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Voss K, Bartkowiak T, Sewell AE, Chi C, Landis MD, Schaefer S, Pua HH, Connelly JA, Irish JM, Rathmell JC, Kaviany S. Peripheral T Cell Development and Immunophenotyping of Twins with Heterozygous FOXN1 Mutations. Immunohorizons 2024; 8:492-499. [PMID: 39008056 DOI: 10.4049/immunohorizons.2400006] [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: 04/16/2024] [Accepted: 06/09/2024] [Indexed: 07/16/2024] Open
Abstract
The transcription factor FOXN1 plays an established role in thymic epithelial development to mediate selection of maturing thymocytes. Patients with heterozygous loss-of-function FOXN1 variants are associated with T cell lymphopenia at birth and low TCR excision circles that can ultimately recover. Although CD4+ T cell reconstitution in these patients is not completely understood, a lower proportion of naive T cells in adults has suggested a role for homeostatic proliferation. In this study, we present an immunophenotyping study of fraternal twins with low TCR excision circles at birth. Targeted primary immunodeficiency testing revealed a heterozygous variant of uncertain significance in FOXN1 (c.1205del, p.Pro402Leufs*148). We present the immune phenotypes of these two patients, as well as their father who carries the same FOXN1 variant, to demonstrate an evolving immune environment over time. While FOXN1 haploinsufficiency may contribute to thymic defects and T cell lymphopenia, we characterized the transcriptional activity and DNA binding of the heterozygous FOXN1 variant in 293T cells and found the FOXN1 variant to have different effects across several target genes. These data suggest multiple mechanisms for similar FOXN1 variants pathogenicity that may be mutation specific. Increased understanding of how these variants drive transcriptional regulation to impact immune cell populations will guide the potential need for therapeutics, risk for infection or autoimmunity over time, and help inform clinical decisions for other variants that might arise.
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Affiliation(s)
- Kelsey Voss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Todd Bartkowiak
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Allison E Sewell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Channing Chi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Madelyn D Landis
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Samuel Schaefer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Heather H Pua
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - James A Connelly
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Saara Kaviany
- Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
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Mojica EA, Kültz D. A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms. J Proteome Res 2023. [PMID: 37624673 DOI: 10.1021/acs.jproteome.3c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in nonmodel organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 214 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 91.59% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in nonmodel organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.
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Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
| | - Dietmar Kültz
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
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Scheuermann S, Lehmann JM, Ramani Mohan R, Reißfelder C, Rückert F, Langejürgen J, Pallavi P. TissueGrinder, a novel technology for rapid generation of patient-derived single cell suspensions from solid tumors by mechanical tissue dissociation. Front Med (Lausanne) 2022; 9:721639. [PMID: 36582292 PMCID: PMC9793748 DOI: 10.3389/fmed.2022.721639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction Recent advances hold promise of making personalized medicine a step closer to implementation in clinical settings. However, traditional sample preparation methods are not robust and reproducible. In this study, the TissueGrinder, a novel mechanical semi-automated benchtop device, which can isolate cells from tissue in a very fast and enzyme-free way is tested for cell isolation from surgically resected tumor tissues. Methods Thirty-three surgically resected tumor tissues from various but mainly pancreatic, liver or colorectal origins were processed by both novel TissueGrinder and explant method. An optimized processing program for tumors from pancreatic, liver or colorectal cancer was developed. The viability and morphological characteristics of the isolated cells were evaluated microscopically. Expression of pancreatic cancer markers was evaluated in cells isolated from pancreatic tumors. Finally, the effect of mechanical stress on the cells was evaluated by assessing apoptosis markers via western blotting. Results TissueGinder was more efficient in isolating cells from tumor tissue with a success rate of 75% when compared to explant method 45% in terms of cell outgrowth six weeks after processing. Cells isolated with TissueGinder had a higher abundance and were more heterogeneous in composition as compared to explant method. Mechanical processing of the cells with TissueGrinder does not lead to apoptosis but causes slight stress to the cells. Discussion Our results show that TissueGrinder can process solid tumor tissues more rapidly and efficiently and with higher success rate compared to the conventionally used explant method. The results of the study suggest that the TissueGrinder might be a suitable method for obtaining cells, which is important for its application in individualized therapy. Due to the great variance in different tumor entities and the associated individual tissue characteristics, a further development of the dissociation protocol for other types of tumors and normal tissue will be targeted.
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Affiliation(s)
- Stefan Scheuermann
- Clinical Health Technologies, Fraunhofer IPA, Mannheim, Germany,*Correspondence: Stefan Scheuermann,
| | | | - Ramkumar Ramani Mohan
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christoph Reißfelder
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Felix Rückert
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Prama Pallavi
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany,Prama Pallavi,
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Parashar P, Das MK, Tripathi P, Kataria T, Gupta D, Sarin D, Hazari PP, Tandon V. DMA, a Small Molecule, Increases Median Survival and Reduces Radiation-Induced Xerostomia via the Activation of the ERK1/2 Pathway in Oral Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14194908. [PMID: 36230831 PMCID: PMC9562201 DOI: 10.3390/cancers14194908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/24/2022] [Accepted: 07/09/2022] [Indexed: 11/16/2022] Open
Abstract
Survival, recurrence, and xerostomia are considerable problems in the treatment of oral squamous carcinoma patients. In this study, we investigated the role of DMA (5-(4-methylpiperazin-1-yl)-2-[2′-(3,4-dimethoxyphenyl)5″benzimidazoyl]benzimidazole) as a salivary gland cytoprotectant in a patient-derived xenograft mouse model. A significant increase in saliva secretion was observed in the DMA-treated xenograft compared to radiation alone. Repeated doses of DMA with a high dose of radiation showed a synergistic effect on mice survival and reduced tumor growth. The mean survival rate of tumor-bearing mice was significantly enhanced. The increased number of Ki-67-stained cells in the spleen, intestine, and lungs compared to the tumor suggests DMA ablates the tumor but protects other organs. The expression of aquaporin-5 was restored in tumor-bearing mice injected with DMA before irradiation. The reduced expression of αvβ3 integrin and CD44 in DMA alone and DMA with radiation-treated mice suggests a reduced migration of cells and stemness of cancer cells. DMA along with radiation treatment results in the activation of the Ras/Raf/MEK/ERK pathway in the tumor, leading to apoptosis through caspase upregulation. In conclusion, DMA has strong potential for use as an adjuvant in radiotherapy in OSCC patients.
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Affiliation(s)
- Palak Parashar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Monoj Kumar Das
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pragya Tripathi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Tejinder Kataria
- Division of Radiation Oncology, Medanta―The Medicity, Gurgaon 122001, India
| | - Deepak Gupta
- Division of Radiation Oncology, Medanta―The Medicity, Gurgaon 122001, India
| | - Deepak Sarin
- Head and Neck OncoSurgery, Medanta―The Medicity, Gurgaon 122001, India
| | - Puja Panwar Hazari
- Defence Research and Development Organization, Institute of Nuclear Medicine and Allied Sciences, Delhi 110054, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
- Correspondence: ; Tel.: +91-11-26742181
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Rana R, Huirem RS, Kant R, Chauhan K, Sharma S, Yashavarddhan MH, Chhabra SS, Acharya R, Kalra SK, Gupta A, Jain S, Ganguly NK. Cytochrome C as a potential clinical marker for diagnosis and treatment of glioma. Front Oncol 2022; 12:960787. [PMID: 36176404 PMCID: PMC9513483 DOI: 10.3389/fonc.2022.960787] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Gliomas are the most prevalent kind of malignant and severe brain cancer. Apoptosis regulating mechanisms are disturbed in malignant gliomas, as they are in added forms of malignancy. Understanding apoptosis and other associated processes are thought to be critical for understanding the origins of malignant tumors and designing anti-cancerous drugs for the treatment. The purpose of this study was to evaluate the variation in the expression level of several apoptotic proteins that are responsible for apoptosis in low to high-grade glioma. This suggests a significant change in the expression of five apoptotic proteins: Clusterin, HSP27, Catalase, Cytochrome C, and SMAC. Cytochrome C, one of the five substantially altered proteins, is a crucial component of the apoptotic cascade. The complex enzyme Cytochrome C is involved in metabolic pathways such as respiration and cell death. The results demonstrated that Cytochrome C expression levels are lower in glioma tissues than in normal tissues. What’s more intriguing is that the expression level decreases with an increase in glioma grades. As a result, the discovery shows that Cytochrome C may be a target for glioma prognostic biomarkers.
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
- *Correspondence: Rashmi Rana, ;
| | | | - Ravi Kant
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Kirti Chauhan
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Swati Sharma
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | | | | | - Rajesh Acharya
- Department of Neurosurgery, Sir Ganga Ram Hospital, New Delhi, India
| | - Samir Kumar Kalra
- Department of Neurosurgery, Sir Ganga Ram Hospital, New Delhi, India
| | - Anshul Gupta
- Department of Neurosurgery, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunila Jain
- Department of Histopathology, Sir Ganga Ram Hospital, New Delhi, India
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Zhang X, Soutto M, Chen Z, Bhat N, Zhu S, Eissmann MF, Ernst M, Lu H, Peng D, Xu Z, El-Rifai W. Induction of Fibroblast Growth Factor Receptor 4 by Helicobacter pylori via Signal Transducer and Activator of Transcription 3 With a Feedforward Activation Loop Involving SRC Signaling in Gastric Cancer. Gastroenterology 2022; 163:620-636.e9. [PMID: 35588797 PMCID: PMC9629135 DOI: 10.1053/j.gastro.2022.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 04/07/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Helicobacter pylori (H pylori) infection is the main risk factor for gastric cancer. The role of fibroblast growth factor receptors (FGRFs) in H pylori-mediated gastric tumorigenesis remains largely unknown. This study investigated the molecular and mechanistic links between H pylori, inflammation, and FGFR4 in gastric cancer. METHODS Cell lines, human and mouse gastric tissue samples, and gastric organoids models were implemented. Infection with H pylori was performed using in vitro and in vivo models. Western blot, real-time quantitative reverse-transcription polymerase chain reaction, flow cytometry, immunofluorescence, immunohistochemistry, chromatin immunoprecipitation, and luciferase reporter assays were used for molecular, mechanistic, and functional studies. RESULTS Analysis of FGFR family members using The Cancer Genome Atlas data, followed by validation, indicated that FGFR4 messenger (m)RNA was the most significantly overexpressed member in human gastric cancer tissue samples (P < .001). We also detected high levels of Fgfr4 mRNA and protein in gastric dysplasia and adenocarcinoma lesions in mouse models. Infection with J166, 7.13, and PMSS1 cytotoxin-associated gene A (CagA)+ H pylori strains induced FGFR4 mRNA and protein expression in in vitro and in vivo models. This was associated with a concordant activation of signal transducer and activator of transcription 3 (STAT3). Analysis of the FGFR4 promoter suggested several putative binding sites for STAT3. Using chromatin immunoprecipitation assay and an FGFR-promoter luciferase reporter containing putative STAT3 binding sites and their mutants, we confirmed a direct functional binding of STAT3 on the FGFR4 promoter. Mechanistically, we also discovered a feedforward activation loop between FGFR4 and STAT3 where the fibroblast growth factor 19–FGFR4 axis played an essential role in activating STAT3 in a SRC proto-oncogene non-receptor tyrosine kinase dependent manner. Functionally, we found that FGFR4 protected against H pylori-induced DNA damage and cell death. CONCLUSIONS Our findings demonstrated a link between infection, inflammation, and FGFR4 activation, where a feedforward activation loop between FGFR4 and STAT3 is established via SRC proto-oncogene non-receptor tyrosine kinase in response to H pylori infection. Given the relevance of FGFR4 to the etiology and biology of gastric cancer, we propose FGFR4 as a druggable molecular vulnerability that can be tested in patients with gastric cancer.
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Affiliation(s)
- Xing Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China; Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida; Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mohammed Soutto
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Zheng Chen
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Nadeem Bhat
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Shoumin Zhu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Moritz F Eissmann
- Cancer and Inflammation Laboratory, Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
| | - Matthias Ernst
- Cancer and Inflammation Laboratory, Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Heidelberg, Victoria, Australia
| | - Heng Lu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Dunfa Peng
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida; Department of Veterans Affairs, Miami Healthcare System, Miami, Florida; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.
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Kaundal B, Karmakar S, Roy Choudhury S. Mitochondria-targeting nano therapy altering IDH2-mediated EZH2/EZH1 interaction as precise epigenetic regulation in glioblastoma. Biomater Sci 2022; 10:5301-5317. [PMID: 35917200 DOI: 10.1039/d1bm02006d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glioblastoma (GBM) is a complex brain cancer with frequent relapses and high mortality and still awaits effective treatment. Mitochondria dysfunction is a pathogenic condition in GBM and could be a prime therapeutic target for ceasing GBM progression. Strategies to overcome brain solid tumor barriers and selectively target mitochondria within specific cell types may improve GBM treatment. Here, we present hypericin-conjugated gold nanoparticles (PEG-AuNPs@Hyp) where hypericin is a mitochondrion-targeting agent exhibiting multimodal therapy by critically impacting the IDH2 gene (Isocitrate dehydrogenase) and its interaction with polycomb methyltransferase EZH1/2 for GBM therapy. It significantly localizes in mitochondria by enhanced cellular uptake in the human GBM cell lines/three-dimensional (3D) culture model under red-light exposure. It triggers oxidative stress and changes the mitochondrial potential, with increased Bax/Bcl2 ratio enhancing GBM cell death. The suppressed expression of mutated IDH2 and polycomb group of proteins upon PEG-AuNPs@Hyp/light exposure regulates mitochondria-targeting-mediated GBM metabolism with epigenetic repression of complex machinery function. Polyubiquitination and proteasomal degradation of EZH1 indicate the implication of these polycomb proteins in GBM progression. Chromatin immunoprecipitation reveals the IDH2 and EZH1/EZH2 direct interaction, confirming the role played by IDH2 in modulating the expression of EZH1 and EZH2. In vivo studies further displayed better tumor ablation in a GBM tumor-bearing nude mouse model. The present multimodal nanoformulation compromised the functional dependency of polycomb on mitochondrial IDH2 and established the mechanism of GBM inhibition.
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Affiliation(s)
- Babita Kaundal
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab-140306, India.
| | - Surajit Karmakar
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab-140306, India.
| | - Subhasree Roy Choudhury
- Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali, Punjab-140306, India.
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Kaviany S, Bartkowiak T, Dulek DE, Khan YW, Hayes MJ, Schaefer SG, Ye X, Dahunsi DO, Connelly JA, Irish JM, Rathmell JC. Systems Immunology Analyses of STAT1 Gain-of-Function Immune Phenotypes Reveal Heterogeneous Response to IL-6 and Broad Immunometabolic Roles for STAT1. Immunohorizons 2022; 6:447-464. [PMID: 35840326 PMCID: PMC9623573 DOI: 10.4049/immunohorizons.2200041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Patients with STAT1 gain-of-function (GOF) pathogenic variants have enhanced or prolonged STAT1 phosphorylation following cytokine stimulation and exhibit increased yet heterogeneous susceptibility to infections, autoimmunity, and cancer. Although disease phenotypes are diverse and other genetic factors contribute, how STAT1 GOF affects cytokine sensitivity and cell biology remains poorly defined. In this study, we analyzed the immune and immunometabolic profiles of two patients with known pathogenic heterozygous STAT1 GOF mutation variants. A systems immunology approach of peripheral blood cells from these patients revealed major changes in multiple immune cell compartments relative to healthy adult and pediatric donors. Although many phenotypes of STAT1 GOF donors were shared, including increased Th1 cells but decreased class-switched B cells and plasmacytoid dendritic cell populations, others were heterogeneous. Mechanistically, hypersensitivity for cytokine-induced STAT1 phosphorylation in memory T cell populations was particularly evident in response to IL-6 in one STAT1 GOF patient. Immune cell metabolism directly influences cell function, and the STAT1 GOF patients shared an immunometabolic phenotype of heightened glucose transporter 1 (GLUT1) and carnitine palmitoyl transferase 1A (CPT1a) expression across multiple immune cell lineages. Interestingly, the metabolic phenotypes of the pediatric STAT1 GOF donors more closely resembled or exceeded those of healthy adult than healthy age-similar pediatric donors, which had low expression of these metabolic markers. These results define new features of STAT1 GOF patients, including a differential hypersensitivity for IL-6 and a shared increase in markers of metabolism in many immune cell types that suggests a role for STAT1 in metabolic regulation of immunity.
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Affiliation(s)
- Saara Kaviany
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.,Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Todd Bartkowiak
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN; and
| | - Daniel E Dulek
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Yasmin W Khan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Madeline J Hayes
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN; and
| | - Samuel G Schaefer
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Debolanle O Dahunsi
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - James A Connelly
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.,Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN
| | - Jonathan M Irish
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN; .,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN; and
| | - Jeffrey C Rathmell
- Vanderbilt Human Immunology Discovery Initiative of the Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN; .,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN
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9
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Kumar PR, Saad M, Hellmich C, Mistry JJ, Moore JA, Conway S, Morris CJ, Bowles KM, Moncrieff MD, Rushworth SA. PGC-1α induced mitochondrial biogenesis in stromal cells underpins mitochondrial transfer to melanoma. Br J Cancer 2022; 127:69-78. [PMID: 35347324 PMCID: PMC9276678 DOI: 10.1038/s41416-022-01783-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/21/2022] [Accepted: 03/08/2022] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Progress in the knowledge of metabolic interactions between cancer and its microenvironment is ongoing and may lead to novel therapeutic approaches. Until recently, melanoma was considered a glycolytic tumour due to mutations in mitochondrial-DNA, however, these malignant cells can regain OXPHOS capacity via the transfer of mitochondrial-DNA, a process that supports their proliferation in-vitro and in-vivo. Here we study how melanoma cells acquire mitochondria and how this process is facilitated from the tumour microenvironment. METHODS Primary melanoma cells, and MSCs derived from patients were obtained. Genes' expression and DNA quantification was analysed using Real-time PCR. MSC migration, melanoma proliferation and tumour volume, in a xenograft subcutaneous mouse model, were monitored through bioluminescent live animal imaging. RESULTS Human melanoma cells attract bone marrow-derived stromal cells (MSCs) to the primary tumour site where they stimulate mitochondrial biogenesis in the MSCs through upregulation of PGC1a. Mitochondria are transferred to the melanoma cells via direct contact with the MSCs. Moreover, inhibition of MSC-derived PGC1a was able to prevent mitochondrial transfer and improve NSG melanoma mouse tumour burden. CONCLUSION MSC mitochondrial biogenesis stimulated by melanoma cells is prerequisite for mitochondrial transfer and subsequent tumour growth, where targeting this pathway may provide an effective novel therapeutic approach in melanoma.
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Affiliation(s)
- Prakrit R Kumar
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mona Saad
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
- Department of Plastic and Reconstructive Surgery, Norfolk and Norwich University Hospitals NHS Trust, Colney Lane, Norwich, NR4 7UY, UK
| | - Charlotte Hellmich
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
- Department of Haematology, Norfolk and Norwich University Hospitals NHS Trust, Colney Lane, Norwich, NR4 7UY, UK
| | - Jayna J Mistry
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jamie A Moore
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Shannon Conway
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Christopher J Morris
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Kristian M Bowles
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
- Department of Haematology, Norfolk and Norwich University Hospitals NHS Trust, Colney Lane, Norwich, NR4 7UY, UK
| | - Marc D Moncrieff
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK.
- Department of Plastic and Reconstructive Surgery, Norfolk and Norwich University Hospitals NHS Trust, Colney Lane, Norwich, NR4 7UY, UK.
| | - Stuart A Rushworth
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK.
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10
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Yaigoub H, Tirichen H, Xin X, Shi S, Wu C, Li R, Li Y. Isolation of Viable Single Cells With High Yield and Purity Using a Small Amount of Human Kidney Tissue Biopsy. Front Cell Dev Biol 2022; 10:822275. [PMID: 35620054 PMCID: PMC9127796 DOI: 10.3389/fcell.2022.822275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Establishment of an efficient method of preparing human kidney single cell suspension, using a very small amount of tissue puncture. Methods: Samples of human kidney tissue puncture were cut into pieces, and then 80 μL of the digestive enzyme were added to each punctured tissue to induce enzymatic digestion. The enzyme combination is composed of collagenases, DNase and hyaluronidase and the sample was incubated 20 min at 37°C. The obtained cell suspension was filtered through a 70 μm cell strainer, centrifuged at 300 g for 5 min and the supernatant was removed, then the pellet was resuspended in 3 ml of DMEM (Dulbecco's Modified Eagle's Medium). Cell suspension was sorted and purified by flow sorting to remove dead cells and obtain a cell suspension with higher viability rate. Results: We found that 1) diverse single cells of human kidney can be obtained by the digestive enzyme, as observed under the light microscope, with different sizes, normal cell morphology and good dispersion. 2) (2-3) × 106 single cells can be extracted from one fresh punctured kidney tissue of about 10 mg, with a cell viability rate of more than 80%. Conclusion: In this work we generated a comprehensive and high-resolution single-cell method, which is simple and efficient for preparing single cell suspension from a minimal amount of human kidney tissue. This method can facilitate the study of renal cell biology and the pathogenesis of kidney diseases.
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Affiliation(s)
- Hasnaa Yaigoub
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Hasna Tirichen
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Xiaohong Xin
- Department of Nephrology, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China.,Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Shuhong Shi
- Core Laboratory, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Rongshan Li
- Department of Nephrology, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China.,Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Yafeng Li
- Department of Nephrology, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China.,Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China.,Academy of Microbial Ecology, Shanxi Medical University, Taiyuan, China.,Core Laboratory, The Fifth Hospital (Shanxi Provincial People's Hospital) of Shanxi Medical University, Taiyuan, China
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11
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Zhou W, Xu Y, Zhang J, Zhang P, Yao Z, Yan Z, Wang H, Chu J, Yao S, Zhao S, Yang S, Guo Y, Miao J, Liu K, Chan WC, Xia Q, Liu Y. MiRNA-363-3p/DUSP10/JNK axis mediates chemoresistance by enhancing DNA damage repair in diffuse large B-cell lymphoma. Leukemia 2022; 36:1861-1869. [PMID: 35488020 PMCID: PMC9252898 DOI: 10.1038/s41375-022-01565-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022]
Abstract
Anthracycline-based chemotherapy resistance represents a major challenge in diffuse large B-cell lymphoma (DLBCL). MiRNA and gene expression profiles (n = 47) were determined to uncover potential chemoresistance mechanisms and therapeutic approaches. An independent correlation between high expression of miRNA-363-3p and chemoresistance was observed and validated in a larger cohort (n = 106). MiRNA-363-3p was shown to reduce doxorubicin-induced apoptosis and tumor shrinkage in in vitro and in vivo experiments by ectopic expression and CRISPR/Cas9-mediated knockout in DLBCL cell lines. DNA methylation was found to participate in transcriptional regulation of miRNA-363-3p. Further investigation revealed that dual specificity phosphatase 10 (DUSP10) is a target of miRNA-363-3p and its suppression promotes the phosphorylation of c-Jun N-terminal kinase (JNK). The miRNA-363-3p/DUSP10/JNK axis was predominantly associated with negative regulation of homologous recombination (HR) and DNA repair pathways. Ectopic expression of miRNA-363-3p more effectively repaired doxorubicin-induced double-strand break (DSB) while enhancing non-homologous end joining repair and reducing HR repair. Targeting JNK and poly (ADP-ribose) polymerase 1 significantly inhibited doxorubicin-induced DSB repair, increased doxorubicin-induced cell apoptosis and tumor shrinkage, and improved the survival of tumor-bearing mice. In conclusion, the miRNA-363-3p/DUSP10/JNK axis is a novel chemoresistance mechanism in DLBCL that may be reversed by targeted therapy.
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Affiliation(s)
- Wenping Zhou
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China.,Department of Lymphoma Research, Henan Cancer Institute, Zhengzhou, Henan, China
| | - Yuanlin Xu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Jiuyang Zhang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Peipei Zhang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China.,Department of Lymphoma Research, Henan Cancer Institute, Zhengzhou, Henan, China
| | - Zhihua Yao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Zheng Yan
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Haiying Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Junfeng Chu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Shuna Yao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Shuang Zhao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Shujun Yang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Yongjun Guo
- Department of Molecule and Pathology, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Jinxin Miao
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Kangdong Liu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Qingxin Xia
- Department of Molecule and Pathology, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China.
| | - Yanyan Liu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China. .,Department of Lymphoma Research, Henan Cancer Institute, Zhengzhou, Henan, China.
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12
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Rozowsky JS, Meesters-Ensing JI, Lammers JAS, Belle ML, Nierkens S, Kranendonk MEG, Kester LA, Calkoen FG, van der Lugt J. A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies. Front Immunol 2022; 13:864423. [PMID: 35464481 PMCID: PMC9022116 DOI: 10.3389/fimmu.2022.864423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The prognosis of pediatric central nervous system (CNS) malignancies remains dismal due to limited treatment options, resulting in high mortality rates and long-term morbidities. Immunotherapies, including checkpoint inhibition, cancer vaccines, engineered T cell therapies, and oncolytic viruses, have promising results in some hematological and solid malignancies, and are being investigated in clinical trials for various high-grade CNS malignancies. However, the role of the tumor immune microenvironment (TIME) in CNS malignancies is mostly unknown for pediatric cases. In order to successfully implement immunotherapies and to eventually predict which patients would benefit from such treatments, in-depth characterization of the TIME at diagnosis and throughout treatment is essential. In this review, we provide an overview of techniques for immune profiling of CNS malignancies, and detail how they can be utilized for different tissue types and studies. These techniques include immunohistochemistry and flow cytometry for quantifying and phenotyping the infiltrating immune cells, bulk and single-cell transcriptomics for describing the implicated immunological pathways, as well as functional assays. Finally, we aim to describe the potential benefits of evaluating other compartments of the immune system implicated by cancer therapies, such as cerebrospinal fluid and blood, and how such liquid biopsies are informative when designing immune monitoring studies. Understanding and uniformly evaluating the TIME and immune landscape of pediatric CNS malignancies will be essential to eventually integrate immunotherapy into clinical practice.
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Affiliation(s)
| | | | | | - Muriël L. Belle
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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13
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The molecular underpinning of geminin-overexpressing triple-negative breast cancer cells homing specifically to lungs. Cancer Gene Ther 2022; 29:304-325. [PMID: 33723406 DOI: 10.1038/s41417-021-00311-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/23/2021] [Accepted: 02/12/2021] [Indexed: 01/31/2023]
Abstract
Triple-negative breast cancer (TNBCs) display lung metastasis tropism. However, the mechanisms underlying this organ-specific pattern remains to be elucidated. We sought to evaluate the utility of blocking extravasation to prevent lung metastasis. To identify potential geminin overexpression-controlled genetic drivers that promote TNBC tumor homing to lungs, we used the differential/suppression subtractive chain (D/SSC) technique. A geminin overexpression-induced lung metastasis gene signature consists of 24 genes was discovered. We validated overexpression of five of these genes (LGR5, HAS2, CDH11, NCAM2, and DSC2) in worsening lung metastasis-free survival in TNBC patients. Our data demonstrate that LGR5-induced β-catenin signaling and stemness in TNBC cells are geminin-overexpression dependent. They also demonstrate for the first-time expression of RSPO2 in mouse lung tissue only and exacerbation of its secretion in the circulation of mice that develop geminin overexpressing/LGR5+-TNBC lung metastasis. We identified a novel extravasation receptor complex, consists of CDH11, CD44v6, c-Met, and AXL on geminin overexpressing/LGR5+-TNBC lung metastatic precursors, inhibition of any of its receptors prevented geminin overexpressing/LGR5+-TNBC lung metastasis. Overall, we propose that geminin overexpression in normal mammary epithelial (HME) cells promotes the generation of TNBC metastatic precursors that home specifically to lungs by upregulating LGR5 expression and promoting stemness, intravasation, and extravasation in these precursors. Circulating levels of RSPO2 and OPN can be diagnostic biomarkers to improve risk stratification of metastatic TNBC to lungs, as well as identifying patients who may benefit from therapy targeting geminin alone or in combination with any member of the newly discovered extravasation receptor complex to minimize TNBC lung metastasis.
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14
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Chan JA, Vercauteren SM. Processing and Cryopreservation of Blood, Cancer Tissues, and Cancer Cells for Viable Biobanking. Methods Mol Biol 2022; 2508:45-58. [PMID: 35737232 DOI: 10.1007/978-1-0716-2376-3_5] [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] [Indexed: 06/15/2023]
Abstract
Biorepositories of fresh frozen and formalin-fixed paraffin-embedded tissues have been foundational to many molecular cancer research studies. Collections of these materials, however, do not enable the establishment of short-term cultures, cell lines, or patient-derived xenograft models for functional studies. Also, intact dissociated cells that are required for some single-cell analyses cannot be obtained from these material types. Adding viable tumor banking to the repertoire of routine cancer biobanking would increase the value of samples collected. This chapter outlines procedures for processing and storing blood and tissue specimens viably in order to expand the future utility of the samples collected. We provide practical tips that can be used by banks and other researchers seeking to incorporate the cryopreservation of viable materials as part of their overall biobanking strategies.
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Affiliation(s)
- Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada.
| | - Suzanne M Vercauteren
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, BC, Canada
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15
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Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends Biotechnol 2021; 40:647-676. [PMID: 34972597 DOI: 10.1016/j.tibtech.2021.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations with variable molecular profiles, aggressiveness, and proliferation potential coexist and interact. Understanding how heterogeneity influences tumor progression has important clinical implications for improving diagnosis, prognosis, and treatment response prediction. Several recent innovations in data acquisition methods and computational metrics have enabled the quantification of spatiotemporal heterogeneity across different scales of tumor organization. Here, we summarize the most promising efforts from a common experimental and computational perspective, discussing their advantages, shortcomings, and challenges. With personalized medicine entering a new era of unprecedented opportunities, our vision is that of future workflows integrating across modalities, scales, and dimensions to capture intricate aspects of the tumor ecosystem and to open new avenues for improved patient care.
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Affiliation(s)
- Aditya Kashyap
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | | | - Vesna Barros
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Anna Fomitcheva-Khartchenko
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland; Eidgenössische Technische Hochschule (ETH-Zurich), Vladimir-Prelog-Weg 1-5/10, 8099 Zurich, Switzerland
| | | | | | - Maria Gabrani
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | - Michal Rosen-Zvi
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Govind Kaigala
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland.
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16
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Shivange G, Mondal T, Lyerly E, Bhatnagar S, Landen CN, Reddy S, Kim J, Doan B, Riddle P, Tushir-Singh J. A patch of positively charged residues regulates the efficacy of clinical DR5 antibodies in solid tumors. Cell Rep 2021; 37:109953. [PMID: 34731630 PMCID: PMC8720280 DOI: 10.1016/j.celrep.2021.109953] [Citation(s) in RCA: 4] [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: 02/24/2021] [Revised: 07/19/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Receptor clustering is the first and critical step to activate apoptosis by death receptor-5 (DR5). The recent discovery of the autoinhibitory DR5 ectodomain has challenged the long-standing view of its mechanistic activation by the natural ligand Apo2L. Because the autoinhibitory residues have remained unknown, here we characterize a crucial patch of positively charged residues (PPCR) in the highly variable domain of DR5. The PPCR electrostatically separates DR5 receptors to autoinhibit their clustering in the absence of ligand and antibody binding. Mutational substitution and antibody-mediated PPCR interference resulted in increased apoptotic cytotoxic function. A dually specific antibody that enables sustained tampering with PPCR function exceptionally enhanced DR5 clustering and apoptotic activation and distinctively improved the survival of animals bearing aggressive metastatic and recurrent tumors, whereas clinically tested DR5 antibodies without PPCR blockade function were largely ineffective. Our study provides mechanistic insights into DR5 activation and a therapeutic analytical design for potential clinical success.
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MESH Headings
- A549 Cells
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/metabolism
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibody Specificity
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/metabolism
- Antineoplastic Agents, Immunological/pharmacology
- Apoptosis/drug effects
- Epitopes
- Humans
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, SCID
- Neoplasms/drug therapy
- Neoplasms/immunology
- Neoplasms/metabolism
- Receptors, TNF-Related Apoptosis-Inducing Ligand/antagonists & inhibitors
- Receptors, TNF-Related Apoptosis-Inducing Ligand/immunology
- Receptors, TNF-Related Apoptosis-Inducing Ligand/metabolism
- Signal Transduction
- Tumor Burden/drug effects
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Gururaj Shivange
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA
| | - Tanmoy Mondal
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Department of Medical Microbiology and Immunology, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA
| | - Evan Lyerly
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA; Blavatnik Institute, Harvard Medical School, Boston MA
| | - Sanchita Bhatnagar
- Department of Medical Microbiology and Immunology, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA
| | | | - Shivani Reddy
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Jonathan Kim
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Britney Doan
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Paula Riddle
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Undergraduate Research Program Volunteers, University of Virginia, Charlottesville VA
| | - Jogender Tushir-Singh
- Laboratory of Novel Biologics, Medical Microbiology and Immunology, University of California, Davis, Davis, CA 95616, USA; Department of Medical Microbiology and Immunology, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville VA 22908, USA; University of Virginia Comprehensive Cancer Center, Charlottesville VA; UC Davis Comprehensive Cancer Center, University of California School of Medicine, University of California, Davis, Davis, CA 95616, USA.
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17
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Ferreira-Facio CDS, Botafogo V, Ferrão PM, Canellas MC, Milito CB, Romano S, Lopes DV, Teixeira LC, Oliveira E, Bruno-Riscarolli E, Mello FV, Siqueira PFR, Moura P, Macedo FN, Forny DN, Simião L, Pureza AL, Land MGP, Pedreira CE, van Dongen JJM, Orfao A, da Costa ES. Flow Cytometry Immunophenotyping for Diagnostic Orientation and Classification of Pediatric Cancer Based on the EuroFlow Solid Tumor Orientation Tube (STOT). Cancers (Basel) 2021; 13:cancers13194945. [PMID: 34638431 PMCID: PMC8508207 DOI: 10.3390/cancers13194945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022] Open
Abstract
Simple Summary Pediatric solid tumors are a heterogenous group of diseases that comprise ≈ 40% of all pediatric cancers, early diagnosis being key for improved survival. Here we designed, tested, and validated a single eight-color tube for the diagnostic screening of pediatric cancer—solid tumor orientation tube (STOT)—based on multiparameter flow cytometry vs. conventional diagnostic procedures. Prospective clinical validation of STOT in 149 samples (63 tumor mass, 38 bone marrow, 30 lymph node, and 18 body fluid samples) screened for pediatric cancer, apart from 26 blood specimens that were excluded from analysis, showed concordant results with the final WHO/ICCC-3 diagnosis in 138/149 cases (92.6%). This included correct diagnostic orientation by STOT in 43/44 (98%) malignant and 4/4 (100%) benign non-hematopoietic tumors, together with 28/38 (74%) leukemia/lymphoma cases. The only recurrently missed diagnosis was Hodgkin lymphoma (0/8), which would require additional markers. These results support the use of STOT as a complementary tool for fast and accurate diagnostic screening, orientation, and classification of pediatric cancer in suspicious patients. Abstract Early diagnosis of pediatric cancer is key for adequate patient management and improved outcome. Although multiparameter flow cytometry (MFC) has proven of great utility in the diagnosis and classification of hematologic malignancies, its application to non-hematopoietic pediatric tumors remains limited. Here we designed and prospectively validated a new single eight-color antibody combination—solid tumor orientation tube, STOT—for diagnostic screening of pediatric cancer by MFC. A total of 476 samples (139 tumor mass, 138 bone marrow, 86 lymph node, 58 peripheral blood, and 55 other body fluid samples) from 296 patients with diagnostic suspicion of pediatric cancer were analyzed by MFC vs. conventional diagnostic procedures. STOT was designed after several design–test–evaluate–redesign cycles based on a large panel of monoclonal antibody combinations tested on 301 samples. In its final version, STOT consists of a single 8-color/12-marker antibody combination (CD99-CD8/numyogenin/CD4-EpCAM/CD56/GD2/smCD3-CD19/cyCD3-CD271/CD45). Prospective validation of STOT in 149 samples showed concordant results with the patient WHO/ICCC-3 diagnosis in 138/149 cases (92.6%). These included: 63/63 (100%) reactive/disease-free samples, 43/44 (98%) malignant and 4/4 (100%) benign non-hematopoietic tumors together with 28/38 (74%) leukemia/lymphoma cases; the only exception was Hodgkin lymphoma that required additional markers to be stained. In addition, STOT allowed accurate discrimination among the four most common subtypes of malignant CD45− CD56++ non-hematopoietic solid tumors: 13/13 (GD2++ numyogenin− CD271−/+ nuMyoD1− CD99− EpCAM−) neuroblastoma samples, 5/5 (GD2− numyogenin++ CD271++ nuMyoD1++ CD99−/+ EpCAM−) rhabdomyosarcomas, 2/2 (GD2−/+ numyogenin− CD271+ nuMyoD1− CD99+ EpCAM−) Ewing sarcoma family of tumors, and 7/7 (GD2− numyogenin− CD271+ nuMyoD1− CD99− EpCAM+) Wilms tumors. In summary, here we designed and validated a new standardized antibody combination and MFC assay for diagnostic screening of pediatric solid tumors that might contribute to fast and accurate diagnostic orientation and classification of pediatric cancer in routine clinical practice.
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Affiliation(s)
- Cristiane de Sá Ferreira-Facio
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Vitor Botafogo
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Patrícia Mello Ferrão
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Maria Clara Canellas
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Cristiane B. Milito
- Department of Pathology, Faculty of Medicine, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil;
| | - Sérgio Romano
- Laboratory of Anatomical Pathology and Cytopathology, Instituto Nacional de Câncer (INCa), Rio de Janeiro 20220-400, Brazil;
| | - Daiana V. Lopes
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Lisandra C. Teixeira
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Elen Oliveira
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Enrico Bruno-Riscarolli
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Fabiana V. Mello
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Patrícia F. R. Siqueira
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Patrícia Moura
- I’Dor Institute, Hospital Estadual da Criança, Rio de Janeiro 21330-400, Brazil; (P.M.); (F.N.M.)
| | - Francisco Nicanor Macedo
- I’Dor Institute, Hospital Estadual da Criança, Rio de Janeiro 21330-400, Brazil; (P.M.); (F.N.M.)
| | - Danielle N. Forny
- Department of Pediatric Surgery, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil;
| | - Luíza Simião
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Ana Luíza Pureza
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
| | - Marcelo Gerardin Poirot Land
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
| | - Carlos Eduardo Pedreira
- Systems and Computing Engineering Department (COPPE-PESC), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, Brazil;
| | - Jacques J. M. van Dongen
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands;
| | - Alberto Orfao
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (A.O.); (E.S.d.C.); Tel.: +34-9232-9481 (A.O.); +55-21-3938-4725 (E.S.d.C.)
| | - Elaine Sobral da Costa
- Internal Medicine Postgraduate Program, Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-617, Brazil; (C.d.S.F.-F.); (V.B.); (L.C.T.); (E.O.); (E.B.-R.); (P.F.R.S.); (M.G.P.L.)
- Cytometry Service, Institute of Paediatrics and Puericultura Martagão Gesteira (IPPMG), Faculty of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-612, Brazil; (P.M.F.); (M.C.C.); (D.V.L.); (F.V.M.); (L.S.); (A.L.P.)
- Correspondence: (A.O.); (E.S.d.C.); Tel.: +34-9232-9481 (A.O.); +55-21-3938-4725 (E.S.d.C.)
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18
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Karmakar T, Banerjee S, Brahma S, Dey D, Radhakrishnan V, Chandy M, Ghara N, Krishnan S, Mukherjee G, Mishra DK, Arora N. A Pilot Study to Determine the Utility of Automated Tissue Dissociator for Flowcytometry Based Evaluation of Hematolymphoid Tumor Tissue Biopsies. Indian J Hematol Blood Transfus 2021; 38:403-410. [PMID: 35496962 PMCID: PMC9001761 DOI: 10.1007/s12288-021-01481-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 08/06/2021] [Indexed: 11/29/2022] Open
Abstract
Routine diagnostic biopsy tissue processing, conventional histology/immunohistochemistry (IHC) method is a multi-step and time consuming practice. With the advanced tissue dissociation protocols and panel designing, flow cytometric immunophenotyping (FCI) can be performed on diagnostic hematolymphoid tissue samples using single cell suspensions that economize steps and the time taken. Diagnostic tissue samples from lymph node, mediastinal mass, testicular biopsies and similar sites were dissociated using gentle MACS Octo-dissociator and FCI was performed thereafter. Oral tissue biopsy samples were also processed as a validation set for the protocol. 21 prospective tissue biopsy samples with suspected involvement by a known hematolymphoid neoplasm were processed and evaluated. These included B lymphoblastic lymphoma (n = 12), T lymphoblastic lymphomas (n = 3), Burkitts lymphoma (n = 3) and one case each of granulocytic sarcoma, Hodgkin lymphoma and granulomatous disease. Tissue FCI and IHC were found concordant with identified profile FCI obtained from blood/bone marrow analyses. FCI can produce a highly sensitive and reliable report, within hours, by processing fresh tumor tissue samples from suspected hematolymphoid malignancies. This method can be considered as an effective adjunct to IHC and can be applicable in routine clinical diagnostics, especially in cases that needs quick diagnosis and immediate clinical treatment.
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Affiliation(s)
- Tanusri Karmakar
- Department of Laboratory Hematology and Molecular Genetics, Tata Medical Center, Kolkata, 700160 India
| | - Sambhunath Banerjee
- Department of Laboratory Hematology and Molecular Genetics, Tata Medical Center, Kolkata, 700160 India
| | - Subhajit Brahma
- Department of Laboratory Hematology and Molecular Genetics, Tata Medical Center, Kolkata, 700160 India
| | - Debdeep Dey
- Department of Histopathology, Tata Medical Center, Kolkata, India
| | - Vivek Radhakrishnan
- Department of Clinical Hematology Oncology and HCT, Tata Medical Center, Kolkata, India
| | - Mammen Chandy
- Department of Clinical Hematology Oncology and HCT, Tata Medical Center, Kolkata, India
| | - Niharendu Ghara
- Department of Pediatric Oncology, Tata Medical Center, Kolkata, India
| | - Shekhar Krishnan
- Department of Pediatric Oncology, Tata Medical Center, Kolkata, India
| | | | - Deepak Kumar Mishra
- Department of Laboratory Hematology and Molecular Genetics, Tata Medical Center, Kolkata, 700160 India
| | - Neeraj Arora
- Department of Laboratory Hematology and Molecular Genetics, Tata Medical Center, Kolkata, 700160 India
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19
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Roe CE, Hayes MJ, Barone SM, Irish JM. Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. ACTA ACUST UNITED AC 2021; 93:e71. [PMID: 32250555 DOI: 10.1002/cpcy.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article presents a single experiment designed to introduce a trainee to multiple advanced bench and analysis techniques, including high-dimensional cytometry, profiling cell signaling networks, functional assays with primary human tissue, and single-cell analysis with machine learning tools. The trainee is expected to have only minimal laboratory experience and is not required to have any prior training in flow cytometry, immunology, or data science. This article aims to introduce the advanced research areas with a design that is robust enough that novice trainees will succeed, flexible enough to allow some project customization, and fundamental enough that the skills and knowledge gained will provide a template for future experiments. For advanced users, the updated phospho-flow protocol and the established controls, best practices, and expected outcomes presented here also provide a framework for adapting these tools in new areas with unexplored biology. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Phospho-protein stimulation and mass cytometry data collection Support Protocol: Analysis of signaling mass cytometry data.
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Affiliation(s)
- Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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20
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Yi B, Cheng H, Wyczechowska D, Yu Q, Li L, Ochoa AC, Riker AI, Xi Y. Sulindac Modulates the Response of Proficient MMR Colorectal Cancer to Anti-PD-L1 Immunotherapy. Mol Cancer Ther 2021; 20:1295-1304. [PMID: 33879557 PMCID: PMC8295201 DOI: 10.1158/1535-7163.mct-20-0934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/26/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
Immune-checkpoint inhibitor (ICI) therapy has been widely used to treat different human cancers, particularly advanced solid tumors. However, clinical studies have reported that ICI immunotherapy benefits only ∼15% of patients with colorectal cancer, specifically those with tumors characterized by microsatellite instability (MSI), a molecular marker of defective DNA mismatch repair (dMMR). For the majority of patients with colorectal cancer who carry proficient MMR (pMMR), ICIs have shown little clinical benefit. In this study, we examined the efficacy of sulindac to enhance the response of pMMR colorectal cancer to anti-PD-L1 immunotherapy. We utilized a CT26 syngeneic mouse tumor model to compare the inhibitory effects of PD-L1 antibody (Ab), sulindac, and their combination on pMMR colorectal cancer tumor growth. We found that mice treated with combination therapy showed a significant reduction in tumor volume, along with increased infiltration of CD8+ T lymphocytes in the tumor tissues. We also demonstrated that sulindac could downregulate PD-L1 by blocking NF-κB signaling, which in turn led to a decrease in exosomal PD-L1. Notably, PD-L1 Ab can be bound and consumed by exosomal PD-L1 in the blood circulation. Therefore, in combination therapy, sulindac downregulating PD-L1 leads to increased availability of PD-L1 Ab, which potentially improves the overall efficacy of anti-PD-L1 therapy. We also show that low-dose sulindac does not appear to have a systemic inhibitory effect on prostaglandin E2 (PGE2). In conclusion, our findings provide unique insights into the mechanism of action and efficacy for sulindac as an immunomodulatory agent in combination with anti-PD-L1 therapy for the treatment of pMMR colorectal cancer.
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Affiliation(s)
- Bin Yi
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Hao Cheng
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Dorota Wyczechowska
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Qingzhao Yu
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Li Li
- Ochsner Clinical School, University of Queensland, and Institute for Translational Research, Ochsner Clinic Foundation, New Orleans, Louisiana
| | - Augusto C Ochoa
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Adam I Riker
- Geaton and JoAnn DeCesaris Cancer Institute, Anne Arundel Medical Center, Luminis Health, Annapolis, Maryland
| | - Yaguang Xi
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana.
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana
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21
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Wogsland CE, Lien HE, Pedersen L, Hanjra P, Grondal SM, Brekken RA, Lorens JB, Halberg N. High-dimensional immunotyping of tumors grown in obese and non-obese mice. Dis Model Mech 2021; 14:dmm048977. [PMID: 33653826 PMCID: PMC8033414 DOI: 10.1242/dmm.048977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/20/2022] Open
Abstract
Obesity is a disease characterized by chronic low-grade systemic inflammation and has been causally linked to the development of 13 cancer types. Several studies have been undertaken to determine whether tumors evolving in obese environments adapt differential interactions with immune cells and whether this can be connected to disease outcome. Most of these studies have been limited to single-cell lines and tumor models and analysis of limited immune cell populations. Given the multicellular complexity of the immune system and its dysregulation in obesity, we applied high-dimensional suspension mass cytometry to investigate how obesity affects tumor immunity. We used a 36-marker immune-focused mass cytometry panel to interrogate the immune landscape of orthotopic syngeneic mouse models of pancreatic and breast cancer. Unanchored batch correction was implemented to enable simultaneous analysis of tumor cohorts to uncover the immunotypes of each cancer model and reveal remarkably model-specific immune regulation. In the E0771 breast cancer model, we demonstrate an important link to obesity with an increase in two T-cell-suppressive cell types and a decrease in CD8 T cells.
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Affiliation(s)
- Cara E. Wogsland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Hilde E. Lien
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Line Pedersen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Pahul Hanjra
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Sturla M. Grondal
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Rolf A. Brekken
- Division of Surgical Oncology, Department of Surgery, and Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James B. Lorens
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
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22
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Mondal T, Shivange GN, Tihagam RGT, Lyerly E, Battista M, Talwar D, Mosavian R, Urbanek K, Rashid NS, Harrell JC, Bos PD, Stelow EB, Stack MS, Bhatnagar S, Tushir‐Singh J. Unexpected PD-L1 immune evasion mechanism in TNBC, ovarian, and other solid tumors by DR5 agonist antibodies. EMBO Mol Med 2021; 13:e12716. [PMID: 33587338 PMCID: PMC7933954 DOI: 10.15252/emmm.202012716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Lack of effective immune infiltration represents a significant barrier to immunotherapy in solid tumors. Thus, solid tumor-enriched death receptor-5 (DR5) activating antibodies, which generates tumor debulking by extrinsic apoptotic cytotoxicity, remains a crucial alternate therapeutic strategy. Over past few decades, many DR5 antibodies moved to clinical trials after successfully controlling tumors in immunodeficient tumor xenografts. However, DR5 antibodies failed to significantly improve survival in phase-II trials, leading in efforts to generate second generation of DR5 agonists to supersize apoptotic cytotoxicity in tumors. Here we have discovered that clinical DR5 antibodies activate an unexpected immunosuppressive PD-L1 stabilization pathway, which potentially had contributed to their limited success in clinics. The DR5 agonist stimulated caspase-8 signaling not only activates ROCK1 but also undermines proteasome function, both of which contributes to increased PD-L1 stability on tumor cell surface. Targeting DR5-ROCK1-PD-L1 axis markedly increases immune effector T-cell function, promotes tumor regression, and improves overall survival in animal models. These insights have identified a potential clinically viable combinatorial strategy to revive solid cancer immunotherapy using death receptor agonism.
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Affiliation(s)
- Tanmoy Mondal
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | - Gururaj N Shivange
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | - Rachisan GT Tihagam
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | - Evan Lyerly
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Michael Battista
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Divpriya Talwar
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Roxanna Mosavian
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- Undergraduate Research ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Karol Urbanek
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
| | | | - J Chuck Harrell
- Department of PathologyMassey Cancer Center, VCURichmondVAUSA
| | - Paula D Bos
- Department of PathologyMassey Cancer Center, VCURichmondVAUSA
| | - Edward B Stelow
- Department of PathologyUniversity of VirginiaCharlottesvilleVAUSA
| | - M Sharon Stack
- Harper Cancer Research InstituteUniversity of Notre DameNotre DameINUSA
| | - Sanchita Bhatnagar
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- University of Virginia Cancer Center and Medical SchoolCharlottesvilleVAUSA
| | - Jogender Tushir‐Singh
- Laboratory of Novel BiologicsUniversity of VirginiaCharlottesvilleVAUSA
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVAUSA
- University of Virginia Cancer Center and Medical SchoolCharlottesvilleVAUSA
- DoD Ovarian Cancer Academy Early Career InvestigatorCharlottesvilleVAUSA
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23
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Galdieri L, Jash A, Malkova O, Mao DD, DeSouza P, Chu YE, Salter A, Campian JL, Naegle KM, Brennan CW, Wakimoto H, Oh ST, Kim AH, Chheda MG. Defining phenotypic and functional heterogeneity of glioblastoma stem cells by mass cytometry. JCI Insight 2021; 6:128456. [PMID: 33400685 PMCID: PMC7934942 DOI: 10.1172/jci.insight.128456] [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: 03/19/2019] [Accepted: 12/29/2020] [Indexed: 01/09/2023] Open
Abstract
Most patients with glioblastoma (GBM) die within 2 years. A major therapeutic goal is to target GBM stem cells (GSCs), a subpopulation of cells that contribute to treatment resistance and recurrence. Since their discovery in 2003, GSCs have been isolated using single-surface markers, such as CD15, CD44, CD133, and α6 integrin. It remains unknown how these single-surface marker-defined GSC populations compare with each other in terms of signaling and function and whether expression of different combinations of these markers is associated with different functional capacity. Using mass cytometry and fresh operating room specimens, we found 15 distinct GSC subpopulations in patients, and they differed in their MEK/ERK, WNT, and AKT pathway activation status. Once in culture, some subpopulations were lost and previously undetectable ones materialized. GSCs that highly expressed all 4 surface markers had the greatest self-renewal capacity, WNT inhibitor sensitivity, and in vivo tumorigenicity. This work highlights the potential signaling and phenotypic diversity of GSCs. Larger patient sample sizes and antibody panels are required to confirm these findings.
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Affiliation(s)
| | | | - Olga Malkova
- Center for Human Immunology and Immunotherapy Programs, and
| | - Diane D Mao
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Yunli E Chu
- Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Amber Salter
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jian L Campian
- Department of Medicine.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kristen M Naegle
- Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Cameron W Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hiroaki Wakimoto
- Brain Tumor Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stephen T Oh
- Center for Human Immunology and Immunotherapy Programs, and.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Albert H Kim
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri, USA.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Milan G Chheda
- Department of Medicine.,Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA.,Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
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24
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Biernacka A, Skrzypczak M, Zhu Y, Pasero P, Rowicka M, Ginalski K. High-resolution, ultrasensitive and quantitative DNA double-strand break labeling in eukaryotic cells using i-BLESS. Nat Protoc 2021; 16:1034-1061. [PMID: 33349705 PMCID: PMC8088906 DOI: 10.1038/s41596-020-00448-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/09/2020] [Indexed: 11/09/2022]
Abstract
DNA double-strand breaks (DSBs) are implicated in various physiological processes, such as class-switch recombination or crossing-over during meiosis, but also present a threat to genome stability. Extensive evidence shows that DSBs are a primary source of chromosome translocations or deletions, making them a major cause of genomic instability, a driving force of many diseases of civilization, such as cancer. Therefore, there is a great need for a precise, sensitive, and universal method for DSB detection, to enable both the study of their mechanisms of formation and repair as well as to explore their therapeutic potential. We provide a detailed protocol for our recently developed ultrasensitive and genome-wide DSB detection method: immobilized direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing (i-BLESS), which relies on the encapsulation of cells in agarose beads and labeling breaks directly and specifically with biotinylated linkers. i-BLESS labels DSBs with single-nucleotide resolution, allows detection of ultrarare breaks, takes 5 d to complete, and can be applied to samples from any organism, as long as a sufficient amount of starting material can be obtained. We also describe how to combine i-BLESS with our qDSB-Seq approach to enable the measurement of absolute DSB frequencies per cell and their precise genomic coordinates at the same time. Such normalization using qDSB-Seq is especially useful for the evaluation of spontaneous DSB levels and the estimation of DNA damage induced rather uniformly in the genome (e.g., by irradiation or radiomimetic chemotherapeutics).
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Affiliation(s)
- Anna Biernacka
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Yingjie Zhu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Montpellier, France
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland.
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25
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Gonder S, Fernandez Botana I, Wierz M, Pagano G, Gargiulo E, Cosma A, Moussay E, Paggetti J, Largeot A. Method for the Analysis of the Tumor Microenvironment by Mass Cytometry: Application to Chronic Lymphocytic Leukemia. Front Immunol 2020; 11:578176. [PMID: 33193376 PMCID: PMC7606286 DOI: 10.3389/fimmu.2020.578176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
In the past 20 years, the interest for the tumor microenvironment (TME) has exponentially increased. Indeed, it is now commonly admitted that the TME plays a crucial role in cancer development, maintenance, immune escape and resistance to therapy. This stands true for hematological malignancies as well. A considerable amount of newly developed therapies are directed against the cancer-supporting TME instead of targeting tumor cells themselves. However, the TME is often not clearly defined. In addition, the unique phenotype of each tumor and the variability among patients limit the success of such therapies. Recently, our group took advantage of the mass cytometry technology to unveil the specific TME in the context of chronic lymphocytic leukemia (CLL) in mice. We found the enrichment of LAG3 and PD1, two immune checkpoints. We tested an antibody-based immunotherapy, targeting these two molecules. This combination of antibodies was successful in the treatment of murine CLL. In this methods article, we provide a detailed protocol for the staining of CLL TME cells aiming at their characterization using mass cytometry. We include panel design and validation, sample preparation and acquisition, machine set-up, quality control, and analysis. Additionally, we discuss different advantages and pitfalls of this technique.
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MESH Headings
- Animals
- Antigens, CD/metabolism
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- Flow Cytometry
- Immune Checkpoint Inhibitors/pharmacology
- Immunotherapy
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mice
- Programmed Cell Death 1 Receptor/metabolism
- Tumor Microenvironment
- Lymphocyte Activation Gene 3 Protein
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Affiliation(s)
- Susanne Gonder
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Iria Fernandez Botana
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marina Wierz
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Giulia Pagano
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ernesto Gargiulo
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Antonio Cosma
- National Cytometry Platform, Quantitative Biology Unit, Transversal Activities, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Etienne Moussay
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jerome Paggetti
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anne Largeot
- Tumor Stroma Interactions, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
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26
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Zhou W, Zhang C, Zhang D, Peng J, Ma S, Wang X, Guan X, Li P, Li D, Jia G, Jia W. Comprehensive analysis of the immunological landscape of pituitary adenomas: implications of immunotherapy for pituitary adenomas. J Neurooncol 2020; 149:473-487. [PMID: 33034841 DOI: 10.1007/s11060-020-03636-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022]
Abstract
PURPOSES Immunotherapies for solid tumor are gaining traction in the clinic, however, the immunological landscape of pituitary adenomas (PAs) is not well defined. In the present study, we used the RNA-seq data of PAs to investigate the impact of immunological landscape on clinical features of pituitary adenomas and aim to evaluate the potential immunotherapy for PAs. METHODS We analyzed tumor-infiltrating immune cells in 115 PA samples using RNA-seq. Main immune cell types (B cells, CD8+ T cells, CD4+ T cells, macrophages and NK cells) were detected from the expression of genes. The association between immune cells abundance and immune checkpoint, as well as inflammatory factors were analyzed. 10 additional patients were enrolled for validation. RESULTS In RNA sequencing data, landscape of PAs were identified. Our computationally inferred immune infiltrates significantly associate with patient clinical features. Growth hormone-secreting adenomas (GHomas) were found with higher B cells and CD8+ T cells infiltration. Moreover, GHomas showed relative different genetic background, significant invasive behavior and independently correlated with reduced progress-free time. Tumor progression was related to increased expression of PD-1/PD-L1 and was associated with higher immune infiltration. Analysis of cancer-testis antigen expression and CD8+ T-cell abundance suggested CTAG2 and TSPYL6 were potential immunotherapeutic targets in GHomas and non-functioning adenomas, respectively. CONCLUSIONS Tumor-infiltrating immune cells confer important clinical and biological implications. Our results of immune-infiltrate levels in PAs may inform effective cancer vaccine and checkpoint blockade therapies and make it possible to take immunotherapy into invasive PAs.
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Affiliation(s)
- Wenjianlong Zhou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Dainan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jiayi Peng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shunchang Ma
- China National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, China.,Beijing Neurosurgical Institute, 199 West Road, South Fourth Ring Road, Beijing, China
| | - Xi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiudong Guan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | - Deling Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guijun Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wang Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. .,China National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, China. .,Beijing Neurosurgical Institute, 199 West Road, South Fourth Ring Road, Beijing, China.
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27
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Frutoso M, Mair F, Prlic M. OMIP-070: NKp46-Based 27-Color Phenotyping to Define Natural Killer Cells Isolated From Human Tumor Tissues. Cytometry A 2020; 97:1052-1056. [PMID: 32978859 PMCID: PMC7702032 DOI: 10.1002/cyto.a.24230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/05/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022]
Abstract
This 27-color panel has been validated and optimized to comprehensively profile natural killer (NK) cells isolated from human tumors using a collagenase Type II-based digestion protocol. We confirmed that detection of protein expression by antibodies used in our final panel was not affected during tissue digestion. During this evaluation process, we found that detection of CD56, a biomarker typically used to identify NK cells, was affected substantially by collagenase-based digestion. Thus, our panel is centered around expression of NKp46, which is sufficient to identify NK cells and not affected by the tissue collagenase digestion step. Our panel further includes biomarkers used to extrapolate NK-cell maturation, differentiation, migration, homing potential, and functional state. Our panel is intended to provide in-depth characterization of human NK cells isolated from tissues, which we specifically tested using oral squamous cell carcinomas tissues, but it is compatible with other tissues that can be dissociated with a collagenase Type II-based protocol. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Marie Frutoso
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWashington98109USA
| | - Florian Mair
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWashington98109USA
| | - Martin Prlic
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWashington98109USA
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28
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Leelatian N, Sinnaeve J, Mistry AM, Barone SM, Brockman AA, Diggins KE, Greenplate AR, Weaver KD, Thompson RC, Chambless LB, Mobley BC, Ihrie RA, Irish JM. Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells. eLife 2020; 9:56879. [PMID: 32573435 PMCID: PMC7340505 DOI: 10.7554/elife.56879] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
A goal of cancer research is to reveal cell subsets linked to continuous clinical outcomes to generate new therapeutic and biomarker hypotheses. We introduce a machine learning algorithm, Risk Assessment Population IDentification (RAPID), that is unsupervised and automated, identifies phenotypically distinct cell populations, and determines whether these populations stratify patient survival. With a pilot mass cytometry dataset of 2 million cells from 28 glioblastomas, RAPID identified tumor cells whose abundance independently and continuously stratified patient survival. Statistical validation within the workflow included repeated runs of stochastic steps and cell subsampling. Biological validation used an orthogonal platform, immunohistochemistry, and a larger cohort of 73 glioblastoma patients to confirm the findings from the pilot cohort. RAPID was also validated to find known risk stratifying cells and features using published data from blood cancer. Thus, RAPID provides an automated, unsupervised approach for finding statistically and biologically significant cells using cytometry data from patient samples.
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Affiliation(s)
- Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Justine Sinnaeve
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States
| | - Akshitkumar M Mistry
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States
| | - Asa A Brockman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States
| | - Kirsten E Diggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States
| | - Allison R Greenplate
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Kyle D Weaver
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Reid C Thompson
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Lola B Chambless
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Bret C Mobley
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Rebecca A Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, United States
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, United States.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
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29
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Targeting AXL and RAGE to prevent geminin overexpression-induced triple-negative breast cancer metastasis. Sci Rep 2019; 9:19150. [PMID: 31844158 PMCID: PMC6915698 DOI: 10.1038/s41598-019-55702-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023] Open
Abstract
Dissemination of metastatic precursors from primaries is the primary reason for patient death. Dissemination encompasses tumor cells invasion of stroma, followed by intravasation through the endothelium barrier into the bloodstream. Here, we describe how geminin-overexpressing tumor cells acquire dissemination ability. Acetylated HMGB1 (Ac-HMGB1) secreted by geminin-overexpressing cells activates RAGE and CXCR4 expression on mesenchymal stem cells (MSCs) located in tumor stroma. Through secreting CXCL12, geminin-overexpressing cells recruit these CXCR4+-MSCs into the tumor. Within the tumor, MSCs differentiate into S100A4-secreting cancer-associated fibroblasts (CAFs). S100A4, in a reciprocal manner, activates geminin-overexpressing cells to secrete CCL2 that recruits M0-macrophages from the stroma into the tumor. Within the tumor, CCL2 polarizes M0-macrophages into Gas6-secreting M2-tumor-associated macrophages (M2-TAMs). In concert, geminin-overexpression, S100A4/RAGE and Gas6/AXL signaling promote the invasive and intravasation abilities in geminin-overexpressing cells through exacerbating their stemness and epithelial-to-mesenchymal phenotypes and enhancing expression and functional interaction of CD151 and α3β1-integrin in geminin-overexpressing cells. Tumors formed following injection of geminin-overexpressing cells admixed with MSCs/CAFs grew faster, metastasized earlier, especially to lungs, and were extremely sensitive to anti-c-Abl, anti-RAGE, and anti-AXL drugs. These data support an intrinsic ability in geminin-overexpressing tumor cells to promote their metastatic potential through recruitment and bi-directional interactions with MSCs/CAFs and M2-TAMs.
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30
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Maby P, Corneau A, Galon J. Phenotyping of tumor infiltrating immune cells using mass-cytometry (CyTOF). Methods Enzymol 2019; 632:339-368. [PMID: 32000904 DOI: 10.1016/bs.mie.2019.07.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The anti-tumor immune response plays a crucial role in cancer patient outcome as well as in response to the growing family of immunotherapeutic treatments. Improving patient prognostic and therapeutic management requires a better knowledge of the tumor microenvironment, for which a deep characterization of tumor-infiltrating immune populations is instrumental. Mass cytometry represents an excellent tool in tumor Immunology, as it allows the simultaneous analysis of >40 markers on single cells. In this chapter, we review challenging technical aspects of the mass cytometry phenotyping of tumor infiltrating immune cells, focusing on fresh human solid tumor samples. We first explain how to design mass cytometry experiments, then provide detailed protocols to isolate mononuclear immune cells from solid tissues and to stain them for an acquisition on a mass cytometer. We also discuss how to optimize the preparation of single immune cell samples, and how to ensure the reproducibility of data generated from distinct fresh human samples. Finally, we provide troubleshooting suggestions for difficult sample acquisitions on a mass cytometer.
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Affiliation(s)
- Pauline Maby
- INSERM, Laboratory of Integrative Cancer Immunology, Équipe Labellisée Ligue Contre le Cancer, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, Paris, France.
| | - Aurélien Corneau
- Sorbonne-Université, UMS037 PASS, Plateforme de Cytometrie CyPS, Faculté des Sciences Sorbonne-Université, Paris, France
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Équipe Labellisée Ligue Contre le Cancer, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, Paris, France
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31
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Ahuja K, Rather GM, Lin Z, Sui J, Xie P, Le T, Bertino JR, Javanmard M. Toward point-of-care assessment of patient response: a portable tool for rapidly assessing cancer drug efficacy using multifrequency impedance cytometry and supervised machine learning. MICROSYSTEMS & NANOENGINEERING 2019; 5:34. [PMID: 31645995 PMCID: PMC6799891 DOI: 10.1038/s41378-019-0073-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/31/2019] [Accepted: 03/25/2019] [Indexed: 05/07/2023]
Abstract
We present a novel method to rapidly assess drug efficacy in targeted cancer therapy, where antineoplastic agents are conjugated to antibodies targeting surface markers on tumor cells. We have fabricated and characterized a device capable of rapidly assessing tumor cell sensitivity to drugs using multifrequency impedance spectroscopy in combination with supervised machine learning for enhanced classification accuracy. Currently commercially available devices for the automated analysis of cell viability are based on staining, which fundamentally limits the subsequent characterization of these cells as well as downstream molecular analysis. Our approach requires as little as 20 μL of volume and avoids staining allowing for further downstream molecular analysis. To the best of our knowledge, this manuscript presents the first comprehensive attempt to using high-dimensional data and supervised machine learning, particularly phase change spectra obtained from multi-frequency impedance cytometry as features for the support vector machine classifier, to assess viability of cells without staining or labelling.
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Affiliation(s)
- Karan Ahuja
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Gulam M. Rather
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Zhongtian Lin
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Jianye Sui
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Pengfei Xie
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Tuan Le
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Joseph R. Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Mehdi Javanmard
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
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32
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Rushing GV, Brockman AA, Bollig MK, Leelatian N, Mobley BC, Irish JM, Ess KC, Fu C, Ihrie RA. Location-dependent maintenance of intrinsic susceptibility to mTORC1-driven tumorigenesis. Life Sci Alliance 2019; 2:2/2/e201800218. [PMID: 30910807 PMCID: PMC6435042 DOI: 10.26508/lsa.201800218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 01/18/2023] Open
Abstract
Per-cell quantification of mTORC1 signaling activity in neural stem/progenitor cells reveals differential signaling, proliferative, and tumor-forming capability between dorsal and ventral cells within a single niche. Neural stem/progenitor cells (NSPCs) of the ventricular–subventricular zone (V-SVZ) are candidate cells of origin for many brain tumors. However, whether NSPCs in different locations within the V-SVZ differ in susceptibility to tumorigenic mutations is unknown. Here, single-cell measurements of signal transduction intermediates in the mechanistic target of rapamycin complex 1 (mTORC1) pathway reveal that ventral NSPCs have higher levels of signaling than dorsal NSPCs. These features are linked with differences in mTORC1-driven disease severity: introduction of a pathognomonic Tsc2 mutation only results in formation of tumor-like masses from the ventral V-SVZ. We propose a direct link between location-dependent intrinsic growth properties imbued by mTORC1 and predisposition to tumor development.
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Affiliation(s)
- Gabrielle V Rushing
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Asa A Brockman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Madelyn K Bollig
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nalin Leelatian
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bret C Mobley
- Department of Pathology, Immunology, and Microbiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Pathology, Immunology, and Microbiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kevin C Ess
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cary Fu
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca A Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA .,Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
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33
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Implementation of Mass Cytometry for Immunoprofiling of Patients with Solid Tumors. J Immunol Res 2019; 2019:6705949. [PMID: 30886872 PMCID: PMC6388349 DOI: 10.1155/2019/6705949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 11/22/2022] Open
Abstract
Monitoring immune responses to solid cancers may be a better prognostic tool than conventional staging criteria, and it can also serve as an important criterion for the selection of individualized therapy. Multiparametric phenotyping by mass cytometry extended possibilities for immunoprofiling. However, careful optimization of each step of such method is necessary for obtaining reliable results. Also, with respect to procedure length and costs, sample preparation, staining, and storage should be optimized. Here, we designed a panel of 31 antibodies which allows for identification of several subpopulations of lymphoid and myeloid cells in a solid tumor and peripheral blood simultaneously. For sample preparation, disaggregation of tumor tissue with two different collagenases combined with DNase I was compared, and removal of dead or tumor cells by magnetic separation was evaluated. Two possible procedures of barcoding for single-tube staining of several samples were examined. While the palladium-based barcoding affected the stability of several antigens, the staining with two differently labeled CD45 antibodies was suitable for cells isolated from a patient's blood and tumor. The storage of samples in the intercalation solution for up to two weeks did not influence results of the analysis, which allowed the measurement of samples collected within this interval on the same day. This procedure optimized on samples from patients with head and neck squamous cell carcinoma enabled identification of various immune cells including rare subpopulations.
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34
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Mistry AM, Greenplate AR, Ihrie RA, Irish JM. Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors. FEBS J 2019; 286:1523-1539. [PMID: 30549207 DOI: 10.1111/febs.14730] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/17/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022]
Abstract
Single-cell technologies that can quantify features of individual cells within a tumor are critical for treatment strategies aiming to target cancer cells while sparing or activating beneficial cells. Given that key players in protein networks are often the primary targets of precision oncology strategies, it is imperative to transcend the nucleic acid message and read cellular actions in human solid tumors. Here, we review the advantages of multiplex, single-cell mass cytometry in tissue and solid tumor investigations. Mass cytometry can quantitatively probe nearly any cellular feature or target. In discussing the ability of mass cytometry to reveal and characterize a broad spectrum of cell types, identify rare cells, and study functional behavior through protein signaling networks in millions of individual cells from a tumor, this review surveys publications of scientific advances in solid tumor biology made with the aid of mass cytometry. Advances discussed include functional identification of rare tumor and tumor-infiltrating immune cells and dissection of cellular mechanisms of immunotherapy in solid tumors and the periphery. The review concludes by highlighting ways to incorporate single-cell mass cytometry in solid tumor precision oncology efforts and rapidly developing cytometry techniques for quantifying cell location and sequenced nucleic acids.
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Affiliation(s)
- Akshitkumar M Mistry
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison R Greenplate
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca A Ihrie
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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35
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Reichard A, Asosingh K. Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry. Cytometry A 2018; 95:219-226. [PMID: 30523671 DOI: 10.1002/cyto.a.23690] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/26/2018] [Accepted: 11/02/2018] [Indexed: 01/02/2023]
Abstract
Preparing a single cell suspension is a critical step in any solid tissue flow cytometry experiment. Tissue dissection, enzymatic digestion, and mechanical dissociation are three significant steps leading to the degradation of the extracellular matrix and the isolation of single cells, allowing the generation of high-quality flow cytometry data. Cells and the extracellular matrix contain various proteins and other structures which must be considered when designing a tissue digestion protocol to preserve the viability of cells and the presence of relevant antigens while digesting matrix components and cleaving cell-cell junctions. Evaluation of the single cell suspension is essential before proceeding with the labeling of the cells as high viability and absence of cell debris and aggregates are critical for flow cytometry. The information presented should be used as a general guide of steps to consider when preparing a single cell suspension from solid tissues for flow cytometry experiments. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Andrew Reichard
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Kewal Asosingh
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio.,Flow Cytometry Core, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio
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36
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Greenplate AR, McClanahan DD, Oberholtzer BK, Doxie DB, Roe CE, Diggins KE, Leelatian N, Rasmussen ML, Kelley MC, Gama V, Siska PJ, Rathmell JC, Ferrell PB, Johnson DB, Irish JM. Computational Immune Monitoring Reveals Abnormal Double-Negative T Cells Present across Human Tumor Types. Cancer Immunol Res 2018; 7:86-99. [PMID: 30413431 DOI: 10.1158/2326-6066.cir-17-0692] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 07/17/2018] [Accepted: 11/05/2018] [Indexed: 12/22/2022]
Abstract
Advances in single-cell biology have enabled measurements of >40 protein features on millions of immune cells within clinical samples. However, the data analysis steps following cell population identification are susceptible to bias, time-consuming, and challenging to compare across studies. Here, an ensemble of unsupervised tools was developed to evaluate four essential types of immune cell information, incorporate changes over time, and address diverse immune monitoring challenges. The four complementary properties characterized were (i) systemic plasticity, (ii) change in population abundance, (iii) change in signature population features, and (iv) novelty of cellular phenotype. Three systems immune monitoring studies were selected to challenge this ensemble approach. In serial biopsies of melanoma tumors undergoing targeted therapy, the ensemble approach revealed enrichment of double-negative (DN) T cells. Melanoma tumor-resident DN T cells were abnormal and phenotypically distinct from those found in nonmalignant lymphoid tissues, but similar to those found in glioblastoma and renal cell carcinoma. Overall, ensemble systems immune monitoring provided a robust, quantitative view of changes in both the system and cell subsets, allowed for transparent review by human experts, and revealed abnormal immune cells present across multiple human tumor types.
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Affiliation(s)
- Allison R Greenplate
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daniel D McClanahan
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Brian K Oberholtzer
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Deon B Doxie
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Caroline E Roe
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kirsten E Diggins
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nalin Leelatian
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Megan L Rasmussen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Mark C Kelley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt Center for Stem Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Peter J Siska
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Jeffrey C Rathmell
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - P Brent Ferrell
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Douglas B Johnson
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan M Irish
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee. .,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, Tennessee
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37
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Doxie DB, Greenplate AR, Gandelman JS, Diggins KE, Roe CE, Dahlman KB, Sosman JA, Kelley MC, Irish JM. BRAF and MEK inhibitor therapy eliminates Nestin-expressing melanoma cells in human tumors. Pigment Cell Melanoma Res 2018; 31:708-719. [PMID: 29778085 PMCID: PMC6188784 DOI: 10.1111/pcmr.12712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/18/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
Abstract
Little is known about the in vivo impacts of targeted therapy on melanoma cell abundance and protein expression. Here, 21 antibodies were added to an established melanoma mass cytometry panel to measure 32 cellular features, distinguish malignant cells, and characterize dabrafenib and trametinib responses in BRAFV600mut melanoma. Tumor cells were biopsied before neoadjuvant therapy and compared to cells surgically resected from the same site after 4 weeks of therapy. Approximately 50,000 cells per tumor were characterized by mass cytometry and computational tools t-SNE/viSNE, FlowSOM, and MEM. The resulting single-cell view of melanoma treatment response revealed initially heterogeneous melanoma tumors were consistently cleared of Nestin-expressing melanoma cells. Melanoma cell subsets that persisted to week 4 were heterogeneous but expressed SOX2 or SOX10 proteins and specifically lacked surface expression of MHC I proteins by MEM analysis. Traditional histology imaging of tissue microarrays from the same tumors confirmed mass cytometry results, including persistence of NES- SOX10+ S100β+ melanoma cells. This quantitative single-cell view of melanoma treatment response revealed protein features of malignant cells that are not eliminated by targeted therapy.
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Affiliation(s)
- Deon B. Doxie
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Allison R. Greenplate
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jocelyn S. Gandelman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kirsten E. Diggins
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline E. Roe
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kimberly B. Dahlman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey A. Sosman
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark C. Kelley
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Hematology-Oncology, Northwestern University, Feinberg School of Medicine, Evanston, IL, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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38
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Brodie TM, Tosevski V, Medová M. OMIP-045: Characterizing human head and neck tumors and cancer cell lines with mass cytometry. Cytometry A 2018; 93:406-410. [PMID: 29648681 DOI: 10.1002/cyto.a.23336] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/29/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Tess M Brodie
- Department of Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, and University of Bern, 3008 Bern, Switzerland.,Mass Cytometry Facility, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vinko Tosevski
- Mass Cytometry Facility, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, and University of Bern, 3008 Bern, Switzerland
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