1
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Krishnaraj A, Nair SJ. Quantifying Intracellular Platinum Accumulation Using Inductively Coupled Mass Spectrometry. Curr Protoc 2024; 4:e70012. [PMID: 39240240 DOI: 10.1002/cpz1.70012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
The platinum-based anticancer drug cisplatin and its analog carboplatin are the most used chemotherapeutic agents worldwide. It is estimated that approximately half of all cancer patients are treated with platinum drugs at some point during the therapy regimen. Cisplatin covalently binds to purine nucleobases to form DNA adducts. Cisplatin therapy is faced with two key challenges. First, despite the initial response, many patients develop cisplatin resistance. Reduced cellular accumulation of cisplatin is one common cause of therapy resistance. Second, cisplatin treatment causes general cytotoxicity, leading to severe side effects. Monitoring the subcellular concentration of platinum chemotherapeutics will help yield clinical efficacy with the minimum possible dose. Inductively coupled plasma-mass spectrometry (ICP-MS) is an analytical technique to quantify the elemental composition of various types of liquified bulk samples with high sensitivity. This article describes quantifying cisplatin accumulation in chromatin and total cell lysate using ICP-MS. The method involves treating cells with cisplatin, isolating RNA-free DNA, digesting samples, ICP-MS instrumentation, and data analysis. Although we describe these steps in one cancer cell line, the protocol can be adapted to any cell line or tissue. The protocol should be a valuable resource for investigators interested in accurate measurement of subcellular concentration of platinum and other metallo-drugs. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Cell culture conditions for A2780 cells and cisplatin treatment Basic Protocol 2: Isolating cellular fractions and sample quantitation Basic Protocol 3: Sample digestion, ICP-MS data collection, and analysis.
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Affiliation(s)
- Arun Krishnaraj
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservior Rd NW, Washington, District of Columbia, USA, 20057
| | - Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservior Rd NW, Washington, District of Columbia, USA, 20057
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2
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Wu C, Yu H, Liang F, Huang X, Jiang B, Lou Z, Liu Y, Wu Z, Wang Q, Shen H, Chen M, Wu P, Wu M. Hypoxia inhibits the iMo/cDC2/CD8+ TRMs immune axis in the tumor microenvironment of human esophageal cancer. J Immunother Cancer 2024; 12:e008889. [PMID: 38964786 PMCID: PMC11227851 DOI: 10.1136/jitc-2024-008889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Esophageal cancer (ESCA) is a form of malignant tumor associated with chronic inflammation and immune dysregulation. However, the specific immune status and key mechanisms of immune regulation in this disease require further exploration. METHODS To investigate the features of the human ESCA tumor immune microenvironment and its possible regulation, we performed mass cytometry by time of flight, single-cell RNA sequencing, multicolor fluorescence staining of tissue, and flow cytometry analyses on tumor and paracancerous tissue from treatment-naïve patients. RESULTS We depicted the immune landscape of the ESCA and revealed that CD8+ (tissue-resident memory CD8+ T cells (CD8+ TRMs) were closely related to disease progression. We also revealed the heterogeneity of CD8+ TRMs in the ESCA tumor microenvironment (TME), which was associated with their differentiation and function. Moreover, the subset of CD8+ TRMs in tumor (called tTRMs) that expressed high levels of granzyme B and immune checkpoints was markedly decreased in the TME of advanced ESCA. We showed that tTRMs are tumor effector cells preactivated in the TME. We then demonstrated that conventional dendritic cells (cDC2s) derived from intermediate monocytes (iMos) are essential for maintaining the proliferation of CD8+ TRMs in the TME. Our preliminary study showed that hypoxia can promote the apoptosis of iMos and impede the maturation of cDC2s, which in turn reduces the proliferative capacity of CD8+ TRMs, thereby contributing to the progression of cancer. CONCLUSIONS Our study revealed the essential antitumor roles of CD8+ TRMs and preliminarily explored the regulation of the iMo/cDC2/CD8+ TRM immune axis in the human ESCA TME.
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Affiliation(s)
- Chuanqiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Huan Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Fuxiang Liang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xiancong Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, People's Republic of China
| | - Bin Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital, Jinan, Shandong Province, People's Republic of China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yafei Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zixiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Qi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Hong Shen
- Department of Medical Oncology, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
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3
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Zhu D, Lu Y, Yang S, Hu T, Tan C, Liang R, Wang Y. PAD4 Inhibitor-Functionalized Layered Double Hydroxide Nanosheets for Synergistic Sonodynamic Therapy/Immunotherapy Of Tumor Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401064. [PMID: 38708711 PMCID: PMC11234469 DOI: 10.1002/advs.202401064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Sonodynamic therapy (SDT) is demonstrated to trigger the systemic immune response of the organism and facilitate the treatment of metastatic tumors. However, SDT-mediated neutrophil extracellular traps (NETs) formation can promote tumor cell spread, thus weakening the therapeutic effectiveness of metastatic tumors. Herein, the amorphous CoW-layered double hydroxide (a-CoW-LDH) nanosheets are functionalized with a peptidyl arginine deiminase 4 (PAD4) inhibitor, i.e., YW3-56, to construct a multifunctional nanoagent (a-LDH@356) for synergistic SDT/immunotherapy. Specifically, a-CoW-LDH nanosheets can act as a sonosensitizer to generate abundant reactive oxygen species (ROS) under US irradiation. After loading with YW3-56, a-LDH@356 plus US irradiation not only effectively induces ROS generation and immunogenic cell death, but also inhibits the elevation of citrullinated histone H3 (H3cit) and the release of NETs, enabling a synergistic enhancement of anti-tumor metastasis effect. Using 4T1 tumor model, it is demonstrated that combining a-CoW-LDH with YW3-56 stimulates an anti-tumor response by upregulating the proportion of immune-activated cells and inducing polarization of M1 macrophages, and inhibits immune escape by downregulating the expression of PD-1 on immune cells under US irradiation, which not only arrests primary tumor progression with a tumor inhibition rate of 69.5% but also prevents tumor metastasis with the least number of lung metastatic nodules.
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Affiliation(s)
- Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing, 100069, P. R. China
| | - Yu Lu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing, 100069, P. R. China
| | - Shuqing Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Tingting Hu
- Department Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077, P. R. China
| | - Chaoliang Tan
- Department Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077, P. R. China
| | - Ruizheng Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
- Quzhou Institute for Innovation in Resource Chemical Engineering, Quzhou, 324000, P. R. China
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing, 100069, P. R. China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Laboratory for Clinical Medicine, Capital Medical University, Beijing Laboratory of Oral Health, Beijing, 100069, P. R. China
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4
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Stepanenko AA, Sosnovtseva AO, Valikhov MP, Chernysheva AA, Abramova OV, Pavlov KA, Chekhonin VP. Systemic and local immunosuppression in glioblastoma and its prognostic significance. Front Immunol 2024; 15:1326753. [PMID: 38481999 PMCID: PMC10932993 DOI: 10.3389/fimmu.2024.1326753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/06/2024] [Indexed: 04/07/2024] Open
Abstract
The effectiveness of tumor therapy, especially immunotherapy and oncolytic virotherapy, critically depends on the activity of the host immune cells. However, various local and systemic mechanisms of immunosuppression operate in cancer patients. Tumor-associated immunosuppression involves deregulation of many components of immunity, including a decrease in the number of T lymphocytes (lymphopenia), an increase in the levels or ratios of circulating and tumor-infiltrating immunosuppressive subsets [e.g., macrophages, microglia, myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs)], as well as defective functions of subsets of antigen-presenting, helper and effector immune cell due to altered expression of various soluble and membrane proteins (receptors, costimulatory molecules, and cytokines). In this review, we specifically focus on data from patients with glioblastoma/glioma before standard chemoradiotherapy. We discuss glioblastoma-related immunosuppression at baseline and the prognostic significance of different subsets of circulating and tumor-infiltrating immune cells (lymphocytes, CD4+ and CD8+ T cells, Tregs, natural killer (NK) cells, neutrophils, macrophages, MDSCs, and dendritic cells), including neutrophil-to-lymphocyte ratio (NLR), focus on the immune landscape and prognostic significance of isocitrate dehydrogenase (IDH)-mutant gliomas, proneural, classical and mesenchymal molecular subtypes, and highlight the features of immune surveillance in the brain. All attempts to identify a reliable prognostic immune marker in glioblastoma tissue have led to contradictory results, which can be explained, among other things, by the unprecedented level of spatial heterogeneity of the immune infiltrate and the significant phenotypic diversity and (dys)functional states of immune subpopulations. High NLR is one of the most repeatedly confirmed independent prognostic factors for shorter overall survival in patients with glioblastoma and carcinoma, and its combination with other markers of the immune response or systemic inflammation significantly improves the accuracy of prediction; however, more prospective studies are needed to confirm the prognostic/predictive power of NLR. We call for the inclusion of dynamic assessment of NLR and other blood inflammatory markers (e.g., absolute/total lymphocyte count, platelet-to-lymphocyte ratio, lymphocyte-to-monocyte ratio, systemic immune-inflammation index, and systemic immune response index) in all neuro-oncology studies for rigorous evaluation and comparison of their individual and combinatorial prognostic/predictive significance and relative superiority.
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Affiliation(s)
- Aleksei A. Stepanenko
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasiia O. Sosnovtseva
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marat P. Valikhov
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia A. Chernysheva
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga V. Abramova
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Konstantin A. Pavlov
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir P. Chekhonin
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N. I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
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5
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Feng S, Calinawan A, Pugliese P, Wang P, Ceccarelli M, Petralia F, Gosline SJC. Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution. CELL REPORTS METHODS 2024; 4:100708. [PMID: 38412834 PMCID: PMC10921018 DOI: 10.1016/j.crmeth.2024.100708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/29/2024]
Abstract
Tumor deconvolution enables the identification of diverse cell types that comprise solid tumors. To date, however, both the algorithms developed to deconvolve tumor samples, and the gold-standard datasets used to assess the algorithms are geared toward the analysis of gene expression (e.g., RNA sequencing) rather than protein levels. Despite the popularity of gene expression datasets, protein levels often provide a more accurate view of rare cell types. To facilitate the use, development, and reproducibility of multiomic deconvolution algorithms, we introduce Decomprolute, a Common Workflow Language framework that leverages containerization to compare tumor deconvolution algorithms across multiomic datasets. Decomprolute incorporates the large-scale multiomic datasets produced by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which include matched mRNA expression and proteomic data from thousands of tumors across multiple cancer types to build a fully open-source, containerized proteogenomic tumor deconvolution benchmarking platform. http://pnnl-compbio.github.io/decomprolute.
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Affiliation(s)
- Song Feng
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Anna Calinawan
- Icahn School of Medicine at Mount Sinai School, New York, NY, USA
| | | | - Pei Wang
- Icahn School of Medicine at Mount Sinai School, New York, NY, USA
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6
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Na S, Choo Y, Yoon TH, Paek E. CyGate Provides a Robust Solution for Automatic Gating of Single Cell Cytometry Data. Anal Chem 2023; 95:16918-16926. [PMID: 37946317 PMCID: PMC10666088 DOI: 10.1021/acs.analchem.3c03006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
To gain a better understanding of the complex human immune system, it is necessary to measure and interpret numerous cellular protein expressions at the single cell level. Mass cytometry is a relatively new technology that offers unprecedented information about the protein expression of a single cell. Conversely, the analysis of high-dimensional and multiparametric mass cytometric data sets presents a new computational challenge. For instance, conventional "manual gating" analysis was inefficient and unreliable for multiparametric phenotyping of the heterogeneous immune cellular system; consequently, automated methods have been developed to address the high dimensionality of mass cytometry data and enhance the reproducibility of the analysis. Here, we present CyGate, a semiautomated method for classifying single cells into their respective cell types. CyGate learns a gating strategy from a reference data set, trains a model for cell classification, and then automatically analyzes additional data sets using the trained model. CyGate also supports the machine learning framework for the classification of "ungated" cells, which are typically disregarded by automated methods. CyGate's utility was demonstrated by its high performance in cell type classification and the lowest generalization error on various public data sets when compared to the state-of-the-art semiautomated methods. Notably, CyGate had the shortest execution time, allowing it to scale with a growing number of samples. CyGate is available at https://github.com/seungjinna/cygate.
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Affiliation(s)
- Seungjin Na
- Institute
for Artificial Intelligence Research, Hanyang
University, Seoul 04763, Republic
of Korea
- Department
of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Yujin Choo
- Department
of Artificial Intelligence, Hanyang University, Seoul 04763, Republic of Korea
| | - Tae Hyun Yoon
- Department
of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Republic
of Korea
- Institute
of Next Generation Material Design, Hanyang
University, Seoul 04763, Republic of Korea
- Yoon
Idea
Lab Co., Ltd., Seoul 04763, Republic of Korea
| | - Eunok Paek
- Institute
for Artificial Intelligence Research, Hanyang
University, Seoul 04763, Republic
of Korea
- Department
of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
- Department
of Artificial Intelligence, Hanyang University, Seoul 04763, Republic of Korea
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7
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Li N, Zhu J, Chen P, Bao C, Wang J, Abdelaal T, Chen D, Zhu S, Wang W, Mao J, Scicluna BP, Koning F, Li F, Lei L. High-dimensional analysis reveals an immune atlas and novel neutrophil clusters in the lungs of model animals with Actinobacillus pleuropneumoniae-induced pneumonia. Vet Res 2023; 54:76. [PMID: 37705063 PMCID: PMC10500746 DOI: 10.1186/s13567-023-01207-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/24/2023] [Indexed: 09/15/2023] Open
Abstract
Due to the increase in bacterial resistance, improving the anti-infectious immunity of the host is rapidly becoming a new strategy for the prevention and treatment of bacterial pneumonia. However, the specific lung immune responses and key immune cell subsets involved in bacterial infection are obscure. Actinobacillus pleuropneumoniae (APP) can cause porcine pleuropneumonia, a highly contagious respiratory disease that has caused severe economic losses in the swine industry. Here, using high-dimensional mass cytometry, the major immune cell repertoire in the lungs of mice with APP infection was profiled. Various phenotypically distinct neutrophil subsets and Ly-6C+ inflammatory monocytes/macrophages accumulated post-infection. Moreover, a linear differentiation trajectory from inactivated to activated to apoptotic neutrophils corresponded with the stages of uninfected, onset, and recovery of APP infection. CD14+ neutrophils, which mainly increased in number during the recovery stage of infection, were revealed to have a stronger ability to produce cytokines, especially IL-10 and IL-21, than their CD14- counterparts. Importantly, MHC-II+ neutrophils with antigen-presenting cell features were identified, and their numbers increased in the lung after APP infection. Similar results were further confirmed in the lungs of piglets infected with APP and Klebsiella pneumoniae infection by using a single-cell RNA-seq technique. Additionally, a correlation analysis between cluster composition and the infection process yielded a dynamic and temporally associated immune landscape where key immune clusters, including previously unrecognized ones, marked various stages of infection. Thus, these results reveal the characteristics of key neutrophil clusters and provide a detailed understanding of the immune response to bacterial pneumonia.
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Affiliation(s)
- Na Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Junhui Zhu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Peiru Chen
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Chuntong Bao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jun Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, The Netherlands
| | - Dexi Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Sibo Zhu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jiangnan Mao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Brendon P Scicluna
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei Hospital, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fengyang Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
| | - Liancheng Lei
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China.
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8
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Wang H, Luo F, Shao X, Gao Y, Jiang N, Jia C, Li H, Chen R. Integrated Proteomics and Single-Cell Mass Cytometry Analysis Dissects the Immune Landscape of Ankylosing Spondylitis. Anal Chem 2023; 95:7702-7714. [PMID: 37126452 DOI: 10.1021/acs.analchem.3c00809] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mass cytometry is a powerful single-cell technology widely adopted to depict immune cell heterogeneity in different contexts. However, this method is only capable of examining several dozens of proteins simultaneously and requires a prior knowledge of the markers to be analyzed. Here we propose that the integration of mass cytometry with shot-gun proteomics may serve as a valuable tool to achieve an in-depth understanding of the immune system. By implementing such a strategy, we investigated the immune landscape of ankylosing spondylitis (AS), a chronic inflammatory arthritis with unclear etiology. The proteome alteration in peripheral blood mononuclear cells (PBMCs) was investigated by quantitative proteomics, and then mass cytometry analysis was conducted to decipher the immunome by considering the signaling molecules identified with differential expression by proteomics. As a result, we identified a wide spectrum of proteins dysregulated in AS, e.g., upregulation of glycolytic enzymes, downregulation of lipid transporters, and dysregulation of chemokine signaling molecules involved in proinflammatory cytokine production and leucocyte migration. Moreover, the single-cell analysis showed the upregulation of chemokine signaling regulators in subclusters of both innate and adaptive immune cells in AS. In addition, correlation analysis unveiled the interplay among Phenograph-identified subclusters of monocytes, CD4+ T cells, and CD8+ T cells. Taken together, our findings demonstrated that the integration of mass spectrometry-based proteomics and single-cell mass cytometry may serve as a useful tool to reveal clinically relevant information regarding useful targets and cellular phenotypes that could be further exploited to develop novel therapeutic strategies.
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Affiliation(s)
- Hao Wang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou 450008, China
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Fengting Luo
- Department of Clinical Laboratory, Tianjin Hospital, Tianjin 300142, China
| | - Xianfeng Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Na Jiang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Chenxi Jia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Hongle Li
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou 450008, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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9
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Fallahzadeh R, Bidoki NH, Stelzer IA, Becker M, Marić I, Chang AL, Culos A, Phongpreecha T, Xenochristou M, Francesco DD, Espinosa C, Berson E, Verdonk F, Angst MS, Gaudilliere B, Aghaeepour N. In-silico generation of high-dimensional immune response data in patients using a deep neural network. Cytometry A 2023; 103:392-404. [PMID: 36507780 PMCID: PMC10182197 DOI: 10.1002/cyto.a.24709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/14/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Technologies for single-cell profiling of the immune system have enabled researchers to extract rich interconnected networks of cellular abundance, phenotypical and functional cellular parameters. These studies can power machine learning approaches to understand the role of the immune system in various diseases. However, the performance of these approaches and the generalizability of the findings have been hindered by limited cohort sizes in translational studies, partially due to logistical demands and costs associated with longitudinal data collection in sufficiently large patient cohorts. An evolving challenge is the requirement for ever-increasing cohort sizes as the dimensionality of datasets grows. We propose a deep learning model derived from a novel pipeline of optimal temporal cell matching and overcomplete autoencoders that uses data from a small subset of patients to learn to forecast an entire patient's immune response in a high dimensional space from one timepoint to another. In our analysis of 1.08 million cells from patients pre- and post-surgical intervention, we demonstrate that the generated patient-specific data are qualitatively and quantitatively similar to real patient data by demonstrating fidelity, diversity, and usefulness.
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Affiliation(s)
- Ramin Fallahzadeh
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Neda H. Bidoki
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Ina A. Stelzer
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
| | - Martin Becker
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Ivana Marić
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Alan L. Chang
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Anthony Culos
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Maria Xenochristou
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Davide De Francesco
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Eloise Berson
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Franck Verdonk
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
| | - Martin S. Angst
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Pediatrics, Stanford University, Stanford, California, USA
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10
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Palomino-Segura M, Sicilia J, Ballesteros I, Hidalgo A. Strategies of neutrophil diversification. Nat Immunol 2023; 24:575-584. [PMID: 36959290 PMCID: PMC10139675 DOI: 10.1038/s41590-023-01452-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/03/2023] [Indexed: 03/25/2023]
Abstract
Neutrophils are formidable defenders. Their vast numbers, constant production, high cytotoxicity and capacity to produce extracellular traps, underlie their ability to efficiently protect in a microorganism-rich world. However, neutrophils are much more than immune sentinels, as evidenced by the expanding repertoire of functions discovered in the context of tissue homeostasis, regeneration or chronic pathologies. In this Perspective, we discuss general functional features of the neutrophil compartment that may be relevant in most, if not all, physiological scenarios in which they participate, including specialization in naïve tissues, transcriptional noise in the bloodstream as a potential strategy for diversification and functional bias in inflammatory sites. We intentionally present the reader with more questions than answers and propose models and approaches that we hope will shed new light onto the biology of these fascinating cells and spark new directions of research.
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Affiliation(s)
- Miguel Palomino-Segura
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.
- Immunophysiology Research Group, Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE) and Department of Physiology, Faculty of Sciences, University of Extremadura, Badajoz, Spain.
| | - Jon Sicilia
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Iván Ballesteros
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Andrés Hidalgo
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.
- Vascular Biology and Therapeutics Program and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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11
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Alexander MR, Dale BL, Smart CD, Elijovich F, Wogsland CE, Lima SM, Irish JM, Madhur MS. Immune Profiling Reveals Decreases in Circulating Regulatory and Exhausted T Cells in Human Hypertension. JACC Basic Transl Sci 2023; 8:319-336. [PMID: 37034287 PMCID: PMC10077123 DOI: 10.1016/j.jacbts.2022.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 01/06/2023]
Abstract
Evidence from nonhuman animal models demonstrates an important role for immune cells in hypertension, but immune cell changes in human hypertension are less clear. Using mass cytometry, we demonstrate novel and selective reductions in CCR10+ regulatory T cells (Tregs) and PD-1+CD57-CD8+ memory T cells. RNA sequencing reveals that CCR10+ Tregs exhibit gene expression changes consistent with enhanced immunosuppressive function. In addition, CITE-Seq demonstrates that PD-1+CD57-CD8+ memory T cells exhibit features of T-cell exhaustion. Taken together, these results provide novel evidence for decreases in anti-inflammatory and/or hypofunctional T-cell populations that may contribute to enhanced inflammation in human hypertension.
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Affiliation(s)
- Matthew R. Alexander
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Bethany L. Dale
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
- Current affiliation: Pirche, Berlin, Germany
| | - Charles D. Smart
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Fernando Elijovich
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cara E. Wogsland
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Current affiliation: KinN Therapeutics, Bergen, Norway
| | - Sierra M. Lima
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jonathan M. Irish
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Meena S. Madhur
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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12
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Rong D, Wang Y, Liu L, Cao H, Huang T, Liu H, Hao X, Sun G, Sun G, Zheng Z, Kang J, Xia Y, Chen Z, Tang W, Wang X. GLIS1 intervention enhances anti-PD1 therapy for hepatocellular carcinoma by targeting SGK1-STAT3-PD1 pathway. J Immunother Cancer 2023; 11:jitc-2022-005126. [PMID: 36787938 PMCID: PMC9930610 DOI: 10.1136/jitc-2022-005126] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND GLI-similar 1 (GLIS1) is one of of Krüppel-like zinc finger proteins, which are either stimulators or inhibitors of genetic transcription. Nevertheless, its effects on T cell were elusive. METHODS In this study, we intend to explore the effects of GLIS1 on modulating the anticancer potency of CD8+ T cells in hepatocellular carcinoma (HCC). The expression of GLIS1 in CD8 peripheral blood mononuclear cell and CD8 tumor-infiltrating lymphocytes of HCC tissues was validated by quantificational real-time-PCR and flow cytometry. The anticancer potency of CD8+ T cells with GLIS1 knock down was confirmed in C57BL/6 mouse model and HCC patient-derived xenograft mice model. GLIS1-/- C57BL/6 mice was applied to explore the effects GLIS1 on tumor immune microenvironment. Chromatin immunoprecipitation and RNA transcriptome sequencing analysis were both performed in GLIS1-knock down of CD8+ T cells. RESULTS GLIS1 was upregulated in exhausted CD8+ T cells in HCC. GLIS1 downregulation in CD8+ T cells repressed cancer development, elevated the infiltrate ability of CD8+ T cells, mitigated CD8+ T cell exhaustion and ameliorated the anti-PD1 reaction of CD8+ T cells in HCC. The causal link beneath this included transcriptional regulation of SGK1-STAT3-PD1 pathway by GLIS1, thereby maintaining the abundant PD1 expression on the surface of CD8+ T cells. CONCLUSION Our study revealed that GLIS1 promoted CD8+ T cell exhaustion in HCC through transcriptional regulating SGK1-STAT3-PD1 pathway. Downregulating the expression of GLIS1 in CD8+ T cells exerted an effect with anti-PD1 treatment synergistically, revealing a prospective method for HCC immune therapy.
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Affiliation(s)
- Dawei Rong
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Yuliang Wang
- School of Basic Medicine, Nanjing Medical University, Nanjing, China
| | - Li Liu
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hengsong Cao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Tian Huang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Hanyuan Liu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Xiaopei Hao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Guangshun Sun
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Guoqiang Sun
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Zhiying Zheng
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Junwei Kang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Yongxiang Xia
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Ziyi Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Weiwei Tang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
| | - Xuehao Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing, China
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13
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De Thoré MG, Meziani L, Deutsch E, Mondini M. Cytofluorometric characterization of the myeloid compartment of irradiated mouse tumors. Methods Cell Biol 2023; 174:17-30. [PMID: 36710048 DOI: 10.1016/bs.mcb.2022.08.004] [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: 12/03/2022]
Abstract
The use of ionizing radiation (IR) is a cornerstone for the treatment of cancer and radiotherapy (RT) is used in roughly 50% of cancer patients. It is now well established that RT exerts widespread effects on the tumor stroma, including the immune environment. Together with its deeply characterized effects on the lymphoid compartment, RT also deeply affects the myeloid cell compartment. Fluorescence-activated flow cytometry is one of the most widely used technologies in immunology, allowing the multiparametric analysis of cells on a cell-by-cell basis. Here, we provide a detailed flow cytometry protocol to analyze the myeloid cell populations of human papillomavirus (HPV)-positive TC1/Luc tumors engrafted in the oral mucosa of immunocompetent mice, and to evaluate their modulations in response to RT. The same method, with slight modifications, can be used to study the tumor myeloid cells from a variety of other mouse tumors.
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Affiliation(s)
| | - Lydia Meziani
- Gustave Roussy, INSERM U1030, Université Paris-Saclay, Villejuif, France
| | - Eric Deutsch
- Gustave Roussy, INSERM U1030, Université Paris-Saclay, Villejuif, France.
| | - Michele Mondini
- Gustave Roussy, INSERM U1030, Université Paris-Saclay, Villejuif, France.
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14
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Barbetta A, Rocque B, Sarode D, Bartlett JA, Emamaullee J. Revisiting transplant immunology through the lens of single-cell technologies. Semin Immunopathol 2023; 45:91-109. [PMID: 35980400 PMCID: PMC9386203 DOI: 10.1007/s00281-022-00958-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
Solid organ transplantation (SOT) is the standard of care for end-stage organ disease. The most frequent complication of SOT involves allograft rejection, which may occur via T cell- and/or antibody-mediated mechanisms. Diagnosis of rejection in the clinical setting requires an invasive biopsy as there are currently no reliable biomarkers to detect rejection episodes. Likewise, it is virtually impossible to identify patients who exhibit operational tolerance and may be candidates for reduced or complete withdrawal of immunosuppression. Emerging single-cell technologies, including cytometry by time-of-flight (CyTOF), imaging mass cytometry, and single-cell RNA sequencing, represent a new opportunity for deep characterization of pathogenic immune populations involved in both allograft rejection and tolerance in clinical samples. These techniques enable examination of both individual cellular phenotypes and cell-to-cell interactions, ultimately providing new insights into the complex pathophysiology of allograft rejection. However, working with these large, highly dimensional datasets requires expertise in advanced data processing and analysis using computational biology techniques. Machine learning algorithms represent an optimal strategy to analyze and create predictive models using these complex datasets and will likely be essential for future clinical application of patient level results based on single-cell data. Herein, we review the existing literature on single-cell techniques in the context of SOT.
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Affiliation(s)
- Arianna Barbetta
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA
- University of Southern California, Los Angeles, CA, USA
| | - Brittany Rocque
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA
- University of Southern California, Los Angeles, CA, USA
| | - Deepika Sarode
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA
- University of Southern California, Los Angeles, CA, USA
| | - Johanna Ascher Bartlett
- Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Juliet Emamaullee
- Department of Surgery, Division of Abdominal Organ Transplant, University of Southern California, 1510 San Pablo St. Suite 412, Los Angeles, CA, 90033, USA.
- University of Southern California, Los Angeles, CA, USA.
- Division of Hepatobiliary and Abdominal Organ Transplantation Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA.
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15
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Rocha-Hasler M, Müller L, Wagner A, Tu A, Stanek V, Campion NJ, Bartosik T, Zghaebi M, Stoshikj S, Gompelmann D, Zech A, Mei H, Kratochwill K, Spittler A, Idzko M, Schneider S, Eckl-Dorna J. Using mass cytometry for the analysis of samples of the human airways. Front Immunol 2022; 13:1004583. [PMID: 36578479 PMCID: PMC9791368 DOI: 10.3389/fimmu.2022.1004583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Mass cytometry (MC) is a powerful method for mapping complex cellular systems at single-cell levels, based on the detection of cellular proteins. Numerous studies have been performed using human blood, but there is a lack of protocols describing the processing and labeling of bronchoalveolar lavage fluid (BALF) and nasal polyps (NP) for acquisition by MC. These specimens are essential in the investigation of immune cell characteristics in airway diseases such as asthma and chronic rhinosinusitis with NP (CRSwNP). Here we optimized a workflow for processing, labeling, and acquisition of BALF and NP cells by MC. Among three methods tested for NP digestion, combined enzymatic/mechanical processing yielded maximum cell recovery, viability and labeling patterns compared to the other methods. Treatment with DNAse improved sample acquisition by MC. In a final step, we performed a comparison of blood, BALF and NP cell composition using a 31-marker MC antibody panel, revealing expected differences between the different tissue but also heterogeneity among the BALF and NP samples. We here introduce an optimized workflow for the MC analysis of human NP and BALF, which enables comparative analysis of different samples in larger cohorts. A deeper understanding of immune cell characteristics in these samples may guide future researchers and clinicians to a better disease management.
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Affiliation(s)
- Marianne Rocha-Hasler
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Lena Müller
- Core Facility Flow Cytometry & Department of Surgery, Research Lab, Medical University of Vienna, Vienna, Austria
| | - Anja Wagner
- Core Facility Proteomics, Medical University of Vienna, Vienna, Austria,Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Aldine Tu
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Victoria Stanek
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Nicholas James Campion
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Tina Bartosik
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Mohammed Zghaebi
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
| | - Slagjana Stoshikj
- Division of Pulmonology, Department of Internal Medicine II, Medical University Vienna, Vienna, Austria
| | - Daniela Gompelmann
- Division of Pulmonology, Department of Internal Medicine II, Medical University Vienna, Vienna, Austria
| | - Andreas Zech
- Division of Pulmonology, Department of Internal Medicine II, Medical University Vienna, Vienna, Austria
| | - Henrik Mei
- German Rheumatism Research Center Berlin, Berlin, Germany
| | - Klaus Kratochwill
- Core Facility Proteomics, Medical University of Vienna, Vienna, Austria,Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Andreas Spittler
- Core Facility Flow Cytometry & Department of Surgery, Research Lab, Medical University of Vienna, Vienna, Austria
| | - Marco Idzko
- Division of Pulmonology, Department of Internal Medicine II, Medical University Vienna, Vienna, Austria
| | - Sven Schneider
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria,*Correspondence: Sven Schneider,
| | - Julia Eckl-Dorna
- Allergology and Sinusitis Research Lab, Department of Otorhinolaryngology, Medical University of Vienna, Vienna, Austria
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16
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Clases D, Gonzalez de Vega R. Facets of ICP-MS and their potential in the medical sciences-Part 2: nanomedicine, immunochemistry, mass cytometry, and bioassays. Anal Bioanal Chem 2022; 414:7363-7386. [PMID: 36042038 PMCID: PMC9427439 DOI: 10.1007/s00216-022-04260-8] [Citation(s) in RCA: 4] [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: 06/11/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022]
Abstract
Inductively coupled-plasma mass spectrometry (ICP-MS) has transformed our knowledge on the role of trace and major elements in biology and has emerged as the most versatile technique in elemental mass spectrometry. The scope of ICP-MS has dramatically changed since its inception, and nowadays, it is a mature platform technology that is compatible with chromatographic and laser ablation (LA) systems. Over the last decades, it kept pace with various technological advances and was inspired by interdisciplinary approaches which endorsed new areas of applications. While the first part of this review was dedicated to fundamentals in ICP-MS, its hyphenated techniques and the application in biomonitoring, isotope ratio analysis, elemental speciation analysis, and elemental bioimaging, this second part will introduce relatively current directions in ICP-MS and their potential to provide novel perspectives in the medical sciences. In this context, current directions for the characterisation of novel nanomaterials which are considered for biomedical applications like drug delivery and imaging platforms will be discussed while considering different facets of ICP-MS including single event analysis and dedicated hyphenated techniques. Subsequently, immunochemistry techniques will be reviewed in their capability to expand the scope of ICP-MS enabling analysis of a large range of biomolecules alongside elements. These methods inspired mass cytometry and imaging mass cytometry and have the potential to transform diagnostics and treatment by offering new paradigms for personalised medicine. Finally, the interlacing of immunochemistry methods, single event analysis, and functional nanomaterials has opened new horizons to design novel bioassays which promise potential as assets for clinical applications and larger screening programs and will be discussed in their capabilities to detect low-level proteins and nucleic acids.
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Affiliation(s)
- David Clases
- Nano Mirco LAB, Institute of Chemistry, University of Graz, Graz, Austria.
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17
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Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Bodenmiller B, Robinson MD. An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res 2022; 9:1263. [PMID: 36072920 PMCID: PMC9411975 DOI: 10.12688/f1000research.26073.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, preprocessing of raw files is commonly performed in independent standalone tools, which makes it difficult to reproduce. Here, we present an R pipeline based on an updated version of CATALYST that covers all preprocessing steps required for downstream mass cytometry analysis in a fully reproducible way. This new version of CATALYST is based on Bioconductor’s SingleCellExperiment class and fully unit tested. The R-based pipeline includes file concatenation, bead-based normalization, single-cell deconvolution, spillover compensation and live cell gating after debris and doublet removal. Importantly, this pipeline also includes different quality checks to assess machine sensitivity and staining performance while allowing also for batch correction. This pipeline is based on open source R packages and can be easily be adapted to different study designs. It therefore has the potential to significantly facilitate the work of CyTOF users while increasing the quality and reproducibility of data generated with this technology.
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Affiliation(s)
- Helena L. Crowell
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D. Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
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18
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Ge P, Liu C, Chan L, Pang Y, Li H, Zhang Q, Ye X, Wang J, Wang R, Zhang Y, Wang W, Zhang D, Zhao J. High-Dimensional Immune Profiling by Mass Cytometry Revealed the Circulating Immune Cell Landscape in Patients With Intracranial Aneurysm. Front Immunol 2022; 13:922000. [PMID: 35833148 PMCID: PMC9271834 DOI: 10.3389/fimmu.2022.922000] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022] Open
Abstract
Background Increasing evidence supports a critical role of chronic inflammation in intracranial aneurysm (IA). Understanding how the immunological alterations in IA provides opportunities for targeted treatment. However, there is a lack of comprehensive and detailed characterization of the changes in circulating immune cells in IA. Objective To perform a comprehensive and detailed characterization of the changes in circulating immune cells in patients with IA. Methods Peripheral blood mononuclear cell samples from IA patients (n = 26) and age-and sex-matched healthy controls (HCs, n = 20) were analyzed using high dimensional mass cytometry, and the frequency and phenotype of immune cell subtypes were assessed. Results We identified 28 cell clusters and found that the immune signature of IA consists of cluster changes. IA patients exhibited dysfunction of immunity, with dysregulation of CD4+ T-cell clusters, increased B cells and monocytes, and decreased CD8+ T cells, DNT cells, and DPT cells. Moreover, compared with findings in HC, IA was associated with enhanced lymphocyte and monocyte immune activation, with a higher expression of HLA-DR, CXCR3, and CX3CR1. In addition, the expression of TLR4, p-STAT3, and the exhaustion marker PD1 was increased in T cells, B cells, and NK cells in IA patients. Conclusions Our data provide an overview of the circulating immune cell landscape of IA patients, and reveal that the dysfunction of circulating immunity may play a potential role in the development of IA.
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Affiliation(s)
- Peicong Ge
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Chenglong Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Liujia Chan
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Yuheng Pang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Hao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Qian Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Xun Ye
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Jia Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Rong Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Yan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China
- *Correspondence: Wenjing Wang, ; Dong Zhang, ; Jizong Zhao,
| | - Dong Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
- Department of Neurosurgery, Beijing Hospital, Beijing, China
- *Correspondence: Wenjing Wang, ; Dong Zhang, ; Jizong Zhao,
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Wenjing Wang, ; Dong Zhang, ; Jizong Zhao,
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19
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Xiao F, Farag MA, Xiao J, Yang X, Liu Y, Shen J, Lu B. The influence of phytochemicals on cell heterogeneity in chronic inflammation-associated diseases: the prospects of single cell sequencing. J Nutr Biochem 2022; 108:109091. [PMID: 35718097 DOI: 10.1016/j.jnutbio.2022.109091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/25/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
Chronic inflammation-associated diseases include, but is not limited to cardiovascular disease, cancer, obesity, diabetes, etc. Cell heterogeneity is a prerequisite for understanding the physiological and pathological development of cell metabolism, and its response to external stimuli. Recently, dietary habits based on phytochemicals became increasingly recognized to play a pivotal role in chronic inflammation. Phytochemicals can relieve chronic inflammation by regulating inflammatory cell differentiation and immune cell response, but the influence of phytochemicals on cell heterogeneity from in vitro and ex vivo studies cannot simulate the complexity of cell differentiation in vivo due to the differences in cell lines and extracellular environment. Therefore, there is no consensus on the regulation mechanism of phytochemicals on chronic diseases based on cell heterogeneity. The purpose of this review is to summarize cell heterogeneity in common chronic inflammation-associated diseases and trace the effects of phytochemicals on cell differentiation in chronic diseases development. More importantly, by discussing the problems and challenges which hinder the study of cell heterogeneity in recent nutritional assessment experiments, we propose new prospects based on the drawbacks of existing research to optimize the research on the regulation mechanism of phytochemicals on chronic diseases. The need to explore precise measurements of cell heterogeneity is a key pillar in understanding the influence of phytochemicals on certain diseases. In the future, deeper understanding of cell-to-cell variation and the impact of food components and their metabolites on cell function by single-cell genomics and epigenomics with the focus on individual differences will open new avenues for the next generation of health care.
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Affiliation(s)
- Fan Xiao
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini st., P.B. 11562, Cairo, Egypt; Department of Chemistry, School of Sciences & Engineering, American University in Cairo, New Cairo 11835, Egypt
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, E-32004 Ourense, Spain
| | - Xuan Yang
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Yan Liu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Jianfu Shen
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Baiyi Lu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou, China; Ningbo Research Institute, Zhejiang University, Ningbo, China.
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20
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Novel Techniques and Future Perspective for Investigating Critical-Size Bone Defects. Bioengineering (Basel) 2022; 9:bioengineering9040171. [PMID: 35447731 PMCID: PMC9027954 DOI: 10.3390/bioengineering9040171] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/31/2023] Open
Abstract
A critical-size bone defect is a challenging clinical problem in which a gap between bone ends will not heal and will become a nonunion. The current treatment is to harvest and transplant an autologous bone graft to facilitate bone bridging. To develop less invasive but equally effective treatment options, one needs to first have a comprehensive understanding of the bone healing process. Therefore, it is imperative to leverage the most advanced technologies to elucidate the fundamental concepts of the bone healing process and develop innovative therapeutic strategies to bridge the nonunion gap. In this review, we first discuss the current animal models to study critical-size bone defects. Then, we focus on four novel analytic techniques and discuss their strengths and limitations. These four technologies are mass cytometry (CyTOF) for enhanced cellular analysis, imaging mass cytometry (IMC) for enhanced tissue special imaging, single-cell RNA sequencing (scRNA-seq) for detailed transcriptome analysis, and Luminex assays for comprehensive protein secretome analysis. With this new understanding of the healing of critical-size bone defects, novel methods of diagnosis and treatment will emerge.
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21
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Ung N, Goldbeck C, Man C, Hoeflich J, Sun R, Barbetta A, Matasci N, Katz J, Lee JSH, Chopra S, Asgharzadeh S, Warren M, Sher L, Kohli R, Akbari O, Genyk Y, Emamaullee J. Adaptation of Imaging Mass Cytometry to Explore the Single Cell Alloimmune Landscape of Liver Transplant Rejection. Front Immunol 2022; 13:831103. [PMID: 35432320 PMCID: PMC9009043 DOI: 10.3389/fimmu.2022.831103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022] Open
Abstract
Rejection continues to be an important cause of graft loss in solid organ transplantation, but deep exploration of intragraft alloimmunity has been limited by the scarcity of clinical biopsy specimens. Emerging single cell immunoprofiling technologies have shown promise in discerning mechanisms of autoimmunity and cancer immunobiology. Within these applications, Imaging Mass Cytometry (IMC) has been shown to enable highly multiplexed, single cell analysis of immune phenotypes within fixed tissue specimens. In this study, an IMC panel of 10 validated markers was developed to explore the feasibility of IMC in characterizing the immune landscape of chronic rejection (CR) in clinical tissue samples obtained from liver transplant recipients. IMC staining was highly specific and comparable to traditional immunohistochemistry. A single cell segmentation analysis pipeline was developed that enabled detailed visualization and quantification of 109,245 discrete cells, including 30,646 immune cells. Dimensionality reduction identified 11 unique immune subpopulations in CR specimens. Most immune subpopulations were increased and spatially related in CR, including two populations of CD45+/CD3+/CD8+ cytotoxic T-cells and a discrete CD68+ macrophage population, which were not observed in liver with no rejection (NR). Modeling via principal component analysis and logistic regression revealed that single cell data can be utilized to construct statistical models with high consistency (Wilcoxon Rank Sum test, p=0.000036). This study highlights the power of IMC to investigate the alloimmune microenvironment at a single cell resolution during clinical rejection episodes. Further validation of IMC has the potential to detect new biomarkers, identify therapeutic targets, and generate patient-specific predictive models of clinical outcomes in solid organ transplantation.
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Affiliation(s)
- Nolan Ung
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States
| | - Cameron Goldbeck
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Cassandra Man
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Julianne Hoeflich
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ren Sun
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States
| | - Arianna Barbetta
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Naim Matasci
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jonathan Katz
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jerry S. H. Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Chemical Engineering and Material Sciences, University of Southern California, Los Angeles, CA, United States
| | - Shefali Chopra
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pathology, University of Southern California, Los Angeles, CA, United States
| | - Shahab Asgharzadeh
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pediatrics, Children’s Hospital-Los Angeles, Los Angeles, CA, United States
| | - Mika Warren
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pathology, Children’s Hospital-Los Angeles, Los Angeles, CA, United States
| | - Linda Sher
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Rohit Kohli
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pediatrics, Children’s Hospital-Los Angeles, Los Angeles, CA, United States
| | - Omid Akbari
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA, United States
| | - Yuri Genyk
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Juliet Emamaullee
- Division of Hepatobiliary and Abdominal Organ Transplant Surgery, Department of Surgery, University of Southern California, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Juliet Emamaullee,
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22
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Determining clinically relevant features in cytometry data using persistent homology. PLoS Comput Biol 2022; 18:e1009931. [PMID: 35312683 PMCID: PMC9009779 DOI: 10.1371/journal.pcbi.1009931] [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: 07/19/2021] [Revised: 04/14/2022] [Accepted: 02/16/2022] [Indexed: 11/19/2022] Open
Abstract
Cytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of cellular subsets is the current standard for cytometry data analysis. However, this approach is unable to capture more subtle topological features hidden in data, especially if those features are further masked by data transforms or significant batch effects or donor-to-donor variations in clinical data. We present that persistent homology, a mathematical structure that summarizes the topological features, can distinguish different sources of data, such as from groups of healthy donors or patients, effectively. Analysis of publicly available cytometry data describing non-naïve CD8+ T cells in COVID-19 patients and healthy controls shows that systematic structural differences exist between single cell protein expressions in COVID-19 patients and healthy controls. We identify proteins of interest by a decision-tree based classifier, sample points randomly and compute persistence diagrams from these sampled points. The resulting persistence diagrams identify regions in cytometry datasets of varying density and identify protruded structures such as ‘elbows’. We compute Wasserstein distances between these persistence diagrams for random pairs of healthy controls and COVID-19 patients and find that systematic structural differences exist between COVID-19 patients and healthy controls in the expression data for T-bet, Eomes, and Ki-67. Further analysis shows that expression of T-bet and Eomes are significantly downregulated in COVID-19 patient non-naïve CD8+ T cells compared to healthy controls. This counter-intuitive finding may indicate that canonical effector CD8+ T cells are less prevalent in COVID-19 patients than healthy controls. This method is applicable to any cytometry dataset for discovering novel insights through topological data analysis which may be difficult to ascertain otherwise with a standard gating strategy or existing bioinformatic tools. Identifying differences between cytometry data seen as a point cloud can be complicated by random variations in data collection and data sources. We apply persistent homology used in topological data analysis to describe the shape and structure of the data representing immune cells in healthy donors and COVID-19 patients. By looking at how the shape and structure differ between healthy donors and COVID-19 patients, we are able to definitively conclude how these groups differ despite random variations in the data. Furthermore, these results are novel in their ability to capture shape and structure of cytometry data, something not described by other analyses.
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23
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Qin Y, Gao C, Luo J. Metabolism Characteristics of Th17 and Regulatory T Cells in Autoimmune Diseases. Front Immunol 2022; 13:828191. [PMID: 35281063 PMCID: PMC8913504 DOI: 10.3389/fimmu.2022.828191] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
The abnormal number and functional deficiency of immune cells are the pathological basis of various diseases. Recent years, the imbalance of Th17/regulatory T (Treg) cell underlies the occurrence and development of inflammation in autoimmune diseases (AID). Currently, studies have shown that material and energy metabolism is essential for maintaining cell survival and normal functions and the altered metabolic state of immune cells exists in a variety of AID. This review summarizes the biology and functions of Th17 and Treg cells in AID, with emphasis on the advances of the roles and regulatory mechanisms of energy metabolism in activation, differentiation and physiological function of Th17 and Treg cells, which will facilitate to provide targets for the treatment of immune-mediated diseases.
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Affiliation(s)
- Yan Qin
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Jing Luo
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Jing Luo,
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24
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Docampo MJ, Lutterotti A, Sospedra M, Martin R. Mechanistic and Biomarker Studies to Demonstrate Immune Tolerance in Multiple Sclerosis. Front Immunol 2022; 12:787498. [PMID: 35069562 PMCID: PMC8766750 DOI: 10.3389/fimmu.2021.787498] [Citation(s) in RCA: 4] [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: 09/30/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
The induction of specific immunological tolerance represents an important therapeutic goal for multiple sclerosis and other autoimmune diseases. Sound knowledge of the target antigens, the underlying pathomechanisms of the disease and the presumed mechanisms of action of the respective tolerance-inducing approach are essential for successful translation. Furthermore, suitable tools and assays to evaluate the induction of immune tolerance are key aspects for the development of such treatments. However, investigation of the mechanisms of action underlying tolerance induction poses several challenges. The optimization of sensitive, robust methods which allow the assessment of low frequency autoreactive T cells and the long-term reduction or change of their responses, the detection of regulatory cell populations and their immune mediators, as well as the validation of specific biomarkers indicating reduction of inflammation and damage, are needed to develop tolerance-inducing approaches successfully to patients. This short review focuses on how to demonstrate mechanistic proof-of-concept in antigen-specific tolerance-inducing therapies in MS.
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Affiliation(s)
| | | | | | - Roland Martin
- Neuroimmunology and Multiple Sclerosis Research Section, Neurology Clinic, University Hospital Zurich & University of Zurich, Zurich, Switzerland
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25
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An Immune Atlas of Nephrolithiasis: Single-Cell Mass Cytometry on SIRT3 Knockout and Calcium Oxalate-Induced Renal Injury. J Immunol Res 2021; 2021:1260140. [PMID: 34849375 PMCID: PMC8627562 DOI: 10.1155/2021/1260140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/25/2021] [Accepted: 10/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background As a common urological disease with a high recurrence rate, nephrolithiasis caused by CaOx may elicit a strong immunologic response. We present a CyTOF-based atlas of the immune landscape in nephrolithiasis models to understand how the immune system contributes to, and is affected by, the underlying response caused by SIRT3 knockout and CaOx inducement. Materials and Methods We performed a large-scale CyTOF analysis of immune cell abundance profiles in nephrolithiasis. The immunophenotyping data were collected from four different mouse models, including the SIRT3 wild-type or knockout, including and excluding CaOx inducement. Unsupervised analysis strategies, such as SPADE and viSNE, revealed the intrarenal resident immune components and the immune alterations caused by SIRT3 knockout and CaOx-induced renal injury. Results An overview analysis of the immune landscape identified T cells and macrophages as the main immune cell population in nephrolithiasis models. Highly similar phenotypes were observed among CD4+ and CD8+ T cell subsets, including cells expressing Ki67, Ly6C, Siglec-F, and TCRβ. Macrophages expressed a characteristic panel of markers with varied expression levels including MHC II, SIRPα, CD11c, Siglec-F, F4/80, CD64, and CD11b, indicating more subtle differences in marker expression than T cells. The SIRT3KO/CaOx and SIRT3WT/CaOx groups exhibited global differences in the intrarenal immune landscape, whereas only small differences existed between the SIRT3KO/CaOx and SIRT3KO/Ctrl groups. Among the major immune lineages, the response of CD4+ T cells, NK cells, monocytes, and M1 to CaOx inducement was regulated by SIRT3 expression in contrast to the expression changes of B cells, DCs, and granulocytes caused by CaOx inducement. The panel of immune markers influenced by CaOx inducement significantly varied with and without SIRT3 knockout. Conclusion In a CaOx-induced nephrolithiasis model, SIRT3 has a critical role in regulating the immune system, especially in reducing inflammatory injury. The characteristic panel of altered immune clusters and markers provides novel insights leading to improved prediction and management of nephrolithiasis.
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26
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Special Focus Issue - Performing flow cytometry in clinical trials. Bioanalysis 2021; 13:1585-1586. [PMID: 34747189 DOI: 10.4155/bio-2021-0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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Li X, Yang Y, Huang Q, Deng Y, Guo F, Wang G, Liu M. Crosstalk Between the Tumor Microenvironment and Cancer Cells: A Promising Predictive Biomarker for Immune Checkpoint Inhibitors. Front Cell Dev Biol 2021; 9:738373. [PMID: 34692696 PMCID: PMC8529050 DOI: 10.3389/fcell.2021.738373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) have changed the landscape of cancer treatment and are emerging as promising curative treatments in different type of cancers. However, only a small proportion of patients have benefited from ICIs and there is an urgent need to find robust biomarkers for individualized immunotherapy and to explore the causes of immunotherapy resistance. In this article, we review the roles of immune cells in the tumor microenvironment (TME) and discuss the effects of ICIs on these cell populations. We discuss the potential of the functional interaction between the TME and cancer cells as a predictive biomarker for ICIs. Furthermore, we outline the potential personalized strategies to improve the effectiveness of ICIs with precision.
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Affiliation(s)
- Xiaoying Li
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yueyao Yang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, China
| | - Qian Huang
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Deng
- School of Basic Medical Science, Chengdu University, Chengdu, China
| | - Fukun Guo
- Division of Experimental Hematology and Cancer Biology, Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Gang Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, China
| | - Ming Liu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
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28
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Cannarile MA, Gomes B, Canamero M, Reis B, Byrd A, Charo J, Yadav M, Karanikas V. Biomarker Technologies to Support Early Clinical Immuno-oncology Development: Advances and Interpretation. Clin Cancer Res 2021; 27:4147-4159. [PMID: 33766813 DOI: 10.1158/1078-0432.ccr-20-2345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022]
Abstract
Today, there is a huge effort to develop cancer immunotherapeutics capable of combating cancer cells as well as the biological environment in which they can grow, adapt, and survive. For such treatments to benefit more patients, there is a great need to dissect the complex interplays between tumor cells and the host's immune system. Monitoring mechanisms of resistance to immunotherapeutics can delineate the evolution of key players capable of driving an efficacious antitumor immune response. In doing so, simultaneous and systematic interrogation of multiple biomarkers beyond single biomarker approaches needs to be undertaken. Zooming into cell-to-cell interactions using technological advancements with unprecedented cellular resolution such as single-cell spatial transcriptomics, advanced tissue histology approaches, and new molecular immune profiling tools promises to provide a unique level of molecular granularity of the tumor environment and may support better decision-making during drug development. This review will focus on how such technological tools are applied in clinical settings, to inform the underlying tumor-immune biology of patients and offer a deeper understanding of cancer immune responsiveness to immuno-oncology treatments.
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Affiliation(s)
- Michael A Cannarile
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bruno Gomes
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | - Marta Canamero
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bernhard Reis
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Jehad Charo
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland
| | | | - Vaios Karanikas
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland.
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29
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Benedé S, Lozano-Ojalvo D, Cristobal S, Costa J, D'Auria E, Velickovic TC, Garrido-Arandia M, Karakaya S, Mafra I, Mazzucchelli G, Picariello G, Romero-Sahagun A, Villa C, Roncada P, Molina E. New applications of advanced instrumental techniques for the characterization of food allergenic proteins. Crit Rev Food Sci Nutr 2021; 62:8686-8702. [PMID: 34060381 DOI: 10.1080/10408398.2021.1931806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Current approaches based on electrophoretic, chromatographic or immunochemical principles have allowed characterizing multiple allergens, mapping their epitopes, studying their mechanisms of action, developing detection and diagnostic methods and therapeutic strategies for the food and pharmaceutical industry. However, some of the common structural features related to the allergenic potential of food proteins remain unknown, or the pathological mechanism of food allergy is not yet fully understood. In addition, it is also necessary to evaluate new allergens from novel protein sources that may pose a new risk for consumers. Technological development has allowed the expansion of advanced technologies for which their whole potential has not been entirely exploited and could provide novel contributions to still unexplored molecular traits underlying both the structure of food allergens and the mechanisms through which they sensitize or elicit adverse responses in human subjects, as well as improving analytical techniques for their detection. This review presents cutting-edge instrumental techniques recently applied when studying structural and functional aspects of proteins, mechanism of action and interaction between biomolecules. We also exemplify their role in the food allergy research and discuss their new possible applications in several areas of the food allergy field.
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Affiliation(s)
- Sara Benedé
- Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
| | - Daniel Lozano-Ojalvo
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, Jaffe Food Allergy Institute, New York, NY, USA
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Faculty of Medicine, Linköping University, Linköping, Sweden.,IKERBASQUE, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Enza D'Auria
- Clinica Pediatrica, Ospedale dei Bambini Vittore Buzzi, Università degli Studi, Milano, Italy
| | - Tanja Cirkovic Velickovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia.,Ghent University Global Campus, Incheon, South Korea.,Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Sibel Karakaya
- Department of Food Engineering, Ege University, Izmir, Turkey
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege, Belgium
| | - Gianluca Picariello
- Institute of Food Sciences, National Research Council (CNR), Avellino, Italy
| | - Alejandro Romero-Sahagun
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paola Roncada
- Department of Health Sciences, University Magna Graecia, Catanzaro, Italy
| | - Elena Molina
- Instituto de Investigación en Ciencias de la Alimentación (CIAL, CSIC-UAM), Madrid, Spain
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30
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Rouers A, Chng MHY, Lee B, Rajapakse MP, Kaur K, Toh YX, Sathiakumar D, Loy T, Thein TL, Lim VW, Singhal A, Yeo TW, Leo YS, Vora KA, Casimiro D, Lim B, Tucker-Kellogg L, Rivino L, Newell EW, Fink K. Immune cell phenotypes associated with disease severity and long-term neutralizing antibody titers after natural dengue virus infection. CELL REPORTS MEDICINE 2021; 2:100278. [PMID: 34095880 PMCID: PMC8149372 DOI: 10.1016/j.xcrm.2021.100278] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/08/2021] [Accepted: 04/21/2021] [Indexed: 12/20/2022]
Abstract
Prior immunological exposure to dengue virus can be both protective and disease-enhancing during subsequent infections with different dengue virus serotypes. We provide here a systematic, longitudinal analysis of B cell, T cell, and antibody responses in the same patients. Antibody responses as well as T and B cell activation differentiate primary from secondary responses. Hospitalization is associated with lower frequencies of activated, terminally differentiated T cells and higher percentages of effector memory CD4 T cells. Patients with more severe disease tend to have higher percentages of plasmablasts. This does not translate into long-term antibody titers, since neutralizing titers after 6 months correlate with percentages of specific memory B cells, but not with acute plasmablast activation. Overall, our unbiased analysis reveals associations between cellular profiles and disease severity, opening opportunities to study immunopathology in dengue disease and the potential predictive value of these parameters.
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Affiliation(s)
- Angeline Rouers
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- A∗STAR ID Labs, Agency for Science, Technology and Research, Singapore 138468, Singapore
| | - Melissa Hui Yen Chng
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Menaka P. Rajapakse
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Kaval Kaur
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Ying Xiu Toh
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Durgalakshmi Sathiakumar
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Thomas Loy
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- A∗STAR ID Labs, Agency for Science, Technology and Research, Singapore 138468, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tun-Linn Thein
- National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Vanessa W.X. Lim
- National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Amit Singhal
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- A∗STAR ID Labs, Agency for Science, Technology and Research, Singapore 138468, Singapore
- Lee Kong Chian School of Medicine, Singapore 308232, Singapore
| | - Tsin Wen Yeo
- Lee Kong Chian School of Medicine, Singapore 308232, Singapore
- Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore 308442, Singapore
- Lee Kong Chian School of Medicine, Singapore 308232, Singapore
- Tan Tock Seng Hospital, Singapore 308433, Singapore
- Yong Loo Lin School of Medicine, Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, Singapore 117549, Singapore
| | - Kalpit A. Vora
- Department of Infectious Diseases and Vaccines Research, Merck, Kenilworth, NJ, USA
| | - Danilo Casimiro
- Department of Infectious Diseases and Vaccines Research, Merck, Kenilworth, NJ, USA
| | - Bing Lim
- Merck Sharp & Dohme Translational Medicine Research Centre, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Lisa Tucker-Kellogg
- Cancer and Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Laura Rivino
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Evan W. Newell
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
- Corresponding author
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31
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Mukherjee S, Wethington D, Dey TK, Das J. Determining clinically relevant features in cytometry data using persistent homology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33948593 DOI: 10.1101/2021.04.26.441473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of cellular subsets is the current standard for cytometry data analysis. However, this approach is unable to capture more subtle topological features hidden in data, especially if those features are further masked by data transforms or significant batch effects or donor-to-donor variations in clinical data. We present that persistent homology, a mathematical structure that summarizes the topological features, can distinguish different sources of data, such as from groups of healthy donors or patients, effectively. Analysis of publicly available cytometry data describing non-naïve CD8+ T cells in COVID-19 patients and healthy controls shows that systematic structural differences exist between single cell protein expressions in COVID-19 patients and healthy controls. Our method identifies proteins of interest by a decision-tree based classifier and passes them to a kernel-density estimator (KDE) for sampling points from the density distribution. We then compute persistence diagrams from these sampled points. The resulting persistence diagrams identify regions in cytometry datasets of varying density and identify protruded structures such as 'elbows'. We compute Wasserstein distances between these persistence diagrams for random pairs of healthy controls and COVID-19 patients and find that systematic structural differences exist between COVID-19 patients and healthy controls in the expression data for T-bet, Eomes, and Ki-67. Further analysis shows that expression of T-bet and Eomes are significantly downregulated in COVID-19 patient non-naïve CD8+ T cells compared to healthy controls. This counter-intuitive finding may indicate that canonical effector CD8+ T cells are less prevalent in COVID-19 patients than healthy controls. This method is applicable to any cytometry dataset for discovering novel insights through topological data analysis which may be difficult to ascertain otherwise with a standard gating strategy or in the presence of large batch effects. Author summary Identifying differences between cytometry data seen as a point cloud can be complicated by random variations in data collection and data sources. We apply persistent homology used in topological data analysis to describe the shape and structure of the data representing immune cells in healthy donors and COVID-19 patients. By looking at how the shape and structure differ between healthy donors and COVID-19 patients, we are able to definitively conclude how these groups differ despite random variations in the data. Furthermore, these results are novel in their ability to capture shape and structure of cytometry data, something not described by other analyses.
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Fu W, Wang W, Li H, Jiao Y, Weng J, Huo R, Yan Z, Wang J, Xu H, Wang S, Wang J, Chen D, Cao Y, Zhao J. CyTOF Analysis Reveals a Distinct Immunosuppressive Microenvironment in IDH Mutant Anaplastic Gliomas. Front Oncol 2021; 10:560211. [PMID: 33614475 PMCID: PMC7890006 DOI: 10.3389/fonc.2020.560211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
The immune microenvironment is important for the development, progression, and prognosis of anaplastic glioma (AG). This complex milieu has not been fully elucidated, and a high-dimensional analysis is urgently required. Utilizing mass cytometry (CyTOF), we performed an analysis of immune cells from 5 patients with anaplastic astrocytoma, IDH-mutant (AAmut) and 10 patients with anaplastic oligodendroglioma, IDH-mutant and 1p/19q codeletion (AOD) and their paired peripheral blood mononuclear cells (PBMCs). Based on a panel of 33 biomarkers, we demonstrated the tumor-driven immune changes in the AG immune microenvironment. Our study confirmed that mononuclear phagocytes and T cells are the most abundant immunocytes in the AG immune microenvironment. Glioma-associated microglia/macrophages in both AAmut and AOD samples showed highly immunosuppressive characteristics. Compared to those in the PBMCs, the ratios of immune checkpoint-positive exhausted CD4+ T cells and CD8+ T cells were higher at the AG tumor sites. The AAmut immune milieu exhibits more immunosuppressive characteristics than that in AOD.
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Affiliation(s)
- Weilun Fu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China.,Organ Transplantation Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yuming Jiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiancong Weng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Ran Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zihan Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jie Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Hongyuan Xu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Shuo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiangfei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Dexi Chen
- Beijing Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China.,Organ Transplantation Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
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Di Zeo-Sánchez DE, Sánchez-Núñez P, Stephens C, Lucena MI. Characterizing Highly Cited Papers in Mass Cytometry through H-Classics. BIOLOGY 2021; 10:biology10020104. [PMID: 33540586 PMCID: PMC7912900 DOI: 10.3390/biology10020104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/22/2022]
Abstract
Mass cytometry (CyTOF) is a relatively novel technique for the multiparametric analysis of single-cell features with an increasing central role in cell biology, immunology, pharmacology, and biomedicine. This technique mixes the fundamentals of flow cytometry with mass spectrometry and is mainly used for in-depth studies of the immune system and diseases with a significant immune load, such as cancer, autoimmune diseases, and viral diseases like HIV or the recently emerged COVID-19, produced by the SARS-CoV-2 coronavirus. The objective of this study was to provide a useful insight into the evolution of the mass cytometry research field, revealing the knowledge structure (conceptual and social) and authors, countries, sources, documents, and organizations that have made the most significant contribution to its development. We retrieved 937 articles from the Web of Science (2010-2019), analysed 71 Highly Cited Papers (HCP) through the H-Classics methodology and computed the data by using Bibliometrix R package. HCP sources corresponded to high-impact journals, such as Nature Biotechnology and Cell, and its production was concentrated in the US, and specifically Stanford University, affiliation of the most relevant authors in the field. HCPs analysis confirmed great interest in the study of the immune system and complex data processing in the mass cytometry research field.
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Affiliation(s)
- Daniel E. Di Zeo-Sánchez
- Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Facultad de Medicina, Universidad de Málaga, 29010 Malaga, Spain; (C.S.); (M.I.L.)
- Correspondence:
| | - Pablo Sánchez-Núñez
- Departamento de Comunicación Audiovisual y Publicidad, Facultad de Ciencias de la Comunicación, Universidad de Málaga, 29010 Malaga, Spain;
- Centro de Investigación Social Aplicada (CISA), Edificio de Investigación Ada Byron, Universidad de Málaga, 29010 Malaga, Spain
| | - Camilla Stephens
- Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Facultad de Medicina, Universidad de Málaga, 29010 Malaga, Spain; (C.S.); (M.I.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - M. Isabel Lucena
- Servicio de Farmacología Clínica, Hospital Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Facultad de Medicina, Universidad de Málaga, 29010 Malaga, Spain; (C.S.); (M.I.L.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- UICEC IBIMA, Plataforma ISCiii de Investigación Clínica, 28020 Madrid, Spain
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34
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Delgado-Gonzalez A, Sanchez-Martin RM. Mass Cytometry Tags: Where Chemistry Meets Single-Cell Analysis. Anal Chem 2021; 93:657-664. [PMID: 33320535 DOI: 10.1021/acs.analchem.0c03560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass cytometry is a highly multiparametric proteomic technology that allows the measurement and quantification of nearly 50 markers with single-cell resolution. Mass cytometry reagents are probes tagged with metal isotopes of defined mass and act as reporters. Metals are detected using inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS). Many different types of mass-tag reagents have been developed to afford myriad applications. We have classified these compounds into polymer-based mass-tag reagents, nonpolymer-based mass-tag reagents, and inorganic nanoparticles. Metal-chelating polymers (MCPs) are widely used to profile and quantify cellular biomarkers; however, both the range of metals that can be detected and the metal signals have to be improved. Several strategies such as the inclusion of chelating agents or highly branched polymers may overcome these issues. Biocompatible materials such as polystyrene and inorganic nanoparticles are also of profound interest in mass cytometry. While polystyrene allows the inclusion of a wide variety of metals, the high metal content of inorganic nanoparticles offers an excellent opportunity to increase the signal from the metals to detect low-abundance biomarkers. Nonpolymer-based mass-tag reagents offer multiple applications: cell detection, cell cycle property determination, biomarker detection, and mass-tag cellular barcoding (MCB). Recent developments have been achieved in live cell barcoding by targeting proteins (CD45, b2m, and CD298), by using small and nonpolar probes or by ratiometric barcoding. From this perspective, the principal applications, strengths, and shortcomings of mass-tag reagents are highlighted, summarized, and discussed, with special emphasis on mass-tag reagents for MCB. Thereafter, the future perspectives of mass-tag reagents are discussed considering the current state-of-the-art technologies.
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Affiliation(s)
- Antonio Delgado-Gonzalez
- Department of Medicinal and Organic Chemistry, Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment", Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain.,GENYO, Pfizer-University of Granada-Junta de Andalucia Centre for Genomics and Oncological Research, P.T. Ciencias de la Salud 114, 18016 Granada, Spain
| | - Rosario M Sanchez-Martin
- Department of Medicinal and Organic Chemistry, Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment", Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain.,GENYO, Pfizer-University of Granada-Junta de Andalucia Centre for Genomics and Oncological Research, P.T. Ciencias de la Salud 114, 18016 Granada, Spain
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35
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Potentiality of multiple modalities for single-cell analyses to evaluate the tumor microenvironment in clinical specimens. Sci Rep 2021; 11:341. [PMID: 33431933 PMCID: PMC7801605 DOI: 10.1038/s41598-020-79385-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022] Open
Abstract
Single-cell level analysis is powerful tool to assess the heterogeneity of cellular components in tumor microenvironments (TME). In this study, we investigated immune-profiles using the single-cell analyses of endoscopically- or surgically-resected tumors, and peripheral blood mononuclear cells from gastric cancer patients. Furthermore, we technically characterized two distinct platforms of the single-cell analysis; RNA-seq-based analysis (scRNA-seq), and mass cytometry-based analysis (CyTOF), both of which are broadly embraced technologies. Our study revealed that the scRNA-seq analysis could cover a broader range of immune cells of TME in the biopsy-resected small samples of tumors, detecting even small subgroups of B cells or Treg cells in the tumors, although CyTOF could distinguish the specific populations in more depth. These findings demonstrate that scRNA-seq analysis is a highly-feasible platform for elucidating the complexity of TME in small biopsy tumors, which would provide a novel strategies to overcome a therapeutic difficulties against cancer heterogeneity in TME.
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36
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Hu-Lieskovan S, Bhaumik S, Dhodapkar K, Grivel JCJB, Gupta S, Hanks BA, Janetzki S, Kleen TO, Koguchi Y, Lund AW, Maccalli C, Mahnke YD, Novosiadly RD, Selvan SR, Sims T, Zhao Y, Maecker HT. SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. J Immunother Cancer 2020; 8:e000705. [PMID: 33268350 PMCID: PMC7713206 DOI: 10.1136/jitc-2020-000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Since the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients.
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Affiliation(s)
- Siwen Hu-Lieskovan
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kavita Dhodapkar
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | | | - Sumati Gupta
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Brent A Hanks
- Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Yoshinobu Koguchi
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Amanda W Lund
- Oregon Health and Science University, Portland, Oregon, USA
| | | | | | | | | | - Tasha Sims
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
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37
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Belanger MC, Anbaei P, Dunn AF, Kinman AW, Pompano RR. Spatially Resolved Analytical Chemistry in Intact, Living Tissues. Anal Chem 2020; 92:15255-15262. [PMID: 33201681 PMCID: PMC7864589 DOI: 10.1021/acs.analchem.0c03625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tissues are an exciting frontier for bioanalytical chemistry, one in which spatial distribution is just as important as total content. Intact tissue preserves the native cellular and molecular organization and the cell-cell contacts found in vivo. Live tissue, in particular, offers the potential to analyze dynamic events in a spatially resolved manner, leading to fundamental biological insights and translational discoveries. In this Perspective, we provide a tutorial on the four fundamental challenges for the bioanalytical chemist working in living tissue samples as well as best practices for mitigating them. The challenges include (i) the complexity of the sample matrix, which contributes myriad interfering species and causes nonspecific binding of reagents; (ii) hindered delivery and mixing; (iii) the need to maintain physiological conditions; and (iv) tissue reactivity. This framework is relevant to a variety of methods for spatially resolved chemical analysis, including optical imaging, inserted sensors and probes such as electrodes, and surface analyses such as sensing arrays. The discussion focuses primarily on ex vivo tissues, though many considerations are relevant in vivo as well. Our goal is to convey the exciting potential of analytical chemistry to contribute to understanding the functions of live, intact tissues.
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Affiliation(s)
- Maura C. Belanger
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Parastoo Anbaei
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Austin F. Dunn
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Andrew W.L. Kinman
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
| | - Rebecca R. Pompano
- Department of Chemistry, University of Virginia, PO BOX 400319, Charlottesville, VA 22904
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38
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Humrich JY, Bernardes JP, Ludwig RJ, Klatzmann D, Scheffold A. Phenotyping of Adaptive Immune Responses in Inflammatory Diseases. Front Immunol 2020; 11:604464. [PMID: 33324421 PMCID: PMC7723922 DOI: 10.3389/fimmu.2020.604464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Immunophenotyping on the molecular and cellular level is a central aspect for characterization of patients with inflammatory diseases, both to better understand disease etiopathogenesis and based on this to develop diagnostic and prognostic biomarkers which allow patient stratification and tailor-made treatment strategies. Technology-driven developments have considerably expanded the range of analysis tools. Especially the analysis of adaptive immune responses, often regarded as central though mostly poorly characterized disease drivers, is a major focus of personalized medicine. The identification of the disease-relevant antigens and characterization of corresponding antigen-specific lymphocytes in individual patients benefits significantly from recent developments in cytometry by sequencing and proteomics. The aim of this workshop was to identify the important developments for state-of-the-art immunophenotyping for clinical application and precision medicine. We focused here on recent key developments in analysis of antigen-specific lymphocytes, sequencing, and proteomics approaches, their relevance in precision medicine and the discussion of the major challenges and opportunities for the future.
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Affiliation(s)
- Jens Y. Humrich
- Department of Rheumatology and Clinical Immunology, University Hospital Schleswig-Holstein—Campus Lübeck, Lübeck, Germany
| | - Joana P. Bernardes
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ralf J. Ludwig
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, Lübeck, Germany
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
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39
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Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Bodenmiller B, Robinson MD. An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res 2020; 9:1263. [PMID: 36072920 PMCID: PMC9411975 DOI: 10.12688/f1000research.26073.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2022] [Indexed: 07/20/2023] Open
Abstract
Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, preprocessing of raw files is commonly performed in independent standalone tools, which makes it difficult to reproduce. Here, we present an R pipeline based on an updated version of CATALYST that covers all preprocessing steps required for downstream mass cytometry analysis in a fully reproducible way. This new version of CATALYST is based on Bioconductor's SingleCellExperiment class and fully unit tested. The R-based pipeline includes file concatenation, bead-based normalization, single-cell deconvolution, spillover compensation and live cell gating after debris and doublet removal. Importantly, this pipeline also includes different quality checks to assess machine sensitivity and staining performance while allowing also for batch correction. This pipeline is based on open source R packages and can be easily be adapted to different study designs. It therefore has the potential to significantly facilitate the work of CyTOF users while increasing the quality and reproducibility of data generated with this technology.
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Affiliation(s)
- Helena L. Crowell
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D. Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
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40
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Simoni Y, Becht E, Li S, Loh CY, Yeong JPS, Lim TKH, Takano A, Tan DSW, Newell EW. Partial absence of PD-1 expression by tumor-infiltrating EBV-specific CD8 + T cells in EBV-driven lymphoepithelioma-like carcinoma. Clin Transl Immunology 2020; 9:e1175. [PMID: 32995000 PMCID: PMC7503213 DOI: 10.1002/cti2.1175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/15/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Objectives Lymphoepithelioma‐like carcinoma (LELC) is an uncommon lung cancer, typically observed in young, non‐smoking Asian populations. LELC is associated with Epstein–Barr virus (EBV) infection of lung tumor cells of epithelial origin, suggesting a carcinogenic role of EBV as observed in nasopharyngeal carcinoma (NPC). Here, we studied the antigen specificity and phenotype of EBV‐specific CD8+ T cells in blood and tumor of one LELC patient positive for EBV infection in lung tumor cells. Methods Using multiplex MHC class I tetramers, mass cytometry and mRNA sequencing, we studied EBV‐specific CD8+ T cells at the transcriptomic and phenotypic levels in blood and tumor tissues of the LELC patient. Results Lymphoepithelioma‐like carcinoma lung tumor cells were positive for EBV infection. In both blood and tumor tissues, we detected two populations of EBV‐specific CD8+ T cells targeting the EBV lytic cycle proteins: BRLF1 and BMLF1. Transcriptomic analyses of these two populations in the tumor, which can be considered as tumor‐specific, revealed their distinct exhausted profile and polyclonal TCR repertoire. High‐dimensional phenotypical analysis revealed the distinct phenotype of these cells between blood and tumor tissues. In tumor tissue, EBV‐specific CD8+ TILs were phenotypically heterogeneous, but consistently expressed CD39. Unexpectedly, although the LELC tumor cells expressed abundant PD‐L1, these tumor‐specific CD8+ tumor‐infiltrating lymphocytes (TILs) mostly did not express PD‐1. Conclusion Epstein–Barr virus‐specific CD8+ TILs in EBV‐driven tumor are heterogeneous and partially lack PD‐1 expression, suggesting that anti‐PD1/PD‐L1 immunotherapy may not be an appropriate strategy for disinhibiting EBV‐specific cells in the treatment of LELC patients.
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Affiliation(s)
- Yannick Simoni
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore.,ImmunoScape Pte Ltd Singapore
| | - Etienne Becht
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore
| | - Shamin Li
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore
| | - Chiew Yee Loh
- Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore
| | - Joe Poh Sheng Yeong
- Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore.,Department of Anatomical Pathology Singapore General Hospital Singapore General Hospital Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology Singapore General Hospital Singapore General Hospital Singapore
| | - Angela Takano
- Department of Anatomical Pathology Singapore General Hospital Singapore General Hospital Singapore
| | - Daniel Shao Weng Tan
- Division of Medical Oncology National Cancer Centre Singapore (NCCS) Singapore.,Agency for Science, Technology and Research (ASTAR) Genome Institute of Singapore (GIS) Singapore
| | - Evan W Newell
- Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle WA USA.,Agency for Science, Technology and Research Singapore (ASTAR) Singapore Immunology Network (SIgN) Singapore.,Senior Corresponding Author
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41
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Nieman DC, Pence BD. Exercise immunology: Future directions. JOURNAL OF SPORT AND HEALTH SCIENCE 2020; 9:432-445. [PMID: 32928447 PMCID: PMC7498623 DOI: 10.1016/j.jshs.2019.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 05/07/2023]
Abstract
Several decades of research in the area of exercise immunology have shown that the immune system is highly responsive to acute and chronic exercise training. Moderate exercise bouts enhance immunosurveillance and when repeated over time mediate multiple health benefits. Most of the studies prior to 2010 relied on a few targeted outcomes related to immune function. During the past decade, technologic advances have created opportunities for a multi-omics and systems biology approach to exercise immunology. This article provides an overview of metabolomics, lipidomics, and proteomics as they pertain to exercise immunology, with a focus on immunometabolism. This review also summarizes how the composition and diversity of the gut microbiota can be influenced by exercise, with applications to human health and immunity. Exercise-induced improvements in immune function may play a critical role in countering immunosenescence and the development of chronic diseases, and emerging omics technologies will more clearly define the underlying mechanisms. This review summarizes what is currently known regarding a multi-omics approach to exercise immunology and provides future directions for investigators.
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Affiliation(s)
- David C Nieman
- Human Performance Laboratory, Appalachian State University, North Carolina Research Campus, Kannapolis, NC 28081, USA.
| | - Brandt D Pence
- School of Health Studies, University of Memphis, Memphis, TN 38152, USA
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42
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Salomon R, Martelotto L, Valdes-Mora F, Gallego-Ortega D. Genomic Cytometry and New Modalities for Deep Single-Cell Interrogation. Cytometry A 2020; 97:1007-1016. [PMID: 32794624 DOI: 10.1002/cyto.a.24209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 06/28/2020] [Accepted: 08/07/2020] [Indexed: 11/08/2022]
Abstract
In the past few years, the rapid development of single-cell analysis techniques has allowed for increasingly in-depth analysis of DNA, RNA, protein, and epigenetic states, at the level of the individual cell. This unprecedented characterization ability has been enabled through the combination of cytometry, microfluidics, genomics, and informatics. Although traditionally discrete, when properly integrated, these fields create the synergistic field of Genomic Cytometry. In this review, we look at the individual methods that together gave rise to the broad field of Genomic Cytometry. We further outline the basic concepts that drive the field and provide a framework to understand this increasingly complex, technology-intensive space. Thus, we introduce Genomic Cytometry as an emerging field and propose that synergistic rationalization of disparate modalities of cytometry, microfluidics, genomics, and informatics under one banner will enable massive leaps forward in the understanding of complex biology. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Robert Salomon
- Institute for Biomedical Materials and Devices, The University of Technology Sydney, Ultimo, New South Wales, 2006, Australia.,ACRF Child Cancer Liquid Biopsy Program, Children's Cancer Institute. Lowy Cancer Research Centre, University of New South Wales (UNSW) Sydney, Randwick, New South Wales, 2031, Australia
| | - Luciano Martelotto
- Centre for Cancer Research, University of Melbourne, Parkville, Victoria, Australia
| | - Fatima Valdes-Mora
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Darlinghurst, New South Wales, 2010, Australia.,Cancer Epigenetic Biology and Therapeutics. Personalised Medicine Theme. Children's Cancer Institute. Lowy Cancer Research Centre, University of New South Wales (UNSW) Sydney, Randwick, New South Wales, 2031, Australia
| | - David Gallego-Ortega
- Institute for Biomedical Materials and Devices, The University of Technology Sydney, Ultimo, New South Wales, 2006, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Darlinghurst, New South Wales, 2010, Australia.,Tumour Development Lab, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, 2010, Australia
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43
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Bortolomeazzi M, Keddar MR, Ciccarelli FD, Benedetti L. Identification of non-cancer cells from cancer transcriptomic data. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194445. [PMID: 31654804 PMCID: PMC7346884 DOI: 10.1016/j.bbagrm.2019.194445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Interactions between cancer cells and non-cancer cells composing the tumour microenvironment play a primary role in determining cancer progression and shaping the response to therapy. The qualitative and quantitative characterisation of the different cell populations in the tumour microenvironment is therefore crucial to understand its role in cancer. In recent years, many experimental and computational approaches have been developed to identify the cell populations composing heterogeneous tissue samples, such as cancer. In this review, we describe the state-of-the-art approaches for the quantification of non-cancer cells from bulk and single-cell cancer transcriptomic data, with a focus on immune cells. We illustrate the main features of these approaches and highlight their applications for the analysis of the tumour microenvironment in solid cancers. We also discuss techniques that are complementary and alternative to RNA sequencing, particularly focusing on approaches that can provide spatial information on the distribution of the cells within the tumour in addition to their qualitative and quantitative measurements. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - Mohamed Reda Keddar
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK.
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK.
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44
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Yu X, Zhang L, Chaudhry A, Rapaport AS, Ouyang W. Unravelling the heterogeneity and dynamic relationships of tumor-infiltrating T cells by single-cell RNA sequencing analysis. J Leukoc Biol 2020; 107:917-932. [PMID: 32272497 PMCID: PMC7317876 DOI: 10.1002/jlb.6mr0320-234r] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
T cells are crucial for the success of immune-based cancer therapy. Reinvigorating antitumor T cell activity by blocking checkpoint inhibitory receptors has provided clinical benefits for many cancer patients. However, the efficacy of these treatments varies in cancer patients and the mechanisms underlying these diverse responses remain elusive. The density and status of tumor-infiltrating T cells have been shown to positively correlate with patient response to checkpoint blockades. Therefore, further understanding of the heterogeneity, clonal expansion, migration, and effector functions of tumor-infiltrating T cells will provide fundamental insights into antitumor immune responses. To this end, recent advances in single-cell RNA sequencing technology have enabled profound and extensive characterization of intratumoral immune cells and have improved our understanding of their dynamic relationships. Here, we summarize recent progress in single-cell RNA sequencing technology and current strategies to uncover heterogeneous tumor-infiltrating T cell subsets. In particular, we discuss how the coupling of deep transcriptome information with T cell receptor (TCR)-based lineage tracing has furthered our understanding of intratumoral T cell populations. We also discuss the functional implications of various T cell subsets in tumors and highlight the identification of novel T cell markers with therapeutic or prognostic potential.
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Affiliation(s)
- Xin Yu
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
| | - Lei Zhang
- Beijing Advanced Innovation Center for GenomicsPeking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Ashutosh Chaudhry
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
| | - Aaron S. Rapaport
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
| | - Wenjun Ouyang
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
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45
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Russano M, Napolitano A, Ribelli G, Iuliani M, Simonetti S, Citarella F, Pantano F, Dell'Aquila E, Anesi C, Silvestris N, Argentiero A, Solimando AG, Vincenzi B, Tonini G, Santini D. Liquid biopsy and tumor heterogeneity in metastatic solid tumors: the potentiality of blood samples. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:95. [PMID: 32460897 PMCID: PMC7254767 DOI: 10.1186/s13046-020-01601-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
Abstract
In a large number of cancer types, treatment selection depends on the presence of specific tumor biomarkers. Due to the dynamic nature of cancer, very often these predictive biomarkers are not uniformly present in all cancer cells. Tumor heterogeneity represents indeed one of the main causes of therapeutic failure, and its decoding remains a major ongoing challenge in the field. Liquid biopsy is the sampling and analysis of non-solid biological tissue often through rapid and non-invasive methods, which allows the assessment in real-time of the evolving landscape of cancer. Samples can be obtained from blood and most other bodily fluids. A blood-based liquid biopsy can capture circulating tumor cells and leukocytes, as well as circulating tumor-derived nucleic acids. In this review, we discuss the current and possibly future applications of blood-based liquid biopsy in oncology, its advantages and its limitations in clinical practice. We specifically focused on its role as a tool to capture tumor heterogeneity in metastatic cancer patients.
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Affiliation(s)
- Marco Russano
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Andrea Napolitano
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Giulia Ribelli
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy.
| | - Michele Iuliani
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Sonia Simonetti
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Fabrizio Citarella
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Francesco Pantano
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Emanuela Dell'Aquila
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Cecilia Anesi
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, IRCCS-Istituto Tumori "Giovanni Paolo II" of Bari, 70124, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', 70124, Bari, Italy
| | - Antonella Argentiero
- Medical Oncology Unit, IRCCS-Istituto Tumori "Giovanni Paolo II" of Bari, 70124, Bari, Italy
| | - Antonio Giovanni Solimando
- Medical Oncology Unit, IRCCS-Istituto Tumori "Giovanni Paolo II" of Bari, 70124, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, Section of Internal Medicine 'G. Baccelli', University of Bari Medical School, 70124, Bari, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Giuseppe Tonini
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Daniele Santini
- Department of Medical Oncology, Campus Bio-Medico University of Rome, Álvaro del Portillo, 21, 00128, Rome, Italy
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Fu W, Wang W, Li H, Jiao Y, Huo R, Yan Z, Wang J, Wang S, Wang J, Chen D, Cao Y, Zhao J. Single-Cell Atlas Reveals Complexity of the Immunosuppressive Microenvironment of Initial and Recurrent Glioblastoma. Front Immunol 2020; 11:835. [PMID: 32457755 PMCID: PMC7221162 DOI: 10.3389/fimmu.2020.00835] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/14/2020] [Indexed: 11/14/2022] Open
Abstract
The Glioblastoma (GBM) immune microenvironment plays a critical role in tumor development, progression, and prognosis. A comprehensive understanding of the intricate milieu and its interactions remains unclear, and single-cell analysis is crucially needed. Leveraging mass cytometry (CyTOF), we analyzed immunocytes from 13 initial and three recurrent GBM samples and their matched peripheral blood mononuclear cells (pPBMCs). Using a panel of 30 markers, we provide a high-dimensional view of the complex GBM immune microenvironment. Hematoxylin and eosin staining and polychromatic immunofluorescence were used for verification of the key findings. In the initial and recurrent GBMs, glioma-associated microglia/macrophages (GAMs) constituted 59.05 and 27.87% of the immunocytes, respectively; programmed cell death-ligand 1 (PD-L1), T cell immunoglobulin domain and mucin domain-3 (TIM-3), lymphocyte activation gene-3 (LAG-3), interleukin-10 (IL-10) and transforming growth factor-β (TGFβ) demonstrated different expression levels in the GAMs among the patients. GAMs could be subdivided into different subgroups with different phenotypes. Both the exhausted T cell and regulatory T (Treg) cell percentages were significantly higher in tumors than in pPBMCs. The natural killer (NK) cells that infiltrated into the tumor lesions expressed higher levels of CXC chemokine receptor 3 (CXCR3), as these cells expressed lower levels of interferon-γ (IFNγ). The immune microenvironment in the initial and recurrent GBMs displayed similar suppressive changes. Our study confirmed that GAMs, as the dominant infiltrating immunocytes, present great inter- and intra-tumoral heterogeneity and that GAMs, increased exhausted T cells, infiltrating Tregs, and nonfunctional NK cells contribute to local immune suppressive characteristics. Recurrent GBMs share similar immune signatures with the initial GBMs except the proportion of GAMs decreases.
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Affiliation(s)
- Weilun Fu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wenjing Wang
- Institute of Hepatology, Capital Medical University Affiliated Beijing You'an Hospital, Beijing, China
| | - Hao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yuming Jiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Ran Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zihan Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jie Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Shuo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiangfei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Dexi Chen
- Institute of Hepatology, Capital Medical University Affiliated Beijing You'an Hospital, Beijing, China
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
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47
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Characterization of pulmonary immune responses to hyperoxia by high-dimensional mass cytometry analyses. Sci Rep 2020; 10:4677. [PMID: 32170168 PMCID: PMC7070092 DOI: 10.1038/s41598-020-61489-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/25/2020] [Indexed: 11/25/2022] Open
Abstract
Prolonged exposure to hyperoxia has deleterious effects on the lung, provoking both inflammation and alveolar injury. The elements of hyperoxic injury, which result in high rates of lethality in experimental models, are thought to include multicellular immune responses. To characterize these alterations in immune cell populations, we performed time-of-flight mass cytometry (CyTOF) analysis of CD45-expressing immune cells in whole lung parenchyma and the bronchoalveolar space of mice, exposed to 48 hours of hyperoxia together with normoxic controls. At the tested time point, hyperoxia exposure resulted in decreased abundance of immunoregulatory populations (regulatory B cells, myeloid regulatory cells) in lung parenchyma and markedly decreased proliferation rates of myeloid regulatory cells, monocytes and alveolar macrophages. Additionally, hyperoxia caused a shift in the phenotype of alveolar macrophages, increasing proportion of cells with elevated CD68, CD44, CD11c, PD-L1, and CD205 expression levels. These changes occurred in the absence of histologically evident alveolar damage and abundance of neutrophils in the parenchyma or alveolar space did not change at these time points. Collectively, these findings demonstrate that pulmonary response to hyperoxia involves marked changes in specific subsets of myeloid and lymphoid populations. These findings have important implications for therapeutic targeting in acute lung injury.
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48
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Fu W, Wang W, Li H, Jiao Y, Weng J, Huo R, Yan Z, Wang J, Xu H, Wang S, Wang J, Chen D, Cao Y, Zhao J. High Dimensional Mass Cytometry Analysis Reveals Characteristics of the Immunosuppressive Microenvironment in Diffuse Astrocytomas. Front Oncol 2020; 10:78. [PMID: 32117733 PMCID: PMC7010913 DOI: 10.3389/fonc.2020.00078] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
The tumor immune microenvironment (TIME) plays a pivotal role in tumor development, progression, and prognosis. However, the characteristics of the TIME in diffuse astrocytoma (DA) are still unclear. Leveraging mass cytometry with a panel of 33 markers, we analyzed the infiltrating immune cells from 10 DA and 4 oligodendroglioma (OG) tissues and provided a single cell-resolution landscape of the intricate immune microenvironment. Our study profiled the composition of the TIME in DA and confirmed the presence of immune cells, such as glioma-associated microglia/macrophages (GAMs), CD8+ T cells, CD4+ T cells, regulatory T cells (Tregs), and natural killer cells. Increased percentages of PD-1+ CD8+ T cells, TIM-3+ CD4+ T cell subpopulations, Tregs and pro-tumor phenotype GAMs substantially contribute to the local immunosuppressive microenvironment in DA. DAs and OGs share similar compositions in terms of immune cells, while GAMs in DA exhibit more inhibitory characteristics than those in OG.
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Affiliation(s)
- Weilun Fu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Wenjing Wang
- Institute of Hepatology, Capital Medical University Affiliated Beijing You'an Hospital, Beijing, China
| | - Hao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yuming Jiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiancong Weng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Ran Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Zihan Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jie Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Hongyuan Xu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Shuo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiangfei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Dexi Chen
- Institute of Hepatology, Capital Medical University Affiliated Beijing You'an Hospital, Beijing, China
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
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Lacroix-Desmazes S, Voorberg J, Lillicrap D, Scott DW, Pratt KP. Tolerating Factor VIII: Recent Progress. Front Immunol 2020; 10:2991. [PMID: 31998296 PMCID: PMC6965068 DOI: 10.3389/fimmu.2019.02991] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/05/2019] [Indexed: 02/02/2023] Open
Abstract
Development of neutralizing antibodies against biotherapeutic agents administered to prevent or treat various clinical conditions is a longstanding and growing problem faced by patients, medical providers and pharmaceutical companies. The hemophilia A community has deep experience with attempting to manage such deleterious immune responses, as the lifesaving protein drug factor VIII (FVIII) has been in use for decades. Hemophilia A is a bleeding disorder caused by genetic mutations that result in absent or dysfunctional FVIII. Prophylactic treatment consists of regular intravenous FVIII infusions. Unfortunately, 1/4 to 1/3 of patients develop neutralizing anti-FVIII antibodies, referred to clinically as “inhibitors,” which result in a serious bleeding diathesis. Until recently, the only therapeutic option for these patients was “Immune Tolerance Induction,” consisting of intensive FVIII administration, which is extraordinarily expensive and fails in ~30% of cases. There has been tremendous recent progress in developing novel potential clinical alternatives for the treatment of hemophilia A, ranging from encouraging results of gene therapy trials, to use of other hemostatic agents (either promoting coagulation or slowing down anti-coagulant or fibrinolytic pathways) to “bypass” the need for FVIII or supplement FVIII replacement therapy. Although these approaches are promising, there is widespread agreement that preventing or reversing inhibitors remains a high priority. Risk profiles of novel therapies are still unknown or incomplete, and FVIII will likely continue to be considered the optimal hemostatic agent to support surgery and manage trauma, or to combine with other therapies. We describe here recent exciting studies, most still pre-clinical, that address FVIII immunogenicity and suggest novel interventions to prevent or reverse inhibitor development. Studies of FVIII uptake, processing and presentation on antigen-presenting cells, epitope mapping, and the roles of complement, heme, von Willebrand factor, glycans, and the microbiome in FVIII immunogenicity are elucidating mechanisms of primary and secondary immune responses and suggesting additional novel targets. Promising tolerogenic therapies include development of FVIII-Fc fusion proteins, nanoparticle-based therapies, oral tolerance, and engineering of regulatory or cytotoxic T cells to render them FVIII-specific. Importantly, these studies are highly applicable to other scenarios where establishing immune tolerance to a defined antigen is a clinical priority.
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Affiliation(s)
| | - Jan Voorberg
- Sanquin Research and Landsteiner Laboratory, Department of Molecular and Cellular Hemostasis, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - David Lillicrap
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - David W Scott
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kathleen P Pratt
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying. Nat Commun 2019; 10:5710. [PMID: 31836712 PMCID: PMC6911020 DOI: 10.1038/s41467-019-13651-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/14/2019] [Indexed: 01/24/2023] Open
Abstract
Sensitive simultaneous assessment of multiple signaling pathways within the same cells requires orthogonal reporters that can assay over large dynamic ranges. Luciferases are such genetically encoded candidates due to their sensitivity, versatility, and cost-effectiveness. We expand luciferase multiplexing in post-lysis endpoint luciferase assays from two to six. Light emissions are distinguished by a combination of distinct substrates and emission spectra deconvolution. All six luciferase reporter units are stitched together into one plasmid facilitating delivery of all reporter units through a process we termed solotransfection, minimizing experimental errors. We engineer a multiplex hextuple luciferase assay to probe pathway fluxes through five transcriptional response elements against a control constitutive promoter. We can monitor effects of siRNA, ligand, and chemical compound treatments on their target pathways along with the four other probed cellular pathways. We demonstrate the effectiveness and adaptiveness of multiplex luciferase assaying, and its broad application across different research fields. Multiplexed detection of luciferase-based sensors in the same sample is challenging and limited by the substrates’ emission spectra. Here the authors establish a system based on three different luciferases and sequential detection to achieve measurements of up to six parameters within the same experiment.
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