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Filippi J, Casti P, Antonelli G, Murdocca M, Mencattini A, Corsi F, D'Orazio M, Pecora A, De Luca M, Curci G, Ghibelli L, Sangiuolo F, Neale SL, Martinelli E. Cell Electrokinetic Fingerprint: A Novel Approach Based on Optically Induced Dielectrophoresis (ODEP) for In-Flow Identification of Single Cells. SMALL METHODS 2024; 8:e2300923. [PMID: 38693090 DOI: 10.1002/smtd.202300923] [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: 07/22/2023] [Revised: 04/04/2024] [Indexed: 05/03/2024]
Abstract
A novel optically induced dielectrophoresis (ODEP) system that can operate under flow conditions is designed for automatic trapping of cells and subsequent induction of 2D multi-frequency cell trajectories. Like in a "ping-pong" match, two virtual electrode barriers operate in an alternate mode with varying frequencies of the input voltage. The so-derived cell motions are characterized via time-lapse microscopy, cell tracking, and state-of-the-art machine learning algorithms, like the wavelet scattering transform (WST). As a cell-electrokinetic fingerprint, the dynamic of variation of the cell displacements happening, over time, is quantified in response to different frequency values of the induced electric field. When tested on two biological scenarios in the cancer domain, the proposed approach discriminates cellular dielectric phenotypes obtained, respectively, at different early phases of drug-induced apoptosis in prostate cancer (PC3) cells and for differential expression of the lectine-like oxidized low-density lipoprotein receptor-1 (LOX-1) transcript levels in human colorectal adenocarcinoma (DLD-1) cells. The results demonstrate increased discrimination of the proposed system and pose an additional basis for making ODEP-based assays addressing cancer heterogeneity for precision medicine and pharmacological research.
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Affiliation(s)
- Joanna Filippi
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
| | - Paola Casti
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
| | - Gianni Antonelli
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
| | - Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, Rome, 00133, Italy
| | - Arianna Mencattini
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
| | - Francesca Corsi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133, Italy
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Michele D'Orazio
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
| | - Alessandro Pecora
- Italian Nation Research Council (CNR), Via del Fosso del Cavaliere 100, Rome, 00133, Italy
| | - Massimiliano De Luca
- Italian Nation Research Council (CNR), Via del Fosso del Cavaliere 100, Rome, 00133, Italy
| | - Giorgia Curci
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
| | - Lina Ghibelli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, Rome, 00133, Italy
| | - Steven L Neale
- James Watt School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Eugenio Martinelli
- Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, Rome, 00133, Italy
- Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), Via del Politecnico 1, Rome, 00133, Italy
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2
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Advances in Mass Spectrometry-Based Single Cell Analysis. BIOLOGY 2023; 12:biology12030395. [PMID: 36979087 PMCID: PMC10045136 DOI: 10.3390/biology12030395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.
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3
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Mehmood S, Aslam S, Dilshad E, Ismail H, Khan AN. Transforming Diagnosis and Therapeutics Using Cancer Genomics. Cancer Treat Res 2023; 185:15-47. [PMID: 37306902 DOI: 10.1007/978-3-031-27156-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In past quarter of the century, much has been understood about the genetic variation and abnormal genes that activate cancer in humans. All the cancers somehow possess alterations in the DNA sequence of cancer cell's genome. In present, we are heading toward the era where it is possible to obtain complete genome of the cancer cells for their better diagnosis, categorization and to explore treatment options.
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Affiliation(s)
- Sabba Mehmood
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan.
| | - Shaista Aslam
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Erum Dilshad
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
| | - Hammad Ismail
- Departments of Biochemistry and Biotechnology, University of Gujrat (UOG) Gujrat, Gujrat, Pakistan
| | - Amna Naheed Khan
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
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4
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Qin R, Zhao H, He Q, Li F, Li Y, Zhao H. Advances in single-cell sequencing technology in the field of hepatocellular carcinoma. Front Genet 2022; 13:996890. [PMID: 36303541 PMCID: PMC9592975 DOI: 10.3389/fgene.2022.996890] [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: 07/18/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Tumors are a class of diseases characterized by altered genetic information and uncontrolled growth. Sequencing technology provide researchers with a better way to explore specific tumor pathogenesis. In recent years, single-cell sequencing technology has shone in tumor research, especially in the study of liver cancer, revealing phenomena that were unexplored by previous studies. Single-cell sequencing (SCS) is a technique for sequencing the cellular genome, transcriptome, epigenome, proteomics, or metabolomics after dissociation of tissues into single cells. Compared with traditional bulk sequencing, single-cell sequencing can dissect human tumors at single-cell resolution, finely delineate different cell types, and reveal the heterogeneity of tumor cells. In view of the diverse pathological types and complex pathogenesis of hepatocellular carcinoma (HCC), the study of the heterogeneity among tumor cells can help improve its clinical diagnosis, treatment and prognostic judgment. On this basis, SCS has revolutionized our understanding of tumor heterogeneity, tumor immune microenvironment, and clonal evolution of tumor cells. This review summarizes the basic process and development of single-cell sequencing technology and its increasing role in the field of hepatocellular carcinoma.
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Affiliation(s)
- Rongyi Qin
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Haichao Zhao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qizu He
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Feng Li
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Yanjun Li
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Yanjun Li, ; Haoliang Zhao,
| | - Haoliang Zhao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Yanjun Li, ; Haoliang Zhao,
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5
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SFRP4 + stromal cell subpopulation with IGF1 signaling in human endometrial regeneration. Cell Discov 2022; 8:95. [PMID: 36163341 PMCID: PMC9512788 DOI: 10.1038/s41421-022-00438-7] [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: 01/05/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Our understanding of full-thickness endometrial regeneration after injury is limited by an incomplete molecular characterization of the cell populations responsible for the organ functions. To help fill this knowledge gap, we characterized 10,551 cells of full-thickness normal human uterine from two menstrual phases (proliferative and secretory phase) using unbiased single cell RNA-sequencing. We dissected cell heterogeneity of main cell types (epithelial, stromal, endothelial, and immune cells) of the full thickness uterine tissues, cell population architectures of human uterus cells across the menstrual cycle. We identified an SFRP4+ stromal cell subpopulation that was highly enriched in the regenerative stage of the human endometria during the menstrual cycle, and the SFRP4+ stromal cells could significantly enhance the proliferation of human endometrial epithelial organoid in vitro, and promote the regeneration of endometrial epithelial glands and full-thickness endometrial injury through IGF1 signaling pathway in vivo. Our cell atlas of full-thickness uterine tissues revealed the cellular heterogeneities, cell population architectures, and their cell-cell communications during the monthly regeneration of the human endometria, which provide insight into the biology of human endometrial regeneration and the development of regenerative medicine treatments against endometrial damage and intrauterine adhesion.
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Corker A, Neff LS, Broughton P, Bradshaw AD, DeLeon-Pennell KY. Organized Chaos: Deciphering Immune Cell Heterogeneity's Role in Inflammation in the Heart. Biomolecules 2021; 12:11. [PMID: 35053159 PMCID: PMC8773626 DOI: 10.3390/biom12010011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/18/2021] [Indexed: 12/24/2022] Open
Abstract
During homeostasis, immune cells perform daily housekeeping functions to maintain heart health by acting as sentinels for tissue damage and foreign particles. Resident immune cells compose 5% of the cellular population in healthy human ventricular tissue. In response to injury, there is an increase in inflammation within the heart due to the influx of immune cells. Some of the most common immune cells recruited to the heart are macrophages, dendritic cells, neutrophils, and T-cells. In this review, we will discuss what is known about cardiac immune cell heterogeneity during homeostasis, how these cell populations change in response to a pathology such as myocardial infarction or pressure overload, and what stimuli are regulating these processes. In addition, we will summarize technologies used to evaluate cell heterogeneity in models of cardiovascular disease.
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Affiliation(s)
- Alexa Corker
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC 29425, USA; (A.C.); (L.S.N.); (P.B.); (A.D.B.)
| | - Lily S. Neff
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC 29425, USA; (A.C.); (L.S.N.); (P.B.); (A.D.B.)
| | - Philip Broughton
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC 29425, USA; (A.C.); (L.S.N.); (P.B.); (A.D.B.)
| | - Amy D. Bradshaw
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC 29425, USA; (A.C.); (L.S.N.); (P.B.); (A.D.B.)
- Ralph H. Johnson Veterans Affairs Medical Center, Medical University of South Carolina, Charleston, SC 29401, USA
| | - Kristine Y. DeLeon-Pennell
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC 29425, USA; (A.C.); (L.S.N.); (P.B.); (A.D.B.)
- Ralph H. Johnson Veterans Affairs Medical Center, Medical University of South Carolina, Charleston, SC 29401, USA
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7
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Ichimura T, Kakizuka T, Horikawa K, Seiriki K, Kasai A, Hashimoto H, Fujita K, Watanabe TM, Nagai T. Exploring rare cellular activity in more than one million cells by a transscale scope. Sci Rep 2021; 11:16539. [PMID: 34400683 PMCID: PMC8368064 DOI: 10.1038/s41598-021-95930-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
In many phenomena of biological systems, not a majority, but a minority of cells act on the entire multicellular system causing drastic changes in the system properties. To understand the mechanisms underlying such phenomena, it is essential to observe the spatiotemporal dynamics of a huge population of cells at sub-cellular resolution, which is difficult with conventional tools such as microscopy and flow cytometry. Here, we describe an imaging system named AMATERAS that enables optical imaging with an over-one-centimeter field-of-view and a-few-micrometer spatial resolution. This trans-scale-scope has a simple configuration, composed of a low-power lens for machine vision and a hundred-megapixel image sensor. We demonstrated its high cell-throughput, capable of simultaneously observing more than one million cells. We applied it to dynamic imaging of calcium ions in HeLa cells and cyclic-adenosine-monophosphate in Dictyostelium discoideum, and successfully detected less than 0.01% of rare cells and observed multicellular events induced by these cells.
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Affiliation(s)
- T Ichimura
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan.
- PRESTO, Japan Science and Technology Agency, Tokyo, 113-0033, Japan.
| | - T Kakizuka
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - K Horikawa
- Department of Optical Imaging, Advanced Research Promotion Center, Tokushima University, Kuramoto-cho 3-18-15, Tokushima, Tokushima, 770-8503, Japan
| | - K Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - A Kasai
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - H Hashimoto
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
- Institute for Transdisciplinary Graduate Degree Programs, Osaka University, Yamadaoka 1-1, Suita, Osaka, 565-0871, Japan
| | - K Fujita
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - T M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Minatomachi-minami 2-2-3, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8553, Japan
| | - T Nagai
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan.
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan.
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8
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Li Y, Wu B, An C, Jiang D, Gong L, Liu Y, Liu Y, Li J, Ouyang H, Zou X. Mass cytometry and transcriptomic profiling reveal body-wide pathology induced by Loxl1 deficiency. Cell Prolif 2021; 54:e13077. [PMID: 34105806 PMCID: PMC8249785 DOI: 10.1111/cpr.13077] [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: 12/19/2020] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022] Open
Abstract
Objective The loss of LOXL1 expression reportedly leads to the prolapse of pelvic organs or to exfoliation syndrome glaucoma. Increasing evidence suggests that LOXL1 deficiency is associated with the pathogenesis of several other diseases. However, the characterization of the systemic functions of LOXL1 is limited by the lack of relevant investigative technologies. Materials and Methods To determine the functions of LOXL1, a novel method for body‐wide organ transcriptome profiling, combined with single‐cell mass cytometry, was developed. A body‐wide organ transcriptomic (BOT) map was created by RNA‐Seq of tissues from 17 organs from both Loxl1 knockout (KO) and wild‐type mice. Results The BOT results indicated the systemic upregulation of genes encoding proteins associated with the immune response and proliferation processes in multiple tissues of KO mice, and histological and immune staining confirmed the hyperplasia and infiltration of local immune cells in the tissues of KO mice. Furthermore, mass cytometry analysis of peripheral blood samples revealed systemic immune changes in KO mice. These findings were well correlated with results obtained from cancer databases. Patients with tumours had higher Loxl1 mutation frequencies, and patients with Loxl1‐mutant tumours showed the upregulation of immune processes and cell proliferation and lower survival rates. Conclusion This study provides an effective strategy for the screening of gene functions in multiple organs and also illustrates the important biological roles of LOXL1 in the cells of multiple organs as well as in systemic immunity.
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Affiliation(s)
- Yu Li
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Bingbing Wu
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Chengrui An
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Deming Jiang
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Lin Gong
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Yanshan Liu
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Yixiao Liu
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Jun Li
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
| | - Hongwei Ouyang
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute, Hangzhou, China.,China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, China
| | - XiaoHui Zou
- Clinical Research Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regeneration Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Tissue Engineering and Regenerative Medicine, Hangzhou, China
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9
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Geng Z, Tao Y, Zheng F, Wu L, Wang Y, Wang Y, Sun Y, Fu S, Wang W, Xie C, Zhang Y, Gong F. Altered Monocyte Subsets in Kawasaki Disease Revealed by Single-cell RNA-Sequencing. J Inflamm Res 2021; 14:885-896. [PMID: 33758528 PMCID: PMC7981157 DOI: 10.2147/jir.s293993] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/09/2021] [Indexed: 11/23/2022] Open
Abstract
Background Kawasaki disease (KD) is characterized by a disorder of immune response, and its etiology remains unknown. Monocyte is an important member of the body’s innate immune system; however its role in KD is still elusive due to its ambiguous heterogeneity and complex functions. We aim to comprehensively delineate monocyte heterogeneity in healthy and KD infants and to reveal the underlying mechanism for KD. Methods Peripheral monocytes were enriched from peripheral blood samples of two healthy infants and two KD infants. scRNA-seq was performed to acquire the transcriptomic atlas of monocytes. Bio-information analysis was utilized to identify monocyte subsets and explore their functions and differentiation states. SELL+CD14+CD16- monocytes were validated using flow cytometry. Results Three monocyte subsets were identified in healthy infants, including CD14+CD16- monocytes, CD14+CD16+ monocytes, and CD14LowCD16+ monocytes. Cell trajectory analysis revealed that the three monocyte subsets represent a linear differentiation, and possess different biological functions. Furthermore, SELL+CD14+CD16- monocytes, which were poorly differentiated and relating to neutrophil activation, were found to be expanded in KD. Conclusion Our findings provide a valuable resource for deciphering the monocyte heterogeneity in healthy infants and uncover the altered monocyte subsets in KD patients, suggesting potential biomarkers for KD diagnosis and treatment.
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Affiliation(s)
- Zhimin Geng
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Yijing Tao
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Fenglei Zheng
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Linlin Wu
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Wang
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Yujia Wang
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Yameng Sun
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Songling Fu
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Wei Wang
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Chunhong Xie
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Yiying Zhang
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
| | - Fangqi Gong
- Department of Cardiology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, People's Republic of China
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10
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Wu M, Xia M, Li W, Li H. Single-Cell Sequencing Applications in the Inner Ear. Front Cell Dev Biol 2021; 9:637779. [PMID: 33644075 PMCID: PMC7907461 DOI: 10.3389/fcell.2021.637779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/21/2021] [Indexed: 01/29/2023] Open
Abstract
Genomics studies face specific challenges in the inner ear due to the multiple types and limited amounts of inner ear cells that are arranged in a very delicate structure. However, advances in single-cell sequencing (SCS) technology have made it possible to analyze gene expression variations across different cell types as well as within specific cell groups that were previously considered to be homogeneous. In this review, we summarize recent advances in inner ear research brought about by the use of SCS that have delineated tissue heterogeneity, identified unknown cell subtypes, discovered novel cell markers, and revealed dynamic signaling pathways during development. SCS opens up new avenues for inner ear research, and the potential of the technology is only beginning to be explored.
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Affiliation(s)
- Mingxuan Wu
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Mingyu Xia
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Wenyan Li
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Huawei Li
- ENT Institute and Department of Otorhinolaryngology, Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China.,The Institutes of Brain Science and The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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11
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High-Dimensional Immune Monitoring for Chimeric Antigen Receptor T Cell Therapies. Curr Hematol Malig Rep 2021; 16:112-116. [PMID: 33449291 DOI: 10.1007/s11899-020-00602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE OF REVIEW High-dimensional flow cytometry experiments have become a method of choice for high-throughput integration and characterization of cell populations. Here, we present a summary of state-of-the-art R-based pipelines used for differential analyses of cytometry data, largely based on chimeric antigen receptor (CAR) T cell therapies. These pipelines are based on publicly available R libraries, put together in a systematic and functional fashion, therefore free of cost. RECENT FINDINGS In recent years, existing tools tailored to analyze complex high-dimensional data such as single-cell RNA sequencing (scRNAseq) have been successfully ported to cytometry studies due to the similar nature of flow cytometry and scRNAseq platforms. Existing environments like Cytobank (Kotecha et al., 2010), FlowJo (FlowJo™ Software) and FCS Express (https://denovosoftware.com) already offer a variety of these ported tools, but they either come at a premium or are fairly complicated to manage by an inexperienced user. To mitigate these limitations, experienced cytometrists and bioinformaticians usually incorporate these functions into an RShiny (https://shiny.rstudio.com) application that ultimately offers a user-friendly, intuitive environment that can be used to analyze flow cytometry data. Computational tools and Shiny-based tools are the perfect answer to the ever-growing dimensionality and complexity of flow cytometry data, by offering a dynamic, yet user-friendly exploratory space, tailored to bridge the space between the lab experimental world and the computational, machine learning space.
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12
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Huang N, Perez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Domínguez Conde C, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado J, LaFont B, Padilla R, Murrah V, Maile R, Lovell W, Wallet S, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann R, Cannon G, Anderson C, Marchesan J, Bush M, Freire M, Kimple A, Herr DL, Rabin J, Grazioli A, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt S, Burbelo PD, Chertow D, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM. Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020. [PMID: 33140061 DOI: 10.1101/2020.10.26.20219089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite signs of infection, the involvement of the oral cavity in COVID-19 is poorly understood. To address this, single-cell RNA sequencing data-sets were integrated from human minor salivary glands and gingiva to identify 11 epithelial, 7 mesenchymal, and 15 immune cell clusters. Analysis of SARS-CoV-2 viral entry factor expression showed enrichment in epithelia including the ducts and acini of the salivary glands and the suprabasal cells of the mucosae. COVID-19 autopsy tissues confirmed in vivo SARS-CoV-2 infection in the salivary glands and mucosa. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibiting ACE2 expression and SARS-CoV-2 RNA. Matched nasopharyngeal and saliva samples found distinct viral shedding dynamics and viral burden in saliva correlated with COVID-19 symptoms including taste loss. Upon recovery, this cohort exhibited salivary antibodies against SARS-CoV-2 proteins. Collectively, the oral cavity represents a robust site for COVID-19 infection and implicates saliva in viral transmission.
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13
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Abstract
The immune system is composed of heterogeneous populations of immune cells that regulate physiological processes and protect organisms against diseases. Single cell technologies have been used to assess immune cell responses at the single cell level, which are crucial for identifying the causes of diseases and elucidating underlying biological mechanisms to facilitate medical therapy. In the present review we first discuss the most recent advances in the development of single cell technologies to investigate cell signaling, cell-cell interactions and cell migration. Each technology's advantages and limitations and its applications in immunology are subsequently reviewed. The latest progress toward commercialization, the remaining challenges and future perspectives for single cell technologies in immunology are also briefly discussed.
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Affiliation(s)
- Jane Ru Choi
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.,Department of Mechanical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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14
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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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15
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Peng G, Cui G, Ke J, Jing N. Using Single-Cell and Spatial Transcriptomes to Understand Stem Cell Lineage Specification During Early Embryo Development. Annu Rev Genomics Hum Genet 2020; 21:163-181. [PMID: 32339035 DOI: 10.1146/annurev-genom-120219-083220] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Embryonic development and stem cell differentiation provide a paradigm to understand the molecular regulation of coordinated cell fate determination and the architecture of tissue patterning. Emerging technologies such as single-cell RNA sequencing and spatial transcriptomics are opening new avenues to dissect cell organization, the divergence of morphological and molecular properties, and lineage allocation. Rapid advances in experimental and computational tools have enabled researchers to make many discoveries and revisit old hypotheses. In this review, we describe the use of single-cell RNA sequencing in studies of molecular trajectories and gene regulation networks for stem cell lineages, while highlighting the integratedexperimental and computational analysis of single-cell and spatial transcriptomes in the molecular annotation of tissue lineages and development during postimplantation gastrulation.
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Affiliation(s)
- Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; .,Center for Cell Lineage and Atlas, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guizhong Cui
- Center for Cell Lineage and Atlas, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Jincan Ke
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China;
| | - Naihe Jing
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; .,Center for Cell Lineage and Atlas, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China;
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16
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Zheng Z, Chen E, Lu W, Mouradian G, Hodges M, Liang M, Liu P, Lu Y. Single-Cell Transcriptomic Analysis. Compr Physiol 2020; 10:767-783. [PMID: 32163201 DOI: 10.1002/cphy.c190037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-cell sequencing measures the sequence information from individual cells using optimized single-cell isolation protocols and next-generation sequencing technologies. Recent advancement in single-cell sequencing has transformed biomedical research, providing insights into diverse biological processes such as mammalian development, immune system function, cellular diversity and heterogeneity, and disease pathogenesis. In this article, we introduce and describe popular commercial platforms for single-cell RNA sequencing, general workflow for data analysis, repositories and databases, and applications for these approaches in biomedical research. © 2020 American Physiological Society. Compr Physiol 10:767-783, 2020.
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Affiliation(s)
- Zhihong Zheng
- Department of Gynecologic Oncology, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Enguo Chen
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China
| | - Weiguo Lu
- Department of Gynecologic Oncology, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Gary Mouradian
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Matthew Hodges
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mingyu Liang
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China.,Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yan Lu
- Department of Gynecologic Oncology, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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17
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Bujko K, Kucia M, Ratajczak J, Ratajczak MZ. Hematopoietic Stem and Progenitor Cells (HSPCs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1201:49-77. [PMID: 31898781 DOI: 10.1007/978-3-030-31206-0_3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hematopoietic stem/progenitor cells (HSPCs) isolated from bone marrow have been successfully employed for 50 years in hematological transplantations. Currently, these cells are more frequently isolated from mobilized peripheral blood or umbilical cord blood. In this chapter, we overview several topics related to these cells including their phenotype, methods for isolation, and in vitro and in vivo assays to evaluate their proliferative potential. The successful clinical application of HSPCs is widely understood to have helped establish the rationale for the development of stem cell therapies and regenerative medicine.
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Affiliation(s)
- Kamila Bujko
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Magda Kucia
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Janina Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA. .,Department of Regenerative Medicine, Center for Preclinical Research and Technology, Warsaw Medical University, Warsaw, Poland.
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18
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Voskamp AL, Kormelink TG, van Wijk RG, Hiemstra PS, Taube C, de Jong EC, Smits HH. Modulating local airway immune responses to treat allergic asthma: lessons from experimental models and human studies. Semin Immunopathol 2020; 42:95-110. [PMID: 32020335 PMCID: PMC7066288 DOI: 10.1007/s00281-020-00782-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/14/2020] [Indexed: 12/17/2022]
Abstract
With asthma affecting over 300 million individuals world-wide and estimated to affect 400 million by 2025, developing effective, long-lasting therapeutics is essential. Allergic asthma, where Th2-type immunity plays a central role, represents 90% of child and 50% of adult asthma cases. Research based largely on animal models of allergic disease have led to the generation of a novel class of drugs, so-called biologicals, that target essential components of Th2-type inflammation. Although highly efficient in subclasses of patients, these biologicals and other existing medication only target the symptomatic stage of asthma and when therapy is ceased, a flare-up of the disease is often observed. Therefore, it is suggested to target earlier stages in the inflammatory cascade underlying allergic airway inflammation and to focus on changing and redirecting the initiation of type 2 inflammatory responses against allergens and certain viral agents. This focus on upstream aspects of innate immunity that drive development of Th2-type immunity is expected to have longer-lasting and disease-modifying effects, and may potentially lead to a cure for asthma. This review highlights the current understanding of the contribution of local innate immune elements in the development and maintenance of inflammatory airway responses and discusses available leads for successful targeting of those pathways for future therapeutics.
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Affiliation(s)
- A L Voskamp
- Department of Parasitology, Leiden University Medical Center, Albinusdreef 2 2333 ZA, Leiden, The Netherlands
| | - T Groot Kormelink
- Department of Experimental Immunology, Amsterdam University Medical Centers, AMC, Amsterdam, The Netherlands
| | - R Gerth van Wijk
- Department of Internal Medicine, Section Allergology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - C Taube
- Department of Pulmonary Medicine, University Hospital Essen - Ruhrklinik, Essen, Germany
| | - E C de Jong
- Department of Experimental Immunology, Amsterdam University Medical Centers, AMC, Amsterdam, The Netherlands
| | - Hermelijn H Smits
- Department of Parasitology, Leiden University Medical Center, Albinusdreef 2 2333 ZA, Leiden, The Netherlands.
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19
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Yasen A, Aini A, Wang H, Li W, Zhang C, Ran B, Tuxun T, Maimaitinijiati Y, Shao Y, Aji T, Wen H. Progress and applications of single-cell sequencing techniques. INFECTION GENETICS AND EVOLUTION 2020; 80:104198. [PMID: 31958516 DOI: 10.1016/j.meegid.2020.104198] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 01/06/2023]
Abstract
Single-cell sequencing (SCS) is a next-generation sequencing method that is mainly used to analyze differences in genetic and protein information between cells, to obtain genetic information on microorganisms that are difficult to cultivate at a single-cell level and to better understand their specific roles in the microenvironment. By sequencing the whole genome, transcriptome and epigenome of a single cell, the complex heterogeneous mechanisms involved in disease occurrence and progression can be revealed, further improving disease diagnosis, prognosis prediction and monitoring of the therapeutic effects of drugs. In this study, we mainly summarized the methods and application fields of SCS, which may provide potential references for its future clinical applications, including the analysis of embryonic and organ development, the immune system, cancer progression, and parasitic and infectious diseases as well as stem cell research, antibody screening, and therapeutic research and development.
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Affiliation(s)
- Aimaiti Yasen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Abudusalamu Aini
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Hui Wang
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Wending Li
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Chuanshan Zhang
- Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Bo Ran
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Tuerhongjiang Tuxun
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Yusufukadier Maimaitinijiati
- The first affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Yingmei Shao
- Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China
| | - Tuerganaili Aji
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China.
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, 393 Xin Yi Road, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China; Department of Hepatobiliary and Hydatid Disease, Digestive and Vascular Surgery Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang Uyghur Autonomous Region, People's Republic of China.
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20
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Duan T, Pinto JP, Xie X. Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures. Bioinformatics 2019; 35:953-961. [PMID: 30165477 DOI: 10.1093/bioinformatics/bty702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/20/2018] [Accepted: 08/22/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been applied to the data, they face challenges in the following aspects: (i) the clustering quality still needs to be improved; (ii) most models need prior knowledge on number of clusters, which is not always available; (iii) there is a demand for faster computational speed. RESULTS We propose to tackle these challenges with Parallelized Split Merge Sampling on Dirichlet Process Mixture Model (the Para-DPMM model). Unlike classic DPMM methods that perform sampling on each single data point, the split merge mechanism samples on the cluster level, which significantly improves convergence and optimality of the result. The model is highly parallelized and can utilize the computing power of high performance computing (HPC) clusters, enabling massive inference on huge datasets. Experiment results show the model outperforms current widely used models in both clustering quality and computational speed. AVAILABILITY AND IMPLEMENTATION Source code is publicly available on https://github.com/tiehangd/Para_DPMM/tree/master/Para_DPMM_package. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tiehang Duan
- Department of Computer Science, University of California, Irvine, CA, USA
| | - José P Pinto
- SysBioLab, Centre for Biomedical Research (CBMR), University of Algarve, Faro, Algarve, Portugal
| | - Xiaohui Xie
- Department of Computer Science, University of California, Irvine, CA, USA
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21
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Lee KCM, Lau AKS, Tang AHL, Wang M, Mok ATY, Chung BMF, Yan W, Shum HC, Cheah KSE, Chan GCF, So HKH, Wong KKY, Tsia KK. Multi-ATOM: Ultrahigh-throughput single-cell quantitative phase imaging with subcellular resolution. JOURNAL OF BIOPHOTONICS 2019; 12:e201800479. [PMID: 30719868 PMCID: PMC7065649 DOI: 10.1002/jbio.201800479] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 02/01/2019] [Indexed: 05/10/2023]
Abstract
A growing body of evidence has substantiated the significance of quantitative phase imaging (QPI) in enabling cost-effective and label-free cellular assays, which provides useful insights into understanding the biophysical properties of cells and their roles in cellular functions. However, available QPI modalities are limited by the loss of imaging resolution at high throughput and thus run short of sufficient statistical power at the single-cell precision to define cell identities in a large and heterogeneous population of cells-hindering their utility in mainstream biomedicine and biology. Here we present a new QPI modality, coined multiplexed asymmetric-detection time-stretch optical microscopy (multi-ATOM) that captures and processes quantitative label-free single-cell images at ultrahigh throughput without compromising subcellular resolution. We show that multi-ATOM, based upon ultrafast phase-gradient encoding, outperforms state-of-the-art QPI in permitting robust phase retrieval at a QPI throughput of >10 000 cell/sec, bypassing the need for interferometry which inevitably compromises QPI quality under ultrafast operation. We employ multi-ATOM for large-scale, label-free, multivariate, cell-type classification (e.g. breast cancer subtypes, and leukemic cells vs peripheral blood mononuclear cells) at high accuracy (>94%). Our results suggest that multi-ATOM could empower new strategies in large-scale biophysical single-cell analysis with applications in biology and enriching disease diagnostics.
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Affiliation(s)
- Kelvin C. M. Lee
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Andy K. S. Lau
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Anson H. L. Tang
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Maolin Wang
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Aaron T. Y. Mok
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Bob M. F. Chung
- Department of Mechanical Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Wenwei Yan
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Ho C. Shum
- Department of Mechanical Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Kathryn S. E. Cheah
- School of Biomedical Sciences, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Godfrey C. F. Chan
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Hayden K. H. So
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Kenneth K. Y. Wong
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
| | - Kevin K. Tsia
- Department of Electrical and Electronic Engineering, Faculty of EngineeringThe University of Hong KongHong Kong
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22
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Niu J, Straubinger RM, Mager DE. Pharmacodynamic Drug-Drug Interactions. Clin Pharmacol Ther 2019; 105:1395-1406. [PMID: 30912119 PMCID: PMC6529235 DOI: 10.1002/cpt.1434] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/13/2019] [Indexed: 01/01/2023]
Abstract
Pharmacodynamic drug-drug interactions (DDIs) occur when the pharmacological effect of one drug is altered by that of another drug in a combination regimen. DDIs often are classified as synergistic, additive, or antagonistic in nature, albeit these terms are frequently misused. Within a complex pathophysiological system, the mechanism of interaction may occur at the same target or through alternate pathways. Quantitative evaluation of pharmacodynamic DDIs by employing modeling and simulation approaches is needed to identify and optimize safe and effective combination therapy regimens. This review investigates the opportunities and challenges in pharmacodynamic DDI studies and highlights examples of quantitative methods for evaluating pharmacodynamic DDIs, with a particular emphasis on the use of mechanism-based modeling and simulation in DDI studies. Advancements in both experimental and computational techniques will enable the application of better, model-informed assessments of pharmacodynamic DDIs in drug discovery, development, and therapeutics.
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Affiliation(s)
- Jin Niu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Robert M. Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Donald E. Mager
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
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23
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Yin L, Zhang Z, Liu Y, Gao Y, Gu J. Recent advances in single-cell analysis by mass spectrometry. Analyst 2019; 144:824-845. [PMID: 30334031 DOI: 10.1039/c8an01190g] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.
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Affiliation(s)
- Lei Yin
- Research Institute of Translational Medicine, The First Hospital of Jilin University, Jilin University, Dongminzhu Street, Changchun 130061, PR China.
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Lee KCM, Wang M, Cheah KSE, Chan GCF, So HKH, Wong KKY, Tsia KK. Quantitative Phase Imaging Flow Cytometry for Ultra-Large-Scale Single-Cell Biophysical Phenotyping. Cytometry A 2019; 95:510-520. [PMID: 31012276 DOI: 10.1002/cyto.a.23765] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 12/21/2022]
Abstract
Cellular biophysical properties are the effective label-free phenotypes indicative of differences in cell types, states, and functions. However, current biophysical phenotyping methods largely lack the throughput and specificity required in the majority of cell-based assays that involve large-scale single-cell characterization for inquiring the inherently complex heterogeneity in many biological systems. Further confounded by the lack of reported robust reproducibility and quality control, widespread adoption of single-cell biophysical phenotyping in mainstream cytometry remains elusive. To address this challenge, here we present a label-free imaging flow cytometer built upon a recently developed ultrafast quantitative phase imaging (QPI) technique, coined multi-ATOM, that enables label-free single-cell QPI, from which a multitude of subcellularly resolvable biophysical phenotypes can be parametrized, at an experimentally recorded throughput of >10,000 cells/s-a capability that is otherwise inaccessible in current QPI. With the aim to translate multi-ATOM into mainstream cytometry, we report robust system calibration and validation (from image acquisition to phenotyping reproducibility) and thus demonstrate its ability to establish high-dimensional single-cell biophysical phenotypic profiles at ultra-large-scale (>1,000,000 cells). Such a combination of throughput and content offers sufficiently high label-free statistical power to classify multiple human leukemic cell types at high accuracy (~92-97%). This system could substantiate the significance of high-throughput QPI flow cytometry in enabling next frontier in large-scale image-derived single-cell analysis applied in biological discovery and cost-effective clinical diagnostics. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Kelvin C M Lee
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Maolin Wang
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kathryn S E Cheah
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Godfrey C F Chan
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hayden K H So
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kenneth K Y Wong
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong
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25
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Zeeshan S, Xiong R, Liang BT, Ahmed Z. 100 Years of evolving gene-disease complexities and scientific debutants. Brief Bioinform 2019; 21:885-905. [PMID: 30972412 DOI: 10.1093/bib/bbz038] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022] Open
Abstract
It's been over 100 years since the word `gene' is around and progressively evolving in several scientific directions. Time-to-time technological advancements have heavily revolutionized the field of genomics, especially when it's about, e.g. triple code development, gene number proposition, genetic mapping, data banks, gene-disease maps, catalogs of human genes and genetic disorders, CRISPR/Cas9, big data and next generation sequencing, etc. In this manuscript, we present the progress of genomics from pea plant genetics to the human genome project and highlight the molecular, technical and computational developments. Studying genome and epigenome led to the fundamentals of development and progression of human diseases, which includes chromosomal, monogenic, multifactorial and mitochondrial diseases. World Health Organization has classified, standardized and maintained all human diseases, when many academic and commercial online systems are sharing information about genes and linking to associated diseases. To efficiently fathom the wealth of this biological data, there is a crucial need to generate appropriate gene annotation repositories and resources. Our focus has been how many gene-disease databases are available worldwide and which sources are authentic, timely updated and recommended for research and clinical purposes. In this manuscript, we have discussed and compared 43 such databases and bioinformatics applications, which enable users to connect, explore and, if possible, download gene-disease data.
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Affiliation(s)
- Saman Zeeshan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Ruoyun Xiong
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Bruce T Liang
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA.,Pat and Jim Calhoun Cardiology Center, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
| | - Zeeshan Ahmed
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center, Farmington Ave, Farmington, CT, USA
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26
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Duval C, Watanabe M, Donati G. Buried myoepithelial stem cells as a reservoir for repairing the exposed airway epithelium. Stem Cell Investig 2019; 5:45. [PMID: 30701180 DOI: 10.21037/sci.2018.11.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/09/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Carlotta Duval
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.,Molecular Biotechnology Center, University of Turin, Torino, Italy
| | - Mika Watanabe
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.,Molecular Biotechnology Center, University of Turin, Torino, Italy
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy.,Molecular Biotechnology Center, University of Turin, Torino, Italy
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Lee D, Cheng A, Lawlor N, Bolisetty M, Ucar D. Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA). Sci Rep 2018; 8:17040. [PMID: 30451954 PMCID: PMC6242813 DOI: 10.1038/s41598-018-35365-9] [Citation(s) in RCA: 6] [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: 12/04/2017] [Accepted: 11/01/2018] [Indexed: 01/01/2023] Open
Abstract
Single cell RNA-sequencing (scRNA-seq) precisely characterizes gene expression levels and dissects variation in expression associated with the state (technical or biological) and the type of the cell, which is averaged out in bulk measurements. Multiple and correlated sources contribute to gene expression variation in single cells, which makes their estimation difficult with the existing methods developed for batch correction (e.g., surrogate variable analysis (SVA)) that estimate orthogonal transformations of these sources. We developed iteratively adjusted surrogate variable analysis (IA-SVA) that can estimate hidden factors even when they are correlated with other sources of variation by identifying a set of genes associated with each hidden factor in an iterative manner. Analysis of scRNA-seq data from human cells showed that IA-SVA could accurately capture hidden variation arising from technical (e.g., stacked doublet cells) or biological sources (e.g., cell type or cell-cycle stage). Furthermore, IA-SVA delivers a set of genes associated with the detected hidden source to be used in downstream data analyses. As a proof of concept, IA-SVA recapitulated known marker genes for islet cell subsets (e.g., alpha, beta), which improved the grouping of subsets into distinct clusters. Taken together, IA-SVA is an effective and novel method to dissect multiple and correlated sources of variation in scRNA-seq data.
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Affiliation(s)
- Donghyung Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA.
| | - Anthony Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, 06030, CT, USA
| | - Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, 06030, CT, USA.
- Institute of Systems Genomics, University of Connecticut Health Center, Farmington, 06030, CT, USA.
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Raeven RHM, van Riet E, Meiring HD, Metz B, Kersten GFA. Systems vaccinology and big data in the vaccine development chain. Immunology 2018; 156:33-46. [PMID: 30317555 PMCID: PMC6283655 DOI: 10.1111/imm.13012] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/03/2018] [Indexed: 02/06/2023] Open
Abstract
Systems vaccinology has proven a fascinating development in the last decade. Where traditionally vaccine development has been dominated by trial and error, systems vaccinology is a tool that provides novel and comprehensive understanding if properly used. Data sets retrieved from systems‐based studies endorse rational design and effective development of safe and efficacious vaccines. In this review we first describe different omics‐techniques that form the pillars of systems vaccinology. In the second part, the application of systems vaccinology in the different stages of vaccine development is described. Overall, this review shows that systems vaccinology has become an important tool anywhere in the vaccine development chain.
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Affiliation(s)
- René H M Raeven
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Elly van Riet
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Hugo D Meiring
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Bernard Metz
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands
| | - Gideon F A Kersten
- Intravacc (Institute for Translational Vaccinology), Bilthoven, The Netherlands.,Leiden Academic Center for Drug Research, Division of Biotherapeutics, Leiden University, Leiden, The Netherlands
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29
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Danova M, Torchio M, Comolli G, Sbrana A, Antonuzzo A, Mazzini G. The role of automated cytometry in the new era of cancer immunotherapy. Mol Clin Oncol 2018; 9:355-361. [PMID: 30233791 DOI: 10.3892/mco.2018.1701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
The introduction in the clinical practice of several new approaches to cancer immunotherapy has greatly increased the interest in analytical methodologies that can define the immunological profile of patients in the clinical setting. This requires huge effort to obtain reliable monitoring tools that could be used to improve the patient's clinical outcome. The clinical applications of flow cytometry (FCM) in oncology started with the measurement of DNA content for the evaluation of both ploidy and cell cycle profile as potential prognostic parameters in the majority of human solid cancer types. The availability of monoclonal antibodies widely broadened the spectrum of clinical applications of this technique, which rapidly became a fundamental tool for the diagnosis and prognosis of malignant hematological diseases. Among the emerging clinical applications of FCM, the study of minimal residual disease in hematological malignancies, the quantification of blood dendritic cells in various types of tumors, the study of metastatic spread in solid tumors throughout both the analysis of circulating endothelial progenitor cells and the identification and characterization of circulating tumor cells, all appear very promising. More recently, an advanced single cell analysis technique has been developed that combines the precision of mass spectrometry with the unique advantages of FCM. This approach, termed mass cytometry, utilizes antibodies conjugated to heavy metal ions for the analysis of cellular proteins by a mass spectrometer. It provides measurement of over 100 simultaneous cellular parameters in a single sample and has evolved from a promising technology to a high recognized platform for multi-dimensional single-cell analysis. Should a careful standardization of the analytical procedures be reached, both FCM and mass cytometry could effectively become ideal tools for the optimization of new immunotherapeutic approaches in cancer patients.
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Affiliation(s)
- Marco Danova
- Department of Internal Medicine and Medical Oncology, Vigevano Civic Hospital, ASST of Pavia, I-27029 Vigevano, Italy
| | - Martina Torchio
- Department of Internal Medicine and Medical Oncology, Vigevano Civic Hospital, ASST of Pavia, I-27029 Vigevano, Italy
| | - Giuditta Comolli
- Department of Microbiology and Virology and Biotechnology Laboratories, IRCCS San Matteo Foundation, I-27100 Pavia, Italy
| | - Andrea Sbrana
- Department of Medical Oncology 2, University Hospital of Pisa, I-56126 Pisa, Italy
| | - Andrea Antonuzzo
- Department of Medical Oncology 2, University Hospital of Pisa, I-56126 Pisa, Italy
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30
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Bioinspired, nanoscale approaches in contemporary bioanalytics (Review). Biointerphases 2018; 13:040801. [DOI: 10.1116/1.5037582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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31
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Nasteska D, Hodson DJ. The role of beta cell heterogeneity in islet function and insulin release. J Mol Endocrinol 2018; 61:R43-R60. [PMID: 29661799 PMCID: PMC5976077 DOI: 10.1530/jme-18-0011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022]
Abstract
It is becoming increasingly apparent that not all insulin-secreting beta cells are equal. Subtle differences exist at the transcriptomic and protein expression levels, with repercussions for beta cell survival/proliferation, calcium signalling and insulin release. Notably, beta cell heterogeneity displays plasticity during development, metabolic stress and type 2 diabetes mellitus (T2DM). Thus, heterogeneity or lack thereof may be an important contributor to beta cell failure during T2DM in both rodents and humans. The present review will discuss the molecular and cellular features of beta cell heterogeneity at both the single-cell and islet level, explore how this influences islet function and insulin release and look into the alterations that may occur during obesity and T2DM.
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Affiliation(s)
- Daniela Nasteska
- Institute of Metabolism and Systems Research (IMSR)University of Birmingham, Edgbaston, UK
- Centre for EndocrinologyDiabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
- COMPARE University of Birmingham and University of Nottingham MidlandsBirmingham, UK
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR)University of Birmingham, Edgbaston, UK
- Centre for EndocrinologyDiabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
- COMPARE University of Birmingham and University of Nottingham MidlandsBirmingham, UK
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32
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Vegh P, Haniffa M. The impact of single-cell RNA sequencing on understanding the functional organization of the immune system. Brief Funct Genomics 2018; 17:265-272. [PMID: 29547972 PMCID: PMC6063276 DOI: 10.1093/bfgp/ely003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Application of single-cell genomics technologies has revolutionized our approach to study the immune system. Unravelling the functional diversity of immune cells and their coordinated response is key to understanding immunity. Single-cell transcriptomics technologies provide high-dimensional assessment of the transcriptional states of immune cells and have been successfully applied to discover new immune cell types, reveal haematopoietic lineages, identify gene modules dictating immune responses and investigate lymphocyte antigen receptor diversity. In this review, we discuss the impact and applications of single-cell RNA sequencing technologies in immunology.
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Affiliation(s)
- Peter Vegh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Department of Dermatology, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
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33
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Circulating tumor microemboli: Progress in molecular understanding and enrichment technologies. Biotechnol Adv 2018; 36:1367-1389. [DOI: 10.1016/j.biotechadv.2018.05.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 04/16/2018] [Accepted: 05/09/2018] [Indexed: 02/07/2023]
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34
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Kolodziejczyk AA, Lönnberg T. Global and targeted approaches to single-cell transcriptome characterization. Brief Funct Genomics 2018; 17:209-219. [PMID: 29028866 PMCID: PMC6063303 DOI: 10.1093/bfgp/elx025] [Citation(s) in RCA: 21] [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] [Indexed: 12/31/2022] Open
Abstract
Analysing transcriptomes of cell populations is a standard molecular biology approach to understand how cells function. Recent methodological development has allowed performing similar experiments on single cells. This has opened up the possibility to examine samples with limited cell number, such as cells of the early embryo, and to obtain an understanding of heterogeneity within populations such as blood cell types or neurons. There are two major approaches for single-cell transcriptome analysis: quantitative reverse transcription PCR (RT-qPCR) on a limited number of genes of interest, or more global approaches targeting entire transcriptomes using RNA sequencing. RT-qPCR is sensitive, fast and arguably more straightforward, while whole-transcriptome approaches offer an unbiased perspective on a cell's expression status.
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Affiliation(s)
| | - Tapio Lönnberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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35
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Kunz DJ, Gomes T, James KR. Immune Cell Dynamics Unfolded by Single-Cell Technologies. Front Immunol 2018; 9:1435. [PMID: 29997618 PMCID: PMC6028612 DOI: 10.3389/fimmu.2018.01435] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
The single-cell revolution is paving the way towards the molecular characterisation of every cell type in the human body, revealing relationships between cell types and states at high resolution. Changes in cellular phenotypes are particularly prevalent in the immune system and can be observed in its continuous remodelling up to adulthood, response to disease and development of immunological memory. In this review, we delve into the world of cellular dynamics of the immune system. We discuss current single-cell experimental and computational approaches in this area, giving insights into plasticity and commitment of cell fates. Finally, we provide an outlook on upcoming technological developments and predict how these will improve our understanding of the immune system.
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Affiliation(s)
- Daniel J. Kunz
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kylie R. James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Abstract
Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools for single-cell analysis, especially in the RNA sequencing field. Every improvement increases sensitivity and throughput. Collecting a large amount of data also stimulates the development of new approaches for bioinformatic analysis and interpretation. However, the essential requirement for any analysis is the collection of single cells of high quality. The single-cell isolation must be fast, effective, and gentle to maintain the native expression profiles. Classical methods for single-cell isolation are micromanipulation, microdissection, and fluorescence-activated cell sorting (FACS). In the last decade several new and highly efficient approaches have been developed, which not just supplement but may fully replace the traditional ones. These new techniques are based on microfluidic chips, droplets, micro-well plates, and automatic collection of cells using capillaries, magnets, an electric field, or a punching probe. In this review we summarize the current methods and developments in this field. We discuss the advantages of the different commercially available platforms and their applicability, and also provide remarks on future developments.
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37
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Schultze JL, Aschenbrenner AC. Systems immunology allows a new view on human dendritic cells. Semin Cell Dev Biol 2018; 86:15-23. [PMID: 29448068 DOI: 10.1016/j.semcdb.2018.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 11/23/2017] [Accepted: 02/10/2018] [Indexed: 01/12/2023]
Abstract
As the most important antigen-presenting cells, dendritic cells connect the innate and adaptive part of our immune system and play a pivotal role in our course of action against invading pathogens as well as during successful vaccination. Immunologists have therefore studied these cells in great detail using flow cytometry-based analyses, in vitro assays and in vivo models, both in murine models and in humans. Albeit, sophisticated, classical immunological, and molecular approaches were often unable to unequivocally determine the subpopulation structure of the dendritic cell lineage and not surprisingly, conflicting results about dendritic cell subsets co-existed throughout the last decades. With the advent of systems approaches and the most recent introduction of -omics approaches on the single cell level combined with multi-colour flow cytometry or mass cytometry, we now enter an era allowing us to define cell population structures with an unprecedented precision. We will report here on the most recent studies applying these technologies to human dendritic cells. Proper delineation of and definition of molecular signatures for the different human dendritic cell subsets will greatly facilitate studying these cells in the future: understanding their function under physiological as well as pathological conditions.
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Affiliation(s)
- Joachim L Schultze
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Str. 31, 53115 Bonn, Germany; Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and University of Bonn, Sigmund-Freud-Str. 27, 53175 Bonn, Germany.
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Carl-Troll-Str. 31, 53115 Bonn, Germany.
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Abstract
Purpose of review Hematopoietic stem cell (HSC) transplantation has yielded tremendous information on experimental properties of HSCs. Yet, it remains unclear whether transplantation reflects the physiology of hematopoiesis. A limitation is the difficulty in accessing HSC functions without isolation, in-vitro manipulation and readout for potential. New genetic fate mapping and clonal marking techniques now shed light on hematopoiesis under physiological conditions. Recent findings Transposon-based genetic marks were introduced across the entire hematopoietic system to follow the clonal dynamics of these tags over time. A polyclonal source downstream from stem cells was found responsible for the production of at least granulocytes. In independent experiments, HSCs were genetically marked in adult mice, and the kinetics of label emergence throughout the system was followed over time. These experiments uncovered that during physiological steady-state hematopoiesis large numbers of HSCs yield differentiated progeny. Individual HSCs were active only rarely, indicating their very slow periodicity of differentiation rather than quiescence. Summary Noninvasive genetic experiments in mice have identified a major role of stem and progenitor cells downstream from HSCs as drivers of adult hematopoiesis, and revealed that post-transplantation hematopoiesis differs quantitatively from normal steady-state hematopoiesis.
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Gabel M, Regoes RR, Graw F. More or less-On the influence of labelling strategies to infer cell population dynamics. PLoS One 2017; 12:e0185523. [PMID: 29045427 PMCID: PMC5646766 DOI: 10.1371/journal.pone.0185523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open
Abstract
The adoptive transfer of labelled cell populations has been an essential tool to determine and quantify cellular dynamics. The experimental methods to label and track cells over time range from fluorescent dyes over congenic markers towards single-cell labelling techniques, such as genetic barcodes. While these methods have been widely used to quantify cell differentiation and division dynamics, the extent to which the applied labelling strategy actually affects the quantification of the dynamics has not been determined so far. This is especially important in situations where measurements can only be obtained at a single time point, as e.g. due to organ harvest. To this end, we studied the appropriateness of various labelling strategies as characterised by the number of different labels and the initial number of cells per label to quantify cellular dynamics. We simulated adoptive transfer experiments in systems of various complexity that assumed either homoeostatic cellular turnover or cell expansion dynamics involving various steps of cell differentiation and proliferation. Re-sampling cells at a single time point, we determined the ability of different labelling strategies to recover the underlying kinetics. Our results indicate that cell transition and expansion rates are differently affected by experimental shortcomings, such as loss of cells during transfer or sampling, dependent on the labelling strategy used. Furthermore, uniformly distributed labels in the transferred population generally lead to more robust and less biased results than non-equal label sizes. In addition, our analysis indicates that certain labelling approaches incorporate a systematic bias for the identification of complex cell expansion dynamics.
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Affiliation(s)
- Michael Gabel
- Center for Modelling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, 69120 Heidelberg, Germany
- * E-mail: (MG); (FG)
| | - Roland R. Regoes
- Institute for Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Frederik Graw
- Center for Modelling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, 69120 Heidelberg, Germany
- * E-mail: (MG); (FG)
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Rizzetto S, Eltahla AA, Lin P, Bull R, Lloyd AR, Ho JWK, Venturi V, Luciani F. Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. Sci Rep 2017; 7:12781. [PMID: 28986563 PMCID: PMC5630586 DOI: 10.1038/s41598-017-12989-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/14/2017] [Indexed: 11/12/2022] Open
Abstract
Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% − 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.
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Affiliation(s)
- Simone Rizzetto
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Auda A Eltahla
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Peijie Lin
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, UNSW, Sydney, Australia
| | - Rowena Bull
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Andrew R Lloyd
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, UNSW, Sydney, Australia
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Fabio Luciani
- School of Medical Sciences, UNSW, Sydney, Australia. .,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia.
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42
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Miragaia RJ, Teichmann SA, Hagai T. Single-cell insights into transcriptomic diversity in immunity. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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43
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Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol 2017; 18:35-45. [DOI: 10.1038/nri.2017.76] [Citation(s) in RCA: 692] [Impact Index Per Article: 98.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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44
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Unravelling HIV-1 Latency, One Cell at a Time. Trends Microbiol 2017; 25:932-941. [PMID: 28668335 DOI: 10.1016/j.tim.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/22/2017] [Accepted: 06/01/2017] [Indexed: 12/14/2022]
Abstract
A single virus is capable of infecting and replicating in a single cell. Recent advances across single-cell omics technologies - genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics - will offer unprecedented opportunities to gain more insights into the various aspects of the life cycle of viruses and their impact on the host cell. Here, using the human immunodeficiency virus type 1 (HIV-1) as an example, we summarize the current knowledge and the future potential of single-cell omics in the investigation of an important aspect of the life cycle of HIV-1 that represents a major hurdle in achieving viral eradication, HIV-1 latency.
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45
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Stikvoort A, Chen Y, Rådestad E, Törlén J, Lakshmikanth T, Björklund A, Mikes J, Achour A, Gertow J, Sundberg B, Remberger M, Sundin M, Mattsson J, Brodin P, Uhlin M. Combining Flow and Mass Cytometry in the Search for Biomarkers in Chronic Graft-versus-Host Disease. Front Immunol 2017; 8:717. [PMID: 28674539 PMCID: PMC5474470 DOI: 10.3389/fimmu.2017.00717] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/02/2017] [Indexed: 01/02/2023] Open
Abstract
Chronic graft-versus-host disease (cGVHD) is a debilitating complication arising in around half of all patients treated with an allogeneic hematopoietic stem cell transplantation. Even though treatment of severe cGVHD has improved during recent years, it remains one of the main causes of morbidity and mortality in affected patients. Biomarkers in blood that could aid in the diagnosis and classification of cGVHD severity are needed for the development of novel treatment strategies that can alleviate symptoms and reduce the need for painful and sometimes complicated tissue biopsies. Methods that comprehensively profile complex biological systems such as the immune system can reveal unanticipated markers when used with the appropriate methods of data analysis. Here, we used mass cytometry, flow cytometry, enzyme-linked immunosorbent assay, and multiplex assays to systematically profile immune cell populations in 68 patients with varying grades of cGVHD. We identified multiple subpopulations across T, B, and NK-cell lineages that distinguished patients with cGVHD from those without cGVHD and which were associated in varying ways with severity of cGVHD. Specifically, initial flow cytometry demonstrated that patients with more severe cGVHD had lower mucosal-associated T cell frequencies, with a concomitant higher level of CD38 expression on T cells. Mass cytometry could identify unique subpopulations specific for cGVHD severity albeit with some seemingly conflicting results. For instance, patients with severe cGVHD had an increased frequency of activated B cells compared to patients with moderate cGVHD while activated B cells were found at a reduced frequency in patients with mild cGVHD compared to patients without cGVHD. Moreover, results indicate it may be possible to validate mass cytometry results with clinically viable, smaller flow cytometry panels. Finally, no differences in levels of blood soluble markers could be identified, with the exception for the semi-soluble combined marker B-cell activating factor/B cell ratio, which was increased in patients with mild cGVHD compared to patients without cGVHD. These findings suggest that interdependencies between such perturbed subpopulations of cells play a role in cGVHD pathogenesis and can serve as future diagnostic and therapeutic targets.
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Affiliation(s)
- Arwen Stikvoort
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Emelie Rådestad
- Department of Clinical Sciences, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
| | - Johan Törlén
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.,Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital, Stockholm, Sweden
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Jaromir Mikes
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Jens Gertow
- Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital, Stockholm, Sweden
| | - Berit Sundberg
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Mats Remberger
- Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Sundin
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Huddinge, Sweden.,Hematology/Immunology/HSCT Section, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Mattsson
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.,Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Neonatology, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Uhlin
- Department of Clinical Sciences, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden.,Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Huddinge, Sweden.,Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
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46
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Suffiotti M, Carmona SJ, Jandus C, Gfeller D. Identification of innate lymphoid cells in single-cell RNA-Seq data. Immunogenetics 2017; 69:439-450. [PMID: 28534222 DOI: 10.1007/s00251-017-1002-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/11/2017] [Indexed: 12/20/2022]
Abstract
Innate lymphoid cells (ILCs) consist of natural killer (NK) cells and non-cytotoxic ILCs that are broadly classified into ILC1, ILC2, and ILC3 subtypes. These cells recently emerged as important early effectors of innate immunity for their roles in tissue homeostasis and inflammation. Over the last few years, ILCs have been extensively studied in mouse and human at the functional and molecular level, including gene expression profiling. However, sorting ILCs with flow cytometry for gene expression analysis is a delicate and time-consuming process. Here we propose and validate a novel framework for studying ILCs at the transcriptomic level using single-cell RNA-Seq data. Our approach combines unsupervised clustering and a new cell type classifier trained on mouse ILC gene expression data. We show that this approach can accurately identify different ILCs, especially ILC2 cells, in human lymphocyte single-cell RNA-Seq data. Our new model relies only on genes conserved across vertebrates, thereby making it in principle applicable in any vertebrate species. Considering the rapid increase in throughput of single-cell RNA-Seq technology, our work provides a computational framework for studying ILC2 cells in single-cell transcriptomic data and may help exploring their conservation in distant vertebrate species.
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Affiliation(s)
- Madeleine Suffiotti
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Santiago J Carmona
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Camilla Jandus
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland
| | - David Gfeller
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
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47
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Gnjatic S, Bronte V, Brunet LR, Butler MO, Disis ML, Galon J, Hakansson LG, Hanks BA, Karanikas V, Khleif SN, Kirkwood JM, Miller LD, Schendel DJ, Tanneau I, Wigginton JM, Butterfield LH. Identifying baseline immune-related biomarkers to predict clinical outcome of immunotherapy. J Immunother Cancer 2017; 5:44. [PMID: 28515944 PMCID: PMC5432988 DOI: 10.1186/s40425-017-0243-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/26/2017] [Indexed: 12/31/2022] Open
Abstract
As cancer strikes, individuals vary not only in terms of factors that contribute to its occurrence and development, but as importantly, in their capacity to respond to treatment. While exciting new therapeutic options that mobilize the immune system against cancer have led to breakthroughs for a variety of malignancies, success is limited to a subset of patients. Pre-existing immunological features of both the host and the tumor may contribute to how patients will eventually fare with immunotherapy. A broad understanding of baseline immunity, both in the periphery and in the tumor microenvironment, is needed in order to fully realize the potential of cancer immunotherapy. Such interrogation of the tumor, blood, and host immune parameters prior to treatment is expected to identify biomarkers predictive of clinical outcome as well as to elucidate why some patients fail to respond to immunotherapy. To approach these opportunities for progress, the Society for Immunotherapy of Cancer (SITC) reconvened the Immune Biomarkers Task Force. Comprised of an international multidisciplinary panel of experts, Working Group 4 sought to make recommendations that focus on the complexity of the tumor microenvironment, with its diversity of immune genes, proteins, cells, and pathways naturally present at baseline and in circulation, and novel tools to aid in such broad analyses.
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Affiliation(s)
- Sacha Gnjatic
- Department of Hematology/Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, S5-105, 1470 Madison Avenue, Box 1128, New York, NY 10029 USA
| | - Vincenzo Bronte
- Head of Immunology Section, University of Verona, Piazzale Le L. A. Scuro, 10, Verona, Italy
| | - Laura Rosa Brunet
- Immodulon Therapeutics Ltd, Stockley Park, 6-9 The Square, Uxbridge, UK
| | - Marcus O Butler
- Princess Margaret Hospital/Ontario Cancer Institute, RM 9-622, 610 University Ave, Toronto, ON Canada
| | - Mary L Disis
- University of Washington, Tumor Vaccine Group, 850 Mercer Street, Box 358050, Seattle, WA 98109 USA
| | - Jérôme Galon
- INSERM - Cordeliers Research Center, Integrative Cancer Immunology Laboratory, 15 rue de l'Ecole de Médecine, Paris, France
| | - Leif G Hakansson
- CanImGuide Therapeutics AB, Domkyrkovägen 23, Hoellviken, Sweden
| | - Brent A Hanks
- Duke University Medical Center, 308 Research Drive, LSRC, Room C203, Box 3819, Durham, NC 27708 USA
| | - Vaios Karanikas
- Roche Innovation Center Zurich, Wagistrasse 18, Schlieren, Switzerland
| | - Samir N Khleif
- Georgia Cancer Center, Augusta University, 1120 15th Street, CN-2101A, Augusta, GA 30912 USA
| | - John M Kirkwood
- University of Pittsburgh, Hillman Cancer Center-Research Pavilion, 5117 Centre Avenue, Suite 1.32, Pittsburg, PA 15213 USA
| | - Lance D Miller
- Wake Forest School of Medicine, 1 Medical Center Blvd, Winston Salem, NC 27157 USA
| | - Dolores J Schendel
- Medigene Immunotherapies GmbH, Lochhamer Strasse 11, Planegg-Martinsried, Germany
| | | | - Jon M Wigginton
- MacroGenics, Inc., 9704 Medical Center Drive, Rockville, MD 20850 USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
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48
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49
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Johnston NR, Mitchell RK, Haythorne E, Pessoa MP, Semplici F, Ferrer J, Piemonti L, Marchetti P, Bugliani M, Bosco D, Berishvili E, Duncanson P, Watkinson M, Broichhagen J, Trauner D, Rutter GA, Hodson DJ. Beta Cell Hubs Dictate Pancreatic Islet Responses to Glucose. Cell Metab 2016; 24:389-401. [PMID: 27452146 PMCID: PMC5031557 DOI: 10.1016/j.cmet.2016.06.020] [Citation(s) in RCA: 314] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 05/17/2016] [Accepted: 06/23/2016] [Indexed: 12/02/2022]
Abstract
The arrangement of β cells within islets of Langerhans is critical for insulin release through the generation of rhythmic activity. A privileged role for individual β cells in orchestrating these responses has long been suspected, but not directly demonstrated. We show here that the β cell population in situ is operationally heterogeneous. Mapping of islet functional architecture revealed the presence of hub cells with pacemaker properties, which remain stable over recording periods of 2 to 3 hr. Using a dual optogenetic/photopharmacological strategy, silencing of hubs abolished coordinated islet responses to glucose, whereas specific stimulation restored communication patterns. Hubs were metabolically adapted and targeted by both pro-inflammatory and glucolipotoxic insults to induce widespread β cell dysfunction. Thus, the islet is wired by hubs, whose failure may contribute to type 2 diabetes mellitus.
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Affiliation(s)
- Natalie R Johnston
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Ryan K Mitchell
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Elizabeth Haythorne
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Maria Paiva Pessoa
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Francesca Semplici
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Jorge Ferrer
- Beta Cell Genome Regulation Lab, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Lorenzo Piemonti
- Diabetes Research Institute (HSR-DRI), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56126 Pisa, Italy
| | - Marco Bugliani
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56126 Pisa, Italy
| | - Domenico Bosco
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva University Hospitals and University of Geneva, 1205 Geneva, Switzerland
| | - Ekaterine Berishvili
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva University Hospitals and University of Geneva, 1205 Geneva, Switzerland
| | - Philip Duncanson
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael Watkinson
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Johannes Broichhagen
- Department of Chemistry, Ludwig-Maximilians-Universität München, and Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München, and Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - David J Hodson
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College London, London W12 0NN, UK; Institute of Metabolism and Systems Research (IMSR) and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TT, UK; Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham B15 2TH, UK.
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50
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Morris DL, Evans-Molina C. Metabolic dysfunction and adipose tissue macrophages: is there more to glean from studying the lean?: Comment on "Adipose tissue infiltration in normal-weight subjects and its impact on metabolic function" by Moreno-Indias et al. Transl Res 2016; 172:1-5. [PMID: 26963742 PMCID: PMC4866879 DOI: 10.1016/j.trsl.2016.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 02/18/2016] [Indexed: 02/06/2023]
Affiliation(s)
- David L Morris
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Ind 46202, USA.
| | - Carmella Evans-Molina
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Ind 46202, USA; The Roudebush VA Medical Center, Indianapolis, Ind 46202, USA; The Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Ind 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Ind 46202, USA; Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Ind 46202, USA.
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