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Kim TW, Koo SY, Riessland M, Chaudhry F, Kolisnyk B, Cho HS, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons. Cell 2024; 187:3671-3689.e23. [PMID: 38866017 DOI: 10.1016/j.cell.2024.05.030] [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: 11/20/2022] [Revised: 12/15/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Ongoing, early-stage clinical trials illustrate the translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, an unresolved challenge is the extensive cell death following transplantation. Here, we performed a pooled CRISPR-Cas9 screen to enhance postmitotic dopamine neuron survival in vivo. We identified p53-mediated apoptotic cell death as a major contributor to dopamine neuron loss and uncovered a causal link of tumor necrosis factor alpha (TNF-α)-nuclear factor κB (NF-κB) signaling in limiting cell survival. As a translationally relevant strategy to purify postmitotic dopamine neurons, we identified cell surface markers that enable purification without the need for genetic reporters. Combining cell sorting and treatment with adalimumab, a clinically approved TNF-α inhibitor, enabled efficient engraftment of postmitotic dopamine neurons with extensive reinnervation and functional recovery in a preclinical PD mouse model. Thus, transient TNF-α inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic hPSC-derived dopamine neurons in PD.
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Affiliation(s)
- Tae Wan Kim
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Department of Interdisciplinary Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - So Yeon Koo
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Markus Riessland
- Department of Neurobiology and Behavior, Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA
| | - Fayzan Chaudhry
- Tri-Institutional PhD program in Computational Biology, New York, NY, USA
| | - Benjamin Kolisnyk
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hyein S Cho
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Marco Vincenzo Russo
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Nathalie Saurat
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doron Betel
- Division of Hematology & Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY 10065, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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2
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Tin E, Lee JB, Khatri I, Na Y, Minden MD, Zhang L. Double-negative T cells utilize a TNFα-JAK1-ICAM-1 cytotoxic axis against acute myeloid leukemia. Blood Adv 2024; 8:3013-3026. [PMID: 38547431 PMCID: PMC11215209 DOI: 10.1182/bloodadvances.2023011739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/15/2024] [Indexed: 06/13/2024] Open
Abstract
ABSTRACT Allogeneic double-negative T cells (DNTs) are a rare T-cell subset that effectively target acute myeloid leukemia (AML) without inducing graft-versus-host disease in an allogeneic setting. A phase 1 clinical trial demonstrated the feasibility, safety, and potential efficacy of allogeneic DNT therapy among patients with relapsed AML. However, the molecular mechanisms of DNT-mediated cytotoxicity against AML remain elusive. Thus, we used a flow cytometry-based high throughput screening to compare the surface molecule expression profile on DNTs during their interaction with DNT-susceptible or -resistant AML cells and identified a tumor necrosis factor α (TNFα)-dependent cytotoxic pathway in DNT-AML interaction. TNFα secreted by DNTs, upon encountering susceptible AML targets, sensitized AML cells to DNT-mediated killing, including those otherwise resistant to DNTs. Mechanistically, TNFα upregulated ICAM-1 on AML cells through a noncanonical JAK1-dependent pathway. DNTs then engaged with AML cells more effectively through an ICAM-1 receptor, lymphocyte function-associated antigen 1, leading to enhanced killing. These results reveal a TNFα-JAK1-ICAM-1 axis in DNT-mediated cytotoxicity against AML to improve therapeutic efficacy.
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Affiliation(s)
- Enoch Tin
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jong Bok Lee
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Ismat Khatri
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Yoosu Na
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Li Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Toyofuku T, Ishikawa T, Nojima S, Kumanogoh A. Efficacy against Lung Cancer Is Augmented by Combining Aberrantly N-Glycosylated T Cells with a Chimeric Antigen Receptor Targeting Fragile X Mental Retardation 1 Neighbor. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:917-927. [PMID: 38214607 PMCID: PMC10876419 DOI: 10.4049/jimmunol.2300618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/17/2023] [Indexed: 01/13/2024]
Abstract
The adaptive transfer of T cells redirected to cancer cells via chimeric Ag receptors (CARs) has produced clinical benefits for the treatment of hematologic diseases. To extend this approach to solid cancer, we screened CARs targeting surface Ags on human lung cancer cells using (to our knowledge) novel expression cloning based on the Ag receptor-induced transcriptional activation of IL-2. Isolated CARs were directed against fragile X mental retardation 1 neighbor (FMR1NB), a cancer-testis Ag that is expressed by malignant cells and adult testicular germ cells. Anti-FMR1NB CAR human T cells demonstrated target-specific cytotoxicity and successfully controlled tumor growth in mouse xenograft models of lung cancer. Furthermore, to protect CAR T cells from immune-inhibitory molecules, which are present in the tumor microenvironment, we introduced anti-FMR1NB CARs into 2-deoxy-glucose (2DG)-treated human T cells. These cells exhibited reduced binding affinity to immune-inhibitory molecules, and the suppressive effects of these molecules were resisted through blockade of the N-glycosylation of their receptors. Anti-FMR1NB CARs in 2DG-treated human T cells augmented target-specific cytotoxicity in vitro and in vivo. Thus, our findings demonstrated the feasibility of eradicating lung cancer cells using 2DG-treated human T cells, which are able to direct tumor-specific FMR1NB via CARs and survive in the suppressive tumor microenvironment.
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Affiliation(s)
- Toshihiko Toyofuku
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, The Center of Medical Innovation and Translational Research, Osaka University, Suita, Osaka, Japan
| | - Takako Ishikawa
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, The Center of Medical Innovation and Translational Research, Osaka University, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
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Slusher GA, Kottke PA, Culberson AL, Chilmonczyk MA, Fedorov AG. Microfluidics enabled multi-omics triple-shot mass spectrometry for cell-based therapies. BIOMICROFLUIDICS 2024; 18:011302. [PMID: 38268742 PMCID: PMC10807926 DOI: 10.1063/5.0175178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/01/2024] [Indexed: 01/26/2024]
Abstract
In recent years, cell-based therapies have transformed medical treatment. These therapies present a multitude of challenges associated with identifying the mechanism of action, developing accurate safety and potency assays, and achieving low-cost product manufacturing at scale. The complexity of the problem can be attributed to the intricate composition of the therapeutic products: living cells with complex biochemical compositions. Identifying and measuring critical quality attributes (CQAs) that impact therapy success is crucial for both the therapy development and its manufacturing. Unfortunately, current analytical methods and tools for identifying and measuring CQAs are limited in both scope and speed. This Perspective explores the potential for microfluidic-enabled mass spectrometry (MS) systems to comprehensively characterize CQAs for cell-based therapies, focusing on secretome, intracellular metabolome, and surfaceome biomarkers. Powerful microfluidic sampling and processing platforms have been recently presented for the secretome and intracellular metabolome, which could be implemented with MS for fast, locally sampled screening of the cell culture. However, surfaceome analysis remains limited by the lack of rapid isolation and enrichment methods. Developing innovative microfluidic approaches for surface marker analysis and integrating them with secretome and metabolome measurements using a common analytical platform hold the promise of enhancing our understanding of CQAs across all "omes," potentially revolutionizing cell-based therapy development and manufacturing for improved efficacy and patient accessibility.
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Affiliation(s)
| | - Peter A. Kottke
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
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de Jong E, Kocer A. Current Methods for Identifying Plasma Membrane Proteins as Cancer Biomarkers. MEMBRANES 2023; 13:409. [PMID: 37103836 PMCID: PMC10142483 DOI: 10.3390/membranes13040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Plasma membrane proteins are a special class of biomolecules present on the cellular membrane. They provide the transport of ions, small molecules, and water in response to internal and external signals, define a cell's immunological identity, and facilitate intra- and intercellular communication. Since they are vital to almost all cellular functions, their mutants, or aberrant expression is linked to many diseases, including cancer, where they are a part of cancer cell-specific molecular signatures and phenotypes. In addition, their surface-exposed domains make them exciting biomarkers for targeting by imaging agents and drugs. This review looks at the challenges in identifying cancer-related cell membrane proteins and the current methodologies that solve most of the challenges. We classified the methodologies as biased, i.e., search cells for the presence of already known membrane proteins. Second, we discuss the unbiased methods that can identify proteins without prior knowledge of what they are. Finally, we discuss the potential impact of membrane proteins on the early detection and treatment of cancer.
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6
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Al-Jazrawe M, Xu S, Poon R, Wei Q, Przybyl J, Varma S, van de Rijn M, Alman BA. CD142 Identifies Neoplastic Desmoid Tumor Cells, Uncovering Interactions Between Neoplastic and Stromal Cells That Drive Proliferation. CANCER RESEARCH COMMUNICATIONS 2023; 3:697-708. [PMID: 37377751 PMCID: PMC10128091 DOI: 10.1158/2767-9764.crc-22-0403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/03/2023] [Accepted: 03/27/2023] [Indexed: 06/29/2023]
Abstract
The interaction between neoplastic and stromal cells within a tumor mass plays an important role in cancer biology. However, it is challenging to distinguish between tumor and stromal cells in mesenchymal tumors because lineage-specific cell surface markers typically used in other cancers do not distinguish between the different cell subpopulations. Desmoid tumors consist of mesenchymal fibroblast-like cells driven by mutations stabilizing beta-catenin. Here we aimed to identify surface markers that can distinguish mutant cells from stromal cells to study tumor-stroma interactions. We analyzed colonies derived from single cells from human desmoid tumors using a high-throughput surface antigen screen, to characterize the mutant and nonmutant cells. We found that CD142 is highly expressed by the mutant cell populations and correlates with beta-catenin activity. CD142-based cell sorting isolated the mutant population from heterogeneous samples, including one where no mutation was previously detected by traditional Sanger sequencing. We then studied the secretome of mutant and nonmutant fibroblastic cells. PTX3 is one stroma-derived secreted factor that increases mutant cell proliferation via STAT6 activation. These data demonstrate a sensitive method to quantify and distinguish neoplastic from stromal cells in mesenchymal tumors. It identifies proteins secreted by nonmutant cells that regulate mutant cell proliferation that could be therapeutically. Significance Distinguishing between neoplastic (tumor) and non-neoplastic (stromal) cells within mesenchymal tumors is particularly challenging, because lineage-specific cell surface markers typically used in other cancers do not differentiate between the different cell subpopulations. Here, we developed a strategy combining clonal expansion with surface proteome profiling to identify markers for quantifying and isolating mutant and nonmutant cell subpopulations in desmoid tumors, and to study their interactions via soluble factors.
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Affiliation(s)
- Mushriq Al-Jazrawe
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Xu
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
| | - Raymond Poon
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
| | - Qingxia Wei
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
| | - Joanna Przybyl
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Benjamin A. Alman
- Hospital for Sick Children, Program in Developmental & Stem Cell Biology, Toronto, Ontario, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Orthopedic Surgery, Duke University, Durham, North Carolina
- Regeneration Next Initiative, Duke University, Durham, North Carolina
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7
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Kim TW, Koo SY, Riessland M, Cho H, Chaudhry F, Kolisnyk B, Russo MV, Saurat N, Mehta S, Garippa R, Betel D, Studer L. TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534819. [PMID: 37034664 PMCID: PMC10081262 DOI: 10.1101/2023.03.29.534819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ongoing, first-in-human clinical trials illustrate the feasibility and translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson's disease (PD). However, a major unresolved challenge in the field is the extensive cell death following transplantation with <10% of grafted dopamine neurons surviving. Here, we performed a pooled CRISPR/Cas9 screen to enhance survival of postmitotic dopamine neurons in vivo . We identified p53-mediated apoptotic cell death as major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival. As a translationally applicable strategy to purify postmitotic dopamine neurons, we performed a cell surface marker screen that enabled purification without the need for genetic reporters. Combining cell sorting with adalimumab pretreatment, a clinically approved and widely used TNFa inhibitor, enabled efficient engraftment of postmitotic dopamine neurons leading to extensive re-innervation and functional recovery in a preclinical PD mouse model. Thus, transient TNFa inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic human PSC-derived dopamine neurons in PD. Highlights In vivo CRISPR-Cas9 screen identifies p53 limiting survival of grafted human dopamine neurons. TNFα-NFκB pathway mediates p53-dependent human dopamine neuron deathCell surface marker screen to enrich human dopamine neurons for translational use. FDA approved TNF-alpha inhibitor rescues in vivo dopamine neuron survival with in vivo function.
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8
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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9
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Köhnke T, Liu X, Haubner S, Bücklein V, Hänel G, Krupka C, Solis-Mezarino V, Herzog F, Subklewe M. Integrated multiomic approach for identification of novel immunotherapeutic targets in AML. Biomark Res 2022; 10:43. [PMID: 35681175 PMCID: PMC9185890 DOI: 10.1186/s40364-022-00390-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/01/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Immunotherapy of acute myeloid leukemia has experienced considerable advances, however novel target antigens continue to be sought after. To this end, unbiased approaches for surface protein detection are limited and integration with other data types, such as gene expression and somatic mutational burden, are poorly utilized. The Cell Surface Capture technology provides an unbiased, discovery-driven approach to map the surface proteins on cells of interest. Yet, direct utilization of primary patient samples has been limited by the considerable number of viable cells needed. METHODS Here, we optimized the Cell Surface Capture protocol to enable direct interrogation of primary patient samples and applied our optimized protocol to a set of samples from patients with acute myeloid leukemia (AML) to generate the AML surfaceome. We then further curated this AML surfaceome to exclude antigens expressed on healthy tissues and integrated mutational burden data from hematologic cancers to further enrich for targets which are likely to be essential to leukemia biology. Finally, we validated our findings in a separate cohort of AML patient samples. RESULTS Our protocol modifications allowed us to double the yield in identified proteins and increased the specificity from 54 to 80.4% compared to previous approaches. Using primary AML patient samples, we were able to identify a total of 621 surface proteins comprising the AML surfaceome. We integrated this data with gene expression and mutational burden data to curate a set of robust putative target antigens. Seventy-six proteins were selected as potential candidates for further investigation of which we validated the most promising novel candidate markers, and identified CD148, ITGA4 and Integrin beta-7 as promising targets in AML. Integrin beta-7 showed the most promising combination of expression in patient AML samples, and low or absent expression on healthy hematopoietic tissue. CONCLUSION Taken together, we demonstrate the feasibility of a highly optimized surfaceome detection method to interrogate the entire AML surfaceome directly from primary patient samples and integrate this data with gene expression and mutational burden data to achieve a robust, multiomic target identification platform. This approach has the potential to accelerate the unbiased target identification for immunotherapy of AML.
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Affiliation(s)
- Thomas Köhnke
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Xilong Liu
- Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Sascha Haubner
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Veit Bücklein
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Gerulf Hänel
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany.,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | - Christina Krupka
- Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany
| | | | - Franz Herzog
- Department of Biochemistry, Gene Center, LMU Munich, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, Marchioninistr 15, 81377, Munich, Germany. .,Laboratory for Translational Cancer Immunology, Gene Center Munich, LMU Munich, Munich, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany.
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10
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Rodriguez-Esteban R, Duarte J, Teixeira PC, Richard F, Koltsova S, So WV. Prediction of standard cell types and functional markers from textual descriptions of flow cytometry gating definitions using machine learning. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2022; 102:220-227. [PMID: 35253974 DOI: 10.1002/cyto.b.22065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND A key step in clinical flow cytometry data analysis is gating, which involves the identification of cell populations. The process of gating produces a set of reportable results, which are typically described by gating definitions. The non-standardized, non-interpreted nature of gating definitions represents a hurdle for data interpretation and data sharing across and within organizations. Interpreting and standardizing gating definitions for subsequent analysis of gating results requires a curation effort from experts. Machine learning approaches have the potential to help in this process by predicting expert annotations associated with gating definitions. METHODS We created a gold-standard dataset by manually annotating thousands of gating definitions with cell type and functional marker annotations. We used this dataset to train and test a machine learning pipeline able to predict standard cell types and functional marker genes associated with gating definitions. RESULTS The machine learning pipeline predicted annotations with high accuracy for both cell types and functional marker genes. Accuracy was lower for gating definitions from assays belonging to laboratories from which limited or no prior data was available in the training. Manual error review ensured that resulting predicted annotations could be reused subsequently as additional gold-standard training data. CONCLUSIONS Machine learning methods are able to consistently predict annotations associated with gating definitions from flow cytometry assays. However, a hybrid automatic and manual annotation workflow would be recommended to achieve optimal results.
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Affiliation(s)
- Raul Rodriguez-Esteban
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - José Duarte
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Priscila C Teixeira
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Fabien Richard
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Svetlana Koltsova
- Curation Department, Rancho BioSciences LLC, San Diego, California, USA
| | - W Venus So
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, USA
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11
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Lopes R, Shi K, Fonseca NA, Gama A, Ramalho JS, Almeida L, Moura V, Simões S, Tidor B, Moreira JN. Modelling the impact of nucleolin expression level on the activity of F3 peptide-targeted pH-sensitive pegylated liposomes containing doxorubicin. Drug Deliv Transl Res 2022; 12:629-646. [PMID: 33860446 DOI: 10.1007/s13346-021-00972-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 01/06/2023]
Abstract
Strategies targeting nucleolin have enabled a significant improvement in intracellular bioavailability of their encapsulated payloads. In this respect, assessment of the impact of target cell heterogeneity and nucleolin homology across species (structurally and functionally) is of major importance. This work also aimed at mathematically modelling the nucleolin expression levels at the cell membrane, binding and internalization of pH-sensitive pegylated liposomes encapsulating doxorubicin and functionalized with the nucleolin-binding F3 peptide (PEGASEMP), and resulting cytotoxicity against cancer cells from mouse, rat, canine, and human origin. Herein, it was shown that nucleolin expression levels were not a limitation on the continuous internalization of F3 peptide-targeted liposomes, despite the saturable nature of the binding mechanism. Modeling enabled the prediction of nucleolin-mediated total doxorubicin exposure provided by the experimental settings of the assessment of PEGASEMP's impact on cell death. The former increased proportionally with nucleolin-binding sites, a measure relevant for patient stratification. This pattern of variation was observed for the resulting cell death in nonsaturating conditions, depending on the cancer cell sensitivity to doxorubicin. This approach differs from standard determination of cytotoxic concentrations, which normally report values of incubation doses rather than the actual intracellular bioactive drug exposure. Importantly, in the context of development of nucleolin-based targeted drug delivery, the structural nucleolin homology (higher than 84%) and functional similarity across species presented herein, emphasized the potential to use toxicological data and other metrics from lower species to infer the dose for a first-in-human trial.
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Affiliation(s)
- Rui Lopes
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Kevin Shi
- Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nuno A Fonseca
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
- TREAT U, SA - Parque Industrial de Taveiro, Lote 44, 3045-508, Coimbra, Portugal
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD), Quinta de Prados, Apartado 1013, 5000-801, Vila Real, Portugal
| | - José S Ramalho
- Laboratory of Cellular and Molecular Biology, NOVA Medical School, New University of Lisbon, Campo Mártires da Pátria, 130, 1169-056, Lisboa, Portugal
| | - Luís Almeida
- Blueclinical, Ltd, 4460-439, Senhora da Hora, Matosinhos, Portugal
| | - Vera Moura
- TREAT U, SA - Parque Industrial de Taveiro, Lote 44, 3045-508, Coimbra, Portugal
| | - Sérgio Simões
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
- UC - University of Coimbra, CIBB, Faculty of Pharmacy, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
| | - Bruce Tidor
- Department of Biological Engineering and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - João N Moreira
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine (Polo 1), Rua Larga, University of Coimbra, 3004-504, Coimbra, Portugal
- UC - University of Coimbra, CIBB, Faculty of Pharmacy, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
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12
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Sato T, Ogawa Y, Ishikawa A, Nagasaka Y, Kinoshita M, Shiokawa I, Shimada S, Momosawa A, Kawamura T. Revisiting the Experimental Methods for Human Skin T Cell Analysis. JID INNOVATIONS 2022; 2:100125. [PMID: 35620704 PMCID: PMC9127406 DOI: 10.1016/j.xjidi.2022.100125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/05/2022] [Accepted: 03/04/2022] [Indexed: 10/27/2022] Open
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13
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Palicelli A, Bonacini M, Croci S, Bisagni A, Zanetti E, De Biase D, Sanguedolce F, Ragazzi M, Zanelli M, Chaux A, Cañete-Portillo S, Bonasoni MP, Ascani S, De Leo A, Gandhi J, Tafuni A, Melli B. What Do We Have to Know about PD-L1 Expression in Prostate Cancer? A Systematic Literature Review. Part 7: PD-L1 Expression in Liquid Biopsy. J Pers Med 2021; 11:1312. [PMID: 34945784 PMCID: PMC8709072 DOI: 10.3390/jpm11121312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is an accessible, non-invasive diagnostic tool for advanced prostate cancer (PC) patients, potentially representing a real-time monitoring test for tumor evolution and response to treatment through the analysis of circulating tumor cells (CTCs) and exosomes. We performed a systematic literature review (PRISMA guidelines) to describe the current knowledge about PD-L1 expression in liquid biopsies of PC patients: 101/159 (64%) cases revealed a variable number of PD-L1+ CTCs. Outcome correlations should be investigated in larger series. Nuclear PD-L1 expression by CTCs was occasionally associated with worse prognosis. Treatment (abiraterone, enzalutamide, radiotherapy, checkpoint-inhibitors) influenced PD-L1+ CTC levels. Discordance in PD-L1 status was detected between primary vs. metastatic PC tissue biopsies and CTCs vs. corresponding tumor tissues. PD-L1 is also released by PC cells through soluble exosomes, which could inhibit the T cell function, causing immune evasion. PD-L1+ PC-CTC monitoring and genomic profiling may better characterize the ongoing aggressive PC forms compared to PD-L1 evaluation on primary tumor biopsies/prostatectomy specimens (sometimes sampled a long time before recurrence/progression). Myeloid-derived suppressor cells and dendritic cells (DCs), which may have immune-suppressive effects in tumor microenvironment, have been found in PC patients circulation, sometimes expressing PD-L1. Occasionally, their levels correlated to clinical outcome. Enzalutamide-progressing castration-resistant PC patients revealed increased PD-1+ T cells and circulating PD-L1/2+ DCs.
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Affiliation(s)
- Andrea Palicelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (A.B.); (E.Z.); (M.R.); (M.Z.); (M.P.B.)
| | - Martina Bonacini
- Clinical Immunology, Allergy and Advanced Biotechnologies Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (M.B.); (S.C.)
| | - Stefania Croci
- Clinical Immunology, Allergy and Advanced Biotechnologies Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (M.B.); (S.C.)
| | - Alessandra Bisagni
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (A.B.); (E.Z.); (M.R.); (M.Z.); (M.P.B.)
| | - Eleonora Zanetti
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (A.B.); (E.Z.); (M.R.); (M.Z.); (M.P.B.)
| | - Dario De Biase
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | | | - Moira Ragazzi
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (A.B.); (E.Z.); (M.R.); (M.Z.); (M.P.B.)
| | - Magda Zanelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (A.B.); (E.Z.); (M.R.); (M.Z.); (M.P.B.)
| | - Alcides Chaux
- Department of Scientific Research, School of Postgraduate Studies, Norte University, Asunción 1614, Paraguay;
| | - Sofia Cañete-Portillo
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Maria Paola Bonasoni
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (A.B.); (E.Z.); (M.R.); (M.Z.); (M.P.B.)
| | - Stefano Ascani
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy;
- Haematopathology Unit, CREO, Azienda Ospedaliera di Perugia, University of Perugia, 06129 Perugia, Italy
| | - Antonio De Leo
- Molecular Diagnostic Unit, Azienda USL Bologna, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy;
| | - Jatin Gandhi
- Department of Pathology and Laboratory Medicine, University of Washington, Seattle, WA 98195, USA;
| | - Alessandro Tafuni
- Pathology Unit, Department of Medicine and Surgery, University of Parma, 43121 Parma, Italy;
| | - Beatrice Melli
- Fertility Center, Department of Obstetrics and Gynecology, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy;
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41121 Modena, Italy
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14
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DePriest BP, Vieira N, Bidgoli A, Paczesny S. An overview of multiplexed analyses of CAR T-cell therapies: insights and potential. Expert Rev Proteomics 2021; 18:767-780. [PMID: 34628995 PMCID: PMC8626704 DOI: 10.1080/14789450.2021.1992276] [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: 01/05/2023]
Abstract
INTRODUCTION Cancer immunotherapy is a rapidly growing field with exponential advancement in engineered immune cell-based therapies. For instance, an engineered chimeric antigen receptor (CAR) can be introduced in T-cells or other immune cells and adoptively transferred to target and kill cancer cells in hematologic malignancies or solid tumors. The first CAR-T-cell (CAR-T) therapy has been developed against CD19, a B-cell marker expressed on lymphoma and lymphoblastic leukemia. To allow for personalized treatment, proteomics approaches could provide insights into biomarkers for CAR-T therapy efficacy and toxicity. AREAS COVERED We researched the most recent technology methods of biomarker evaluation used in the laboratory and clinical setting. Publications of CAR-T biomarkers were then systematically reviewed to provide a narrative of the most validated biomarkers of CAR-T efficacy and toxicity. Examples of biomarkers include CAR-T functionality and phenotype as well as interleukin-6 and other cytokines. EXPERT COMMENTARY Biomarkers of CAR-T efficacy and toxicity have been identified, but still need to be validated and standardized across institutions. Moreover, few are used in the clinical setting due to limitations in real-time technology. Expansion of biomarker research could provide better understanding of patient response and risk of life-threatening side effects with potential for improved precision medicine.
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Affiliation(s)
- Brittany Paige DePriest
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Noah Vieira
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Alan Bidgoli
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Sophie Paczesny
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
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15
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Reza KK, Dey S, Wuethrich A, Behren A, Antaw F, Wang Y, Sina AAI, Trau M. In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment. ACS NANO 2021; 15:11231-11243. [PMID: 34225455 DOI: 10.1021/acsnano.0c10008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cancer is a dynamic disease with heterogenic molecular signatures and constantly evolves during the course of the disease. Single cell proteomic analysis could offer a suitable pathway to monitor cancer cell heterogeneity and deliver critical information for the diagnosis, recurrence, and drug-resistant mechanisms in cancer. Current standard techniques for proteomic analysis such as ELISA, mass spectrometry, and Western blots are time-consuming, expensive, and often require fluorescence labeling that fails to provide accurate information about the multiple protein expression changes at the single cell level. Herein, we report a surface-enhanced Raman spectroscopy-based simple microfluidic device that enables the screening of single circulating tumor cells (CTC) in a dynamic state to precisely understand the heterogeneous expression of multiple protein biomarkers in response to therapy. It further enables identifying intercellular heterogeneous expression of CTC surface proteins which would be highly informative to identify the cancer cells surviving treatment and potentially responsible for drug resistance. Using a bead and cell line-based model system, we successfully detect single bead and single cell spectra when flowed through the device. Using SK-MEL-28 melanoma cells, we demonstrate that our system is capable of monitoring heterogeneous expressions of multiple surface protein markers (MCSP, MCAM, and LNGFR) before and during drug treatment. Integrating a label-free electrochemical system with the device, we also monitor the expression of an intracellular protein (here, BRAFV600E) under drug treatment. Finally, we perform a longitudinal study with 15 samples from five different melanoma patients who underwent therapy. We find that the average expression of receptor proteins in a patient fails to determine the therapy response particularly when the disease progresses. However, single CTC analysis with our device shows a high level of intercellular heterogeneity in the receptor expression profiles of patient-derived CTCs and identifies heterogeneity within CTCs. More importantly, we find that a fraction of CTCs still shows a high expression of these receptor proteins during and after therapy, indicating the presence of resistant CTCs which may evolve after a certain time and progress the disease. We believe this automated assay will have high clinical importance in disease diagnosis and monitoring treatment and will significantly advance the understanding of cancer heterogeneity on the single cell level.
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Affiliation(s)
- K Kamil Reza
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, Queensland 4072, Australia
| | - Shuvashis Dey
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, Queensland 4072, Australia
| | - Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, Queensland 4072, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, Victoria 3084, Australia
| | - Fiach Antaw
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, Queensland 4072, Australia
| | - Yuling Wang
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Abu Ali Ibn Sina
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, Queensland 4072, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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16
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Yao H, Zhao H, Pan X, Zhao X, Feng J, Yang C, Zhang S, Zhang X. Discriminating Leukemia Cellular Heterogeneity and Screening Metabolite Biomarker Candidates using Label-Free Mass Cytometry. Anal Chem 2021; 93:10282-10291. [PMID: 34259005 DOI: 10.1021/acs.analchem.1c01746] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Discriminating various leukocyte subsets with specific functions is critical due to their important roles in the development of many diseases. Here, we proposed a general strategy to unravel leukocytes heterogeneity and screen differentiated metabolites as biomarker candidates for leukocyte subtypes using the label-free mass cytometry (CyESI-MS) combined with a homemade data processing workflow. Taking leukemia cells as an example, metabolic fingerprints of single leukemia cells were obtained from 472 HL-60, 416 THP-1, 313 U937, 356 Jurkat, and 366 Ramos cells, with throughput up to 40 cells/min. Five leukemia subtypes were clearly distinguished by unsupervised learning t-SNE analysis of the single-cell metabolic fingerprints. Cell discrimination in the mixed leukemia cell samples was also realized by supervised learning of the single-cell metabolic fingerprints with high recovery and good repetition (98.31 ± 0.24%, -102.35 ± 4.82%). Statistical analysis and metabolite assignment were carried out to screen characteristic metabolites for discrimination and 36 metabolites with significant differences were annotated. Then, differentiated metabolites for pairwise discrimination of five leukemia subtypes were further selected as biomarker candidates. Furthermore, discriminating cultured leukemia cells from human normal leukocytes, separated from fresh human peripheral blood, was performed based on single-cell metabolic fingerprints as well as the proposed biomarker candidates, unveiling the potential of this strategy in clinical research. This work makes efforts to realize high-throughput single-leukocyte metabolic analysis and metabolite-based discrimination of leukocytes. It is expected to be a powerful means for the clinical molecular diagnosis of hematological diseases.
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Affiliation(s)
- Huan Yao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xu Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Chengdui Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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17
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Soave M, Stoddart LA, White CW, Kilpatrick LE, Goulding J, Briddon SJ, Hill SJ. Detection of genome-edited and endogenously expressed G protein-coupled receptors. FEBS J 2021; 288:2585-2601. [PMID: 33506623 PMCID: PMC8647918 DOI: 10.1111/febs.15729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane receptors and major targets for FDA-approved drugs. The ability to quantify GPCR expression and ligand binding characteristics in different cell types and tissues is therefore important for drug discovery. The advent of genome editing along with developments in fluorescent ligand design offers exciting new possibilities to probe GPCRs in their native environment. This review provides an overview of the recent technical advances employed to study the localisation and ligand binding characteristics of genome-edited and endogenously expressed GPCRs.
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Affiliation(s)
- Mark Soave
- Division of Physiology, Pharmacology and NeuroscienceSchool of Life SciencesUniversity of NottinghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
| | - Leigh A. Stoddart
- Division of Physiology, Pharmacology and NeuroscienceSchool of Life SciencesUniversity of NottinghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
| | - Carl W. White
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
- Harry Perkins Institute of Medical Research and Centre for Medical ResearchQEII Medical CentreThe University of Western AustraliaNedlandsAustralia
- Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Laura E. Kilpatrick
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
- Division of Biomolecular Science and Medicinal ChemistrySchool of Pharmacy, Biodiscovery InstituteUniversity of NottinghamUK
| | - Joëlle Goulding
- Division of Physiology, Pharmacology and NeuroscienceSchool of Life SciencesUniversity of NottinghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
| | - Stephen J. Briddon
- Division of Physiology, Pharmacology and NeuroscienceSchool of Life SciencesUniversity of NottinghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
| | - Stephen J. Hill
- Division of Physiology, Pharmacology and NeuroscienceSchool of Life SciencesUniversity of NottinghamUK
- Centre of Membrane Proteins and Receptors (COMPARE)University of Birmingham and University of NottinghamThe MidlandsUK
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18
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Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmytryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG, Ailles LE. Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21. J Exp Med 2021; 217:151793. [PMID: 32434219 PMCID: PMC7398174 DOI: 10.1084/jem.20191094] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/06/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Recent studies indicate that cancer-associated fibroblasts (CAFs) are phenotypically and functionally heterogeneous. However, little is known about CAF subtypes, the roles they play in cancer progression, and molecular mediators of the CAF “state.” Here, we identify a novel cell surface pan-CAF marker, CD49e, and demonstrate that two distinct CAF states, distinguished by expression of fibroblast activation protein (FAP), coexist within the CD49e+ CAF compartment in high-grade serous ovarian cancers. We show for the first time that CAF state influences patient outcomes and that this is mediated by the ability of FAP-high, but not FAP-low, CAFs to aggressively promote proliferation, invasion and therapy resistance of cancer cells. Overexpression of the FAP-low–specific transcription factor TCF21 in FAP-high CAFs decreases their ability to promote invasion, chemoresistance, and in vivo tumor growth, indicating that it acts as a master regulator of the CAF state. Understanding CAF states in more detail could lead to better patient stratification and novel therapeutic strategies.
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Affiliation(s)
- Ali Hussain
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Poon
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christina Karamboulas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ngoc Hoang Bao Bui
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jalna Meens
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Julia Dmytryshyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Victor W Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kwan Ho Tang
- Laura and Isaac Perlmutter Cancer Center, New York Langone Health, New York, NY
| | - Joshua Paterson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Blaise A Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Division of Gynaecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin G Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Laura and Isaac Perlmutter Cancer Center, New York Langone Health, New York, NY
| | - Laurie E Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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19
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Liu T, Li J, Yu L, Sun HX, Li J, Dong G, Hu Y, Li Y, Shen Y, Wu J, Gu Y. Cross-species single-cell transcriptomic analysis reveals pre-gastrulation developmental differences among pigs, monkeys, and humans. Cell Discov 2021; 7:8. [PMID: 33531465 PMCID: PMC7854681 DOI: 10.1038/s41421-020-00238-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Interspecies blastocyst complementation enables organ-specific enrichment of xenogeneic pluripotent stem cell (PSC) derivatives, which raises an intriguing possibility to generate functional human tissues/organs in an animal host. However, differences in embryo development between human and host species may constitute the barrier for efficient chimera formation. Here, to understand these differences we constructed a complete single-cell landscape of early embryonic development of pig, which is considered one of the best host species for human organ generation, and systematically compared its epiblast development with that of human and monkey. Our results identified a developmental coordinate of pluripotency spectrum among pigs, humans and monkeys, and revealed species-specific differences in: (1) pluripotency progression; (2) metabolic transition; (3) epigenetic and transcriptional regulations of pluripotency; (4) cell surface proteins; and (5) trophectoderm development. These differences may prevent proper recognition and communication between donor human cells and host pig embryos, resulting in low integration and survival of human cells. These results offer new insights into evolutionary conserved and divergent processes during mammalian development and may be helpful for developing effective strategies to overcome low human-pig chimerism, thereby enabling the generation of functional human organs in pigs in the future.
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Affiliation(s)
- Tianbin Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jie Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Hai-Xi Sun
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jing Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Guoyi Dong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China.,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yingying Hu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yong Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ying Gu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518083, China. .,BGI-Shenzhen, Shenzhen, Guangdong, 518083, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, 518120, China. .,Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Bares AJ, Mejooli MA, Pender MA, Leddon SA, Tilley S, Lin K, Dong J, Kim M, Fowell DJ, Nishimura N, Schaffer CB. Hyperspectral multiphoton microscopy for in vivo visualization of multiple, spectrally overlapped fluorescent labels. OPTICA 2020; 7:1587-1601. [PMID: 33928182 PMCID: PMC8081374 DOI: 10.1364/optica.389982] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 09/30/2020] [Indexed: 05/17/2023]
Abstract
The insensitivity of multiphoton microscopy to optical scattering enables high-resolution, high-contrast imaging deep into tissue, including in live animals. Scattering does, however, severely limit the use of spectral dispersion techniques to improve spectral resolution. In practice, this limited spectral resolution together with the need for multiple excitation wavelengths to excite different fluorophores limits multiphoton microscopy to imaging a few, spectrally-distinct fluorescent labels at a time, restricting the complexity of biological processes that can be studied. Here, we demonstrate a hyperspectral multiphoton microscope that utilizes three different wavelength excitation sources together with multiplexed fluorescence emission detection using angle-tuned bandpass filters. This microscope maintains scattering insensitivity, while providing high enough spectral resolution on the emitted fluorescence and capitalizing on the wavelength-dependent nonlinear excitation of fluorescent dyes to enable clean separation of multiple, spectrally overlapping labels, in vivo. We demonstrated the utility of this instrument for spectral separation of closely-overlapped fluorophores in samples containing ten different colors of fluorescent beads, live cells expressing up to seven different fluorescent protein fusion constructs, and in multiple in vivo preparations in mouse cortex and inflamed skin with up to eight different cell types or tissue structures distinguished.
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Affiliation(s)
- Amanda J. Bares
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Menansili A. Mejooli
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Mitchell A. Pender
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Scott A. Leddon
- Center for Vaccine Biology and Immunology, Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Steven Tilley
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Karen Lin
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Jingyuan Dong
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Minsoo Kim
- Center for Vaccine Biology and Immunology, Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Deborah J. Fowell
- Center for Vaccine Biology and Immunology, Dept. of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Nozomi Nishimura
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Chris B. Schaffer
- The Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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21
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Low junctional adhesion molecule-A expression is associated with an epithelial to mesenchymal transition and poorer outcomes in high-grade serous carcinoma of uterine adnexa. Mod Pathol 2020; 33:2361-2377. [PMID: 32514162 DOI: 10.1038/s41379-020-0586-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/17/2022]
Abstract
High-grade serous carcinoma of uterine adnexa (HGSC) is the most frequent histotype of epithelial ovarian cancer and has a poor 5-year survival rate due to late-stage diagnosis and the poor efficacy of standard treatments. Novel biomarkers of cancer outcome are needed to identify new targetable pathways and improve personalized treatments. Cell-surface screening of 26 HGSC cell lines by high-throughput flow cytometry identified junctional adhesion molecule 1 (JAM-A, also known as F11R) as a potential biomarker. Using a multi-labeled immunofluorescent staining coupled with digital image analysis, protein levels of JAM-A were quantified in tissue microarrays from three HGSC patient cohorts: a discovery cohort (n = 101), the Canadian Ovarian Experimental Unified Resource cohort (COEUR, n = 1158), and the Canadian Cancer Trials Group OV16 cohort (n = 267). Low JAM-A level was associated with poorer outcome in the three cohorts by Kaplan-Meier (p = 0.023, p < 0.001, and p = 0.036, respectively) and was an independent marker of shorter survival in the COEUR cohort (HR = 0.517 (0.381-703), p < 0.001). When analyses were restricted to patients treated by taxane-platinum-based chemotherapy, low JAM-A protein expression was associated with poorer responses in the COEUR (p < 0.001) and OV16 cohorts (p = 0.006) by Kaplan-Meier. Decreased JAM-A gene expression was an indicator of poor outcome in gene expression datasets including The Cancer Genome Atlas (n = 606, p = 0.002) and Kaplan-Meier plotter (n = 1816, p = 0.024). Finally, we observed that tumors with decreased JAM-A expression exhibited an enhanced epithelial to mesenchymal transition (EMT) signature. Our results demonstrate that JAM-A expression is a robust prognostic biomarker of HGSC and may be used to discriminate tumors responsive to therapies targeting EMT.
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22
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Ding M, Baker D. Recent advances in high-throughput flow cytometry for drug discovery. Expert Opin Drug Discov 2020; 16:303-317. [PMID: 33054417 DOI: 10.1080/17460441.2021.1826433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION High-throughput flow cytometry (HTFC) has proven to be an important technology in drug discovery. The use of HTFC enables multi-parametric screening of suspension cells containing heterogenous cell populations and coated particles for screening proteins of interest. Novel targets, novel cell markers and compound clusters for drug development have been identified from HTFC screens. AREAS COVERED In this article, the authors focus on reviewing the recent HTFC applications reported during the last 5-6 years, including drug discovery screens and studies for immune, immune-oncology, infectious and inflammatory diseases. The main HTFC approaches, development of HTFC systems, and automated sample preparation systems for HTFC are also discussed. EXPERT OPINION The advance of HTFC technology coupled with automated sample acquisition and sample preparation has demonstrated its utility in screening large numbers of compounds using suspension cells, facilitated screening of disease-relevant human primary cells, and enabled deep understanding of mechanism of action by analyzing multiple parameters. The authors see HTFC as a very valuable tool in immune, immune-oncology, infectious and inflammatory diseases where immune cells play essential roles.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - David Baker
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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23
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Rocha-Resende C, Yang W, Li W, Kreisel D, Adamo L, Mann DL. Developmental changes in myocardial B cells mirror changes in B cells associated with different organs. JCI Insight 2020; 5:139377. [PMID: 32663200 PMCID: PMC7455131 DOI: 10.1172/jci.insight.139377] [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: 04/21/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
The naive heart harbors a population of intravascular B cells that make close contact with the cardiac microvasculature. However, the timing of their appearance and their organ specificity remain unknown. To address this knowledge gap, we performed a systematic analysis of B cells isolated from the myocardium and other organs, from embryonic life to adulthood. We found that the phenotype of myocardial B cells changed dynamically during development. While neonatal heart B cells were mostly CD11b+ and CD11b– CD21–CD23–, adult B cells were predominantly CD11b–CD21+CD23+. Histological analysis and intravital microscopy of lung and liver showed that organ-associated B cells in contact with the microvascular endothelium were not specific to the heart. Flow cytometric analysis of perfused hearts, livers, lungs, and spleen showed that the dynamic changes in B cell subpopulations observed in the heart during development mirrored changes observed in the other organs. Single cell RNA sequencing (scRNAseq) analysis of B cells showed that myocardial B cells were part of a larger population of organ-associated B cells that had a distinct transcriptional profile. These findings broaden our understanding of the biology of myocardial-associated B cells and suggest that current models of the dynamics of naive B cells during development are incomplete. Myocardial B cells are part of a larger population of intravascular organ-associated B cells.
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Affiliation(s)
- Cibele Rocha-Resende
- Center for Cardiovascular Research, Cardiovascular Division, Department of Medicine
| | - Wei Yang
- Genome Technology Access Center, Department of Genetics
| | | | - Daniel Kreisel
- Department of Surgery, and.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Luigi Adamo
- Center for Cardiovascular Research, Cardiovascular Division, Department of Medicine
| | - Douglas L Mann
- Center for Cardiovascular Research, Cardiovascular Division, Department of Medicine
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24
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Krämer M, Plum PS, Velazquez Camacho O, Folz-Donahue K, Thelen M, Garcia-Marquez I, Wölwer C, Büsker S, Wittig J, Franitza M, Altmüller J, Löser H, Schlößer H, Büttner R, Schröder W, Bruns CJ, Alakus H, Quaas A, Chon SH, Hillmer AM. Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics. Mol Oncol 2020; 14:1170-1184. [PMID: 32255255 PMCID: PMC7266280 DOI: 10.1002/1878-0261.12680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/17/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022] Open
Abstract
Single‐cell transcriptomics have revolutionized our understanding of the cell composition of tumors and allowed us to identify new subtypes of cells. Despite rapid technological advancements, single‐cell analysis remains resource‐intense hampering the scalability that is required to profile a sufficient number of samples for clinical associations. Therefore, more scalable approaches are needed to understand the contribution of individual cell types to the development and treatment response of solid tumors such as esophageal adenocarcinoma where comprehensive genomic studies have only led to a small number of targeted therapies. Due to the limited treatment options and late diagnosis, esophageal adenocarcinoma has a poor prognosis. Understanding the interaction between and dysfunction of individual cell populations provides an opportunity for the development of new interventions. In an attempt to address the technological and clinical needs, we developed a protocol for the separation of esophageal carcinoma tissue into leukocytes (CD45+), epithelial cells (EpCAM+), and fibroblasts (two out of PDGFRα, CD90, anti‐fibroblast) by fluorescence‐activated cell sorting and subsequent RNA sequencing. We confirm successful separation of the three cell populations by mapping their transcriptomic profiles to reference cell lineage expression data. Gene‐level analysis further supports the isolation of individual cell populations with high expression of CD3, CD4, CD8, CD19, and CD20 for leukocytes, CDH1 and MUC1 for epithelial cells, and FAP, SMA, COL1A1, and COL3A1 for fibroblasts. As a proof of concept, we profiled tumor samples of nine patients and explored expression differences in the three cell populations between tumor and normal tissue. Interestingly, we found that angiogenesis‐related genes were upregulated in fibroblasts isolated from tumors compared with normal tissue. Overall, we suggest our protocol as a complementary and more scalable approach compared with single‐cell RNA sequencing to investigate associations between clinical parameters and transcriptomic alterations of specific cell populations in esophageal adenocarcinoma.
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Affiliation(s)
- Max Krämer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Patrick S Plum
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany.,Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Oscar Velazquez Camacho
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Kat Folz-Donahue
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Martin Thelen
- Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Germany
| | | | - Christina Wölwer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Sören Büsker
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Jana Wittig
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Marek Franitza
- Cologne Center for Genomics, University of Cologne, Germany
| | | | - Heike Löser
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Hans Schlößer
- Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Wolfgang Schröder
- Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Christiane J Bruns
- Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Seung-Hun Chon
- Department of General, Visceral and Cancer Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany
| | - Axel M Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Germany.,Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
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25
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Yoon JY, Gedye C, Paterson J, Ailles L. Stem/progenitor cell marker expression in clear cell renal cell carcinoma: a potential relationship with the immune microenvironment to be explored. BMC Cancer 2020; 20:272. [PMID: 32245446 PMCID: PMC7119074 DOI: 10.1186/s12885-020-06733-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/10/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a markedly heterogeneous disease in many aspects, including the tumour microenvironment. Our previous study showed the importance of the tumour microenvironment in ccRCC xeno-transplant success rates. In order to better understand the potential relationship between TICs and the immune microenvironment, we employed a multi-modal approach, examining RNA and protein expression (flow cytometry, immunohistochemistry). METHODS We first examined the gene expression pattern of 18 stem/progenitor marker genes in the cancer genome atlas (TCGA) ccRCC cohort. Flow cytometry was next employed to examine lineage-specific expression levels of stem/progenitor markers and immune population makeup in six, disaggregated, primary ccRCC specimens. Immunohistochemistry was performed on a commercial ccRCC tissue microarray (TMA). RESULTS The 18 genes differed with respect to their correlation patterns with one another and to their prognostic significance. By flow cytometry, correlating expression frequency of 12 stem/progenitor markers and CD10 resulted in two clusters-one with CD10 (marker of proximal tubular differentiation), and second cluster containing mostly mesenchymal stem cell (MSC) markers, including CD146. In turn, these clusters differed with respect to their correlation with different CD45+ lineage markers and their expression of immune checkpoint pathway proteins. To confirm these findings, four stem/progenitor marker expression patterns were compared with CD4, CD8 and CD20 in a ccRCC TMA which showed a number of similar trends with respect to frequency of the different tumour-infiltrating leukocytes. CONCLUSION Taken together, we observed heterogeneous but patterned expression levels of different stem/progenitor markers. Our results suggest a non-random relationship between their expression patterns with the immune microenvironment populations in ccRCC.
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Affiliation(s)
- Ju-Yoon Yoon
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, M5S 1A1, Canada.
| | - Craig Gedye
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Joshua Paterson
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Laurie Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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26
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Burgess TL, Amason JD, Rubin JS, Duveau DY, Lamy L, Roberts DD, Farrell CL, Inglese J, Thomas CJ, Miller TW. A homogeneous SIRPα-CD47 cell-based, ligand-binding assay: Utility for small molecule drug development in immuno-oncology. PLoS One 2020; 15:e0226661. [PMID: 32240171 PMCID: PMC7117682 DOI: 10.1371/journal.pone.0226661] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
CD47 is an immune checkpoint protein that downregulates both the innate and adaptive anti-tumor immune response via its counter receptor SIRPα. Biologics, including humanized CD47 monoclonal antibodies and decoy SIRPα receptors, that block the SIRPα-CD47 interaction, are currently being developed as cancer immunotherapy agents. However, adverse side effects and limited penetration of tumor tissue associated with their structure and large size may impede their clinical application. We recently developed a quantitative high throughput screening assay platform to identify small molecules that disrupt the binding of SIRPα and CD47 as an alternative approach to these protein-based therapeutics. Here, we report on the development and optimization of a cell-based binding assay to validate active small molecules from our biochemical screening effort. This assay has a low volume, high capacity homogenous format that relies on laser scanning cytometry (LSC) and associated techniques to enhance signal to noise measurement of cell surface binding. The LSC assay is specific, concentration dependent, and validated for the two major human SIRPα variants (V1 and V2), with results that parallel those of our biochemical data as well as published studies. We also utilized the LSC assay to confirm published studies showing that the inhibition of amino-terminal pyroglutamate formation on CD47 using the glutaminyl cyclase inhibitor SEN177 disrupts SIRPα binding. The SIRPα-CD47 interaction could be quantitatively measured in live and fixed tumor cells. Use of fixed cells reduces the burden of cell maintenance and provides stable cell standards to control for inter- and intra-assay variations. We also demonstrate the utility of the assay to characterize the activity of the first reported small molecule antagonists of the SIRPα-CD47 interaction. This assay will support the screening of thousands of compounds to identify or validate active small molecules as hits, develop structure activity relationships and assist in the optimization of hits to leads by a typical iterative medicinal chemistry campaign.
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Affiliation(s)
- Teresa L. Burgess
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
| | - Joshua D. Amason
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey S. Rubin
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
| | - Damien Y. Duveau
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - Laurence Lamy
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - David D. Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - Craig J. Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - Thomas W. Miller
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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27
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A Fast and Sensitive Luciferase-based Assay for Antibody Engineering and Design of Chimeric Antigen Receptors. Sci Rep 2020; 10:2318. [PMID: 32047180 PMCID: PMC7012821 DOI: 10.1038/s41598-020-59099-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/15/2020] [Indexed: 12/27/2022] Open
Abstract
Success of immunotherapeutic approaches using genetically engineered antibodies and T cells modified with chimeric antigen receptors (CARs) depends, among other things, on the selection of antigen binding domains with desirable expression and binding characteristics. We developed a luciferase-based assay, termed Malibu-Glo Assay, which streamlines the process of optimization of an antigen binding domain with desirable properties and allows the sensitive detection of tumor antigens. The assay involves a recombinant immunoconjugate, termed Malibu-Glo reagent, comprising an immunoglobulin or a non-immunoglobulin based antigen binding domain genetically linked to a marine luciferase. Malibu-Glo reagent can be conveniently produced in mammalian cells as a secreted protein that retains the functional activity of both the antigen binding domain and the luciferase. Moreover, crude supernatant containing the secreted Malibu-Glo reagent can directly be used for detection of cell surface antigens obviating the laborious steps of protein purification and labeling. We further demonstrate the utility of Malibu-Glo assay for the selection of optimal single chain fragment variables (scFvs) with desired affinity characteristics for incorporation into CARs. In summary, Malibu-Glo assay is a fast, simple, sensitive, specific and economical assay for antigen detection with multiple applications in the fields of antibody engineering, antibody humanization and CAR-T cell therapy.
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28
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Bonfim-Silva R, Salomão KB, Pimentel TVCDA, Menezes CCBDO, Palma PVB, Fontes AM. Biological characterization of the UW402, UW473, ONS-76 and DAOY pediatric medulloblastoma cell lines. Cytotechnology 2019; 71:893-903. [PMID: 31346954 PMCID: PMC6787134 DOI: 10.1007/s10616-019-00332-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 07/19/2019] [Indexed: 12/15/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children. Recent advances in molecular technologies allowed to classify MB in 4 major molecular subgroups: WNT, SHH, Group 3 and Group 4. In cancer research, cancer cell lines are important for examining and manipulating molecular and cellular process. However, it is important to know the characteristics of each cancer cell line prior to use, because there are some differences among them, even if they originate from the same cancer type. This study aimed to evaluate the similarities and differences among four human medulloblastoma cell lines, UW402, UW473, DAOY and ONS-76. The medulloblastoma cell lines were analyzed for (1) cell morphology, (2) immunophenotyping by flow cytometry for some specifics surface proteins, (3) expression level of adhesion molecules by RT-qPCR, (4) proliferative potential, (5) cell migration, and (6) in vivo tumorigenic potential. It was observed a relationship between cell growth and CDH1 (E-chaderin) adhesion molecule expression and all MB cell lines showed higher levels of CDH2 (N-chaderin) when compared to other adhesion molecule. ONS-76 showed higher gene expression of CDH5 (VE-chaderin) and higher percentage of CD144/VE-chaderin positive cells when compared to other MB cell lines. All MB cell lines showed low percentage of CD34, CD45, CD31, CD133 positive cells and high percentage of CD44, CD105, CD106 and CD29 positive cells. The DAOY cell line showed the highest migration potential, the ONS-76 cell line showed the highest proliferative potential and only DAOY and ONS-76 cell lines showed tumorigenic potential in vivo. MB cell lines showed functional and molecular differences among them, which it should be considered by the researchers in choosing the most suitable cellular model according to the study proposal.
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Affiliation(s)
- Ricardo Bonfim-Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 Monte Alegre, Ribeirão Preto, São Paulo, ZIP code: 14049-900, Brazil.
| | - Karina Bezerra Salomão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 Monte Alegre, Ribeirão Preto, São Paulo, ZIP code: 14049-900, Brazil
| | - Thais Valéria Costa de Andrade Pimentel
- Department of Medical Clinic, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 Monte Alegre, Ribeirão Preto, São Paulo, ZIP code: 14049-900, Brazil
| | - Camila Cristina Branquinho de Oliveira Menezes
- Ribeirão Preto Blood Center, Clinics Hospital of the Ribeirão Preto Medical School, University of São Paulo, Av. Tenente Catão Roxo, 2501 Monte Alegre, Ribeirão Preto, São Paulo, ZIP code: 14051-140, Brazil
| | - Patrícia Vianna Bonini Palma
- Ribeirão Preto Blood Center, Clinics Hospital of the Ribeirão Preto Medical School, University of São Paulo, Av. Tenente Catão Roxo, 2501 Monte Alegre, Ribeirão Preto, São Paulo, ZIP code: 14051-140, Brazil
| | - Aparecida Maria Fontes
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 Monte Alegre, Ribeirão Preto, São Paulo, ZIP code: 14049-900, Brazil
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Sen M, Hahn F, Black TA, DeMarshall M, Porter W, Snowden E, Yee SS, Tong F, Ferguson M, Fleshman EN, Nakagawa H, Falk GW, Ginsberg GG, Kochman ML, Blaesius R, Rustgi AK, Carpenter EL. Flow based single cell analysis of the immune landscape distinguishes Barrett's esophagus from adjacent normal tissue. Oncotarget 2019; 10:3592-3604. [PMID: 31217895 PMCID: PMC6557213 DOI: 10.18632/oncotarget.26911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/14/2019] [Indexed: 01/21/2023] Open
Abstract
Barrett’s esophagus (BE) is metaplasia of the squamous epithelium to a specialized columnar epithelium. BE progresses through low- and high-grade dysplasia before developing into esophageal adenocarcinoma. The BE microenvironment is not well defined. We compare 12 human clinical BE and adjacent normal squamous epithelium biopsies using single cell immunophenotyping by flow cytometry. A cassette of 19 epithelial and immune cell markers was used to detect differences between cellular compartments in normal and BE tissues. We found that the BE microenvironment has an immunological landscape distinct from adjacent normal epithelium. BE has an increased percentage of epithelial cells with a concomitant decrease in the percentage of immune cells, accompanied by a shift in the immune landscape from a predominantly T cell rich microenvironment in normal tissue to a B cell rich landscape in BE tissue. Hierarchical clustering separates BE and normal samples into two discrete groups based upon our 19-marker panel, but also reveals unexpected, shared phenotypes for three patients. Our results suggest that flow based single cell analysis may have the potential for revealing clinically relevant differences between BE and normal adjacent tissue, and that surface immunophenotypes could identify specific subpopulations from dysplastic tissue for further investigation.
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Affiliation(s)
- Moen Sen
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Friedrich Hahn
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Taylor A Black
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maureen DeMarshall
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Warren Porter
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Eileen Snowden
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Stephanie S Yee
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frances Tong
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Mitchell Ferguson
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Emylee N Fleshman
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hiroshi Nakagawa
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary W Falk
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory G Ginsberg
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael L Kochman
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rainer Blaesius
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erica L Carpenter
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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30
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Nimker S, Sharma K, Saraswathy R, Chandna S. Delineating the Effects of Ionizing Radiation on Erythropoietic Lineage-Implications for Radiation Biodosimetry. HEALTH PHYSICS 2019; 116:677-693. [PMID: 30720544 DOI: 10.1097/hp.0000000000000975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The overall lethality/morbidity of ionizing radiation exposure involves multiple forms of inhibitory or cytotoxic effects that may manifest in different tissues with a varying dose and time response. One of the major systemic effects leading to lethality of radiation includes its suppressive effect on hematopoiesis, which could be observed even at doses as low as 1-2 Gy, whereas effects on gastrointestinal and nervous systems appear at relatively higher doses in the same order. This article reviews the effects of radiation on the three distinct stages of erythropoiesis-formation of erythroid progenitor cells, differentiation of erythroid precursor cells, and terminal maturation. During these stepwise developmental processes, erythroid progenitor cells undergo rapid expansion to form terminally differentiated red blood cells that are continuously replenished from bone marrow into the circulating peripheral blood stream. Cellular radiation response depends upon many factors such as cell lineage, rate of proliferation, and differentiation status. Therefore, we discuss radiation-induced alterations during the progenitor, precursor, and terminal maturation stages and the implications thereof. Since biomarkers of ionizing radiation exposure in human populations are of great interest for assessing normal tissue injury as well as for biodosimetry in the event of accidental or incidental radiation exposures, we also highlight blood-based biomarkers that have potential utility for medical management.
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Affiliation(s)
- Shwetanjali Nimker
- Division of Natural Radiation Response Mechanisms, Institute of Nuclear Medicine and Allied Sciences, Timarpur, Delhi, India
- School of Biosciences and Technology, Vellore Institiute of Technology, Vellore, Tamil Nadu, India
| | - Kanupriya Sharma
- Division of Natural Radiation Response Mechanisms, Institute of Nuclear Medicine and Allied Sciences, Timarpur, Delhi, India
| | - Radha Saraswathy
- School of Biosciences and Technology, Vellore Institiute of Technology, Vellore, Tamil Nadu, India
| | - Sudhir Chandna
- Division of Natural Radiation Response Mechanisms, Institute of Nuclear Medicine and Allied Sciences, Timarpur, Delhi, India
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Lee DF, Chambers MA. Isolation of Alveolar Type II Cells from Adult Bovine Lung. ACTA ACUST UNITED AC 2019; 80:e71. [PMID: 30875462 DOI: 10.1002/cptx.71] [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: 01/05/2023]
Abstract
Alveolar type II (ATII) cells play a key role as part of the distal lung epithelium, including in the innate immune response and as self-renewing progenitors to replace alveolar type I (ATI) cells during epithelial regeneration. Their secretion of surfactant protein helps maintain homeostasis and exerts protective, antimicrobial properties. ATII cells remain difficult to study, partly due to inefficient and expensive isolation methods, a propensity to differentiate into ATI cells, and susceptibility to fibroblast contamination. Published methods of isolation often require specialized technology, negatively impacting the development of in vitro models of disease, including bovine tuberculosis. Presented here is a simple and cost-effective method for generation of bovine primary ATII cells. These cells exhibit an ATII phenotype in 2D and 3D culture and are conducive to further study of the role of ATII cells in bovine respiratory diseases. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Diane Frances Lee
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Mark Andrew Chambers
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
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32
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Alhattab D, Jamali F, Ali D, Hammad H, Adwan S, Rahmeh R, Samarah O, Salah B, Hamdan M, Awidi A. An insight into the whole transcriptome profile of four tissue-specific human mesenchymal stem cells. Regen Med 2019; 14:841-865. [PMID: 30702025 DOI: 10.2217/rme-2018-0137] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: Variations in the clinical outcomes using mesenchymal stem cells (MSCs) treatments exist, reflecting different origins and niches. To date, there is no consensus on the best source of MSCs most suitable to treat a specific disease. Methods: Total transcriptome analysis of human MSCs was performed. MSCs were isolated from two adult sources bone marrow, adipose tissue and two perinatal sources umbilical cord and placenta. Results: Each MSCs type possessed a unique expression pattern that reflects an advantage in terms of their potential therapeutic use. Advantages in immune modulation, neurogenesis and other aspects were found. Discussion: This study is a milestone for evidence-based choice of the type of MSCs used in the treatment of diseases.
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Affiliation(s)
- Dana Alhattab
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Fatima Jamali
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Dema Ali
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Hana Hammad
- Department of Biological Sciences, School of Science, The University of Jordan, Amman, Jordan
| | - Sofia Adwan
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Reem Rahmeh
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Omar Samarah
- Special Surgery Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Bareqa Salah
- General Surgery Department/Plastic & Reconstructive, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | - Mohammad Hamdan
- Special Surgery Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, Jordan.,Department of Hematology & Oncology, Faculty of Medicine, The University of Jordan, Amman, Jordan
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33
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Xi Y, Wang D, Wang T, Huang L, Zhang XE. Quantitative profiling of CD13 on single acute myeloid leukemia cells by super-resolution imaging and its implication in targeted drug susceptibility assessment. NANOSCALE 2019; 11:1737-1744. [PMID: 30623954 DOI: 10.1039/c8nr06526h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantitative profiling of membrane proteins on the cell surface is of great interest in tumor targeted therapy and single cell biology. However, the existing technologies are either of insufficient resolution, or unable to provide precise information on the localization of individual proteins. Here, we report a new method that combines the use of quantum dot labeling, super-resolution microscopy (structured illumination microscopy, SIM) and software modeling. In this proof-of-principle study, we assessed the biological effects of Bestatin on individual cells from different AML cell lines expressing CD13 proteins, a potential target for tumor targeted therapy. Using the proposed method, we found that the different AML cell lines exhibit different CD13 expression densities, ranging from 0.1 to 1.3 molecules per μm2 cell surface, respectively. Importantly, Bestatin treatment assays shows that its effects on cell growth inhibition, apoptosis and cell cycle change are directly proportional to the density of CD13 on the cell surface of these cell lines. The results suggest that the proposed method advances the quantitative analysis of single cell surface proteins, and that the quantitative profiling information of the target protein on single cells has potential value in targeted drug susceptibility assessment.
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Affiliation(s)
- Yan Xi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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34
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Lee JB, Kang H, Fang L, D'Souza C, Adeyi O, Zhang L. Developing Allogeneic Double-Negative T Cells as a Novel Off-the-Shelf Adoptive Cellular Therapy for Cancer. Clin Cancer Res 2019; 25:2241-2253. [DOI: 10.1158/1078-0432.ccr-18-2291] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 11/16/2022]
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Mariñas-Pardo L, García-Castro J, Rodríguez-Hurtado I, Rodríguez-García MI, Núñez-Naveira L, Hermida-Prieto M. Allogeneic Adipose-Derived Mesenchymal Stem Cells (Horse Allo 20) for the Treatment of Osteoarthritis-Associated Lameness in Horses: Characterization, Safety, and Efficacy of Intra-Articular Treatment. Stem Cells Dev 2018; 27:1147-1160. [DOI: 10.1089/scd.2018.0074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Javier García-Castro
- Unidad de Biotecnología Celular, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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36
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Lee DF, Salguero FJ, Grainger D, Francis RJ, MacLellan-Gibson K, Chambers MA. Isolation and characterisation of alveolar type II pneumocytes from adult bovine lung. Sci Rep 2018; 8:11927. [PMID: 30093682 PMCID: PMC6085293 DOI: 10.1038/s41598-018-30234-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
Alveolar type II (ATII) cells play a key role as part of the distal lung epithelium, including roles in the innate immune response and as self-renewing progenitors to replace alveolar type I (ATI) cells during regeneration of the alveolar epithelium. Their secretion of surfactant protein helps to maintain homeostasis in the distal lung and exert protective, antimicrobial properties. Despite the cell's crucial roles, they remain difficult to study, in part due to inefficient and expensive isolation methods, a propensity to differentiate into alveolar type I cells in culture and susceptibility to fibroblast overgrowth from primary isolations. Published methods of isolation often require specialist technology, negatively impacting the development of in vitro models of disease, including bovine tuberculosis (BTB), a serious re-emerging disease in both animals and humans worldwide. We present here a simple and cost-effective method that may be utilised in the generation of bovine primary ATII cells. These exhibit an ATII phenotype in 2D and 3D culture in our studies and are conducive to further study of the role of ATII cells in bovine respiratory diseases.
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Affiliation(s)
- Diane Frances Lee
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, GU2 7AL, England.
| | - Francisco Javier Salguero
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, GU2 7AL, England
| | - Duncan Grainger
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, GU2 7AL, England
| | - Robert James Francis
- National Institute of Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, UK EN6 3QG, England
| | - Kirsty MacLellan-Gibson
- National Institute of Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, UK EN6 3QG, England
| | - Mark Andrew Chambers
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, GU2 7AL, England
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37
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Asthana V, Tang Y, Ferguson A, Bugga P, Asthana A, Evans ER, Chen AL, Stern BS, Drezek RA. An inexpensive, customizable microscopy system for the automated quantification and characterization of multiple adherent cell types. PeerJ 2018; 6:e4937. [PMID: 29888136 PMCID: PMC5993021 DOI: 10.7717/peerj.4937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Cell quantification assays are essential components of most biological and clinical labs. However, many currently available quantification assays, including flow cytometry and commercial cell counting systems, suffer from unique drawbacks that limit their overall efficacy. In order to address the shortcomings of traditional quantification assays, we have designed a robust, low-cost, automated microscopy-based cytometer that quantifies individual cells in a multiwell plate using tools readily available in most labs. Plating and subsequent quantification of various dilution series using the automated microscopy-based cytometer demonstrates the single-cell sensitivity, near-perfect R2 accuracy, and greater than 5-log dynamic range of our system. Further, the microscopy-based cytometer is capable of obtaining absolute counts of multiple cell types in one well as part of a co-culture setup. To demonstrate this ability, we recreated an experiment that assesses the tumoricidal properties of primed macrophages on co-cultured tumor cells as a proof-of-principle test. The results of the experiment reveal that primed macrophages display enhanced cytotoxicity toward tumor cells while simultaneously losing the ability to proliferate, an example of a dynamic interplay between two cell populations that our microscopy-based cytometer is successfully able to elucidate.
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Affiliation(s)
| | - Yuqi Tang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Adam Ferguson
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Pallavi Bugga
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Anantratn Asthana
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Emily R Evans
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Allen L Chen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Brett S Stern
- Department of Bioengineering, Rice University, Houston, TX, USA
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Javarappa KK, Tsallos D, Heckman CA. A Multiplexed Screening Assay to Evaluate Chemotherapy-Induced Myelosuppression Using Healthy Peripheral Blood and Bone Marrow. SLAS DISCOVERY 2018; 23:687-696. [DOI: 10.1177/2472555218777968] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Myelosuppression is a major side effect of chemotherapy in cancer patients and can result in infections, bleeding complications, and increased risk of morbidity and mortality, as well as limit the drug dose and frequency of administration. Chemotherapy-induced myelosuppression is caused by the disruption of normal hematopoiesis. Thus, prior understanding of the adverse effects of chemotherapies on hematopoietic cells is essential to minimize the side effects of cancer treatment. Traditional methods such as colony-forming assays for studying chemotherapy-induced myelosuppression are time-consuming and labor intensive. High-throughput flow cytometry technologies and methods to detect rare hematopoietic cell populations are critical in advancing our understanding of how different blood cell types in complex biological samples respond to chemotherapeutic drugs. In the present study, hematopoietic progenitor cells were induced to differentiate into megakaryocytes and myeloid lineage cells. The expanded cells were then used in a multiplexed assay to monitor the dose-response effects of multiple chemotherapies on different stages of megakaryocyte differentiation and myeloid cell populations in a 96-well plate format. The assay offers an alternative method to evaluate the myelosuppressive potential of novel chemotherapeutic drugs compared to traditional lower throughput and labor-intensive assays.
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Affiliation(s)
- Komal K. Javarappa
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Dimitrios Tsallos
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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39
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Ding M, Clark R, Bardelle C, Backmark A, Norris T, Williams W, Wigglesworth M, Howes R. Application of High-Throughput Flow Cytometry in Early Drug Discovery: An AstraZeneca Perspective. SLAS DISCOVERY 2018; 23:719-731. [PMID: 29787326 DOI: 10.1177/2472555218775074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Flow cytometry is a powerful tool providing multiparametric analysis of single cells or particles. The introduction of faster plate-based sampling technologies on flow cytometers has transformed the technology into one that has become attractive for higher throughput drug discovery screening. This article describes AstraZeneca's perspectives on the deployment and application of high-throughput flow cytometry (HTFC) platforms for small-molecule high-throughput screening (HTS), structure-activity relationship (SAR) and phenotypic screening, and antibody screening. We describe the overarching HTFC workflow, including the associated automation and data analysis, along with a high-level overview of our HTFC assay portfolio. We go on to discuss the practical challenges encountered and solutions adopted in the course of our deployment of HTFC, as well as future enhancements and expansion of the technology to new areas of drug discovery.
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Affiliation(s)
- Mei Ding
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Roger Clark
- 2 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | - Anna Backmark
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Tyrrell Norris
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Wendy Williams
- 4 Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
| | - Mark Wigglesworth
- 3 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Macclesfield, UK
| | - Rob Howes
- 1 Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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40
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Ang YS, Li JJ, Chua PJ, Ng CT, Bay BH, Yung LYL. Localized Visualization and Autonomous Detection of Cell Surface Receptor Clusters Using DNA Proximity Circuit. Anal Chem 2018; 90:6193-6198. [PMID: 29608843 DOI: 10.1021/acs.analchem.8b00722] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell surface receptors play an important role in mediating cell communication and are used as disease biomarkers and therapeutic targets. We present a one-pot molecular toolbox, which we term the split proximity circuit (SPC), for the autonomous detection and visualization of cell surface receptor clusters. Detection was powered by antibody recognition and a series of autonomous DNA hybridization to achieve localized, enzyme-free signal amplification. The system under study was the human epidermal growth factor receptor (HER) family, that is, HER2:HER2 homodimer and HER2:HER3 heterodimer, both in cell lysate and in situ on fixed whole cells. The detection and imaging of receptors were carried out using standard microplate scans and confocal microscopy, respectively. The circuit operated specifically with minimal leakages and successfully captured the receptor expression profiles on three cell types without any intermediate washing steps.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical and Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
| | - Jia'En Jasmine Li
- Department of Chemical and Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
| | - Pei-Jou Chua
- Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117594 , Singapore
| | - Cheng-Teng Ng
- Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117594 , Singapore
| | - Boon-Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117594 , Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical and Biomolecular Engineering , National University of Singapore , Singapore 117585 , Singapore
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41
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Global phenotypic characterisation of human platelet lysate expanded MSCs by high-throughput flow cytometry. Sci Rep 2018; 8:3907. [PMID: 29500387 PMCID: PMC5834600 DOI: 10.1038/s41598-018-22326-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/21/2018] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stromal cells (MSCs) are a promising cell source to develop cell therapy for many diseases. Human platelet lysate (PLT) is increasingly used as an alternative to foetal calf serum (FCS) for clinical-scale MSC production. To date, the global surface protein expression of PLT-expended MSCs (MSC-PLT) is not known. To investigate this, paired MSC-PLT and MSC-FCS were analysed in parallel using high-throughput flow cytometry for the expression of 356 cell surface proteins. MSC-PLT showed differential surface protein expression compared to their MSC-FCS counterpart. Higher percentage of positive cells was observed in MSC-PLT for 48 surface proteins, of which 13 were significantly enriched on MSC-PLT. This finding was validated using multiparameter flow cytometry and further confirmed by quantitative staining intensity analysis. The enriched surface proteins are relevant to increased proliferation and migration capacity, as well as enhanced chondrogenic and osteogenic differentiation properties. In silico network analysis revealed that these enriched surface proteins are involved in three distinct networks that are associated with inflammatory responses, carbohydrate metabolism and cellular motility. This is the first study reporting differential cell surface protein expression between MSC-PLT and MSC-FSC. Further studies are required to uncover the impact of those enriched proteins on biological functions of MSC-PLT.
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42
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Jensen L, Neri E, Bassaneze V, De Almeida Oliveira NC, Dariolli R, Turaça LT, Levy D, Veronez D, Ferraz MSA, Alencar AM, Bydlowski SP, Cestari IA, Krieger JE. Integrated molecular, biochemical, and physiological assessment unravels key extraction method mediated influences on rat neonatal cardiomyocytes. J Cell Physiol 2018; 233:5420-5430. [PMID: 29219187 DOI: 10.1002/jcp.26380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/04/2017] [Indexed: 12/29/2022]
Abstract
Neonatal cardiomyocytes are instrumental for disease modeling, but the effects of different cell extraction methods on basic cell biological processes remain poorly understood. We assessed the influence of two popular methods to extract rat neonatal cardiomyocytes, Pre-plating (PP), and Percoll (PC) on cell structure, metabolism, and function. Cardiomyocytes obtained from PP showed higher gene expression for troponins, titin, and potassium and sodium channels compared to PC. Also, PP cells displayed higher levels of troponin I protein. Cells obtained from PC displayed higher lactate dehydrogenase activity and lactate production than PP cells, indicating higher anaerobic metabolism after 8 days of culture. In contrast, reactive oxygen species levels were higher in PP cells as indicated by ethidium and hydroxyethidium production. Consistent with these data, protein nitration was higher in PP cells, as well as nitrite accumulation in cell medium. Moreover, PP cells showed higher global intracellular calcium under basal and 1 mM isoprenaline conditions. In a calcium-transient assessment under electrical stimulation (0.5 Hz), PP cells displayed higher calcium amplitude than cardiomyocytes obtained from PC and using a traction force microscope technique we observed that PP cardiomyocytes showed the highest relaxation. Collectively, we demonstrated that extraction methods influence parameters related to cell structure, metabolism, and function. Overall, PP derived cells are more active and mature than PC cells, displaying higher contractile function and generating more reactive oxygen species. On the other hand, PC derived cells display higher anaerobic metabolism, despite comparable high yields from both protocols.
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Affiliation(s)
- Leonardo Jensen
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Elida Neri
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Vinicius Bassaneze
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Nathalia C De Almeida Oliveira
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Rafael Dariolli
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Lauro T Turaça
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Débora Levy
- Laboratory of Genetics and Molecular Hematology/LIM 31, Clinics Hospital (HC), University of São Paulo Medical School, São Paulo, Brazil
| | - Douglas Veronez
- Bioengineering Division, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Mariana S A Ferraz
- Laboratory of Microrheology and Molecular Physiology, Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Adriano M Alencar
- Laboratory of Microrheology and Molecular Physiology, Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Sérgio P Bydlowski
- Laboratory of Genetics and Molecular Hematology/LIM 31, Clinics Hospital (HC), University of São Paulo Medical School, São Paulo, Brazil
| | - Idágene A Cestari
- Bioengineering Division, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - José Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
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Abstract
Cell surface proteins are widely studied in the search for new biomarkers and therapeutic targets, but there is little information available about the surfaceome of individual cells, and this is difficult to obtain experimentally, especially in heterogeneous samples. Flow cytometry is a simple and robust tool for assessing cell surface protein expression on a single-cell level in a wide variety of cell types. However, due to the cost and relative scarcity of reagents, it is typically limited to interrogating known markers, screening small curated subsets of likely candidates, or validating targets obtained via other high throughput methods such as transcriptional profiling. Given recent advances in our understanding of stem cells, tumor-initiating cells, and other rare populations in seemingly homogenous samples, and the relative lack of correlation between the transcriptome and the surfaceome, large-scale flow cytometry screens have become an appealing option. A relatively exhaustive microarray-like flow cytometry screening platform can reveal unexpected markers or sub-populations that are not readily detected by other methods. The single-cell resolution, reliability, and simplicity of flow cytometry and the additional benefit of sub-population/heterogeneity discrimination with the addition of functional and/or phenotypic co-stains allow for the rapid generation of very reliable data from a wide variety of samples at a low cost per sample. These larger datasets can be used for more elaborate bioinformatics, such as hierarchical clustering. Here we describe a method for high throughput cell surface profiling using conventional single or multicolor flow cytometry, which can be adapted to an antibody panel of any size.
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Affiliation(s)
- Joshua Paterson
- Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, ON, Canada, M5G 1L7
| | - Laurie E Ailles
- Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, ON, Canada, M5G 1L7.
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High-throughput flow cytometry screening of human hepatocellular carcinoma reveals CD146 to be a novel marker of tumor-initiating cells. Biochem Biophys Rep 2017; 8:107-113. [PMID: 28955945 PMCID: PMC5613743 DOI: 10.1016/j.bbrep.2016.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/02/2016] [Accepted: 08/09/2016] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains a common and lethal cancer. Cancer stem cells, or tumor-initiating cells (TICs), are thought to contribute to the pathogenesis of HCC, but remain to be fully characterized. Unbiased screens of primary human HCC cells for the identification of novel HCC TIC markers have not been reported. We conducted high-throughput flow cytometry (HT-FC) profiling to characterize the expression of 375 CD antigens on tumor cells from 10 different human HCC samples. We selected 91 of these for further analysis based on HT-FC data that showed consistent expression in discrete, rare, sortable populations of HCC cells. Nine of these CD antigens demonstrated significantly increased expression in the EpCAM+ stem/progenitor fraction of a human HCC cell line and were further evaluated in primary human HCC tissues from 30 different patients. Of the nine tested, only CD146 demonstrated significantly increased expression in HCC tumor tissue as compared with matched adjacent non-tumor liver tissue. CD146+CD31−CD45− cells purified from HCC tumors and cell lines demonstrated a unique phenotype distinct from mesenchymal stem cells. As compared with other tumor cell fractions, CD146+CD31−CD45− cells showed significantly increased colony-forming capacity in vitro, consistent with TICs. This study demonstrates that HT-FC screening can be successfully applied to primary human HCC and reveals CD146 to be a novel TIC marker in this disease. Unbiased screens of human HCC cells for novel TIC markers have not been reported. A high-throughput flow cytometry screen of human HCC cells was successfully performed . Candidate TIC markers were further evaluated by RT-PCR and functional assays. Of candidates tested, only CD146 expression was significantly increased in HCC tissues. CD146+ cells had increased colony-forming capacity, consistent with a TIC phenotype.
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45
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Lekishvili T, Campbell JJ. Rapid comparative immunophenotyping of human mesenchymal stromal cells by a modified fluorescent cell barcoding flow cytometric assay. Cytometry A 2017; 93:905-915. [DOI: 10.1002/cyto.a.23248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/30/2017] [Accepted: 09/02/2017] [Indexed: 12/15/2022]
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Schott DS, Pizon M, Pachmann U, Pachmann K. Sensitive detection of PD-L1 expression on circulating epithelial tumor cells (CETCs) could be a potential biomarker to select patients for treatment with PD-1/PD-L1 inhibitors in early and metastatic solid tumors. Oncotarget 2017; 8:72755-72772. [PMID: 29069824 PMCID: PMC5641167 DOI: 10.18632/oncotarget.20346] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/11/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The current cancer research strongly focuses on immune therapies, where the PD-1, with its ligands plays an important role. It is known that PD-L1 is frequently up-regulated in a number of different cancers and the relevance of this pathway has been extensively studied and therapeutic approaches targeting PD-1 and PD-L1 have been developed. We used a non-invasive, real-time biopsy for determining PD-L1 and PD-L2 expression in CETCs of solid cancer patients. METHODS CETCs were determined from blood of 128 patients suffering from breast (72), prostate (27), colorectal (18) and lung (11) cancer. The number of vital CETCs and the expression of PD-L1 and PD-L2 were investigated using the maintrac® method. RESULTS PD-L1 expressing CETCs were detected in 94.5% of breast, 100% of prostate, 95.4% of colorectal and 82% of lung cancer patients whereas only 75% of breast cancer patients had PD-L2 positive CETCs. In the PD-L1 and PD-L2 expressing patients the cell fraction of PD-L1 positive CETCs is significantly higher than the fraction of PD-L2 positive CETCs (54.6% vs. 28.7%; p<0.001). Breast cancer patients with metastatic disease had significantly more PD-L1 positive CETCs as compared to patients without metastasis (median 75% vs. 61.1%; p<0.05). CONCLUSION PD-L1 seems to be a major factor in immune evasion and is highly expressed on CETCs regardless of the type of cancer. Monitoring the frequency of PD-L1 positive CETCs could reflect individual patient's response for an anti-PD-1/PD-L1 therapy and may be a promising target of anticancer treatment.
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Mellisho EA, Velásquez AE, Nuñez MJ, Cabezas JG, Cueto JA, Fader C, Castro FO, Rodríguez-Álvarez L. Identification and characteristics of extracellular vesicles from bovine blastocysts produced in vitro. PLoS One 2017; 12:e0178306. [PMID: 28542562 PMCID: PMC5444795 DOI: 10.1371/journal.pone.0178306] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/10/2017] [Indexed: 12/20/2022] Open
Abstract
Extracellular vesicles (EVs) have been identified within different body fluids and cell culture media. However, there is very little information on the secretion of these vesicles during early embryonic development. The aims of this work were first to demonstrate the secretion of extracellular vesicles by pre-implantation bovine embryos and second to identify and characterize the population of EVs secreted by bovine blastocysts during the period from day seven to nine of embryo culture and its correlation with further embryo development up to day 11. Bovine embryos were produced by in vitro fertilization (IVF) or parthenogenetic activation (PA) and cultured until blastocyst stage. Blastocyst selection was performed at day 7 post IVF/PA considering two variables: stage of development and quality of embryos. Selected blastocysts were cultured in vitro for 48 hours in groups (exp. 1) or individually (exp. 2) in SOF media depleted of exosomes. At day 9 post IVF/PA the media was collected and EVs isolated by ultracentrifugation. Transmission electron microscopy revealed the presence of heterogeneous vesicles of different sizes and population: microvesicles (MVs) and exosomes (EXs) of rounded shape, enclosed by a lipid bi-layer and ranging from 30 to 385 nm of diameter. Flow cytometry analysis allowed identifying CD63 and CD9 proteins as exosome markers. Nanoparticle tracking analysis generated a large number of variables, which required the use of multivariate statistics. The results indicated that the concentration of vesicles is higher in those blastocysts with arrested development from day 9 up to day 11 of in vitro development (6.7 x 108 particles/ml) derived from IVF (p <0.05), compared to PA blastocysts (4.7 x 108 particles/ml). Likewise, the profile (concentration and diameter) of particles secreted by embryos derived from IVF were different from those secreted by PA embryos. In conclusion, we demonstrated that bovine blastocysts secrete MVs/EXs to the culture media. Data suggest that characteristics of the population of EVs vary depending on embryo competence.
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Affiliation(s)
- Edwin A. Mellisho
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Science, University of Concepción, Chillán, Concepción, Chile
| | - Alejandra E. Velásquez
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Science, University of Concepción, Chillán, Concepción, Chile
| | - María J. Nuñez
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Science, University of Concepción, Chillán, Concepción, Chile
| | - Joel G. Cabezas
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Science, University of Concepción, Chillán, Concepción, Chile
| | - Juan A. Cueto
- Laboratory of Cell and Molecular Biology, IHEM-CONICET, Faculty of Medical Sciences, National University of Cuyo, Mendoza, Argentina
| | - Claudio Fader
- Laboratory of Cell and Molecular Biology, IHEM-CONICET, Faculty of Medical Sciences, National University of Cuyo, Mendoza, Argentina
| | - Fidel O. Castro
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Science, University of Concepción, Chillán, Concepción, Chile
| | - Lleretny Rodríguez-Álvarez
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Science, University of Concepción, Chillán, Concepción, Chile
- * E-mail:
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Valdez J, Cook CD, Ahrens CC, Wang AJ, Brown A, Kumar M, Stockdale L, Rothenberg D, Renggli K, Gordon E, Lauffenburger D, White F, Griffith L. On-demand dissolution of modular, synthetic extracellular matrix reveals local epithelial-stromal communication networks. Biomaterials 2017; 130:90-103. [PMID: 28371736 DOI: 10.1016/j.biomaterials.2017.03.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 02/06/2023]
Abstract
Methods to parse paracrine epithelial-stromal communication networks are a vital need in drug development, as disruption of these networks underlies diseases ranging from cancer to endometriosis. Here, we describe a modular, synthetic, and dissolvable extracellular matrix (MSD-ECM) hydrogel that fosters functional 3D epithelial-stromal co-culture, and that can be dissolved on-demand to recover cells and paracrine signaling proteins intact for subsequent analysis. Specifically, synthetic polymer hydrogels, modified with cell-interacting adhesion motifs and crosslinked with peptides that include a substrate for cell-mediated proteolytic remodeling, can be rapidly dissolved by an engineered version of the microbial transpeptidase Sortase A (SrtA) if the crosslinking peptide includes a SrtA substrate motif and a soluble second substrate. SrtA-mediated dissolution affected only 1 of 31 cytokines and growth factors assayed, whereas standard protease degradation methods destroyed about half of these same molecules. Using co-encapsulated endometrial epithelial and stromal cells as one model system, we show that the dynamic cytokine and growth factor response of co-cultures to an inflammatory cue is richer and more nuanced when measured from SrtA-dissolved gel microenvironments than from the culture supernate. This system employs accessible, reproducible reagents and facile protocols; hence, has potential as a tool in identifying and validating therapeutic targets in complex diseases.
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Affiliation(s)
- Jorge Valdez
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christi D Cook
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Caroline Chopko Ahrens
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alex J Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander Brown
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manu Kumar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Linda Stockdale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel Rothenberg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kasper Renggli
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth Gordon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Forest White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Linda Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Interrogation of Functional Cell-Surface Markers Identifies CD151 Dependency in High-Grade Serous Ovarian Cancer. Cell Rep 2017; 18:2343-2358. [DOI: 10.1016/j.celrep.2017.02.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/20/2016] [Accepted: 02/08/2017] [Indexed: 11/21/2022] Open
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Snowden E, Porter W, Hahn F, Ferguson M, Tong F, Parker JS, Middlebrook A, Ghanekar S, Dillmore WS, Blaesius R. Immunophenotyping and Transcriptomic Outcomes in PDX-Derived TNBC Tissue. Mol Cancer Res 2016; 15:429-438. [PMID: 28039356 DOI: 10.1158/1541-7786.mcr-16-0286-t] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/23/2016] [Accepted: 12/21/2016] [Indexed: 11/16/2022]
Abstract
Cancer tissue functions as an ecosystem of a diverse set of cells that interact in a complex tumor microenvironment. Genomic tools applied to biopsies in bulk fail to account for this tumor heterogeneity, whereas single-cell imaging methods limit the number of cells which can be assessed or are very resource intensive. The current study presents methods based on flow cytometric analysis and cell sorting using known cell surface markers (CXCR4/CD184, CD24, THY1/CD90) to identify and interrogate distinct groups of cells in triple-negative breast cancer clinical biopsy specimens from patient-derived xenograft (PDX) models. The results demonstrate that flow cytometric analysis allows a relevant subgrouping of cancer tissue and that sorting of these subgroups provides insights into cancer cell populations with unique, reproducible, and functionally divergent gene expression profiles. The discovery of a drug resistance signature implies that uncovering the functional interaction between these populations will lead to deeper understanding of cancer progression and drug response.Implications: PDX-derived human breast cancer tissue was investigated at the single-cell level, and cell subpopulations defined by surface markers were identified which suggest specific roles for distinct cellular compartments within a solid tumor. Mol Cancer Res; 15(4); 429-38. ©2016 AACR.
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Affiliation(s)
- Eileen Snowden
- BD Technologies, Research Triangle Park, Durham, North Carolina
| | - Warren Porter
- BD Technologies, Research Triangle Park, Durham, North Carolina
| | - Friedrich Hahn
- BD Technologies, Research Triangle Park, Durham, North Carolina
| | | | - Frances Tong
- BD Technologies, Research Triangle Park, Durham, North Carolina
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | | | | | | | - Rainer Blaesius
- BD Technologies, Research Triangle Park, Durham, North Carolina.
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