteomics of archived tissues for translational research, we introduce a hybrid microfluidic platform for high-specificity, high-sensitivity protein detection from individual chemically fixed cells. To streamline processing-to-analysis workflows and minimize signal loss, DropBlot serially integrates sample preparation using droplet-based antigen retrieval from single fixed cells with unified analysis-on-a-chip comprising microwell-based antigen extraction followed by chip-based single-cell western blotting. A water-in-oil droplet formulation proves robust to the harsh chemical (SDS, 6M urea) and thermal conditions (98°C, 1-2 hr.) required for sufficient antigen retrieval, and the electromechanical conditions required for electrotransfer of retrieved antigen from microwell-encapsulated droplets to single-cell electrophoresis. Protein-target retrieval was demonstrated for unfixed, paraformaldehyde-(PFA), and methanol-fixed cells. We observed higher protein electrophoresis separation resolution from PFA-fixed cells with sufficient immunoreactivity confirmed for key targets (HER2, GAPDH, EpCAM, Vimentin) from both fixation chemistries. Multiple forms of EpCAM and Vimentin were detected, a hallmark strength of western-blot analysis. DropBlot of PFA-fixed human-derived breast tumor specimens (n = 5) showed antigen retrieval from cells archived frozen for 6 yrs. DropBlot could provide a precision integrated workflow for single-cell resolution protein-biomarker mining of precious biospecimen repositories.
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7
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Mas G, Man N, Nakata Y, Martinez-Caja C, Karl D, Beckedorff F, Tamiro F, Chen C, Duffort S, Itonaga H, Mookhtiar AK, Kunkalla K, Valencia AM, Collings CK, Kadoch C, Vega F, Kogan SC, Shiekhattar R, Morey L, Bilbao D, Nimer SD. The SWI/SNF chromatin-remodeling subunit DPF2 facilitates NRF2-dependent antiinflammatory and antioxidant gene expression. J Clin Invest 2023; 133:e158419. [PMID: 37200093 PMCID: PMC10313367 DOI: 10.1172/jci158419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
During emergency hematopoiesis, hematopoietic stem cells (HSCs) rapidly proliferate to produce myeloid and lymphoid effector cells, a response that is critical against infection or tissue injury. If unresolved, this process leads to sustained inflammation, which can cause life-threatening diseases and cancer. Here, we identify a role of double PHD fingers 2 (DPF2) in modulating inflammation. DPF2 is a defining subunit of the hematopoiesis-specific BAF (SWI/SNF) chromatin-remodeling complex, and it is mutated in multiple cancers and neurological disorders. We uncovered that hematopoiesis-specific Dpf2-KO mice developed leukopenia, severe anemia, and lethal systemic inflammation characterized by histiocytic and fibrotic tissue infiltration resembling a clinical hyperinflammatory state. Dpf2 loss impaired the polarization of macrophages responsible for tissue repair, induced the unrestrained activation of Th cells, and generated an emergency-like state of HSC hyperproliferation and myeloid cell-biased differentiation. Mechanistically, Dpf2 deficiency resulted in the loss of the BAF catalytic subunit BRG1 from nuclear factor erythroid 2-like 2-controlled (NRF2-controlled) enhancers, impairing the antioxidant and antiinflammatory transcriptional response needed to modulate inflammation. Finally, pharmacological reactivation of NRF2 suppressed the inflammation-mediated phenotypes and lethality of Dpf2Δ/Δ mice. Our work establishes an essential role of the DPF2-BAF complex in licensing NRF2-dependent gene expression in HSCs and immune effector cells to prevent chronic inflammation.
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Affiliation(s)
- Gloria Mas
- Sylvester Comprehensive Cancer Center and
| | - Na Man
- Sylvester Comprehensive Cancer Center and
| | - Yuichiro Nakata
- Sylvester Comprehensive Cancer Center and
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | | | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center and
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | - Chuan Chen
- Sylvester Comprehensive Cancer Center and
| | | | | | | | | | - Alfredo M. Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Chemical Biology Program, Harvard University, Cambridge, Massachusetts, USA
| | - Clayton K. Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Francisco Vega
- Sylvester Comprehensive Cancer Center and
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Scott C. Kogan
- Helen Diller Family Comprehensive Cancer Center and
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center and
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center and
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Daniel Bilbao
- Sylvester Comprehensive Cancer Center and
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Stephen D. Nimer
- Sylvester Comprehensive Cancer Center and
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
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Geben LC, Brockman AA, Chalkley MBL, Sweet SR, Gallagher JE, Scheuing AL, Simerly RB, Ess KC, Irish JM, Ihrie RA. Dephosphorylation of 4EBP1/2 Induces Prenatal Neural Stem Cell Quiescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528513. [PMID: 36824760 PMCID: PMC9948964 DOI: 10.1101/2023.02.14.528513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A limiting factor in the regenerative capacity of the adult brain is the abundance and proliferative ability of neural stem cells (NSCs). Adult NSCs are derived from a subpopulation of embryonic NSCs that temporarily enter quiescence during mid-gestation and remain quiescent until postnatal reactivation. Here we present evidence that the mechanistic/mammalian target of rapamycin (mTOR) pathway regulates quiescence entry in embryonic NSCs of the developing forebrain. Throughout embryogenesis, two downstream effectors of mTOR, p-4EBP1/2 T37/46 and p-S6 S240/244, were mutually exclusive in NSCs, rarely occurring in the same cell. While 4EBP1/2 was phosphorylated in stem cells undergoing mitosis at the ventricular surface, S6 was phosphorylated in more differentiated cells migrating away from the ventricle. Phosphorylation of 4EBP1/2, but not S6, was responsive to quiescence induction in cultured embryonic NSCs. Further, inhibition of p-4EBP1/2, but not p-S6, was sufficient to induce quiescence. Collectively, this work offers new insight into the regulation of quiescence entry in embryonic NSCs and, thereby, correct patterning of the adult brain. These data suggest unique biological functions of specific posttranslational modifications and indicate that the preferential inhibition of such modifications may be a useful therapeutic approach in neurodevelopmental diseases where NSC numbers, proliferation, and differentiation are altered.
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Affiliation(s)
- Laura C. Geben
- Program in Pharmacology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Asa A. Brockman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | | | - Serena R. Sweet
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Julia E. Gallagher
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Alexandra L. Scheuing
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Richard B. Simerly
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN 37235, USA
| | - Kevin C. Ess
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN 37235, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Rebecca A. Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN 37235, USA
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9
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Luque GM, Schiavi-Ehrenhaus LJ, Jabloñski M, Balestrini PA, Novero AG, Torres NI, Osycka-Salut CE, Darszon A, Krapf D, Buffone MG. High-throughput screening method for discovering CatSper inhibitors using membrane depolarization caused by external calcium chelation and fluorescent cell barcoding. Front Cell Dev Biol 2023; 11:1010306. [PMID: 36743410 PMCID: PMC9892719 DOI: 10.3389/fcell.2023.1010306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
The exclusive expression of CatSper in sperm and its critical role in sperm function makes this channel an attractive target for contraception. The strategy of blocking CatSper as a male, non-hormonal contraceptive has not been fully explored due to the lack of robust screening methods to discover novel and specific inhibitors. The reason for this lack of appropriate methodology is the structural and functional complexity of this channel. We have developed a high-throughput method to screen drugs with the capacity to block CatSper in mammalian sperm. The assay is based on removing external free divalent cations by chelation, inducing CatSper to efficiently conduct monovalent cations. Since Na+ is highly concentrated in the extracellular milieu, a sudden influx depolarizes the cell. Using CatSper1 KO sperm we demonstrated that this depolarization depends on CatSper function. A membrane potential (Em) assay was combined with fluorescent cell barcoding (FCB), enabling higher throughput flow cytometry based on unique fluorescent signatures of different sperm samples. These differentially labeled samples incubated in distinct experimental conditions can be combined into one tube for simultaneous acquisition. In this way, acquisition times are highly reduced, which is essential to perform larger screening experiments for drug discovery using live cells. Altogether, a simple strategy for assessing CatSper was validated, and this assay was used to develop a high-throughput drug screening for new CatSper blockers.
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Affiliation(s)
- Guillermina M. Luque
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina,*Correspondence: Guillermina M. Luque, ; Mariano G. Buffone,
| | | | - Martina Jabloñski
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Paula A. Balestrini
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Analia G. Novero
- Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Nicolás I. Torres
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Claudia E. Osycka-Salut
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM-CONICET), Buenos Aires, Argentina
| | | | - Dario Krapf
- Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Mariano G. Buffone
- Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina,*Correspondence: Guillermina M. Luque, ; Mariano G. Buffone,
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10
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Medina S, Ihrie RA, Irish JM. Learning cell identity in immunology, neuroscience, and cancer. Semin Immunopathol 2023; 45:3-16. [PMID: 36534139 PMCID: PMC9762661 DOI: 10.1007/s00281-022-00976-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
Suspension and imaging cytometry techniques that simultaneously measure hundreds of cellular features are powering a new era of cell biology and transforming our understanding of human tissues and tumors. However, a central challenge remains in learning the identities of unexpected or novel cell types. Cell identification rubrics that could assist trainees, whether human or machine, are not always rigorously defined, vary greatly by field, and differentially rely on cell intrinsic measurements, cell extrinsic tissue measurements, or external contextual information such as clinical outcomes. This challenge is especially acute in the context of tumors, where cells aberrantly express developmental programs that are normally time, location, or cell-type restricted. Well-established fields have contrasting practices for cell identity that have emerged from convention and convenience as much as design. For example, early immunology focused on identifying minimal sets of protein features that mark individual, functionally distinct cells. In neuroscience, features including morphology, development, and anatomical location were typical starting points for defining cell types. Both immunology and neuroscience now aim to link standardized measurements of protein or RNA to informative cell functions such as electrophysiology, connectivity, lineage potential, phospho-protein signaling, cell suppression, and tumor cell killing ability. The expansion of automated, machine-driven methods for learning cell identity has further created an urgent need for a harmonized framework for distinguishing cell identity across fields and technology platforms. Here, we compare practices in the fields of immunology and neuroscience, highlight concepts from each that might work well in the other, and propose ways to implement these ideas to study neural and immune cell interactions in brain tumors and associated model systems.
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Affiliation(s)
- Stephanie Medina
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Rebecca A. Ihrie
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Jonathan M. Irish
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
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11
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS NANO 2022; 16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
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12
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Liu R, Sun Y, Berthelet J, Bui LC, Xu X, Viguier M, Dupret JM, Deshayes F, Rodrigues Lima F. Biochemical, Enzymatic, and Computational Characterization of Recurrent Somatic Mutations of the Human Protein Tyrosine Phosphatase PTP1B in Primary Mediastinal B Cell Lymphoma. Int J Mol Sci 2022; 23:ijms23137060. [PMID: 35806064 PMCID: PMC9266312 DOI: 10.3390/ijms23137060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 12/16/2022] Open
Abstract
Human protein tyrosine phosphatase 1B (PTP1B) is a ubiquitous non-receptor tyrosine phosphatase that serves as a major negative regulator of tyrosine phosphorylation cascades of metabolic and oncogenic importance such as the insulin, epidermal growth factor receptor (EGFR), and JAK/STAT pathways. Increasing evidence point to a key role of PTP1B-dependent signaling in cancer. Interestingly, genetic defects in PTP1B have been found in different human malignancies. Notably, recurrent somatic mutations and splice variants of PTP1B were identified in human B cell and Hodgkin lymphomas. In this work, we analyzed the molecular and functional levels of three PTP1B mutations identified in primary mediastinal B cell lymphoma (PMBCL) patients and located in the WPD-loop (V184D), P-loop (R221G), and Q-loop (G259V). Using biochemical, enzymatic, and molecular dynamics approaches, we show that these mutations lead to PTP1B mutants with extremely low intrinsic tyrosine phosphatase activity that display alterations in overall protein stability and in the flexibility of the active site loops of the enzyme. This is in agreement with the key role of the active site loop regions, which are preorganized to interact with the substrate and to enable catalysis. Our study provides molecular and enzymatic evidence for the loss of protein tyrosine phosphatase activity of PTP1B active-site loop mutants identified in human lymphoma.
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Affiliation(s)
- Rongxing Liu
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Yujie Sun
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; (Y.S.); (X.X.)
| | - Jérémy Berthelet
- Université Paris Cité, CNRS, Centre d’Epigénétique et Destin Cellulaire, F-75013 Paris, France;
| | - Linh-Chi Bui
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Ximing Xu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266071, China; (Y.S.); (X.X.)
| | - Mireille Viguier
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Jean-Marie Dupret
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Frédérique Deshayes
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; (R.L.); (L.-C.B.); (M.V.); (J.-M.D.); (F.D.)
- Correspondence:
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13
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Kramer KJ, Wilfong EM, Voss K, Barone SM, Shiakolas AR, Raju N, Roe CE, Suryadevara N, Walker LM, Wall SC, Paulo A, Schaefer S, Dahunsi D, Westlake CS, Crowe JE, Carnahan RH, Rathmell JC, Bonami RH, Georgiev IS, Irish JM. Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine. Nat Commun 2022; 13:3466. [PMID: 35710908 PMCID: PMC9201272 DOI: 10.1038/s41467-022-31142-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/26/2022] [Indexed: 12/15/2022] Open
Abstract
RNA-based vaccines against SARS-CoV-2 have proven critical to limiting COVID-19 disease severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. Here we identify and characterize antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 using multiple single-cell technologies for in depth analysis of longitudinal samples from a cohort of healthy participants. Mass cytometry and unbiased machine learning pinpoint an expanding, population of antigen-specific memory CD4+ and CD8+ T cells with characteristics of follicular or peripheral helper cells. B cell receptor sequencing suggest progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlate with eventual SARS-CoV-2 IgG, and a participant lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms identify an antigen-specific cellular basis of RNA vaccine-based immunity.
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Affiliation(s)
- Kevin J Kramer
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
| | - Erin M Wilfong
- Department of Medicine, Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN, 37232, USA
| | - Kelsey Voss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sierra M Barone
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andrea R Shiakolas
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
| | - Nagarajan Raju
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
| | - Caroline E Roe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | | | - Lauren M Walker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
| | - Steven C Wall
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
| | - Ariana Paulo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
| | - Samuel Schaefer
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA
| | - Debolanle Dahunsi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA
| | - Camille S Westlake
- Department of Medicine, Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN, 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Program in Computational Microbiology and Immunology, Nashville, TN, 37232, USA
| | | | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA.
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN, 37232, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Vanderbilt Program in Computational Microbiology and Immunology, Nashville, TN, 37232, USA.
| | - Rachel H Bonami
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Medicine, Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA.
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN, 37232, USA.
- Vanderbilt Program in Computational Microbiology and Immunology, Nashville, TN, 37232, USA.
| | - Ivelin S Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Vanderbilt Vaccine Center, Nashville, TN, 37232, USA.
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA.
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN, 37232, USA.
- Vanderbilt Program in Computational Microbiology and Immunology, Nashville, TN, 37232, USA.
| | - Jonathan M Irish
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Nashville, TN, 37232, USA.
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, TN, 37232, USA.
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Vanderbilt Program in Computational Microbiology and Immunology, Nashville, TN, 37232, USA.
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14
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Preservation of lymphocyte functional fitness in perinatally-infected and treated HIV+ pediatric patients displaying sub-optimal viral control. COMMUNICATIONS MEDICINE 2022; 2. [PMID: 35434722 PMCID: PMC9012494 DOI: 10.1038/s43856-022-00085-9] [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: 11/09/2022] Open
Abstract
Abstract
Background
Host–pathogen dynamics associated with HIV infection are quite distinct in children versus adults. We interrogated the functional fitness of the lymphocyte responses in two cohorts of perinatally infected HIV+ pediatric subjects with early anti-retroviral therapy (ART) initiation but divergent patterns of virologic control. We hypothesized that sub-optimal viral control would compromise immune functional fitness.
Methods
The immune responses in the two HIV+ cohorts (n = 6 in each cohort) were benchmarked against the responses measured in age-range matched, uninfected healthy control subjects (n = 11) by utilizing tests for normality, and comparison [the Kruskal–Wallis test, and the two-tailed Mann–Whitney U test (where appropriate)]. Lymphocyte responses were examined by intra-cellular cytokine secretion, degranulation assays as well as phosflow. A subset of these data were further queried by an automated clustering algorithm. Finally, we evaluated the humoral immune responses to four childhood vaccines in all three cohorts.
Results
We demonstrate that contrary to expectations pediatric HIV+ patients with sub-optimal viral control display no significant deficits in immune functional fitness. In fact, the patients that display better virologic control lack functional Gag-specific T cell responses and compared to healthy controls they display signaling deficits and an enrichment of mitogen-stimulated CD3 negative and positive lymphocyte clusters with suppressed cytokine production.
Conclusions
These results highlight the immune resilience in HIV+ children on ART with sub-optimal viral control. With respect to HIV+ children on ART with better viral control, our data suggest that this cohort might potentially benefit from targeted interventions that might mitigate cell-mediated immune functional quiescence.
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15
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Reisman BJ, Barone SM, Bachmann BO, Irish JM. DebarcodeR increases fluorescent cell barcoding capacity and accuracy. Cytometry A 2021; 99:946-953. [PMID: 33960644 PMCID: PMC8410645 DOI: 10.1002/cyto.a.24363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/25/2022]
Abstract
Fluorescent cell barcoding (FCB) enables efficient collection of tens to hundreds of flow cytometry samples by covalently marking cells with varying concentration of spectrally distinct dyes. A key consideration in FCB is to balance the density of dye barcodes, the complexity of cells in the sample, and the desired accuracy of the debarcoding. Unfortunately, barcoding bench and computational methods have not benefited from the high dimensional revolution in cytometry due to a lack of automated computational tools that effectively balance these common cytometry needs. DebarcodeR addresses these unmet needs by providing a framework for computational debarcoding augmented by improvements to experimental methods. Adaptive regression modeling accounted for differential dye uptake between different cell types and Gaussian mixture modeling provided a robust method to probabilistically assign cells to samples. Assignment tolerance parameters are available to allow users to balance high cell recovery with accurate assignments. Improvements to experimental methods include: (1) inclusion of an "external standard" control where a pool of all cells was stained a single level of each barcoding dyes and (2) an "internal standard" where each cell is stained with a single level of a separate dye. DebarcodeR significantly improved speed, accuracy, and reproducibility of FCB while avoiding selective loss of unusual cell subsets when debarcoding microtiter plates of cell lines and heterogenous mixtures of primary cells. DebarcodeR is available on Github as an R package that works with flowCore and Cytoverse packages at github.com/cytolab/DebarcodeR.
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Affiliation(s)
| | - Sierra M. Barone
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Jonathan M. Irish
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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16
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Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34341788 DOI: 10.1101/2021.07.28.453981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA-based vaccines against SARS-CoV-2 are critical to limiting COVID-19 severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. We used single-cell technologies to identify and characterized antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 in longitudinal samples from a cohort of healthy donors. Mass cytometry and machine learning pinpointed a novel expanding, population of antigen-specific non-canonical memory CD4 + and CD8 + T cells. B cell sequencing suggested progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlated with eventual SARS-CoV-2 IgG and a donor lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms reveal an antigen-specific cellular basis of RNA vaccine-based immunity. ONE SENTENCE SUMMARY Single-cell profiling reveals the cellular basis of the antigen-specific response to the BNT162b2 SARS-CoV-2 RNA vaccine.
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17
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Roe CE, Hayes MJ, Barone SM, Irish JM. Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. ACTA ACUST UNITED AC 2021; 93:e71. [PMID: 32250555 DOI: 10.1002/cpcy.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article presents a single experiment designed to introduce a trainee to multiple advanced bench and analysis techniques, including high-dimensional cytometry, profiling cell signaling networks, functional assays with primary human tissue, and single-cell analysis with machine learning tools. The trainee is expected to have only minimal laboratory experience and is not required to have any prior training in flow cytometry, immunology, or data science. This article aims to introduce the advanced research areas with a design that is robust enough that novice trainees will succeed, flexible enough to allow some project customization, and fundamental enough that the skills and knowledge gained will provide a template for future experiments. For advanced users, the updated phospho-flow protocol and the established controls, best practices, and expected outcomes presented here also provide a framework for adapting these tools in new areas with unexplored biology. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Phospho-protein stimulation and mass cytometry data collection Support Protocol: Analysis of signaling mass cytometry data.
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Affiliation(s)
- Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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18
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Koenig A, Charmetant X, Barba T, Sicard A, Espi M, Dussurgey S, Thaunat O. Improved cell signaling analysis by biofunctionalized nanospheres and imaging flow cytometry. Cytometry A 2021; 99:1079-1090. [PMID: 33866668 DOI: 10.1002/cyto.a.24354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/16/2021] [Accepted: 04/07/2021] [Indexed: 11/11/2022]
Abstract
The analysis of immune cell signaling is critical for the understanding of the biology and pathology of the immune system, and thus a mandatory step for the development of efficient biomarkers and targeted therapies. Phosflow, which has progressively replaced the traditional western blot approach, relies on flow cytometry to analyze various signaling pathways at a single-cell level. This technique however suffers a lack of sensitivity largely due to the low signal/noise ratio that characterizes cell signaling analysis. In this study, we describe a new technique, which combines the use of biofunctionalized nanospheres (i.e., synthetic particulate antigens, SPAg) to stimulate the immune cells in suspension and imaging flow cytometry to identify homogenously-stimulated cells and quantify the activity of the chosen signaling pathway in selected subcellular regions of interest. Using BCR signaling as model, we demonstrate that SIBERIAN (SPAg-assIsted suB-cEllulaR sIgnaling ANalysis) allows assessing immune cell signaling with unprecedented sensitivity and specificity.
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Affiliation(s)
- Alice Koenig
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Xavier Charmetant
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Thomas Barba
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Antoine Sicard
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Maxime Espi
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Sébastien Dussurgey
- University of Lyon, ENS de Lyon, Inserm, CNRS SFR Biosciences US8 UMS3444, UCBL, Lyon, France
| | - Olivier Thaunat
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
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19
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Glass DR, Tsai AG, Oliveria JP, Hartmann FJ, Kimmey SC, Calderon AA, Borges L, Glass MC, Wagar LE, Davis MM, Bendall SC. An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. Immunity 2021; 53:217-232.e5. [PMID: 32668225 PMCID: PMC7369630 DOI: 10.1016/j.immuni.2020.06.013] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/03/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022]
Abstract
B cells are capable of a wide range of effector functions including antibody secretion, antigen presentation, cytokine production, and generation of immunological memory. A consistent strategy for classifying human B cells by using surface molecules is essential to harness this functional diversity for clinical translation. We developed a highly multiplexed screen to quantify the co-expression of 351 surface molecules on millions of human B cells. We identified differentially expressed molecules and aligned their variance with isotype usage, VDJ sequence, metabolic profile, biosynthesis activity, and signaling response. Based on these analyses, we propose a classification scheme to segregate B cells from four lymphoid tissues into twelve unique subsets, including a CD45RB+CD27− early memory population, a class-switched CD39+ tonsil-resident population, and a CD19hiCD11c+ memory population that potently responds to immune activation. This classification framework and underlying datasets provide a resource for further investigations of human B cell identity and function. A mass cytometry screen reveals 98 surface molecules expressed by human B cells High-dimensional analysis identifies twelve B cell subsets across four tissues CD45RB, CD11c, CD39, CD73, and CD95 define subsets of antigen-experienced B cells Isotype usage, signaling, and metabolism vary in accordance with cell surface phenotype
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Affiliation(s)
- David R Glass
- Immunology Graduate Program, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Albert G Tsai
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - John Paul Oliveria
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA; Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, L8S4K1, Canada
| | - Felix J Hartmann
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Samuel C Kimmey
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA; Department of Developmental Biology, Stanford University, Stanford CA, 94305, USA
| | - Ariel A Calderon
- Immunology Graduate Program, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Marla C Glass
- Department of Surgery, Stanford University, Stanford CA, 94305, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University, Stanford CA, 94305, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford CA, 94305, USA
| | - Sean C Bendall
- Immunology Graduate Program, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA.
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20
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Understanding breast cancer heterogeneity through non-genetic heterogeneity. Breast Cancer 2021; 28:777-791. [PMID: 33723745 DOI: 10.1007/s12282-021-01237-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
Abstract
Intricacy in treatment and diagnosis of breast cancer has been an obstacle due to genotype and phenotype heterogeneity. Understanding of non-genetic heterogeneity mechanisms along with considering role of genetic heterogeneity may fill the gaps in landscape painting of heterogeneity. The main factors contribute to non-genetic heterogeneity including: transcriptional pulsing/bursting or discontinuous transcriptions, stochastic partitioning of components at cell division and various signal transduction from tumor ecosystem. Throughout this review, we desired to provide a conceptual framework focused on non-genetic heterogeneity, which has been intended to offer insight into prediction, diagnosis and treatment of breast cancer.
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21
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Khanolkar A, Wilks JD, Liu G, Simpson BM, Caparelli EA, Kirschmann DA, Bergerson J, Fuleihan RL. A case of aberrant CD8 T cell-restricted IL-7 signaling with a Janus kinase 3 defect-associated atypical severe combined immunodeficiency. Immunol Res 2020; 68:13-27. [PMID: 32215810 DOI: 10.1007/s12026-020-09123-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Severe combined immunodeficiency (SCID) disorders compromise lymphocyte numbers and/or function. One subset of SCID typically affects T cell and Natural Killer (NK) cell development in tandem (T-B+NK-) due to mutations arising in the genes encoding the common γ chain or Janus Kinase 3 (JAK3). In rare circumstances, mutations in the JAK3 gene have been reported to cause atypical SCID that selectively affects T cells (T-B+NK+). Here we describe a case involving a female infant who was referred to our institution on day nine of life following an abnormal newborn screen result for T-SCID. Immunological assessments revealed a T-B+NK+ phenotype and molecular analyses, including whole exome sequencing, identified compound heterozygous JAK3 variants (R117C and E658K). Pre-transplant phosflow analyses revealed a persistent IL-7 signaling defect, based on phospho-STAT5 measurements, only in CD8 but not CD4 T cells. Intriguingly, phospho-STAT5 signals in response to IL-2 stimulation were not affected in either CD4 or CD8 T cells. The pre-transplant clinical course was unremarkable, and the patient received a cord-blood stem cell transplant on day 716 of life. Post-transplant monitoring revealed that despite normalization of lymphocyte counts, the CD8 T cell-restricted IL-7 signaling defect was still evident at day 627 post-transplant (phospho-STAT5 signal in CD8 T cells was > 60% reduced compared with CD4 T cells). The post-transplant clinical course has also been complicated by identification of autoimmune responses and likely GVHD-induced ichthyosis. To the best of our knowledge, this report represents the third case of JAK3-associated atypical SCID reported in the literature.
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Affiliation(s)
- Aaruni Khanolkar
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA. .,Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Chicago, IL, 60611, USA.
| | - Jeffrey D Wilks
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Guorong Liu
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Bridget M Simpson
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Edward A Caparelli
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Dawn A Kirschmann
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Jenna Bergerson
- Department of Pediatrics, Division of Allergy and Immunology, Feinberg School of Medicine, Chicago, IL, 60611, USA.,Primary Immunodeficiency Clinic, NIH/NIAID, 9000 Rockville Pike, Bldg. 10, Room 11N244A MSC 1960, Bethesda, MD, 20892, USA
| | - Ramsay L Fuleihan
- Department of Pediatrics, Division of Allergy and Immunology, Feinberg School of Medicine, Chicago, IL, 60611, USA.,Division of Allergy & Immunology, Sidra Medicine, Doha, Qatar
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22
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Alonso-Alonso R, Rodriguez M, Morillo D, Cordoba R, Piris MA. An analysis of genetic targets for guiding clinical management of follicular lymphoma. Expert Rev Hematol 2020; 13:1361-1372. [PMID: 33176509 DOI: 10.1080/17474086.2020.1850252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Introduction: Follicular lymphoma (FL) is one of the most common non-Hodgkin lymphoma (NHL) types, where genomic studies have accumulated potentially useful information about frequently mutated genes and deregulated pathways, which has allowed to a better understanding of the molecular pathogenesis of this tumor and the complex interrelationship between the tumoral cells and the stroma. Areas covered: The results of the molecular studies performed on Follicular Lymphoma have been here reviewed, summarizing the results of the clinical trials so far developed on this basis and discussing the reasons for the successes and failures. Searches were performed on June 1st, 2020, in PubMed and ClinicalTrials.gov. Expert opinion: Targeted therapy for follicular lymphoma has multiple opportunities including the use of epigenetic drugs, PI3K inhibitors, modifiers of the immune stroma and others. Data currently known on FL pathogenesis suggest that combining these treatments with immunotherapy should be explored in clinical trials, mainly for patients with clinical progression or adverse prognostic markers. Association of targeted trials with dynamic molecular studies of the tumor and serum samples is advised. Chemotherapy-free approaches should also be explored as first-line therapy for FL patients.
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Affiliation(s)
- Ruth Alonso-Alonso
- Services of Pathology and Haematology, Fundación Jimenez Diaz , Madrid, Spain
| | - Marta Rodriguez
- Services of Pathology and Haematology, Fundación Jimenez Diaz , Madrid, Spain
| | - Daniel Morillo
- Services of Pathology and Haematology, Fundación Jimenez Diaz , Madrid, Spain
| | - Raul Cordoba
- Services of Pathology and Haematology, Fundación Jimenez Diaz , Madrid, Spain
| | - Miguel A Piris
- Services of Pathology and Haematology, Fundación Jimenez Diaz , Madrid, Spain
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23
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Klofas LK, Short BP, Snow JP, Sinnaeve J, Rushing GV, Westlake G, Weinstein W, Ihrie RA, Ess KC, Carson RP. DEPDC5 haploinsufficiency drives increased mTORC1 signaling and abnormal morphology in human iPSC-derived cortical neurons. Neurobiol Dis 2020; 143:104975. [PMID: 32574724 PMCID: PMC7462127 DOI: 10.1016/j.nbd.2020.104975] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/21/2020] [Accepted: 06/13/2020] [Indexed: 01/21/2023] Open
Abstract
Mutations in the DEPDC5 gene can cause epilepsy, including forms with and without brain malformations. The goal of this study was to investigate the contribution of DEPDC5 gene dosage to the underlying neuropathology of DEPDC5-related epilepsies. We generated induced pluripotent stem cells (iPSCs) from epilepsy patients harboring heterozygous loss of function mutations in DEPDC5. Patient iPSCs displayed increases in both phosphorylation of ribosomal protein S6 and proliferation rate, consistent with elevated mTORC1 activation. In line with these findings, we observed increased soma size in patient iPSC-derived cortical neurons that was rescued with rapamycin treatment. These data indicate that human cells heterozygous for DEPDC5 loss-of-function mutations are haploinsufficient for control of mTORC1 signaling. Our findings suggest that human pathology differs from mouse models of DEPDC5-related epilepsies, which do not show consistent phenotypic differences in heterozygous neurons, and support the need for human-based models to affirm and augment the findings from animal models of DEPDC5-related epilepsy.
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Affiliation(s)
- Lindsay K Klofas
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Brittany P Short
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John P Snow
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Justine Sinnaeve
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Grant Westlake
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Will Weinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca A Ihrie
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kevin C Ess
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Robert P Carson
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA.
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24
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Beckermann KE, Hongo R, Ye X, Young K, Carbonell K, Healey DCC, Siska PJ, Barone S, Roe CE, Smith CC, Vincent BG, Mason FM, Irish JM, Rathmell WK, Rathmell JC. CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation. JCI Insight 2020; 5:138729. [PMID: 32814710 PMCID: PMC7455120 DOI: 10.1172/jci.insight.138729] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
Metabolic reprogramming dictates the fate and function of stimulated T cells, yet these pathways can be suppressed in T cells in tumor microenvironments. We previously showed that glycolytic and mitochondrial adaptations directly contribute to reducing the effector function of renal cell carcinoma (RCC) CD8+ tumor-infiltrating lymphocytes (TILs). Here we define the role of these metabolic pathways in the activation and effector functions of CD8+ RCC TILs. CD28 costimulation plays a key role in augmenting T cell activation and metabolism, and is antagonized by the inhibitory and checkpoint immunotherapy receptors CTLA4 and PD-1. While RCC CD8+ TILs were activated at a low level when stimulated through the T cell receptor alone, addition of CD28 costimulation greatly enhanced activation, function, and proliferation. CD28 costimulation reprogrammed RCC CD8+ TIL metabolism with increased glycolysis and mitochondrial oxidative metabolism, possibly through upregulation of GLUT3. Mitochondria also fused to a greater degree, with higher membrane potential and overall mass. These phenotypes were dependent on glucose metabolism, as the glycolytic inhibitor 2-deoxyglucose both prevented changes to mitochondria and suppressed RCC CD8+ TIL activation and function. These data show that CD28 costimulation can restore RCC CD8+ TIL metabolism and function through rescue of T cell glycolysis that supports mitochondrial mass and activity.
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Affiliation(s)
| | - Rachel Hongo
- Department of Medicine, Division of Hematology and Oncology, and
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kirsten Young
- Department of Medicine, Division of Hematology and Oncology, and
| | - Katie Carbonell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diana C Contreras Healey
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peter J Siska
- Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sierra Barone
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Christof C Smith
- Lineberger Comprehensive Cancer Center; Department of Medicine Division of Hematology and Oncology, Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center; Department of Medicine Division of Hematology and Oncology, Department of Microbiology and Immunology, Curriculum in Bioinformatics and Computational Biology, Computational Medicine Program, University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, and
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, and.,Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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25
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Leelatian N, Sinnaeve J, Mistry AM, Barone SM, Brockman AA, Diggins KE, Greenplate AR, Weaver KD, Thompson RC, Chambless LB, Mobley BC, Ihrie RA, Irish JM. Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells. eLife 2020; 9:56879. [PMID: 32573435 PMCID: PMC7340505 DOI: 10.7554/elife.56879] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
A goal of cancer research is to reveal cell subsets linked to continuous clinical outcomes to generate new therapeutic and biomarker hypotheses. We introduce a machine learning algorithm, Risk Assessment Population IDentification (RAPID), that is unsupervised and automated, identifies phenotypically distinct cell populations, and determines whether these populations stratify patient survival. With a pilot mass cytometry dataset of 2 million cells from 28 glioblastomas, RAPID identified tumor cells whose abundance independently and continuously stratified patient survival. Statistical validation within the workflow included repeated runs of stochastic steps and cell subsampling. Biological validation used an orthogonal platform, immunohistochemistry, and a larger cohort of 73 glioblastoma patients to confirm the findings from the pilot cohort. RAPID was also validated to find known risk stratifying cells and features using published data from blood cancer. Thus, RAPID provides an automated, unsupervised approach for finding statistically and biologically significant cells using cytometry data from patient samples.
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Affiliation(s)
- Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Justine Sinnaeve
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States
| | - Akshitkumar M Mistry
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Asa A Brockman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States
| | - Kirsten E Diggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States
| | - Allison R Greenplate
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Kyle D Weaver
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Reid C Thompson
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Lola B Chambless
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Bret C Mobley
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Rebecca A Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
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26
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Abstract
The existence of cellular heterogeneity and its central relevance to biological phenomena provides a strong rationale for a need for analytical methods that enable analysis at the single-cell level. Analysis of the genome and transcriptome is possible at the single-cell level, but the comprehensive interrogation of the proteome with this level of resolution remains challenging. Single-cell protein analysis tools are advancing rapidly, however, and providing insights into collections of proteins with great relevance to cell and disease biology. Here, we review single-cell protein analysis technologies and assess their advantages and limitations. The emerging technologies presented have the potential to reveal new insights into tumour heterogeneity and therapeutic resistance, elucidate mechanisms of immune response and immunotherapy, and accelerate drug discovery.
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27
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Cossarizza A, Chang HD, Radbruch A, Acs A, Adam D, Adam-Klages S, Agace WW, Aghaeepour N, Akdis M, Allez M, Almeida LN, Alvisi G, Anderson G, Andrä I, Annunziato F, Anselmo A, Bacher P, Baldari CT, Bari S, Barnaba V, Barros-Martins J, Battistini L, Bauer W, Baumgart S, Baumgarth N, Baumjohann D, Baying B, Bebawy M, Becher B, Beisker W, Benes V, Beyaert R, Blanco A, Boardman DA, Bogdan C, Borger JG, Borsellino G, Boulais PE, Bradford JA, Brenner D, Brinkman RR, Brooks AES, Busch DH, Büscher M, Bushnell TP, Calzetti F, Cameron G, Cammarata I, Cao X, Cardell SL, Casola S, Cassatella MA, Cavani A, Celada A, Chatenoud L, Chattopadhyay PK, Chow S, Christakou E, Čičin-Šain L, Clerici M, Colombo FS, Cook L, Cooke A, Cooper AM, Corbett AJ, Cosma A, Cosmi L, Coulie PG, Cumano A, Cvetkovic L, Dang VD, Dang-Heine C, Davey MS, Davies D, De Biasi S, Del Zotto G, Cruz GVD, Delacher M, Bella SD, Dellabona P, Deniz G, Dessing M, Di Santo JP, Diefenbach A, Dieli F, Dolf A, Dörner T, Dress RJ, Dudziak D, Dustin M, Dutertre CA, Ebner F, Eckle SBG, Edinger M, Eede P, Ehrhardt GR, Eich M, Engel P, Engelhardt B, Erdei A, Esser C, Everts B, Evrard M, Falk CS, Fehniger TA, Felipo-Benavent M, Ferry H, Feuerer M, Filby A, Filkor K, Fillatreau S, Follo M, Förster I, Foster J, Foulds GA, Frehse B, Frenette PS, Frischbutter S, Fritzsche W, Galbraith DW, Gangaev A, Garbi N, Gaudilliere B, Gazzinelli RT, Geginat J, Gerner W, Gherardin NA, Ghoreschi K, Gibellini L, Ginhoux F, Goda K, Godfrey DI, Goettlinger C, González-Navajas JM, Goodyear CS, Gori A, Grogan JL, Grummitt D, Grützkau A, Haftmann C, Hahn J, Hammad H, Hämmerling G, Hansmann L, Hansson G, Harpur CM, Hartmann S, Hauser A, Hauser AE, Haviland DL, Hedley D, Hernández DC, Herrera G, Herrmann M, Hess C, Höfer T, Hoffmann P, Hogquist K, Holland T, Höllt T, Holmdahl R, Hombrink P, Houston JP, Hoyer BF, Huang B, Huang FP, Huber JE, Huehn J, Hundemer M, Hunter CA, Hwang WYK, Iannone A, Ingelfinger F, Ivison SM, Jäck HM, Jani PK, Jávega B, Jonjic S, Kaiser T, Kalina T, Kamradt T, Kaufmann SHE, Keller B, Ketelaars SLC, Khalilnezhad A, Khan S, Kisielow J, Klenerman P, Knopf J, Koay HF, Kobow K, Kolls JK, Kong WT, Kopf M, Korn T, Kriegsmann K, Kristyanto H, Kroneis T, Krueger A, Kühne J, Kukat C, Kunkel D, Kunze-Schumacher H, Kurosaki T, Kurts C, Kvistborg P, Kwok I, Landry J, Lantz O, Lanuti P, LaRosa F, Lehuen A, LeibundGut-Landmann S, Leipold MD, Leung LY, Levings MK, Lino AC, Liotta F, Litwin V, Liu Y, Ljunggren HG, Lohoff M, Lombardi G, Lopez L, López-Botet M, Lovett-Racke AE, Lubberts E, Luche H, Ludewig B, Lugli E, Lunemann S, Maecker HT, Maggi L, Maguire O, Mair F, Mair KH, Mantovani A, Manz RA, Marshall AJ, Martínez-Romero A, Martrus G, Marventano I, Maslinski W, Matarese G, Mattioli AV, Maueröder C, Mazzoni A, McCluskey J, McGrath M, McGuire HM, McInnes IB, Mei HE, Melchers F, Melzer S, Mielenz D, Miller SD, Mills KH, Minderman H, Mjösberg J, Moore J, Moran B, Moretta L, Mosmann TR, Müller S, Multhoff G, Muñoz LE, Münz C, Nakayama T, Nasi M, Neumann K, Ng LG, Niedobitek A, Nourshargh S, Núñez G, O’Connor JE, Ochel A, Oja A, Ordonez D, Orfao A, Orlowski-Oliver E, Ouyang W, Oxenius A, Palankar R, Panse I, Pattanapanyasat K, Paulsen M, Pavlinic D, Penter L, Peterson P, Peth C, Petriz J, Piancone F, Pickl WF, Piconese S, Pinti M, Pockley AG, Podolska MJ, Poon Z, Pracht K, Prinz I, Pucillo CEM, Quataert SA, Quatrini L, Quinn KM, Radbruch H, Radstake TRDJ, Rahmig S, Rahn HP, Rajwa B, Ravichandran G, Raz Y, Rebhahn JA, Recktenwald D, Reimer D, e Sousa CR, Remmerswaal EB, Richter L, Rico LG, Riddell A, Rieger AM, Robinson JP, Romagnani C, Rubartelli A, Ruland J, Saalmüller A, Saeys Y, Saito T, Sakaguchi S, de-Oyanguren FS, Samstag Y, Sanderson S, Sandrock I, Santoni A, Sanz RB, Saresella M, Sautes-Fridman C, Sawitzki B, Schadt L, Scheffold A, Scherer HU, Schiemann M, Schildberg FA, Schimisky E, Schlitzer A, Schlosser J, Schmid S, Schmitt S, Schober K, Schraivogel D, Schuh W, Schüler T, Schulte R, Schulz AR, Schulz SR, Scottá C, Scott-Algara D, Sester DP, Shankey TV, Silva-Santos B, Simon AK, Sitnik KM, Sozzani S, Speiser DE, Spidlen J, Stahlberg A, Stall AM, Stanley N, Stark R, Stehle C, Steinmetz T, Stockinger H, Takahama Y, Takeda K, Tan L, Tárnok A, Tiegs G, Toldi G, Tornack J, Traggiai E, Trebak M, Tree TI, Trotter J, Trowsdale J, Tsoumakidou M, Ulrich H, Urbanczyk S, van de Veen W, van den Broek M, van der Pol E, Van Gassen S, Van Isterdael G, van Lier RA, Veldhoen M, Vento-Asturias S, Vieira P, Voehringer D, Volk HD, von Borstel A, von Volkmann K, Waisman A, Walker RV, Wallace PK, Wang SA, Wang XM, Ward MD, Ward-Hartstonge KA, Warnatz K, Warnes G, Warth S, Waskow C, Watson JV, Watzl C, Wegener L, Weisenburger T, Wiedemann A, Wienands J, Wilharm A, Wilkinson RJ, Willimsky G, Wing JB, Winkelmann R, Winkler TH, Wirz OF, Wong A, Wurst P, Yang JHM, Yang J, Yazdanbakhsh M, Yu L, Yue A, Zhang H, Zhao Y, Ziegler SM, Zielinski C, Zimmermann J, Zychlinsky A. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). Eur J Immunol 2019; 49:1457-1973. [PMID: 31633216 PMCID: PMC7350392 DOI: 10.1002/eji.201970107] [Citation(s) in RCA: 699] [Impact Index Per Article: 139.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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Affiliation(s)
- Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, Univ. of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Andreas Acs
- Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Dieter Adam
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sabine Adam-Klages
- Institut für Transfusionsmedizin, Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | - William W. Agace
- Mucosal Immunology group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Immunology Section, Lund University, Lund, Sweden
| | - Nima Aghaeepour
- Departments of Anesthesiology, Pain and Perioperative Medicine; Biomedical Data Sciences; and Pediatrics, Stanford University, Stanford, CA, USA
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Matthieu Allez
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U1160, and Gastroenterology Department, Hôpital Saint-Louis – APHP, Paris, France
| | | | - Giorgia Alvisi
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Rozzano, Italy
| | | | - Immanuel Andrä
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Achille Anselmo
- Flow Cytometry Core, Humanitas Clinical and Research Center, Milan, Italy
| | - Petra Bacher
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Institut für Klinische Molekularbiologie, Christian-Albrechts Universität zu Kiel, Germany
| | | | - Sudipto Bari
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | | | | | - Wolfgang Bauer
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Sabine Baumgart
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Nicole Baumgarth
- Center for Comparative Medicine & Dept. Pathology, Microbiology & Immunology, University of California, Davis, CA, USA
| | - Dirk Baumjohann
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Planegg-Martinsried, Germany
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mary Bebawy
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney, Sydney, NSW, Australia
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Wolfgang Beisker
- Flow Cytometry Laboratory, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rudi Beyaert
- Department of Biomedical Molecular Biology, Center for Inflammation Research, Ghent University - VIB, Ghent, Belgium
| | - Alfonso Blanco
- Flow Cytometry Core Technologies, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Dominic A. Boardman
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Christian Bogdan
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Erlangen, Germany
- Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Medical Immunology Campus Erlangen, Erlangen, Germany
| | - Jessica G. Borger
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Giovanna Borsellino
- Neuroimmunology and Flow Cytometry Units, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Philip E. Boulais
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, New York, USA
| | | | - Dirk Brenner
- Luxembourg Institute of Health, Department of Infection and Immunity, Experimental and Molecular Immunology, Esch-sur-Alzette, Luxembourg
- Odense University Hospital, Odense Research Center for Anaphylaxis, University of Southern Denmark, Department of Dermatology and Allergy Center, Odense, Denmark
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Ryan R. Brinkman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
| | - Anna E. S. Brooks
- University of Auckland, School of Biological Sciences, Maurice Wilkins Center, Auckland, New Zealand
| | - Dirk H. Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
- Focus Group “Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München, Munich, Germany
| | - Martin Büscher
- Biophysics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Timothy P. Bushnell
- Department of Pediatrics and Shared Resource Laboratories, University of Rochester Medical Center, Rochester, NY, USA
| | - Federica Calzetti
- University of Verona, Department of Medicine, Section of General Pathology, Verona, Italy
| | - Garth Cameron
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Ilenia Cammarata
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
| | - Xuetao Cao
- National Key Laboratory of Medical Immunology, Nankai University, Tianjin, China
| | - Susanna L. Cardell
- Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - Stefano Casola
- The FIRC Institute of Molecular Oncology (FOM), Milan, Italy
| | - Marco A. Cassatella
- University of Verona, Department of Medicine, Section of General Pathology, Verona, Italy
| | - Andrea Cavani
- National Institute for Health, Migration and Poverty (INMP), Rome, Italy
| | - Antonio Celada
- Macrophage Biology Group, School of Biology, University of Barcelona, Barcelona, Spain
| | - Lucienne Chatenoud
- Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | | | - Sue Chow
- Divsion of Medical Oncology and Hematology, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Eleni Christakou
- Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institutes of Health Research Biomedical Research Centre at Guy’s and St. Thomas’ National Health Service, Foundation Trust and King’s College London, UK
| | - Luka Čičin-Šain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mario Clerici
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Department of Physiopathology and Transplants, University of Milan, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | | | - Laura Cook
- BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Anne Cooke
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Andrea M. Cooper
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Antonio Cosma
- National Cytometry Platform, Luxembourg Institute of Health, Department of Infection and Immunity, Esch-sur-Alzette, Luxembourg
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Pierre G. Coulie
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Ana Cumano
- Unit Lymphopoiesis, Department of Immunology, Institut Pasteur, Paris, France
| | - Ljiljana Cvetkovic
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Van Duc Dang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Chantip Dang-Heine
- Clinical Research Unit, Berlin Institute of Health (BIH), Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Martin S. Davey
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Derek Davies
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Sara De Biasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | | | - Gelo Victoriano Dela Cruz
- Novo Nordisk Foundation Center for Stem Cell Biology – DanStem, University of Copenhagen, Copenhagen, Denmark
| | - Michael Delacher
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Germany
| | - Silvia Della Bella
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Paolo Dellabona
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Günnur Deniz
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Immunology, Istanbul, Turkey
| | | | - James P. Di Santo
- Innate Immunty Unit, Department of Immunology, Institut Pasteur, Paris, France
- Institut Pasteur, Inserm U1223, Paris, France
| | - Andreas Diefenbach
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Francesco Dieli
- University of Palermo, Central Laboratory of Advanced Diagnosis and Biomedical Research, Department of Biomedicine, Neurosciences and Advanced Diagnostics, Palermo, Italy
| | - Andreas Dolf
- Flow Cytometry Core Facility, Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Thomas Dörner
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Dept. Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Regine J. Dress
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Diana Dudziak
- Department of Dermatology, Laboratory of Dendritic Cell Biology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Michael Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Charles-Antoine Dutertre
- Program in Emerging Infectious Disease, Duke-NUS Medical School, Singapore
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Friederike Ebner
- Institute of Immunology, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Germany
| | - Sidonia B. G. Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Matthias Edinger
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Germany
| | - Pascale Eede
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Germany
| | | | - Marcus Eich
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Pablo Engel
- University of Barcelona, Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Barcelona, Spain
| | | | - Anna Erdei
- Department of Immunology, University L. Eotvos, Budapest, Hungary
| | - Charlotte Esser
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Christine S. Falk
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Todd A. Fehniger
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mar Felipo-Benavent
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Principe Felipe Research Center, Valencia, Spain
| | - Helen Ferry
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Feuerer
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Germany
| | - Andrew Filby
- The Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Simon Fillatreau
- Institut Necker-Enfants Malades, Université Paris Descartes Sorbonne Paris Cité, Faculté de Médecine, AP-HP, Hôpital Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Paris, France
| | - Marie Follo
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Universitaetsklinikum FreiburgLighthouse Core Facility, Zentrum für Translationale Zellforschung, Klinik für Innere Medizin I, Freiburg, Germany
| | - Irmgard Förster
- Immunology and Environment, LIMES Institute, University of Bonn, Bonn, Germany
| | | | - Gemma A. Foulds
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
| | - Britta Frehse
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Paul S. Frenette
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Stefan Frischbutter
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Dermatology, Venereology and Allergology
| | - Wolfgang Fritzsche
- Nanobiophotonics Department, Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - David W. Galbraith
- School of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, USA
- Honorary Dean of Life Sciences, Henan University, Kaifeng, China
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalio Garbi
- Institute of Experimental Immunology, University of Bonn, Germany
| | - Brice Gaudilliere
- Stanford Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, CA, USA
| | - Ricardo T. Gazzinelli
- Fundação Oswaldo Cruz - Minas, Laboratory of Immunopatology, Belo Horizonte, MG, Brazil
- Department of Mecicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jens Geginat
- INGM - Fondazione Istituto Nazionale di Genetica Molecolare “Ronmeo ed Enrica Invernizzi”, Milan, Italy
| | - Wilhelm Gerner
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
- Christian Doppler Laboratory for Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Kamran Ghoreschi
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lara Gibellini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keisuke Goda
- Department of Bioengineering, University of California, Los Angeles, California, USA
- Department of Chemistry, University of Tokyo, Tokyo, Japan
- Institute of Technological Sciences, Wuhan University, Wuhan, China
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | | | - Jose M. González-Navajas
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Carl S. Goodyear
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Biomedical Research Centre, Glasgow, UK
| | - Andrea Gori
- Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, University of Milan
| | - Jane L. Grogan
- Cancer Immunology Research, Genentech, South San Francisco, CA, USA
| | | | - Andreas Grützkau
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Claudia Haftmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Jonas Hahn
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Hamida Hammad
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Zwijnaarde, Belgium
| | | | - Leo Hansmann
- Berlin Institute of Health (BIH), Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Goran Hansson
- Department of Medicine and Center for Molecular Medicine at Karolinska University Hospital, Solna, Sweden
| | | | - Susanne Hartmann
- Institute of Immunology, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Germany
| | - Andrea Hauser
- Department of Internal Medicine III, University Hospital Regensburg, Germany
| | - Anja E. Hauser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
- Department of Rheumatology and Clinical Immunology, Berlin Institute of Health, Berlin, Germany
| | - David L. Haviland
- Flow Cytometry, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - David Hedley
- Divsion of Medical Oncology and Hematology, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Daniela C. Hernández
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Medical Department I, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Guadalupe Herrera
- Cytometry Service, Incliva Foundation. Clinic Hospital and Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Martin Herrmann
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Christoph Hess
- Immunobiology Laboratory, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Thomas Höfer
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, Heidelberg, Germany
| | - Petra Hoffmann
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Germany
| | - Kristin Hogquist
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Tristan Holland
- Institute of Experimental Immunology, University of Bonn, Germany
| | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Computer Graphics and Visualization, Department of Intelligent Systems, TU Delft, Delft, The Netherlands
| | | | - Pleun Hombrink
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jessica P. Houston
- Department of Chemical & Materials Engineering, New Mexico State University, Las Cruces, NM, USA
| | - Bimba F. Hoyer
- Rheumatologie/Klinische Immunologie, Klinik für Innere Medizin I und Exzellenzzentrum Entzündungsmedizin, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Fang-Ping Huang
- Institute for Advanced Study (IAS), Shenzhen University, Shenzhen, China
| | - Johanna E. Huber
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Planegg-Martinsried, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Hundemer
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Christopher A. Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William Y. K. Hwang
- Department of Hematology, Singapore General Hospital, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore
- Executive Offices, National Cancer Centre Singapore, Singapore
| | - Anna Iannone
- Department of Diagnostic Medicine, Clinical and Public Health, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Florian Ingelfinger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sabine M Ivison
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Peter K. Jani
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Beatriz Jávega
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Stipan Jonjic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Toralf Kaiser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Tomas Kalina
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Thomas Kamradt
- Jena University Hospital, Institute of Immunology, Jena, Germany
| | | | - Baerbel Keller
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven L. C. Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ahad Khalilnezhad
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Srijit Khan
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jan Kisielow
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Paul Klenerman
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jasmin Knopf
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Germany
| | - Jay K. Kolls
- John W Deming Endowed Chair in Internal Medicine, Center for Translational Research in Infection and Inflammation Tulane School of Medicine, New Orleans, LA, USA
| | - Wan Ting Kong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Thomas Korn
- Department of Neurology, Technical University of Munich, Munich, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Hendy Kristyanto
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Kroneis
- Division of Cell Biology, Histology & Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jenny Kühne
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Désirée Kunkel
- Flow & Mass Cytometry Core Facility, Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Berlin, Germany
- BCRT Flow Cytometry Lab, Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Tomohiro Kurosaki
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Christian Kurts
- Institute of Experimental Immunology, University of Bonn, Germany
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jonathan Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olivier Lantz
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, Centre on Aging Sciences and Translational Medicine (Ce.S.I.-Me.T.), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
| | - Francesca LaRosa
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Agnès Lehuen
- Institut Cochin, CNRS8104, INSERM1016, Department of Endocrinology, Metabolism and Diabetes, Université de Paris, Paris, France
| | | | - Michael D. Leipold
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, CA, USA
| | - Leslie Y.T. Leung
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Megan K. Levings
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
| | - Andreia C. Lino
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Dept. Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Yanling Liu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Michael Lohoff
- Inst. f. Med. Mikrobiology and Hospital Hygiene, University of Marburg, Germany
| | - Giovanna Lombardi
- King’s College London, “Peter Gorer” Department of Immunobiology, London, UK
| | | | - Miguel López-Botet
- IMIM(Hospital de Mar Medical Research Institute), University Pompeu Fabra, Barcelona, Spain
| | - Amy E. Lovett-Racke
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Erik Lubberts
- Department of Rheumatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Herve Luche
- Centre d’Immunophénomique - CIPHE (PHENOMIN), Aix Marseille Université (UMS3367), Inserm (US012), CNRS (UMS3367), Marseille, France
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Rozzano, Italy
- Flow Cytometry Core, Humanitas Clinical and Research Center, Milan, Italy
| | - Sebastian Lunemann
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Holden T. Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Orla Maguire
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Florian Mair
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Kerstin H. Mair
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
- Christian Doppler Laboratory for Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Alberto Mantovani
- Istituto Clinico Humanitas IRCCS and Humanitas University, Pieve Emanuele, Milan, Italy
- William Harvey Research Institute, Queen Mary University, London, United Kingdom
| | - Rudolf A. Manz
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Aaron J. Marshall
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Glòria Martrus
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ivana Marventano
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Wlodzimierz Maslinski
- National Institute of Geriatrics, Rheumatology and Rehabilitation, Department of Pathophysiology and Immunology, Warsaw, Poland
| | - Giuseppe Matarese
- Treg Cell Lab, Dipartimento di Medicina Molecolare e Biotecologie Mediche, Università di Napoli Federico II and Istituto per l’Endocrinologia e l’Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli, Italy
| | - Anna Vittoria Mattioli
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
- Lab of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Christian Maueröder
- Cell Clearance in Health and Disease Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Mairi McGrath
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Helen M. McGuire
- Ramaciotti Facility for Human Systems Biology, and Discipline of Pathology, The University of Sydney, Camperdown, Australia
| | - Iain B. McInnes
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Biomedical Research Centre, Glasgow, UK
| | - Henrik E. Mei
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Fritz Melchers
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Susanne Melzer
- Clinical Trial Center Leipzig, University Leipzig, Leipzig, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Stephen D. Miller
- Interdepartmental Immunobiology Center, Dept. of Microbiology-Immunology, Northwestern Univ. Medical School, Chicago, IL, USA
| | - Kingston H.G. Mills
- Trinity College Dublin, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Hans Minderman
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, ANA Futura, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical and Experimental Medine, Linköping University, Linköping, Sweden
| | - Jonni Moore
- Abramson Cancer Center Flow Cytometry and Cell Sorting Shared Resource, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Barry Moran
- Trinity College Dublin, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesu Children’s Hospital, Rome, Italy
| | - Tim R. Mosmann
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Susann Müller
- Centre for Environmental Research - UFZ, Department Environmental Microbiology, Leipzig, Germany
| | - Gabriele Multhoff
- Institute for Innovative Radiotherapy (iRT), Experimental Immune Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Radiation Immuno-Oncology Group, Center for Translational Cancer Research Technische Universität München (TranslaTUM), Klinikum rechts der Isar, Munich, Germany
| | - Luis Enrique Muñoz
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Christian Münz
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba city, Chiba, Japan
| | - Milena Nasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- Discipline of Dermatology, University of Sydney, Sydney, New South Wales, Australia
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Antonia Niedobitek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Sussan Nourshargh
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, the University of Michigan, Ann Arbor, Michigan, USA
| | - José-Enrique O’Connor
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Aaron Ochel
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Oja
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Diana Ordonez
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alberto Orfao
- Department of Medicine, Cancer Research Centre (IBMCC-CSIC/USAL), Cytometry Service, University of Salamanca, CIBERONC and Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Eva Orlowski-Oliver
- Burnet Institute, AMREP Flow Cytometry Core Facility, Melbourne, Victoria, Australia
| | - Wenjun Ouyang
- Inflammation and Oncology, Research, Amgen Inc, South San Francisco, USA
| | | | - Raghavendra Palankar
- Department of Transfusion Medicine, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Isabel Panse
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Kovit Pattanapanyasat
- Center of Excellence for Flow Cytometry, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Malte Paulsen
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Dinko Pavlinic
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Livius Penter
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Christian Peth
- Biophysics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Jordi Petriz
- Functional Cytomics Group, Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain
| | - Federica Piancone
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Winfried F. Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Silvia Piconese
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - A. Graham Pockley
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
- Chromocyte Limited, Electric Works, Sheffield, UK
| | - Malgorzata Justyna Podolska
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
- Department for Internal Medicine 3, Institute for Rheumatology and Immunology, AG Munoz, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Zhiyong Poon
- Department of Hematology, Singapore General Hospital, Singapore
| | - Katharina Pracht
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Sally A. Quataert
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Linda Quatrini
- Department of Immunology, IRCCS Bambino Gesu Children’s Hospital, Rome, Italy
| | - Kylie M. Quinn
- School of Biomedical and Health Sciences, RMIT University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Helena Radbruch
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Germany
| | - Tim R. D. J. Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Susann Rahmig
- Regeneration in Hematopoiesis, Leibniz-Institute on Aging, Fritz-Lipmann-Institute (FLI), Jena, Germany
| | - Hans-Peter Rahn
- Preparative Flow Cytometry, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Bartek Rajwa
- Bindley Biosciences Center, Purdue University, West Lafayette, IN, USA
| | - Gevitha Ravichandran
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yotam Raz
- Department of Internal Medicine, Groene Hart Hospital, Gouda, The Netherlands
| | - Jonathan A. Rebhahn
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Dorothea Reimer
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Ester B.M. Remmerswaal
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Renal Transplant Unit, Division of Internal Medicine, Academic Medical Centre, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisa Richter
- Core Facility Flow Cytometry, Biomedical Center, Ludwig-Maximilians-University Munich, Germany
| | - Laura G. Rico
- Functional Cytomics Group, Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain
| | - Andy Riddell
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Aja M. Rieger
- Department of Medical Microbiology and Immunology, University of Alberta, Alberta, Canada
| | - J. Paul Robinson
- Purdue University Cytometry Laboratories, Purdue University, West Lafayette, IN, USA
| | - Chiara Romagnani
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Medical Department I, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Anna Rubartelli
- Cell Biology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Jürgen Ruland
- Institut für Klinische Chemie und Pathobiochemie, Fakultät für Medizin, Technische Universität München, München, Germany
| | - Armin Saalmüller
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Takashi Saito
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shimon Sakaguchi
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Francisco Sala de-Oyanguren
- Flow Cytometry Facility, Ludwig Cancer Institute, Faculty of Medicine and Biology, University of Lausanne, Epalinges, Switzerland
| | - Yvonne Samstag
- Heidelberg University, Institute of Immunology, Section of Molecular Immunology, Heidelberg, Germany
| | - Sharon Sanderson
- Translational Immunology Laboratory, NIHR BRC, University of Oxford, Kennedy Institute of Rheumatology, Oxford, UK
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Angela Santoni
- Department of Molecular Medicine, Sapienza University of Rome, IRCCS, Neuromed, Pozzilli, Italy
| | - Ramon Bellmàs Sanz
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Marina Saresella
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | | | - Birgit Sawitzki
- Charité – Universitätsmedizin Berlin, and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Linda Schadt
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Alexander Scheffold
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hans U. Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Schiemann
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Frank A. Schildberg
- Clinic for Orthopedics and Trauma Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Andreas Schlitzer
- Quantitative Systems Biology, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Josephine Schlosser
- Institute of Immunology, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Germany
| | - Stephan Schmid
- Internal Medicine I, University Hospital Regensburg, Germany
| | - Steffen Schmitt
- Flow Cytometry Core Facility, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Kilian Schober
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Daniel Schraivogel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wolfgang Schuh
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Reiner Schulte
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
| | - Axel Ronald Schulz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Cristiano Scottá
- King’s College London, “Peter Gorer” Department of Immunobiology, London, UK
| | - Daniel Scott-Algara
- Institut Pasteur, Cellular Lymphocytes Biology, Immunology Departement, Paris, France
| | - David P. Sester
- TRI Flow Cytometry Suite (TRI.fcs), Translational Research Institute, Wooloongabba, QLD, Australia
| | | | - Bruno Silva-Santos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | | | - Katarzyna M. Sitnik
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Silvano Sozzani
- Dept. Molecular Translational Medicine, University of Brescia, Brescia, Italy
| | - Daniel E. Speiser
- Department of Oncology, University of Lausanne and CHUV, Epalinges, Switzerland
| | | | - Anders Stahlberg
- Lundberg Laboratory for Cancer, Department of Pathology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | | | - Natalie Stanley
- Departments of Anesthesiology, Pain and Perioperative Medicine; Biomedical Data Sciences; and Pediatrics, Stanford University, Stanford, CA, USA
| | - Regina Stark
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Christina Stehle
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Medical Department I, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Tobit Steinmetz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Kiyoshi Takeda
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Leonard Tan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Attila Tárnok
- Departement for Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- Department of Precision Instruments, Tsinghua University, Beijing, China
| | - Gisa Tiegs
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Julia Tornack
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- BioGenes GmbH, Berlin, Germany
| | - Elisabetta Traggiai
- Novartis Biologics Center, Mechanistic Immunology Unit, Novartis Institute for Biomedical Research, NIBR, Basel, Switzerland
| | - Mohamed Trebak
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, PA, United States
| | - Timothy I.M. Tree
- Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institutes of Health Research Biomedical Research Centre at Guy’s and St. Thomas’ National Health Service, Foundation Trust and King’s College London, UK
| | | | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Sophia Urbanczyk
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Maries van den Broek
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Edwin van der Pol
- Vesicle Observation Center; Biomedical Engineering & Physics; Laboratory Experimental Clinical Chemistry; Amsterdam University Medical Centers, Location AMC, The Netherlands
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | | | - René A.W. van Lier
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc Veldhoen
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | | | - Paulo Vieira
- Unit Lymphopoiesis, Department of Immunology, Institut Pasteur, Paris, France
| | - David Voehringer
- Department of Infection Biology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Hans-Dieter Volk
- BIH Center for Regenerative Therapies (BCRT) Charité Universitätsmedizin Berlin and Berlin Institute of Health, Core Unit ImmunoCheck
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | | | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | - Paul K. Wallace
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, USA
| | - Sa A. Wang
- Dept of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin M. Wang
- The Scientific Platforms, the Westmead Institute for Medical Research, the Westmead Research Hub, Westmead, New South Wales, Australia
| | | | | | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gary Warnes
- Flow Cytometry Core Facility, Blizard Institute, Queen Mary London University, London, UK
| | - Sarah Warth
- BCRT Flow Cytometry Lab, Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin
| | - Claudia Waskow
- Regeneration in Hematopoiesis, Leibniz-Institute on Aging, Fritz-Lipmann-Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | | | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Leonie Wegener
- Biophysics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Thomas Weisenburger
- Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Annika Wiedemann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Dept. Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Jürgen Wienands
- Institute for Cellular & Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
| | - Anneke Wilharm
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Robert John Wilkinson
- Department of Infectious Disease, Imperial College London, UK
- Wellcome Centre for Infectious Diseases Research in Africa and Department of Medicine, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Republic of South Africa
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Gerald Willimsky
- Cooperation Unit for Experimental and Translational Cancer Immunology, Institute of Immunology (Charité - Universitätsmedizin Berlin) and German Cancer Research Center (DKFZ), Berlin, Germany
| | - James B. Wing
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Rieke Winkelmann
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Thomas H. Winkler
- Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Oliver F. Wirz
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Alicia Wong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Peter Wurst
- University Bonn, Medical Faculty, Bonn, Germany
| | - Jennie H. M. Yang
- Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institutes of Health Research Biomedical Research Centre at Guy’s and St. Thomas’ National Health Service, Foundation Trust and King’s College London, UK
| | - Juhao Yang
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Alice Yue
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Susanne Maria Ziegler
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Christina Zielinski
- German Center for Infection Research (DZIF), Munich, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
- TranslaTUM, Technical University of Munich, Munich, Germany
| | - Jakob Zimmermann
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
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28
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Kruk M, Widstrom N, Jena S, Wolter NL, Blankenhorn JF, Abdalla I, Yang TY, Parker LL. Assays for tyrosine phosphorylation in human cells. Methods Enzymol 2019; 626:375-406. [PMID: 31606083 DOI: 10.1016/bs.mie.2019.06.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tyrosine kinases are important for many cellular processes and disruption of their regulation is a factor in diseases like cancer, therefore they are a major target of anticancer drugs. There are many ways to measure tyrosine kinase activity in cells by monitoring endogenous substrate phosphorylation, or by using peptide substrates and incubating them with cell lysates containing active kinases. However, most of these strategies rely on antibodies and/or are limited in how accurately they model the intracellular environment. In cases in which activity needs to be measured in cells, but endogenous substrates are not known and/or suitable phosphospecific antibodies are not available, cell-deliverable peptide substrates can be an alternative and can provide information on activation and inhibition of kinases in intact, live cells. In this chapter, we review this methodology and provide a protocol for measuring Abl kinase activity in human cells using enzyme-linked immunosorbent assay (ELISA) with a generic antiphosphotyrosine antibody for detection.
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Affiliation(s)
- Monica Kruk
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Naomi Widstrom
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Sampreeti Jena
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Nicole L Wolter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - John F Blankenhorn
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Ibrahim Abdalla
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Tzu-Yi Yang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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29
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The ion channels and transporters gene expression profile indicates a shift in excitability and metabolisms during malignant progression of Follicular Lymphoma. Sci Rep 2019; 9:8586. [PMID: 31197180 PMCID: PMC6565741 DOI: 10.1038/s41598-019-44661-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
The definition of the gene expression profile of genes encoding Ion Channels and Transporters (ICT-GEP) represents a novel and attracting aspect in cancer. We determined the ICT-GEP of Follicular Lymphoma (FL), and compared it with that of the more aggressive Diffuse Large B Cell Lymphoma (DLBCL). cDNA microarray data were collected both from patients enrolled for this study, and from public datasets. In FL the ICT-GEP indicated the overexpression of both the K+ channel encoding gene KCNN4, and SLC2A1, which encodes the Glut1 glucose transporter. SLC2A1 turned out to represent the hub of a functional network, connecting channels and transporters in FL. Relapsed FL patients were characterised by 38 differentially expressed ICT genes, among which ATP9A, SLC2A1 and KCNN4 were under-expressed, indicating a down-regulation of both excitability and glycolysis. A completely different profile of K+ channel encoding genes emerged in DLBCL accompanied by the over-expression of the fatty acid transporter-encoding gene SLC27A1 as well as of the metabolism regulator NCoR1. This indicates a change in excitability and a shift towards an oxidative metabolism in DLBCL. Overall, the ICT-GEP may contribute to identifying novel lymphoma biomarkers related to excitability and metabolic pathways, with particular relevance for drug resistant, relapsed FL.
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30
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Rushing GV, Brockman AA, Bollig MK, Leelatian N, Mobley BC, Irish JM, Ess KC, Fu C, Ihrie RA. Location-dependent maintenance of intrinsic susceptibility to mTORC1-driven tumorigenesis. Life Sci Alliance 2019; 2:2/2/e201800218. [PMID: 30910807 PMCID: PMC6435042 DOI: 10.26508/lsa.201800218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 01/18/2023] Open
Abstract
Per-cell quantification of mTORC1 signaling activity in neural stem/progenitor cells reveals differential signaling, proliferative, and tumor-forming capability between dorsal and ventral cells within a single niche. Neural stem/progenitor cells (NSPCs) of the ventricular–subventricular zone (V-SVZ) are candidate cells of origin for many brain tumors. However, whether NSPCs in different locations within the V-SVZ differ in susceptibility to tumorigenic mutations is unknown. Here, single-cell measurements of signal transduction intermediates in the mechanistic target of rapamycin complex 1 (mTORC1) pathway reveal that ventral NSPCs have higher levels of signaling than dorsal NSPCs. These features are linked with differences in mTORC1-driven disease severity: introduction of a pathognomonic Tsc2 mutation only results in formation of tumor-like masses from the ventral V-SVZ. We propose a direct link between location-dependent intrinsic growth properties imbued by mTORC1 and predisposition to tumor development.
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Affiliation(s)
- Gabrielle V Rushing
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Asa A Brockman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Madelyn K Bollig
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bret C Mobley
- Department of Pathology, Immunology, and Microbiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Pathology, Immunology, and Microbiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kevin C Ess
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cary Fu
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca A Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA .,Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
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31
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Abstract
PURPOSE OF REVIEW The treatment of the germinal center lymphomas, diffuse large B cell (DLBCL) and follicular lymphoma, has changed little beyond the introduction of immunochemotherapies. However, there exists a substantial group of patients within both diseases for which improvements in care will involve appropriate tailoring of treatment. RECENT FINDINGS DLBCL consists of two major subtypes with striking differences in their clinical outcomes paralleling their underlying genetic heterogeneity. Recent studies have seen advances in the stratification of germinal center lymphomas, through comprehensive profiling of 1001 DLBCLs alongside refinements in the identification of high-risk follicular lymphoma patients using m7-FLIPI and 23G models. A new wave of novel therapeutic agents is now undergoing clinical trials for germinal center lymphomas, with BCR and EZH2 inhibitors demonstrating preferential benefit in subgroups of patients. The emergence of cell-free DNA has raised the possibility of dynamic disease monitoring to potentially mitigate the complexity of spatial and temporal heterogeneity, whilst predicting tumor evolution in real time. SUMMARY Altogether knowledge of the genomic landscape of germinal center lymphomas is offering welcome opportunities in patient risk stratification and therapeutics. The challenge ahead is to establish how best to combine upfront or dynamic prognostication with precision therapies, while retaining practicality in clinical trials and the real-world setting.
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32
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Huse K, Wogsland CE, Polikowsky HG, Diggins KE, Smeland EB, Myklebust JH, Irish JM. Human Germinal Center B Cells Differ from Naïve and Memory B Cells in CD40 Expression and CD40L-Induced Signaling Response. Cytometry A 2019; 95:442-449. [PMID: 30838773 DOI: 10.1002/cyto.a.23737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 11/20/2018] [Accepted: 02/08/2019] [Indexed: 12/21/2022]
Abstract
CD40 expression is required for germinal center (GC) formation and function, but the kinetics and magnitude of signaling following CD40 engagement remain poorly characterized in human B cells undergoing GC reactions. Here, differences in CD40 expression and signaling responses were compared across differentiation stages of mature human tonsillar B cells. A combination of mass cytometry and phospho-specific flow cytometry was used to quantify protein expression and CD40L-induced signaling in primary human naïve, GC, and memory B cells. Protein expression signatures of cell subsets were quantified using viSNE and Marker Enrichment Modeling (MEM). This approach revealed enriched expression of CD40 protein in GC B cells, compared to naïve and memory B cells. Despite this, GC B cells responded to CD40L engagement with lower phosphorylation of NFκB p65 during the first 30 min following CD40L activation. Before CD40L stimulation, GC B cells expressed higher levels of suppressor protein IκBα than naïve and memory B cells. Following CD40 activation, IκBα was rapidly degraded and reached equivalently low levels in naïve, GC, and memory B cells at 30 min following CD40L. Quantifying CD40 signaling responses as a function of bound ligand revealed a correlation between bound CD40L and degree of induced NFκB p65 phosphorylation, whereas comparable IκBα degradation occurred at all measured levels of CD40L binding. These results characterize cell-intrinsic signaling differences that exist in mature human B cells undergoing GC reactions. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Kanutte Huse
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Centre for B cell malignancies, University of Oslo, Oslo, Norway
| | - Cara E Wogsland
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hannah G Polikowsky
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kirsten E Diggins
- Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Erlend B Smeland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Centre for B cell malignancies, University of Oslo, Oslo, Norway
| | - June H Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Centre for B cell malignancies, University of Oslo, Oslo, Norway
| | - Jonathan M Irish
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell & Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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33
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Chellappa S, Kushekhar K, Munthe LA, Tjønnfjord GE, Aandahl EM, Okkenhaug K, Taskén K. The PI3K p110δ Isoform Inhibitor Idelalisib Preferentially Inhibits Human Regulatory T Cell Function. THE JOURNAL OF IMMUNOLOGY 2019; 202:1397-1405. [PMID: 30692213 DOI: 10.4049/jimmunol.1701703] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 12/19/2018] [Indexed: 01/01/2023]
Abstract
In chronic lymphocytic leukemia (CLL), signaling through several prosurvival B cell surface receptors activates the PI3K signaling pathway. Idelalisib is a highly selective PI3K (PI3Kδ) isoform-specific inhibitor effective in relapsed/refractory CLL and follicular lymphoma. However, severe autoimmune adverse effects in association with the use of idelalisib in the treatment of CLL, particularly as a first-line therapy, gave indications that idelalisib may preferentially target the suppressive function of regulatory T cells (Tregs). On this background, we examined the effect of idelalisib on the function of human Tregs ex vivo with respect to proliferation, TCR signaling, phenotype, and suppressive function. Our results show that human Tregs are highly susceptible to PI3Kδ inactivation using idelalisib compared with CD4+ and CD8+ effector T cells (Teffs) as evident from effects on anti-CD3/CD28/CD2-induced proliferation (order of susceptibility [IC50]: Treg [.5 μM] > CD4+ Teff [2.0 μM] > CD8+ Teff [6.5 μM]) and acting at the level of AKT and NF-κB phosphorylation. Moreover, idelalisib treatment of Tregs altered their phenotype and reduced their suppressive function against CD4+ and CD8+ Teffs. Phenotyping Tregs from CLL patients treated with idelalisib supported our in vitro findings. Collectively, our data show that human Tregs are more dependent on PI3Kδ-mediated signaling compared with CD4+ and CD8+ Teffs. This Treg-preferential effect could explain why idelalisib produces adverse autoimmune effects by breaking Treg-mediated tolerance. However, balancing effects on Treg sensitivity versus CD8+ Teff insensitivity to idelalisib could still potentially be exploited to enhance inherent antitumor immune responses in patients.
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Affiliation(s)
- Stalin Chellappa
- Department for Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway.,K.G. Jebsen Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,K.G. Jebsen Centre for Cancer Immunotherapy, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, N-0318 Oslo, Norway
| | - Kushi Kushekhar
- Department for Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway.,K.G. Jebsen Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,K.G. Jebsen Centre for Cancer Immunotherapy, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, N-0318 Oslo, Norway
| | - Ludvig A Munthe
- K.G. Jebsen Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital, N-0424 Oslo, Norway
| | - Geir E Tjønnfjord
- K.G. Jebsen Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,Department of Haematology, Oslo University Hospital, N-0424 Oslo, Norway
| | - Einar M Aandahl
- Department for Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway.,K.G. Jebsen Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,K.G. Jebsen Centre for Cancer Immunotherapy, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, N-0318 Oslo, Norway.,Section for Transplantation Surgery, Oslo University Hospital, N-0424 Oslo, Norway; and
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Kjetil Taskén
- Department for Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; .,K.G. Jebsen Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,K.G. Jebsen Centre for Cancer Immunotherapy, Institute for Clinical Medicine, University of Oslo, N-0424 Oslo, Norway.,Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, N-0318 Oslo, Norway
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34
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Mistry AM, Greenplate AR, Ihrie RA, Irish JM. Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors. FEBS J 2019; 286:1523-1539. [PMID: 30549207 DOI: 10.1111/febs.14730] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/17/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022]
Abstract
Single-cell technologies that can quantify features of individual cells within a tumor are critical for treatment strategies aiming to target cancer cells while sparing or activating beneficial cells. Given that key players in protein networks are often the primary targets of precision oncology strategies, it is imperative to transcend the nucleic acid message and read cellular actions in human solid tumors. Here, we review the advantages of multiplex, single-cell mass cytometry in tissue and solid tumor investigations. Mass cytometry can quantitatively probe nearly any cellular feature or target. In discussing the ability of mass cytometry to reveal and characterize a broad spectrum of cell types, identify rare cells, and study functional behavior through protein signaling networks in millions of individual cells from a tumor, this review surveys publications of scientific advances in solid tumor biology made with the aid of mass cytometry. Advances discussed include functional identification of rare tumor and tumor-infiltrating immune cells and dissection of cellular mechanisms of immunotherapy in solid tumors and the periphery. The review concludes by highlighting ways to incorporate single-cell mass cytometry in solid tumor precision oncology efforts and rapidly developing cytometry techniques for quantifying cell location and sequenced nucleic acids.
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Affiliation(s)
- Akshitkumar M Mistry
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison R Greenplate
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca A Ihrie
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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35
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Zhang X, Li Y, Fang H, Wei H, Mu Y, Lang MF, Sun J. The influence of cell morphology on microfluidic single cell analysis. RSC Adv 2018; 9:139-144. [PMID: 35521600 PMCID: PMC9059331 DOI: 10.1039/c8ra08303g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/16/2018] [Indexed: 11/21/2022] Open
Abstract
Microfluidics has been widely used in single cell analysis. Current protocols allow either spread or round cells to be analyzed. However, the contribution of cell morphology to single cell analysis has not been noted. In this study, four proteins (EGFR, PTEN, pAKT, and pS6) in the EGFR signaling pathway are measured simultaneously using microfluidic image cytometry (MIC) in glioblastoma cells U87. The results show that the MIC technology can reveal different subsets of cells corresponding to the four protein expression levels no matter whether they are round or spread at the time of the measurements. However, sharper distinction is obtained from round cells, which implies that cellular heterogeneity can be better resolved with round cells during in situ protein quantification by imaging cytometry. This study calls attention to the role of cell morphology in single cell analysis. Future studies should examine whether differences in data interpretation resulting from cell morphology could reveal altered biological meanings.
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Affiliation(s)
- Xuxin Zhang
- Affiliated Zhongshan Hospital of Dalian University Dalian 116001 China
| | - Yanzhao Li
- Affiliated Zhongshan Hospital of Dalian University Dalian 116001 China
| | - Hanshu Fang
- Medical College, Institute of Microanalysis, Dalian University Dalian 116622 China
| | - Hongquan Wei
- First Hospital of China Medical University Shenyang 110001 China
| | - Ying Mu
- Institute of Cyber-Systems and Control, Zhejiang University Hangzhou 310007 China
| | - Ming-Fei Lang
- Medical College, Institute of Microanalysis, Dalian University Dalian 116622 China
| | - Jing Sun
- The Key Laboratory of Biomarker High-throughput Screening and Target Translation of Breast and Gastrointestinal Tumor of Liaoning Province, Dalian University Dalian 116622 China.,College of Environmental and Chemical Engineering, Institute of Microanalysis, Dalian University Dalian 116622 China
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36
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Doxie DB, Greenplate AR, Gandelman JS, Diggins KE, Roe CE, Dahlman KB, Sosman JA, Kelley MC, Irish JM. BRAF and MEK inhibitor therapy eliminates Nestin-expressing melanoma cells in human tumors. Pigment Cell Melanoma Res 2018; 31:708-719. [PMID: 29778085 PMCID: PMC6188784 DOI: 10.1111/pcmr.12712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/18/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
Abstract
Little is known about the in vivo impacts of targeted therapy on melanoma cell abundance and protein expression. Here, 21 antibodies were added to an established melanoma mass cytometry panel to measure 32 cellular features, distinguish malignant cells, and characterize dabrafenib and trametinib responses in BRAFV600mut melanoma. Tumor cells were biopsied before neoadjuvant therapy and compared to cells surgically resected from the same site after 4 weeks of therapy. Approximately 50,000 cells per tumor were characterized by mass cytometry and computational tools t-SNE/viSNE, FlowSOM, and MEM. The resulting single-cell view of melanoma treatment response revealed initially heterogeneous melanoma tumors were consistently cleared of Nestin-expressing melanoma cells. Melanoma cell subsets that persisted to week 4 were heterogeneous but expressed SOX2 or SOX10 proteins and specifically lacked surface expression of MHC I proteins by MEM analysis. Traditional histology imaging of tissue microarrays from the same tumors confirmed mass cytometry results, including persistence of NES- SOX10+ S100β+ melanoma cells. This quantitative single-cell view of melanoma treatment response revealed protein features of malignant cells that are not eliminated by targeted therapy.
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Affiliation(s)
- Deon B. Doxie
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison R. Greenplate
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jocelyn S. Gandelman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kirsten E. Diggins
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline E. Roe
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kimberly B. Dahlman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey A. Sosman
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark C. Kelley
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Hematology-Oncology, Northwestern University, Feinberg School of Medicine, Evanston, IL, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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37
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Zwang NA, Ganesh BB, Cardenas KT, Chong AS, Finn PW, Perkins DL. An optimized protocol to quantify signaling in human transitional B cells by phospho flow cytometry. J Immunol Methods 2018; 463:112-121. [PMID: 30321549 DOI: 10.1016/j.jim.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND PURPOSE Phospho flow cytometry is a powerful technique to analyze signaling in rare cell populations. This technique, however, requires harsh conditions for cell fixation and permeabilization, which can denature surface antigens or antibody-conjugated fluorochromes. These are among several technical limitations which have been a barrier to quantify signaling in unique B cell subsets. One such immature subset, transitional B cells (TrBs), may play a role in suppressing solid organ transplant rejection, graft-versus-host disease, autoimmunity, and even the immune response to malignancy. Here we sought to optimize a protocol for quantification of signaling in human TrBs compared with mature B cell subsets. RESULTS TrBs were defined by surface marker expression as CD19+CD24hiCD38hi. Key parameters optimized included antibody clone selection, sequence of surface epitope labeling in relation to paraformaldehyde-based fixation and methanol-based permeabilization, photomultiplier tube (PMT) voltages, and compensation. Special attention was paid to labeling of CD38 with regard to these parameters, and an optimized protocol enabled reliable identification of TrBs, naïve (CD24+CD38+), early memory (CD24hiCD38-), and late memory (CD24-CD38-) B cells. Phospho flow cytometry enabled simultaneous quantification of phosphorylation among at least three different signaling molecules within the same sample. Among normal donors, transitional B cells exhibited diminished mitogen activated protein kinase/extracellular signal-regulated kinase and Akt phospho signaling upon nonspecific stimulation with phorbol 12-myristate 13-acetateand ionomycin stimulation. CONCLUSIONS We optimized an effective protocol to quantify B cell subset signaling upon stimulation. Such a protocol may ultimately serve as the basis for assessing dysfunctional B cell signaling in disease, predict clinical outcomes, and monitor response to B cell-directed therapies.
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Affiliation(s)
- Nicholas A Zwang
- Division of Nephrology, Department of Medicine, The University of Illinois at Chicago, 820 South Wood Street (MC 793), Chicago, IL 60612, USA.
| | - Balaji B Ganesh
- Flow Cytometry Core, The University of Illinois at Chicago, Medical Science Building, 835 South Wolcott Avenue (E-25C), Chicago, IL 60612, USA
| | - Kim T Cardenas
- BioLegend, 9727 Pacific Heights Blvd, San Diego, CA 92121, USA
| | - Anita S Chong
- Department of Surgery, Section of Transplantation Surgery, The University of Chicago, 5841 South Maryland Avenue (SBRI J547/MC 5026), Chicago, IL 60637, USA
| | - Patricia W Finn
- Department of Medicine, The University of Illinois at Chicago, 840 South Wood Street Suite 1020N (MC 787), Chicago, IL 60612, USA
| | - David L Perkins
- Division of Nephrology, Department of Medicine, The University of Illinois at Chicago, 820 South Wood Street (MC 793), Chicago, IL 60612, USA
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38
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Gopal AK, Schuster SJ, Fowler NH, Trotman J, Hess G, Hou JZ, Yacoub A, Lill M, Martin P, Vitolo U, Spencer A, Radford J, Jurczak W, Morton J, Caballero D, Deshpande S, Gartenberg GJ, Wang SS, Damle RN, Schaffer M, Balasubramanian S, Vermeulen J, Cheson BD, Salles G. Ibrutinib as Treatment for Patients With Relapsed/Refractory Follicular Lymphoma: Results From the Open-Label, Multicenter, Phase II DAWN Study. J Clin Oncol 2018; 36:2405-2412. [PMID: 29851546 DOI: 10.1200/jco.2017.76.8853] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose The Bruton's tyrosine kinase inhibitor ibrutinib has demonstrated clinical activity in B-cell malignancies. The DAWN study assessed the efficacy and safety of single-agent ibrutinib in chemoimmunotherapy relapsed/refractory follicular lymphoma (FL) patients. Methods DAWN was an open-label, single-arm, phase II study of ibrutinib in patients with FL with two or more prior lines of therapy. Patients received ibrutinib 560 mg daily until progressive disease/unacceptable toxicity. The primary objective was independent review committee-assessed overall response rate (ORR; complete response plus partial response). Exploratory analyses of T-cell subsets in peripheral blood (baseline/cycle 3) and cytokines/chemokines (baseline/cycle 2) were performed for available samples. Results Between March 2013 and May 2016, 110 patients with a median of three prior lines of therapy were enrolled. At median follow-up of 27.7 months, ORR was 20.9% (95% CI, 13.7% to 29.7%, which did not meet the 18% lower-bound threshold for the primary end point). Twelve patients achieved a complete response (11%; 95% CI, 5.8% to 18.3%). Median duration of response was 19.4 months (range, 1 to ≥ 33 months), with a median progression-free survival of 4.6 months and a 30-month overall survival of 61% (95% CI, 0.51% to 0.70%). Lymphoma symptoms resolved in 67%. Seven of 32 patients who experienced initial radiologic progression responded upon continuing therapy (pseudoprogression). The most common adverse events were diarrhea, fatigue, cough, and muscle spasms; 48.2% of patients reported serious adverse events. In patients who experienced a response, regulatory T cells were downregulated at C3D1 ( P = .02), and Th1-promoting (antitumor) cytokines interferon-γ and interleukin-12 increased ( P ≤ .035). Conclusion With an ORR of 20.9%, ibrutinib failed to meet its primary efficacy end point in chemoimmunotherapy in patients with relapsed/refractory FL, although responses were durable and associated with a reduction in regulatory T cells and increases in proinflammatory cytokines.
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Affiliation(s)
- Ajay K Gopal
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Stephen J Schuster
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Nathan H Fowler
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Judith Trotman
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Georg Hess
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Jing-Zhou Hou
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Abdulraheem Yacoub
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Michael Lill
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Peter Martin
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Umberto Vitolo
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Andrew Spencer
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - John Radford
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Wojciech Jurczak
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - James Morton
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Dolores Caballero
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Sanjay Deshpande
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Gary J Gartenberg
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Shean-Sheng Wang
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Rajendra N Damle
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Michael Schaffer
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Sriram Balasubramanian
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Jessica Vermeulen
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Bruce D Cheson
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
| | - Gilles Salles
- Ajay K. Gopal, The University of Washington; Ajay K. Gopal, Fred Hutchinson Cancer Research Center, Seattle, WA; Stephen J. Schuster, Abramson Cancer Center of the University of Pennsylvania, Philadelphia; Jing-Zhou Hou, University of Pittsburgh Medical Center; Jing-Zhou Hou, University of Pittsburgh Cancer Institute, Pittsburgh; Rajendra N. Damle, Michael Schaffer, and Sriram Balasubramanian, Janssen Research & Development, Spring House, PA; Nathan H. Fowler, The University of Texas MD Anderson Cancer Center, Houston, TX; Judith Trotman, Concord Hospital, University of Sydney, Sydney, New South Wales; Andrew Spencer, Alfred Hospital-Monash University, Melbourne, Victoria; James Morton, Haematology and Oncology Clinics of Australia, Milton, Queensland, Australia; Georg Hess, Johannes Gutenberg-University, Mainz, Germany; Abdulraheem Yacoub, Kansas University Medical Center, Kansas City, KS; Michael Lill, Cedars-Sinai Medical Center, Los Angeles, CA; Peter Martin, Weill Cornell Medical College, Cornell University, New York, NY; Umberto Vitolo, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy; John Radford, University of Manchester; John Radford, Christie National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Wojciech Jurczak, Jagiellonian University, Kraków, Poland; Dolores Caballero, Hospital Clínico Universitario, Salamanca, Spain; Sanjay Deshpande, Gary J. Gartenberg, and Shean-Sheng Wang, Janssen Research & Development, Raritan, NJ; Jessica Vermeulen, Janssen Research & Development, Leiden, the Netherlands; Bruce D. Cheson, Georgetown University Hospital, Washington, DC; and Gilles Salles, Hospices Civils de Lyon-Université de Lyon, Pierre-Bénite cedex, Lyon, France
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Huet S, Sujobert P, Salles G. From genetics to the clinic: a translational perspective on follicular lymphoma. Nat Rev Cancer 2018; 18:224-239. [PMID: 29422597 DOI: 10.1038/nrc.2017.127] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Follicular lymphoma (FL) is the most frequent indolent B cell lymphoma and is still considered to be incurable. In recent years, whole-exome sequencing studies of large cohorts of patients have greatly improved our knowledge of the FL mutational landscape. Moreover, the prolonged evolution of this disease has enabled some insights regarding the early pre-lymphoma lesions as well as the clonal evolution after treatment, allowing an evolutionary perspective on lymphomagenesis. Deciphering the earliest initiating lesions and identifying the molecular alterations leading to disease progression currently represent important goals; accomplishing these could help identify the most relevant targets for precision therapy.
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Affiliation(s)
- Sarah Huet
- Cancer Research Center of Lyon, INSERM 1052 CNRS5286, 'Clinical and experimental models of lymphomagenesis' Team, Equipe labellisée Ligue Contre le Cancer Oullins, France
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 165 chemin du Grand Revoyet, Pierre Bénite 69495, France
- Université Lyon-1, ISPB-Faculté de Pharmacie de Lyon, Lyon, France
| | - Pierre Sujobert
- Cancer Research Center of Lyon, INSERM 1052 CNRS5286, 'Clinical and experimental models of lymphomagenesis' Team, Equipe labellisée Ligue Contre le Cancer Oullins, France
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 165 chemin du Grand Revoyet, Pierre Bénite 69495, France
- Université Lyon-1, Faculté de Médecine et de Maïeutique Lyon-Sud Charles Mérieux, Oullins, France
| | - Gilles Salles
- Cancer Research Center of Lyon, INSERM 1052 CNRS5286, 'Clinical and experimental models of lymphomagenesis' Team, Equipe labellisée Ligue Contre le Cancer Oullins, France
- Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 165 chemin du Grand Revoyet, Pierre Bénite 69495, France
- Université Lyon-1, Faculté de Médecine et de Maïeutique Lyon-Sud Charles Mérieux, Oullins, France
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40
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Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nat Med 2018; 24:474-483. [PMID: 29505032 DOI: 10.1038/nm.4505] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/26/2018] [Indexed: 12/13/2022]
Abstract
Insight into the cancer cell populations that are responsible for relapsed disease is needed to improve outcomes. Here we report a single-cell-based study of B cell precursor acute lymphoblastic leukemia at diagnosis that reveals hidden developmentally dependent cell signaling states that are uniquely associated with relapse. By using mass cytometry we simultaneously quantified 35 proteins involved in B cell development in 60 primary diagnostic samples. Each leukemia cell was then matched to its nearest healthy B cell population by a developmental classifier that operated at the single-cell level. Machine learning identified six features of expanded leukemic populations that were sufficient to predict patient relapse at diagnosis. These features implicated the pro-BII subpopulation of B cells with activated mTOR signaling, and the pre-BI subpopulation of B cells with activated and unresponsive pre-B cell receptor signaling, to be associated with relapse. This model, termed 'developmentally dependent predictor of relapse' (DDPR), significantly improves currently established risk stratification methods. DDPR features exist at diagnosis and persist at relapse. By leveraging a data-driven approach, we demonstrate the predictive value of single-cell 'omics' for patient stratification in a translational setting and provide a framework for its application to human cancer.
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Greenplate A, Wang K, Tripathi RM, Palma N, Ali SM, Stephens PJ, Miller VA, Shyr Y, Guo Y, Reddy NM, Kozhaya L, Unutmaz D, Chen X, Irish JM, Davé UP. Genomic Profiling of T-Cell Neoplasms Reveals Frequent JAK1 and JAK3 Mutations With Clonal Evasion From Targeted Therapies. JCO Precis Oncol 2018; 2018. [PMID: 30079384 PMCID: PMC6072266 DOI: 10.1200/po.17.00019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose The promise of precision oncology is that identification of genomic alterations will direct the rational use of molecularly targeted therapy. This approach is particularly applicable to neoplasms that are resistant to standard cytotoxic chemotherapy, like T-cell leukemias and lymphomas. In this study, we tested the feasibility of targeted next-generation sequencing in profiles of diverse T-cell neoplasms and focused on the therapeutic utility of targeting activated JAK1 and JAK3 in an index case. Patients and Methods Using Foundation One and Foundation One Heme assays, we performed genomic profiling on 91 consecutive T-cell neoplasms for alterations in 405 genes. The samples were sequenced to high uniform coverage with an Illumina HiSeq and averaged a coverage depth of greater than 500× for DNA and more than 8M total pairs for RNA. An index case of T-cell prolymphocytic leukemia (T-PLL), which was analyzed by targeted next-generation sequencing, is presented. T-PLL cells were analyzed by RNA-seq, in vitro drug testing, mass cytometry, and phospho-flow. Results One third of the samples had genomic aberrations in the JAK-STAT pathway, most often composed of JAK1 and JAK3 gain-of-function mutations. We present an index case of a patient with T-PLL with a clonal JAK1 V658F mutation that responded to ruxolitinib therapy. After relapse developed, an expanded clone that harbored mutant JAK3 M511I and downregulation of the phosphatase, CD45, was identified. We demonstrate that the JAK missense mutations were activating, caused pathway hyperactivation, and conferred cytokine hypersensitivity. Conclusion These results underscore the utility of profiling occurrences of resistance to standard regimens and support JAK enzymes as rational therapeutic targets for T-cell leukemias and lymphomas.
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Affiliation(s)
| | - Kai Wang
- Foundation Medicine, Cambridge, MA. Origimed, Shanghai, China
| | | | | | | | | | | | - Yu Shyr
- Vanderbilt University Medical Center, Nashville, TN
| | - Yan Guo
- Vanderbilt University Medical Center, Nashville, TN
| | | | | | | | - Xueyan Chen
- University of Washington Medical Center, Seattle, WA
| | | | - Utpal P Davé
- R.L. Roudebush Veterans Affairs Medical Center and Indiana University School of Medicine, Indianapolis, IN
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42
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Zhang Y, Shen F, Mojarad MR, Li D, Liu S, Tao C, Yu Y, Liu H. Systematic identification of latent disease-gene associations from PubMed articles. PLoS One 2018; 13:e0191568. [PMID: 29373609 PMCID: PMC5786305 DOI: 10.1371/journal.pone.0191568] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/08/2018] [Indexed: 12/27/2022] Open
Abstract
Recent scientific advances have accumulated a tremendous amount of biomedical knowledge providing novel insights into the relationship between molecular and cellular processes and diseases. Literature mining is one of the commonly used methods to retrieve and extract information from scientific publications for understanding these associations. However, due to large data volume and complicated associations with noises, the interpretability of such association data for semantic knowledge discovery is challenging. In this study, we describe an integrative computational framework aiming to expedite the discovery of latent disease mechanisms by dissecting 146,245 disease-gene associations from over 25 million of PubMed indexed articles. We take advantage of both Latent Dirichlet Allocation (LDA) modeling and network-based analysis for their capabilities of detecting latent associations and reducing noises for large volume data respectively. Our results demonstrate that (1) the LDA-based modeling is able to group similar diseases into disease topics; (2) the disease-specific association networks follow the scale-free network property; (3) certain subnetwork patterns were enriched in the disease-specific association networks; and (4) genes were enriched in topic-specific biological processes. Our approach offers promising opportunities for latent disease-gene knowledge discovery in biomedical research.
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Affiliation(s)
- Yuji Zhang
- Division of Biostatistics and Bioinformatics, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland, United States of America
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Feichen Shen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Majid Rastegar Mojarad
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Dingcheng Li
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sijia Liu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Cui Tao
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yue Yu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Medical Informatics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Hongfang Liu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
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Myhrvold IK, Cremaschi A, Hermansen JU, Tjønnfjord GE, Munthe LA, Taskén K, Skånland SS. Single cell profiling of phospho-protein levels in chronic lymphocytic leukemia. Oncotarget 2018; 9:9273-9284. [PMID: 29507689 PMCID: PMC5823631 DOI: 10.18632/oncotarget.23949] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/16/2017] [Indexed: 12/26/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) has a high incidence and a steeply growing prevalence in the Western world. The heterogeneity of the disease necessitates individual mapping of biology and predicted drug response in each patient as basis for administration of tailored treatments. Cell signaling aberrations may serve as biological indicators for suitable therapy. By applying phospho-specific flow cytometry, we mapped basal and induced phosphorylation levels of 20 phospho-epitopes on proteins relevant to B-cell signaling in B cells from 22 CLL patients and 25 normal controls. The signaling response of the cytostatic drugs fludarabine, doxorubicin and vincristine was also investigated. CLL cells exerted similar or lower basal phosphorylation levels compared to normal B cells, with the exception of STAT3 (pY705) which was increased. Interestingly, STAT3 inhibitors normalized the STAT3 (pY705) level and reduced cell viability. Vincristine treatment significantly modulated phosphorylation levels in CLL cells, while no effect was observed in controls or after fludarabine or doxorubicin treatment. After BCR stimulation, CLL cells showed a tendency towards impaired phosphorylation levels, significant for several of the analyzed proteins. However, the level of Akt (pS473) was more potently induced in IgHV unmutated CLL (UM-CLL) patient samples and was significantly higher than in M-CLL samples. Importantly, the PI3Kδ inhibitor idelalisib potently reversed the effect of anti-IgM on Akt (pS473). Thus, signaling aberrations could be identified by phosphoflow cytometry and aberrant signaling could be normalized by small molecule drugs. This approach can identify relevant drug targets as well as drug effects in the individual patient.
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Affiliation(s)
- Ida K Myhrvold
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Centre for Inflammation Research, University of Oslo, Oslo, Norway.,K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo, Oslo, Norway
| | - Andrea Cremaschi
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
| | - Johanne U Hermansen
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Centre for Inflammation Research, University of Oslo, Oslo, Norway.,K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo, Oslo, Norway
| | - Geir E Tjønnfjord
- Department of Haematology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ludvig A Munthe
- Centre for Immune Regulation, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjetil Taskén
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Centre for Inflammation Research, University of Oslo, Oslo, Norway.,K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo, Oslo, Norway.,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Sigrid S Skånland
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Centre for Inflammation Research, University of Oslo, Oslo, Norway.,K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo, Oslo, Norway
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44
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Earl DC, Ferrell PB, Leelatian N, Froese JT, Reisman BJ, Irish JM, Bachmann BO. Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics. Nat Commun 2018; 9:39. [PMID: 29295987 PMCID: PMC5750220 DOI: 10.1038/s41467-017-02470-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 12/01/2017] [Indexed: 01/06/2023] Open
Abstract
Discovering bioactive metabolites within a metabolome is challenging because there is generally little foreknowledge of metabolite molecular and cell-targeting activities. Here, single-cell response profiles and primary human tissue comprise a response platform used to discover novel microbial metabolites with cell-type-selective effector properties in untargeted metabolomic inventories. Metabolites display diverse effector mechanisms, including targeting protein synthesis, cell cycle status, DNA damage repair, necrosis, apoptosis, or phosphoprotein signaling. Arrayed metabolites are tested against acute myeloid leukemia patient bone marrow and molecules that specifically targeted blast cells or nonleukemic immune cell subsets within the same tissue biopsy are revealed. Cell-targeting polyketides are identified in extracts from biosynthetically prolific bacteria, including a previously unreported leukemia blast-targeting anthracycline and a polyene macrolactam that alternates between targeting blasts or nonmalignant cells by way of light-triggered photochemical isomerization. High-resolution cell profiling with mass cytometry confirms response mechanisms and is used to validate initial observations.
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Affiliation(s)
- David C Earl
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - P Brent Ferrell
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, TN, 37232, USA
| | - Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-2220 Medical Center North, Nashville, TN, 37232, USA
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37232, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, D-2220 Medical Center North, Nashville, TN, 37232, USA.
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN, 37235, USA.
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45
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Abstract
Cancer immunotherapy fights against cancer by modulating the immune response and is delivering encouraging results in clinical treatments. However, it is challenging to achieve durable response in all cancer patients during treatment due to the diversity and dynamic nature of immune system as well as inter- and intratumor heterogeneity. A comprehensive assessment of system immunity and tumor microenvironment is crucial for effective and safe cancer therapy, which can potentially be resolved by single-cell proteomic analysis. Single-cell proteomic technologies enable system-wide profiling of protein levels in a number of single cells within the immune system and tumor microenvironment, and thereby provide direct assessment of the functional state of the immune cells and tumor-immune interaction that could be used to evaluate efficacy of immunotherapy and to improve clinical outcome. In this chapter, we summarized current single-cell proteomic technologies and their applications in cancer immunotherapy.
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46
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Khanolkar A, Kirschmann DA, Caparelli EA, Wilks JD, Cerullo JM, Bergerson JRE, Jennings LJ, Fuleihan RL. CD4 T cell-restricted IL-2 signaling defect in a patient with a novel IFNGR1 deficiency. J Allergy Clin Immunol 2018; 141:435-439.e7. [PMID: 28927822 DOI: 10.1016/j.jaci.2017.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/08/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Aaruni Khanolkar
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Ill; Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill.
| | - Dawn A Kirschmann
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Edward A Caparelli
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Jeffrey D Wilks
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Jillian M Cerullo
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Jenna R E Bergerson
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Chicago, Ill; Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Lawrence J Jennings
- Department of Pathology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill; Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | - Ramsay L Fuleihan
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Chicago, Ill; Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
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47
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Development of expression-based biomarkers of Dasatinib response in hematologic malignancies. Blood Cancer J 2017; 7:652. [PMID: 29242603 PMCID: PMC5802564 DOI: 10.1038/s41408-017-0013-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/13/2017] [Accepted: 09/20/2017] [Indexed: 12/02/2022] Open
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48
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Josefsson SE, Huse K, Kolstad A, Beiske K, Pende D, Steen CB, Inderberg EM, Lingjærde OC, Østenstad B, Smeland EB, Levy R, Irish JM, Myklebust JH. T Cells Expressing Checkpoint Receptor TIGIT Are Enriched in Follicular Lymphoma Tumors and Characterized by Reversible Suppression of T-cell Receptor Signaling. Clin Cancer Res 2017; 24:870-881. [PMID: 29217528 DOI: 10.1158/1078-0432.ccr-17-2337] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/10/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022]
Abstract
Purpose: T cells infiltrating follicular lymphoma (FL) tumors are considered dysfunctional, yet the optimal target for immune checkpoint blockade is unknown. Characterizing coinhibitory receptor expression patterns and signaling responses in FL T-cell subsets might reveal new therapeutic targets.Experimental Design: Surface expression of 9 coinhibitory receptors governing T-cell function was characterized in T-cell subsets from FL lymph node tumors and from healthy donor tonsils and peripheral blood samples, using high-dimensional flow cytometry. The results were integrated with T-cell receptor (TCR)-induced signaling and cytokine production. Expression of T-cell immunoglobulin and ITIM domain (TIGIT) ligands was detected by immunohistochemistry.Results: TIGIT was a frequently expressed coinhibitory receptor in FL, expressed by the majority of CD8 T effector memory cells, which commonly coexpressed exhaustion markers such as PD-1 and CD244. CD8 FL T cells demonstrated highly reduced TCR-induced phosphorylation (p) of ERK and reduced production of IFNγ, while TCR proximal signaling (p-CD3ζ, p-SLP76) was not affected. The TIGIT ligands CD112 and CD155 were expressed by follicular dendritic cells in the tumor microenvironment. Dysfunctional TCR signaling correlated with TIGIT expression in FL CD8 T cells and could be fully restored upon in vitro culture. The costimulatory receptor CD226 was downregulated in TIGIT+ compared with TIGIT- CD8 FL T cells, further skewing the balance toward immunosuppression.Conclusions: TIGIT blockade is a relevant strategy for improved immunotherapy in FL. A deeper understanding of the interplay between coinhibitory receptors and key T-cell signaling events can further assist in engineering immunotherapeutic regimens to improve clinical outcomes of cancer patients. Clin Cancer Res; 24(4); 870-81. ©2017 AACR.
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Affiliation(s)
- Sarah E Josefsson
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kanutte Huse
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Arne Kolstad
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Klaus Beiske
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Daniela Pende
- Immunology Laboratory, Ospedale Policlinico San Martino, Genova, Italy
| | - Chloé B Steen
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Computer Science, University of Oslo, Oslo, Norway
| | | | - Ole Christian Lingjærde
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Department of Computer Science, University of Oslo, Oslo, Norway
| | - Bjørn Østenstad
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Erlend B Smeland
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ronald Levy
- Division of Oncology, Stanford School of Medicine, Stanford, California
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - June H Myklebust
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway. .,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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49
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Single-agent ibrutinib in relapsed or refractory follicular lymphoma: a phase 2 consortium trial. Blood 2017; 131:182-190. [PMID: 29074501 DOI: 10.1182/blood-2017-09-804641] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/11/2017] [Indexed: 12/27/2022] Open
Abstract
Most patients with follicular lymphoma (FL) experience multiple relapses necessitating subsequent lines of therapy. Ibrutinib, a Bruton tyrosine kinase (BTK) inhibitor approved for the treatment of several B-cell malignancies, showed promising activity in FL in a phase 1 study. We report the results of a phase 2 trial evaluating ibrutinib in recurrent FL. Forty patients with recurrent FL were treated with ibrutinib 560 mg/d until progression or intolerance. The primary end point was overall response rate (ORR). Exploratory analyses included correlations of outcome with recurrent mutations identified in a cancer gene panel that used next-generation sequencing in pretreatment biopsies from 31 patients and results of early interim positron emission tomography/computed tomography scans in 20 patients. ORR was 37.5% with a complete response rate of 12.5%, median progression-free survival (PFS) of 14 months, and 2-year PFS of 20.4%. Response rates were significantly higher among patients whose disease was sensitive to rituximab (52.6%) compared with those who were rituximab refractory (16.7%) (P = .04). CARD11 mutations were present in 16% of patients (5 of 31) and predicted resistance to ibrutinib with only wild-type patients responding (P = .002). Maximum standardized uptake value at cycle 1 day 8 correlated with response and PFS. Ibrutinib was well-tolerated with a toxicity profile similar to labeled indications. Ibrutinib is a well-tolerated treatment with modest activity in relapsed FL. Evaluation of BTK inhibitors in earlier lines of therapy may be warranted on the basis of improved response rates in rituximab-sensitive disease. Somatic mutations such as CARD11 may have an impact on response to ibrutinib, may inform clinical decisions, and should be evaluated in larger data sets. This trial was registered at www.clinicaltrials.gov as #NCT01849263.
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50
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Wogsland CE, Greenplate AR, Kolstad A, Myklebust JH, Irish JM, Huse K. Mass Cytometry of Follicular Lymphoma Tumors Reveals Intrinsic Heterogeneity in Proteins Including HLA-DR and a Deficit in Nonmalignant Plasmablast and Germinal Center B-Cell Populations. CYTOMETRY PART B-CLINICAL CYTOMETRY 2017; 92:79-87. [PMID: 27933753 DOI: 10.1002/cyto.b.21498] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/22/2016] [Accepted: 11/29/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma that has a risk of transformation to more aggressive lymphoma. Relatively little is known about the nonmalignant B-cell and T-cell subset composition within the tumor microenvironment and whether altered phenotypes are associated with patterns of lymphoma B-cell heterogeneity. METHODS Two mass cytometry (CyTOF) panels were designed to immunophenotype B and T cells in FL tumors. Populations of malignant B cells, nonmalignant B cells, and T cells from each FL tumor were identified and their phenotypes compared to B and T cells from healthy human tonsillar tissue. RESULTS Diversity in cellular phenotype between tumors was greater for the malignant B cells than for nonmalignant B or T cells. The malignant B-cell population bore little phenotypic similarity to any healthy B-cell subset, and unexpectedly clustered closer to naïve B-cell populations than GC B-cell populations. Among the nonmalignant B cells within FL tumors, a significant lack of GC and plasmablast B cells was observed relative to tonsil controls. In contrast, nonmalignant T cells in FL tumors were present at levels similar to their cognate tonsillar T-cell subsets. CONCLUSION Mass cytometry revealed that diverse HLA-DR expression on FL cells within individual tumors contributed greatly to tumor heterogeneity. Both malignant and nonmalignant B cells in the tumor bore little phenotypic resemblance to healthy GC B cells despite the presence of T follicular helper cells in the tumor. These findings suggest that ongoing signaling interactions between malignant B cells and intra-tumor T cells shape the tumor microenvironment. © 2016 International Clinical Cytometry Society.
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Affiliation(s)
- Cara Ellen Wogsland
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Allison Rae Greenplate
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Arne Kolstad
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - June Helen Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Jonathan Michael Irish
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Kanutte Huse
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
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