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Colpitts SJ, Budd MA, Monajemi M, Reid KT, Murphy JM, Ivison S, Verchere CB, Levings MK, Crome SQ. Strategies for optimizing CITE-seq for human islets and other tissues. Front Immunol 2023; 14:1107582. [PMID: 36936943 PMCID: PMC10014726 DOI: 10.3389/fimmu.2023.1107582] [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: 11/25/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023] Open
Abstract
Defining the immunological landscape of human tissue is an important area of research, but challenges include the impact of tissue disaggregation on cell phenotypes and the low abundance of immune cells in many tissues. Here, we describe methods to troubleshoot and standardize Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) for studies involving enzymatic digestion of human tissue. We tested epitope susceptibility of 92 antibodies commonly used to differentiate immune lineages and cell states on human peripheral blood mononuclear cells following treatment with an enzymatic digestion cocktail used to isolate islets. We observed CD4, CD8a, CD25, CD27, CD120b, CCR4, CCR6, and PD1 display significant sensitivity to enzymatic treatment, effects that often could not be overcome with alternate antibodies. Comparison of flow cytometry-based CITE-seq antibody titrations and sequencing data supports that for the majority of antibodies, flow cytometry accurately predicts optimal antibody concentrations for CITE-seq. Comparison by CITE-seq of immune cells in enzymatically digested islet tissue and donor-matched spleen not treated with enzymes revealed little digestion-induced epitope cleavage, suggesting increased sensitivity of CITE-seq and/or that the islet structure may protect resident immune cells from enzymes. Within islets, CITE-seq identified immune cells difficult to identify by transcriptional signatures alone, such as distinct tissue-resident T cell subsets, mast cells, and innate lymphoid cells (ILCs). Collectively this study identifies strategies for the rational design and testing of CITE-seq antibodies for single-cell studies of immune cells within islets and other tissues.
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Affiliation(s)
- Sarah J. Colpitts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Matthew A. Budd
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mahdis Monajemi
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Kyle T. Reid
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Julia M. Murphy
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Sabine Ivison
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - C. Bruce Verchere
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Canada and Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
| | - Megan K. Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
| | - Sarah Q. Crome
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
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Montanari M, Burattini S, Ciacci C, Ambrogini P, Carloni S, Balduini W, Lopez D, Panza G, Papa S, Canonico B. Automated–Mechanical Procedure Compared to Gentle Enzymatic Tissue Dissociation in Cell Function Studies. Biomolecules 2022; 12:biom12050701. [PMID: 35625628 PMCID: PMC9138555 DOI: 10.3390/biom12050701] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The first step to obtain a cellular suspension from tissues is the disaggregation procedure. The cell suspension method has to provide a representative sample of the different cellular subpopulations and to maximize the number of viable functional cells. Here, we analyzed specific cell functions in cell suspensions from several rat tissues obtained by two different methods, automated–mechanical and enzymatic disaggregation. Flow cytometric, confocal, and ultrastructural (TEM) analyses were applied to the spleen, testis, liver and other tissues. Samples were treated by an enzymatic trypsin solution or processed by the Medimachine II (MMII). The automated–mechanical and enzymatic disaggregation procedures have shown to work similarly in some tissues, which displayed comparable amounts of apoptotic/necrotic cells. However, cells obtained by the enzyme-free Medimachine II protocols show a better preservation lysosome and mitochondria labeling, whereas the enzymatic gentle dissociation appears to constantly induce a lower amount of intracellular ROS; nevertheless, lightly increased ROS can be recognized as a complimentary signal to promote cell survival. Therefore, MMII represents a simple, fast, and standardized method for tissue processing, which allows to minimize bias arising from the operator’s ability. Our study points out technical issues to be adopted for specific organs and tissues to obtain functional cells.
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Affiliation(s)
- Mariele Montanari
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Sabrina Burattini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Caterina Ciacci
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Patrizia Ambrogini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Silvia Carloni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Walter Balduini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Daniele Lopez
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
- Department of Pure and Applied Sciences (DiSPeA), University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Giovanna Panza
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Stefano Papa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
- Correspondence:
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Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nat Neurosci 2022; 25:306-316. [PMID: 35260865 DOI: 10.1038/s41593-022-01022-8] [Citation(s) in RCA: 161] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples.
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Ferreira-Facio CDS, Botafogo V, Ferrão PM, Canellas MC, Milito CB, Romano S, Lopes DV, Teixeira LC, Oliveira E, Bruno-Riscarolli E, Mello FV, Siqueira PFR, Moura P, Macedo FN, Forny DN, Simião L, Pureza AL, Land MGP, Pedreira CE, van Dongen JJM, Orfao A, da Costa ES. Flow Cytometry Immunophenotyping for Diagnostic Orientation and Classification of Pediatric Cancer Based on the EuroFlow Solid Tumor Orientation Tube (STOT). Cancers (Basel) 2021; 13:cancers13194945. [PMID: 34638431 PMCID: PMC8508207 DOI: 10.3390/cancers13194945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022] Open
Abstract
Simple Summary Pediatric solid tumors are a heterogenous group of diseases that comprise ≈ 40% of all pediatric cancers, early diagnosis being key for improved survival. Here we designed, tested, and validated a single eight-color tube for the diagnostic screening of pediatric cancer—solid tumor orientation tube (STOT)—based on multiparameter flow cytometry vs. conventional diagnostic procedures. Prospective clinical validation of STOT in 149 samples (63 tumor mass, 38 bone marrow, 30 lymph node, and 18 body fluid samples) screened for pediatric cancer, apart from 26 blood specimens that were excluded from analysis, showed concordant results with the final WHO/ICCC-3 diagnosis in 138/149 cases (92.6%). This included correct diagnostic orientation by STOT in 43/44 (98%) malignant and 4/4 (100%) benign non-hematopoietic tumors, together with 28/38 (74%) leukemia/lymphoma cases. The only recurrently missed diagnosis was Hodgkin lymphoma (0/8), which would require additional markers. These results support the use of STOT as a complementary tool for fast and accurate diagnostic screening, orientation, and classification of pediatric cancer in suspicious patients. Abstract Early diagnosis of pediatric cancer is key for adequate patient management and improved outcome. Although multiparameter flow cytometry (MFC) has proven of great utility in the diagnosis and classification of hematologic malignancies, its application to non-hematopoietic pediatric tumors remains limited. Here we designed and prospectively validated a new single eight-color antibody combination—solid tumor orientation tube, STOT—for diagnostic screening of pediatric cancer by MFC. A total of 476 samples (139 tumor mass, 138 bone marrow, 86 lymph node, 58 peripheral blood, and 55 other body fluid samples) from 296 patients with diagnostic suspicion of pediatric cancer were analyzed by MFC vs. conventional diagnostic procedures. STOT was designed after several design–test–evaluate–redesign cycles based on a large panel of monoclonal antibody combinations tested on 301 samples. In its final version, STOT consists of a single 8-color/12-marker antibody combination (CD99-CD8/numyogenin/CD4-EpCAM/CD56/GD2/smCD3-CD19/cyCD3-CD271/CD45). Prospective validation of STOT in 149 samples showed concordant results with the patient WHO/ICCC-3 diagnosis in 138/149 cases (92.6%). These included: 63/63 (100%) reactive/disease-free samples, 43/44 (98%) malignant and 4/4 (100%) benign non-hematopoietic tumors together with 28/38 (74%) leukemia/lymphoma cases; the only exception was Hodgkin lymphoma that required additional markers to be stained. In addition, STOT allowed accurate discrimination among the four most common subtypes of malignant CD45− CD56++ non-hematopoietic solid tumors: 13/13 (GD2++ numyogenin− CD271−/+ nuMyoD1− CD99− EpCAM−) neuroblastoma samples, 5/5 (GD2− numyogenin++ CD271++ nuMyoD1++ CD99−/+ EpCAM−) rhabdomyosarcomas, 2/2 (GD2−/+ numyogenin− CD271+ nuMyoD1− CD99+ EpCAM−) Ewing sarcoma family of tumors, and 7/7 (GD2− numyogenin− CD271+ nuMyoD1− CD99− EpCAM+) Wilms tumors. In summary, here we designed and validated a new standardized antibody combination and MFC assay for diagnostic screening of pediatric solid tumors that might contribute to fast and accurate diagnostic orientation and classification of pediatric cancer in routine clinical practice.
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Affiliation(s)
- Cristiane de Sá Ferreira-Facio
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Vitor Botafogo
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Patrícia Mello Ferrão
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Maria Clara Canellas
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Cristiane B. Milito
- Department of Pathology, Faculty of Medicine, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil;
| | - Sérgio Romano
- Laboratory of Anatomical Pathology and Cytopathology, Instituto Nacional de Câncer (INCa), Rio de Janeiro 20220-400, Brazil;
| | - Daiana V. Lopes
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Lisandra C. Teixeira
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Elen Oliveira
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Enrico Bruno-Riscarolli
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Fabiana V. Mello
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Patrícia F. R. Siqueira
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Patrícia Moura
- I’Dor Institute, Hospital Estadual da Criança, Rio de Janeiro 21330-400, Brazil; (P.M.); (F.N.M.)
| | - Francisco Nicanor Macedo
- I’Dor Institute, Hospital Estadual da Criança, Rio de Janeiro 21330-400, Brazil; (P.M.); (F.N.M.)
| | - Danielle N. Forny
- Department of Pediatric Surgery, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil;
| | - Luíza Simião
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Ana Luíza Pureza
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Marcelo Gerardin Poirot Land
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
| | - Carlos Eduardo Pedreira
- Systems and Computing Engineering Department (COPPE-PESC), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, Brazil;
| | - Jacques J. M. van Dongen
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands;
| | - Alberto Orfao
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (A.O.); (E.S.d.C.); Tel.: +34-9232-9481 (A.O.); +55-21-3938-4725 (E.S.d.C.)
| | - Elaine Sobral da Costa
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
- Correspondence: (A.O.); (E.S.d.C.); Tel.: +34-9232-9481 (A.O.); +55-21-3938-4725 (E.S.d.C.)
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Possamaï D, Pagé G, Panès R, Gagnon É, Lapointe R. CD40L-Stimulated B Lymphocytes Are Polarized toward APC Functions after Exposure to IL-4 and IL-21. THE JOURNAL OF IMMUNOLOGY 2021; 207:77-89. [PMID: 34135061 DOI: 10.4049/jimmunol.2001173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/26/2021] [Indexed: 01/25/2023]
Abstract
B lymphocytes have multiple functions central to humoral immunity, including Ag presentation to T cells, cytokine secretion, and differentiation into Ab-secreting plasma cells. In vitro expansion of human B cells by continuous IL-4 stimulation and engagement of their CD40 receptor by CD40L has allowed the use of these IL-4-CD40-B cells in research for the induction of Ag-specific T cell immune responses. However, in vivo, follicular helper T cells also influence B cell activity through the secretion of IL-21. The impact of both cytokines on multiple B cell functions is not clearly defined. To further understand these cytokines in CD40-B cell biology, we stimulated CD40-B cells with IL-4 or IL-21 or both (Combo) and characterized the proliferation, subsets, and functions of these cells. We demonstrate that IL-21- and Combo-CD40-B cells are highly proliferative cells that can be rapidly expanded to high numbers. We show that IL-21-CD40-B cells polarize to Ab-secreting plasma cells, whereas IL-4- and Combo-CD40-B cells are mostly activated mature B cells that express molecules associated with favorable APC functions. We further demonstrate that both IL-4- and Combo-CD40-B cells are efficient in promoting T cell activation and proliferation compared with IL-21-CD40-B cells. Thus, our study provides a better appreciation of CD40-B cell plasticity and biology. In addition, the stimulation of B cells with CD40L, IL-4, and IL-21 allows for the fast generation of high numbers of efficient APC, therefore providing a prospective tool for research and clinical applications such as cancer immunotherapy.
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Affiliation(s)
- David Possamaï
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Gabriel Pagé
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada.,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Rébecca Panès
- Axe de Recherche en Immunobiologie du Cancer, Institut de Recherche en Immunologie et Cancérologie, Montréal, Québec, Canada; and.,Faculté de Médecine, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Étienne Gagnon
- Axe de Recherche en Immunobiologie du Cancer, Institut de Recherche en Immunologie et Cancérologie, Montréal, Québec, Canada; and.,Faculté de Médecine, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Réjean Lapointe
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada; .,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, Québec, Canada
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Nielsen M, Krarup-Hansen A, Hovgaard D, Petersen MM, Loya AC, Westergaard MCW, Svane IM, Junker N. In vitro 4-1BB stimulation promotes expansion of CD8 + tumor-infiltrating lymphocytes from various sarcoma subtypes. Cancer Immunol Immunother 2020; 69:2179-2191. [PMID: 32472369 DOI: 10.1007/s00262-020-02568-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/03/2020] [Indexed: 12/22/2022]
Abstract
Tumor-specific tumor-infiltrating lymphocytes (TILs) can be in vitro expanded and have the ability to induce complete and durable tumor regression in some patients with melanoma following adoptive cell therapy (ACT). In this preclinical study, we investigated the feasibility of expanding TIL from sarcomas, as well as performing functional in vitro analyses on these. TILs were expanded in vitro by the use of IL2 stimulation with or without the addition of 4-1BB and CD3 antibodies. Phenotypical and functional analyses were mainly performed by flow cytometry. TILs were expanded from 25 of 28 (89%) tumor samples from patients with 9 different sarcoma subtypes. TILs were predominantly αβ T-cells of effector memory subtype with CD4+ dominance. In particular, CD8+ TIL highly expressed LAG3 and to a lesser degree PD-1 and BTLA. In total, 10 of 20 TIL cultures demonstrated in vitro recognition of autologous tumor. In some cases, the fraction of tumor-reactive T cells was more than 20%. 4-1BB stimulation augmented expansion kinetics and favored CD8+ occurrence. In conclusion, TIL expansion from sarcoma is feasible and expanded TILs highly express LAG3 and comprise multifunctional tumor-reactive T-cells.
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Affiliation(s)
- Morten Nielsen
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital Herlev, Herlev, Denmark
| | | | - Dorrit Hovgaard
- Department of Orthopedic Surgery, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Michael Mørk Petersen
- Department of Orthopedic Surgery, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anand Chainsukh Loya
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Inge Marie Svane
- Department of Oncology, National Center for Cancer Immune Therapy (CCIT-DK), Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Niels Junker
- Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
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7
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Abstract
Intracellular cytokine staining (ICS) utilizing fluorescently labeled, cytokine-specific antibodies is a powerful technique utilized to evaluate cytokine expression that provides resolution at the single cell level. Combined with multi-parameter flow cytometry, ICS can provide detailed information on complex cytokine profiles and cellular phenotypes within the tumor microenvironment, particularly for the CD4+ T helper and CD8+ cytotoxic T cell compartments. This technique provides critical information concerning tumor-infiltrating T cell function that is essential for evaluating existing or therapeutically-induced tumor antigen-specific T cell responses in both preclinical models and cancer patients. In this chapter we will discuss in detail the critical steps necessary for a successful ICS assay and outline common protocols for the evaluation of cytokine production from T cell subsets present within the tumor microenvironment.
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8
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Waise S, Parker R, Rose-Zerilli MJJ, Layfield DM, Wood O, West J, Ottensmeier CH, Thomas GJ, Hanley CJ. An Optimized Method to Isolate Human Fibroblasts from Tissue for ex vivo Analysis. Bio Protoc 2019; 9:e3440. [PMID: 33654935 PMCID: PMC7853986 DOI: 10.21769/bioprotoc.3440] [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: 09/26/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 11/02/2022] Open
Abstract
Despite their involvement in many physiological and pathological processes, fibroblasts remain a poorly-characterized cell type. Analysis of primary fibroblasts while maintaining their in vivo phenotype is challenging: standard methods for fibroblast isolation require cell culture in vitro, which is known to alter phenotypes. Previously-described protocols for the dissociation of primary tissues fail to extract sufficient numbers of fibroblasts, instead largely yielding immune cells. Here, we describe an optimized method for generating a fibroblast-enriched single-cell suspension from human tissues using combined mechanical and enzymatic dissociation. This allows analysis of ex vivo fibroblasts without the need for culture in vitro.
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Affiliation(s)
- Sara Waise
- Cancer Sciences Unit, University of Southampton, UK
| | | | | | | | - Oliver Wood
- Cancer Sciences Unit, University of Southampton, UK
| | - Jonathan West
- Cancer Sciences Unit, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Christian H. Ottensmeier
- Cancer Sciences Unit, University of Southampton, UK
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, UK
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9
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Waise S, Parker R, Rose-Zerilli MJJ, Layfield DM, Wood O, West J, Ottensmeier CH, Thomas GJ, Hanley CJ. An optimised tissue disaggregation and data processing pipeline for characterising fibroblast phenotypes using single-cell RNA sequencing. Sci Rep 2019; 9:9580. [PMID: 31270426 PMCID: PMC6610623 DOI: 10.1038/s41598-019-45842-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/13/2019] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) provides a valuable platform for characterising multicellular ecosystems. Fibroblasts are a heterogeneous cell type involved in many physiological and pathological processes, but remain poorly-characterised. Analysis of fibroblasts is challenging: these cells are difficult to isolate from tissues, and are therefore commonly under-represented in scRNA-seq datasets. Here, we describe an optimised approach for fibroblast isolation from human lung tissues. We demonstrate the potential for this procedure in characterising stromal cell phenotypes using scRNA-Seq, analyse the effect of tissue disaggregation on gene expression, and optimise data processing to improve clustering quality. We also assess the impact of in vitro culture conditions on stromal cell gene expression and proliferation, showing that altering these conditions can skew phenotypes.
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Affiliation(s)
- Sara Waise
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Rachel Parker
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Matthew J J Rose-Zerilli
- Cancer Sciences Unit, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - David M Layfield
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Oliver Wood
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Jonathan West
- Cancer Sciences Unit, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Christian H Ottensmeier
- Cancer Sciences Unit, University of Southampton, Southampton, UK
- Cancer Research UK and NIHR Southampton Experimental Cancer Medicine Centre, Southampton, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, University of Southampton, Southampton, UK
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10
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Torres C, Machado R, Lima M. Flow cytometric characterization of the saphenous veins endothelial cells in patients with chronic venous disease and in patients undergoing bypass surgery: an exploratory study. Heart Vessels 2019; 35:1-13. [PMID: 31227876 DOI: 10.1007/s00380-019-01451-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/14/2019] [Indexed: 10/26/2022]
Abstract
Recent findings have suggested that the primary factors for development of chronic venous disease (CVD), which commonly manifests as varicose veins (VV), are due to structural and biochemical modifications of the vessel wall. The aim of this exploratory study was to characterize by flow cytometry the endothelial cells (EC) mechanically extracted from the varicose saphenous veins (VSV) segments of patients submitted to VV surgery, and to compare the expression of cell surface molecules in these EC with that observed in the EC from the graft SV (GSV) of patients undergoing bypass surgery. EC were isolated from distal- (varicose trunk) and from proximal- (nearly normal) VSV segments of 30 patients submitted to VV surgery, and from proximal GSV segments of 20 patients submitted to bypass surgery (control group), using a mechanical method, and their immunophenotype was characterized by flow cytometry. EC were identified as being CD45negCD146brightCD31bright, and analyzed for expression of activation-related (CD54, CD62E, CD106), procoagulant (CD142), and cell junction (CD31, CD146) molecules, and for the scavenger receptor, CD36. The EC harvested from the SV segments of CVD patients had lower expression of all the molecules evaluated, in comparison to controls; these differences were more evident for the EC isolated from the distal-VSV. The EC extracted from the proximal- and distal-VSV segments of the CVD patients also differ from each other, the first having lower levels of CD62E, CD106, CD142 and CD36. Groups did not match for gender and controls were heterogeneous concerning the underlying pathologies, which may have a confounding effect. Our study revealed that the EC isolated from varicose (distal) and nearly normal (proximal) VSV segments of the CVD patients differ phenotypically from each other, and from the EC of the control group. The VSV segments more affected by the CVD have the lowest expression of the studied markers. We hypothesize that CVD is associated with a decrease on the EC surface molecules, causing EC dysfunctionality. Further studies with a large number of gender-matched participants are needed, to confirm the results obtained in this exploratory study.
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Affiliation(s)
- Cláudia Torres
- Laboratório de Citometria, Serviço de Hematologia Clínica, Hospital de Santo António (HSA), Centro Hospitalar Universitário do Porto (CHUP), Rua D. Manuel II 57, 4050-014, Porto, Portugal. .,Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (UMIB/ICBAS/UP), Rua Jorge Viterbo Ferreira 228, 4050-343, Porto, Portugal.
| | - Rui Machado
- Serviço de Angiologia e Cirurgia Vascular, Hospital de Santo António (HSA), Centro Hospitalar Universitário do Porto (CHUP), Largo Prof. Abel Salazar, 4099-001, Porto, Portugal
| | - Margarida Lima
- Laboratório de Citometria, Serviço de Hematologia Clínica, Hospital de Santo António (HSA), Centro Hospitalar Universitário do Porto (CHUP), Rua D. Manuel II 57, 4050-014, Porto, Portugal.,Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (UMIB/ICBAS/UP), Rua Jorge Viterbo Ferreira 228, 4050-343, Porto, Portugal
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11
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Crossey F, Marx S, Hölters S, Schmitt K, Bohle RM, Schmidt T, Stöckle M, Sester U, Sester M, Janssen MWW. Robust method for isolation of tumor infiltrating lymphocytes with a high vital cell yield from small samples of renal cell carcinomas by a new collagenase-free mechanical procedure. Urol Oncol 2018; 36:402.e1-402.e10. [PMID: 30072305 DOI: 10.1016/j.urolonc.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Tumor-infiltrating lymphocytes (TIL) play an important role in the pathogenesis of renal cell carcinoma. Characterization of TIL requires efficient isolation procedures, especially in early stage disease when the tumor is of small in size. Conventional methods for isolating TIL are based on enzymatic tissue digestion, most frequently with collagenase. Collagenase isolation is limited by poor cell recovery, altered expression of cell-surface molecules, and impaired TIL-functionality. To overcome these limitations, we developed and optimized conditions for a robust collagenase-free mechanical procedure for improved isolation of TIL from renal cell carcinoma samples. METHODS TIL from tumor samples and T cells from peripheral blood were collected from 12 patients undergoing partial or radical nephrectomy. Samples were subjected to an enzymatic reference protocol and to a newly established mechanical isolation protocol. After viability staining, TIL-subpopulations were quantified and phenotyped by immunohistochemistry and flow-cytometric analysis, and were compared to characteristics of peripheral blood T cells. As a marker for TIL-functionality, T-cell cytokine induction was quantified after polyclonal stimulation. RESULTS We show that this new technique is rapid and allows identification of CD4 and CD8 T-cell subpopulations including CD4, CD8, and regulatory T cells expressing anergy markers such as programmed death-1 (PD-1) or B- and T-lymphocyte attenuator. When compared to the reference protocol involving collagenase digestion, the yield of TIL after mechanical isolation was higher and the expression of cell-surface markers was better preserved. Moreover, although antitumor activity was not assessed, mechanically isolated TIL are at least equally functional as T cells from peripheral blood, as polyclonal stimulation induced cytokines such as interferon-γ and tumor necrosis factor-α in both TIL and T cells from peripheral blood. CONCLUSION The mechanical procedure may be applied as a robust and rapid alternative to collagenase digestion for isolation of high amounts of phenotypically and functionally intact TIL from fresh tumor samples.
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Affiliation(s)
- Fiona Crossey
- Department of Urology and Pediatric Urology, Saarland University, Homburg (Saar), Germany; Department of Transplant and Infection Immunology, Saarland University, Homburg (Saar), Germany.
| | - Stefanie Marx
- Department of Transplant and Infection Immunology, Saarland University, Homburg (Saar), Germany.
| | - Sebastian Hölters
- Department of Urology and Pediatric Urology, Saarland University, Homburg (Saar), Germany.
| | - Kai Schmitt
- Department of Pathology, Saarland University, Homburg (Saar), Germany.
| | - Rainer M Bohle
- Department of Pathology, Saarland University, Homburg (Saar), Germany.
| | - Tina Schmidt
- Department of Transplant and Infection Immunology, Saarland University, Homburg (Saar), Germany.
| | - Michael Stöckle
- Department of Urology and Pediatric Urology, Saarland University, Homburg (Saar), Germany.
| | - Urban Sester
- Department of Internal Medicine IV, Saarland University, Homburg (Saar), Germany.
| | - Martina Sester
- Department of Transplant and Infection Immunology, Saarland University, Homburg (Saar), Germany.
| | - Martin W W Janssen
- Department of Urology and Pediatric Urology, Saarland University, Homburg (Saar), Germany; Department of Transplant and Infection Immunology, Saarland University, Homburg (Saar), Germany.
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12
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Jamal R, Lapointe R, Cocolakis E, Thébault P, Kazemi S, Friedmann JE, Dionne J, Cailhier JF, Bélanger K, Ayoub JP, Le H, Lambert C, El-Hajjar J, van Kempen LC, Spatz A, Miller WH. Peripheral and local predictive immune signatures identified in a phase II trial of ipilimumab with carboplatin/paclitaxel in unresectable stage III or stage IV melanoma. J Immunother Cancer 2017; 5:83. [PMID: 29157311 PMCID: PMC5696743 DOI: 10.1186/s40425-017-0290-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/04/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Checkpoint blockade with ipilimumab provides long-term survival to a significant proportion of patients with metastatic melanoma. New approaches to increase survival and to predict which patients will benefit from treatment are needed. This phase II trial combined ipilimumab with carboplatin/paclitaxel (CP) to assess its safety, efficacy, and to search for peripheral and tumor-based predictive biomarkers. METHODS Thirty patients with untreated unresectable/metastatic melanoma were treated with ipilimumab and CP. Adverse events (AEs) were monitored and response to treatment was evaluated. Tumor tissue and peripheral blood were collected at specified time points to characterize tumor immune markers by immunohistochemistry and systemic immune activity by multiplex assays and flow cytometry. RESULTS Eighty three percent of patients received all 5 cycles of CP and 93% completed ipilimumab induction. Serious AEs occurred in 13% of patients, and no treatment-related deaths were observed. Best Overall Response Rate (BORR) and Disease Control Rate (DCR) were 27 and 57%, respectively. Median overall survival was 16.2 months. Response to treatment was positively correlated with a higher tumor CD3+ infiltrate (immune score) at baseline. NRAS and BRAF mutations were less frequent in patients who experienced clinical benefit. Assessment of peripheral blood revealed that non-responders had elevated baseline levels of CXCL8 and CCL4, and a higher proportion of circulating late differentiated B cells. Pre-existing high levels of chemokines (CCL3, CCL4 and CXCL8) and advanced B cell differentiation were strongly associated with worse patient overall survival. Elevated proportions of circulating CD8+/PD-1+ T cells during treatment were associated with worse survival. CONCLUSIONS The combination of ipilimumab and CP was well tolerated and revealed novel characteristics associated with patients likely to benefit from treatment. A pre-existing systemic inflammatory state characterized by elevation of selected chemokines and advanced B cell differentiation, was strongly associated with poor patient outcomes, revealing potential predictive circulating biomarkers. TRIAL REGISTRATION Clinicaltrials.gov , NCT01676649 , registered on August 29, 2012.
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Affiliation(s)
- Rahima Jamal
- Hôpital Notre-Dame, Centre de recherche du CHUM, Centre hospitalier de l’Université de Montréal, Montréal, QC Canada
| | - Réjean Lapointe
- Centre de recherche du CHUM, Institut du Cancer de Montréal, Université de Montréal, Montréal, QC Canada
| | - Eftihia Cocolakis
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
| | - Paméla Thébault
- Centre de recherche du CHUM, Institut du Cancer de Montréal, Université de Montréal, Montréal, QC Canada
| | - Shirin Kazemi
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
| | - Jennifer E. Friedmann
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
| | - Jeanne Dionne
- Hôpital Notre-Dame, Centre de recherche du CHUM, Centre hospitalier de l’Université de Montréal, Montréal, QC Canada
| | - Jean-François Cailhier
- Centre de recherche du CHUM, Institut du Cancer de Montréal, Université de Montréal, Montréal, QC Canada
| | - Karl Bélanger
- Hôpital Notre-Dame, Centre de recherche du CHUM, Centre hospitalier de l’Université de Montréal, Montréal, QC Canada
| | - Jean-Pierre Ayoub
- Hôpital Notre-Dame, Centre de recherche du CHUM, Centre hospitalier de l’Université de Montréal, Montréal, QC Canada
| | - Huy Le
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
| | - Caroline Lambert
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
| | - Jida El-Hajjar
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
| | - Léon C. van Kempen
- Department of Pathology, Molecular Pathology Center, Jewish General Hospital, McGill University, Montreal, QC Canada
| | - Alan Spatz
- Department of Pathology, Molecular Pathology Center, Jewish General Hospital, McGill University, Montreal, QC Canada
| | - Wilson H. Miller
- Segal Cancer Center, Jewish General Hospital, Rossy Cancer Network, McGill University, 3755 Côte-St-Catherine, suite E670, Montreal, Québec Canada
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13
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Neutrophils dominate the immune cell composition in non-small cell lung cancer. Nat Commun 2017; 8:14381. [PMID: 28146145 PMCID: PMC5296654 DOI: 10.1038/ncomms14381] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/21/2016] [Indexed: 12/13/2022] Open
Abstract
The response rate to immune checkpoint inhibitor therapy for non-small-cell lung cancer (NSCLC) is just 20%. To improve this figure, several early phase clinical trials combining novel immunotherapeutics with immune checkpoint blockade have been initiated. Unfortunately, these trials have been designed without a strong foundational knowledge of the immune landscape present in NSCLC. Here, we use a flow cytometry panel capable of measuring 51 immune cell populations to comprehensively identify the immune cell composition and function in NSCLC. The results show that the immune cell composition is fundamentally different in lung adenocarcinoma as compared with lung squamous cell carcinoma, and that neutrophils are the most prevalent immune cell type. Using T-cell receptor-β sequencing and tumour reactivity assays, we predict that tumour reactive T cells are frequently present in NSCLC. These results should help to guide the design of clinical trials and the direction of future research in this area.
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14
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Garaud S, Gu-Trantien C, Lodewyckx JN, Boisson A, De Silva P, Buisseret L, Migliori E, Libin M, Naveaux C, Duvillier H, Willard-Gallo K. A simple and rapid protocol to non-enzymatically dissociate fresh human tissues for the analysis of infiltrating lymphocytes. J Vis Exp 2014:52392. [PMID: 25548995 PMCID: PMC4396968 DOI: 10.3791/52392] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The ability of malignant cells to evade the immune system, characterized by tumor escape from both innate and adaptive immune responses, is now accepted as an important hallmark of cancer. Our research on breast cancer focuses on the active role that tumor infiltrating lymphocytes play in tumor progression and patient outcome. Toward this goal, we developed a methodology for the rapid isolation of intact lymphoid cells from normal and abnormal tissues in an effort to evaluate them proximate to their native state. Homogenates prepared using a mechanical dissociator show both increased viability and cell recovery while preserving surface receptor expression compared to enzyme-digested tissues. Furthermore, enzymatic digestion of the remaining insoluble material did not recover additional CD45(+) cells indicating that quantitative and qualitative measurements in the primary homogenate likely genuinely reflect infiltrating subpopulations in the tissue fragment. The lymphoid cells in these homogenates can be easily characterized using immunological (phenotype, proliferation, etc.) or molecular (DNA, RNA and/or protein) approaches. CD45(+) cells can also be used for subpopulation purification, in vitro expansion or cryopreservation. An additional benefit of this approach is that the primary tissue supernatant from the homogenates can be used to characterize and compare cytokines, chemokines, immunoglobulins and antigens present in normal and malignant tissues. This protocol functions extremely well for human breast tissues and should be applicable to a wide variety of normal and abnormal tissues.
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Affiliation(s)
- Soizic Garaud
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Chunyan Gu-Trantien
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Jean-Nicolas Lodewyckx
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Anaïs Boisson
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Pushpamali De Silva
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Laurence Buisseret
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Edoardo Migliori
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Myriam Libin
- Institut d'Immunologie Médicale, Université Libre de Bruxelles
| | - Céline Naveaux
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles
| | - Hugues Duvillier
- Molecular Immunology Unit, Université Libre de Bruxelles; Flow Cytometry Core Facility, Université Libre de Bruxelles
| | - Karen Willard-Gallo
- Molecular Immunology Unit, Université Libre de Bruxelles; Institut Jules Bordet, Université Libre de Bruxelles;
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15
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Ward ST, Li KK, Hepburn E, Weston CJ, Curbishley SM, Reynolds GM, Hejmadi RK, Bicknell R, Eksteen B, Ismail T, Rot A, Adams DH. The effects of CCR5 inhibition on regulatory T-cell recruitment to colorectal cancer. Br J Cancer 2014; 112:319-28. [PMID: 25405854 PMCID: PMC4301825 DOI: 10.1038/bjc.2014.572] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/02/2014] [Accepted: 10/09/2014] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Regulatory T cells (Treg) are enriched in human colorectal cancer (CRC) where they suppress anti-tumour immunity. The chemokine receptor CCR5 has been implicated in the recruitment of Treg from blood into CRC and tumour growth is delayed in CCR5-/- mice, associated with reduced tumour Treg infiltration. METHODS Tissue and blood samples were obtained from patients undergoing resection of CRC. Tumour-infiltrating lymphocytes were phenotyped for chemokine receptors using flow cytometry. The presence of tissue chemokines was assessed. Standard chemotaxis and suppression assays were performed and the effects of CCR5 blockade were tested in murine tumour models. RESULTS Functional CCR5 was highly expressed by human CRC infiltrating Treg and CCR5(high) Treg were more suppressive than their CCR5(low) Treg counterparts. Human CRC-Treg were more proliferative and activated than other T cells suggesting that local proliferation could provide an alternative explanation for the observed tumour Treg enrichment. Pharmacological inhibition of CCR5 failed to reduce tumour Treg infiltration in murine tumour models although it did result in delayed tumour growth. CONCLUSIONS CCR5 inhibition does not mediate anti-tumour effects as a consequence of inhibiting Treg recruitment. Other mechanisms must be found to explain this effect. This has important implications for anti-CCR5 therapy in CRC.
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Affiliation(s)
- S T Ward
- Centre for Liver Research & NIHR Birmingham Biomedical Research Unit, Level 5 Institute for Biomedical Research, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - K K Li
- National Institute for Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - E Hepburn
- National Institute for Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - C J Weston
- National Institute for Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - S M Curbishley
- National Institute for Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - G M Reynolds
- National Institute for Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - R K Hejmadi
- Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Birmingham B15 2WW, UK
| | - R Bicknell
- Institute for Biomedical Research, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - B Eksteen
- Snyder Institute, University of Calgary, Alberta T2N 4N1, Canada
| | - T Ismail
- Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Birmingham B15 2WW, UK
| | - A Rot
- Institute for Biomedical Research, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - D H Adams
- National Institute for Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
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16
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Quatromoni JG, Singhal S, Bhojnagarwala P, Hancock WW, Albelda SM, Eruslanov E. An optimized disaggregation method for human lung tumors that preserves the phenotype and function of the immune cells. J Leukoc Biol 2014; 97:201-9. [PMID: 25359999 DOI: 10.1189/jlb.5ta0814-373] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Careful preparation of human tissues is the cornerstone of obtaining accurate data in immunologic studies. Despite the essential importance of tissue processing in tumor immunology and clinical medicine, current methods of tissue disaggregation have not been rigorously tested for data fidelity. Thus, we critically evaluated the current techniques available in the literature that are used to prepare human lung tumors for immunologic studies. We discovered that these approaches are successful at digesting cellular attachments and ECMs; however, these methods frequently alter the immune cell composition and/or expression of surface molecules. We thus developed a novel approach to prepare human lung tumors for immunologic studies by combining gentle mechanical manipulation with an optimized cocktail of enzymes used at low doses. This enzymatic digestion cocktail optimized cell yield and cell viability, retrieved all major tumor-associated cell populations, and maintained the expression of cell-surface markers for lineage definition and in vivo effector functions. To our knowledge, we present the first rigorously tested disaggregation method designed for human lung tumors.
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Affiliation(s)
- Jon G Quatromoni
- Departments of *Surgery and Medicine, University of Pennsylvania School of Medicine, and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sunil Singhal
- Departments of *Surgery and Medicine, University of Pennsylvania School of Medicine, and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Pratik Bhojnagarwala
- Departments of *Surgery and Medicine, University of Pennsylvania School of Medicine, and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Wayne W Hancock
- Departments of *Surgery and Medicine, University of Pennsylvania School of Medicine, and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Steven M Albelda
- Departments of *Surgery and Medicine, University of Pennsylvania School of Medicine, and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Evgeniy Eruslanov
- Departments of *Surgery and Medicine, University of Pennsylvania School of Medicine, and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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17
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Gu-Trantien C, Loi S, Garaud S, Equeter C, Libin M, de Wind A, Ravoet M, Le Buanec H, Sibille C, Manfouo-Foutsop G, Veys I, Haibe-Kains B, Singhal SK, Michiels S, Rothé F, Salgado R, Duvillier H, Ignatiadis M, Desmedt C, Bron D, Larsimont D, Piccart M, Sotiriou C, Willard-Gallo K. CD4⁺ follicular helper T cell infiltration predicts breast cancer survival. J Clin Invest 2013; 123:2873-92. [PMID: 23778140 DOI: 10.1172/jci67428] [Citation(s) in RCA: 728] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/25/2013] [Indexed: 12/13/2022] Open
Abstract
CD4⁺ T cells are critical regulators of immune responses, but their functional role in human breast cancer is relatively unknown. The goal of this study was to produce an image of CD4⁺ T cells infiltrating breast tumors using limited ex vivo manipulation to better understand the in vivo differences associated with patient prognosis. We performed comprehensive molecular profiling of infiltrating CD4⁺ T cells isolated from untreated invasive primary tumors and found that the infiltrating T cell subpopulations included follicular helper T (Tfh) cells, which have not previously been found in solid tumors, as well as Th1, Th2, and Th17 effector memory cells and Tregs. T cell signaling pathway alterations included a mixture of activation and suppression characterized by restricted cytokine/chemokine production, which inversely paralleled lymphoid infiltration levels and could be reproduced in activated donor CD4⁺ T cells treated with primary tumor supernatant. A comparison of extensively versus minimally infiltrated tumors showed that CXCL13-producing CD4⁺ Tfh cells distinguish extensive immune infiltrates, principally located in tertiary lymphoid structure germinal centers. An 8-gene Tfh signature, signifying organized antitumor immunity, robustly predicted survival or preoperative response to chemotherapy. Our identification of CD4⁺ Tfh cells in breast cancer suggests that they are an important immune element whose presence in the tumor is a prognostic factor.
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Affiliation(s)
- Chunyan Gu-Trantien
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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Domingues PH, Teodósio C, Ortiz J, Sousa P, Otero A, Maillo A, Bárcena P, García-Macias MC, Lopes MC, de Oliveira C, Orfao A, Tabernero MD. Immunophenotypic identification and characterization of tumor cells and infiltrating cell populations in meningiomas. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 181:1749-61. [PMID: 22982440 DOI: 10.1016/j.ajpath.2012.07.033] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/12/2012] [Accepted: 07/06/2012] [Indexed: 11/27/2022]
Abstract
Meningiomas are primary tumors of the central nervous system composed of both neoplastic and other infiltrating cells. We determined the cellular composition of 51 meningioma samples by multiparameter flow cytometric (MFC) immunophenotyping and investigated the potential relationship between mRNA and protein expression levels of neoplastic cells. For immunophenotypic, morphologic, and cytogenetic characterization of individual cell populations, a large panel of markers was used together with phagocytic/endocytic functional assays and MFC sorting. Overall, our results revealed coexistence of CD45(-) neoplastic cells and CD45(+) immune infiltrating cells in all meningiomas. Infiltrating cells included tissue macrophages, with an HLA-DR(+)CD14(+)CD45(+)CD68(+)CD16(-/+)CD33(-/+) phenotype and high phagocytic/endocytic activity, and a small proportion of cytotoxic lymphocytes (mostly T CD8(+) and natural killer cells). Tumor cells expressed multiple cell adhesion proteins, tetraspanins, HLA-I/HLA-DR molecules, complement regulatory proteins, cell surface ectoenzymes, and growth factor receptors. Noteworthy, the relationship between mRNA and protein levels was variable, depending on the proteins evaluated and the level of infiltration by immune cells. In summary, our results indicate that MFC immunophenotyping provides a reliable tool for the characterization of the patterns of protein expression of different cell populations coexisting in meningioma samples, with a more accurate measure of gene expression profiles of tumor cells at the functional/protein level than conventional mRNA microarray, independently of the degree of infiltration of the tumor by immune cells.
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Affiliation(s)
- Patrícia H Domingues
- Centre for Neurosciences and Cell Biology, Faculty of Pharmacy, University of Coimbra, Portugal
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Stimulation of Wnt/ß-catenin pathway in human CD8+ T lymphocytes from blood and lung tumors leads to a shared young/memory phenotype. PLoS One 2012; 7:e41074. [PMID: 22859966 PMCID: PMC3408435 DOI: 10.1371/journal.pone.0041074] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 06/17/2012] [Indexed: 11/19/2022] Open
Abstract
Cancer can be treated by adoptive cell transfer (ACT) of T lymphocytes. However, how to optimally raise human T cells to a differentiation state allowing the best persistence in ACT is a challenge. It is possible to differentiate mouse CD8+ T cells towards stem cell-like memory (TSCM) phenotype upon TCR stimulation with Wnt/ß-catenin pathway activation. Here, we evaluated if TSCM can be obtained from human mature CD8+ T cells following TCR and Wnt/ß-catenin activation through treatment with the chemical agent 4,6-disubstituted pyrrolopyrimidine (TWS119), which inhibits the glycogen synthase kinase-3β (GSK-3β), key inhibitor of the Wnt pathway. Human CD8+ T cells isolated from peripheral blood or tumor-infiltrating lymphocytes (TIL), and treated with TWS119 gave rise to CD62L+CD45RA+ cells, indicative of early differentiated stage, also expressing CD127 which is normally found on memory cells, and CD133, an hematopoietic stem cell marker. TSCM cells raised from either TIL or blood secreted numerous inflammatory mediators, but in lower amounts than those measured without TWS119. Finally, generated TSCM CD8+ T cells expressed elevated Bcl-2 and no detectable caspase-3 activity, suggesting increased persistence. Our data support a role for Wnt/ß-catenin pathway in promoting the TSCM subset in human CD8+ T cells from TIL and the periphery, which are relevant for ACT.
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Long lasting local and systemic inflammation after cerebral hypoxic ischemia in newborn mice. PLoS One 2012; 7:e36422. [PMID: 22567156 PMCID: PMC3342175 DOI: 10.1371/journal.pone.0036422] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 03/31/2012] [Indexed: 11/24/2022] Open
Abstract
Background Hypoxic ischemia (HI) is an important cause of neonatal brain injury and subsequent inflammation affects neurological outcome. In this study we performed investigations of systemic and local activation states of inflammatory cells from innate and adaptive immunity at different time points after neonatal HI brain injury in mice. Methodology/Principal Findings We developed a multiplex flow cytometry based method combined with immunohistochemistry to investigate cellular immune responses in the brain 24 h to 7 months after HI brain injury. In addition, functional studies of ex vivo splenocytes after cerebral hypoxic ischemia were performed. Both central and peripheral activation of CD11b+ and CD11c+ antigen presenting cells were seen with expression of the costimulatory molecule CD86 and MHC-II, indicating active antigen presentation in the damaged hemisphere and in the spleen. After one week, naïve CD45rb+ T-lymphocytes were demonstrated in the damaged brain hemisphere. In a second phase after three months, pronounced activation of CD45rb− T-lymphocytes expressing CD69 and CD25 was seen in the damaged hemisphere. Brain homogenate induced proliferation in splenocytes after HI but not in controls. Conclusions/Significance Our findings demonstrate activation of both local and systemic immune responses months after hypoxic ischemic neonatal brain injury. The long term immune activation observed is of general importance for future studies of the inflammatory response after brain injury as most previous studies have focused on the first few weeks after damage, while the effects of the late inflammation phase may be missed. Furthermore, the self-reactive component raises the question if there is a correlation with development of autoimmune brain disease later in life.
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