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Seo D, Sun H, Choi Y. Simultaneous Protein Colorful Imaging via Raman Signal Classification. NANO LETTERS 2024. [PMID: 38869082 DOI: 10.1021/acs.nanolett.4c01654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Protein imaging aids diagnosis and drug development by revealing protein-drug interactions or protein levels. However, the challenges of imaging multiple proteins, reduced sensitivity, and high reliance on specific protein properties such as Raman peaks or refractive index hinder the understanding. Here, we introduce multiprotein colorful imaging through Raman signal classification. Our method utilized machine learning-assisted classification of Raman signals, which are the distinctive features of label-free proteins. As a result, three types of proteins could be imaged simultaneously. In addition, we could quantify individual proteins from a mixture of multiple proteins over a wide detection range (10 fg/mL-1 μg/mL). These results showed a 1000-fold improvement in sensitivity and a 30-fold increase in the upper limit of detection compared to existing methods. These advances will enhance our understanding of biology and facilitate the development of disease diagnoses and treatments.
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Affiliation(s)
- Dongkwon Seo
- Department of Bio-convergence Engineering, Korea University, Seoul 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, Republic of Korea
| | - Hayeon Sun
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- Department of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yeonho Choi
- Department of Bio-convergence Engineering, Korea University, Seoul 02841, Republic of Korea
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- Department of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
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2
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Sun Y, Kong L, Huang J, Deng H, Bian X, Li X, Cui F, Dou L, Cao C, Zou Q, Zhang Z. A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data. Brief Funct Genomics 2024:elae023. [PMID: 38860675 DOI: 10.1093/bfgp/elae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/29/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
In recent years, the application of single-cell transcriptomics and spatial transcriptomics analysis techniques has become increasingly widespread. Whether dealing with single-cell transcriptomic or spatial transcriptomic data, dimensionality reduction and clustering are indispensable. Both single-cell and spatial transcriptomic data are often high-dimensional, making the analysis and visualization of such data challenging. Through dimensionality reduction, it becomes possible to visualize the data in a lower-dimensional space, allowing for the observation of relationships and differences between cell subpopulations. Clustering enables the grouping of similar cells into the same cluster, aiding in the identification of distinct cell subpopulations and revealing cellular diversity, providing guidance for downstream analyses. In this review, we systematically summarized the most widely recognized algorithms employed for the dimensionality reduction and clustering analysis of single-cell transcriptomic and spatial transcriptomic data. This endeavor provides valuable insights and ideas that can contribute to the development of novel tools in this rapidly evolving field.
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Affiliation(s)
- Yidi Sun
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Lingling Kong
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Jiayi Huang
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Hongyan Deng
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Xinling Bian
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Xingfeng Li
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Feifei Cui
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
| | - Lijun Dou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland, OH 44106, United States
| | - Chen Cao
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 210029, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Zilong Zhang
- School of Computer Science and Technology, Hainan University, Haikou 570228, China
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Valdés JJ, Tchagang AB. Novel machine learning insights into the QM7b and QM9 quantum mechanics datasets. J Comput Chem 2024; 45:1193-1214. [PMID: 38329198 DOI: 10.1002/jcc.27295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024]
Abstract
This paper (i) explores the internal structure of two quantum mechanics datasets (QM7b, QM9), composed of several thousands of organic molecules and described in terms of electronic properties, and (ii) further explores an inverse design approach to molecular design consisting of using machine learning methods to approximate the atomic composition of molecules, using QM9 data. Understanding the structure and characteristics of this kind of data is important when predicting the atomic composition from physical-chemical properties in inverse molecular designs. Intrinsic dimension analysis, clustering, and outlier detection methods were used in the study. They revealed that for both datasets the intrinsic dimensionality is several times smaller than the descriptive dimensions. The QM7b data is composed of well-defined clusters related to atomic composition. The QM9 data consists of an outer region predominantly composed of outliers, and an inner, core region that concentrates clustered inliner objects. A significant relationship exists between the number of atoms in the molecule and its outlier/inliner nature. The spatial structure exhibits a relationship with molecular weight. Despite the structural differences between the two datasets, the predictability of variables of interest for inverse molecular design is high. This is exemplified by models estimating the number of atoms of the molecule from both the original properties and from lower dimensional embedding spaces. In the generative approach the input is given by a set of desired properties of the molecule and the output is an approximation of the atomic composition in terms of its constituent chemical elements. This could serve as the starting region for further search in the huge space determined by the set of possible chemical compounds. The quantum mechanic's dataset QM9 is used in the study, composed of 133,885 small organic molecules and 19 electronic properties. Different multi-target regression approaches were considered for predicting the atomic composition from the properties, including feature engineering techniques in an auto-machine learning framework. High-quality models were found that predict the atomic composition of the molecules from their electronic properties, as well as from a subset of only 52.6% size. Feature selection worked better than feature generation. The results validate the generative approach to inverse molecular design.
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Affiliation(s)
- Julio J Valdés
- National Research Council Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Alain B Tchagang
- National Research Council Canada, Digital Technologies Research Centre, Ottawa, Canada
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4
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Zhou Y, Cheng T, Tang K, Li H, Luo C, Yu F, Xiao F, Jin L, Hung IFN, Lu L, Yuen KY, Chan JFW, Yuan S, Sun H. Integration of metalloproteome and immunoproteome reveals a tight link of iron-related proteins with COVID-19 pathogenesis and immunity. Clin Immunol 2024; 263:110205. [PMID: 38575044 DOI: 10.1016/j.clim.2024.110205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Increasing clinical data show that the imbalance of host metallome is closely associated with different kinds of disease, however, the intrinsic mechanisms of action of metals in immunity and pathogenesis of disease remain largely undefined. There is lack of multiplexed profiling system to integrate the metalloproteome-immunoproteome information at systemic level for exploring the roles of metals in immunity and disease pathogenesis. In this study, we build up a metal-coding assisted multiplexed proteome assay platform for serum metalloproteomic and immunoproteomic profiling. By taking COVID-19 as a showcase, we unbiasedly uncovered the most evident modulation of iron-related proteins, i.e., Ft and Tf, in serum of severe COVID-19 patients, and the value of Ft/Tf could work as a robust biomarker for COVID-19 severity stratification, which overtakes the well-established clinical risk factors (cytokines). We further uncovered a tight association of transferrin with inflammation mediator IL-10 in COVID-19 patients, which was proved to be mainly governed by the monocyte/macrophage of liver, shedding light on new pathophysiological and immune regulatory mechanisms of COVID-19 disease. We finally validated the beneficial effects of iron chelators as anti-viral agents in SARS-CoV-2-infected K18-hACE2 mice through modulation of iron dyshomeostasis and alleviating inflammation response. Our findings highlight the critical role of liver-mediated iron dysregulation in COVID-19 disease severity, providing solid evidence on the involvement of iron-related proteins in COVID-19 pathophysiology and immunity.
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Affiliation(s)
- Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics for Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China
| | - Tianfan Cheng
- Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong, PR China
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics for Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China
| | - Fu Yu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China
| | - Fan Xiao
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong, PR China
| | - Ivan Fan-Ngai Hung
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong, Hong Kong Special Administrative Region, PR China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China; Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, PR China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, PR China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, PR China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China; Guangzhou Laboratory, Guangdong Province, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China; Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, PR China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, PR China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, PR China; Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China; Guangzhou Laboratory, Guangdong Province, China.
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China; Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, PR China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, PR China.
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics for Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, PR China.
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5
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Fan L, Liu J, Hu W, Chen Z, Lan J, Zhang T, Zhang Y, Wu X, Zhong Z, Zhang D, Zhang J, Qin R, Chen H, Zong Y, Zhang J, Chen B, Jiang J, Cheng J, Zhou J, Gao Z, Liu Z, Chai Y, Fan J, Wu P, Chen Y, Zhu Y, Wang K, Yuan Y, Huang P, Zhang Y, Feng H, Song K, Zeng X, Zhu W, Hu X, Yin W, Chen W, Wang J. Targeting pro-inflammatory T cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans. Cell Res 2024; 34:407-427. [PMID: 38491170 PMCID: PMC11143203 DOI: 10.1038/s41422-024-00945-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/24/2024] [Indexed: 03/18/2024] Open
Abstract
Atherosclerosis (AS), a leading cause of cardio-cerebrovascular disease worldwide, is driven by the accumulation of lipid contents and chronic inflammation. Traditional strategies primarily focus on lipid reduction to control AS progression, leaving residual inflammatory risks for major adverse cardiovascular events (MACEs). While anti-inflammatory therapies targeting innate immunity have reduced MACEs, many patients continue to face significant risks. Another key component in AS progression is adaptive immunity, but its potential role in preventing AS remains unclear. To investigate this, we conducted a retrospective cohort study on tumor patients with AS plaques. We found that anti-programmed cell death protein 1 (PD-1) monoclonal antibody (mAb) significantly reduces AS plaque size. With multi-omics single-cell analyses, we comprehensively characterized AS plaque-specific PD-1+ T cells, which are activated and pro-inflammatory. We demonstrated that anti-PD-1 mAb, when captured by myeloid-expressed Fc gamma receptors (FcγRs), interacts with PD-1 expressed on T cells. This interaction turns the anti-PD-1 mAb into a substitute PD-1 ligand, suppressing T-cell functions in the PD-1 ligands-deficient context of AS plaques. Further, we conducted a prospective cohort study on tumor patients treated with anti-PD-1 mAb with or without Fc-binding capability. Our analysis shows that anti-PD-1 mAb with Fc-binding capability effectively reduces AS plaque size, while anti-PD-1 mAb without Fc-binding capability does not. Our work suggests that T cell-targeting immunotherapy can be an effective strategy to resolve AS in humans.
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Affiliation(s)
- Lin Fan
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China
| | - Junwei Liu
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Wei Hu
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zexin Chen
- Center of Clinical Epidemiology and Biostatistics and Department of Scientific Research, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Lan
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, China
- Department of Bioinformatics, The Basic Medical School of Chongqing Medical University, Chongqing, China
| | - Tongtong Zhang
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yang Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianpeng Wu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhiwei Zhong
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Danyang Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jinlong Zhang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Rui Qin
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hui Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Zong
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianmin Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bing Chen
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Jiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jifang Cheng
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingyi Zhou
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhiwei Gao
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhenjie Liu
- Department of Vascular Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Chai
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Junqiang Fan
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinxuan Chen
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuefeng Zhu
- Department of Vascular Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kai Wang
- Department of Respiratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Department of Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pintong Huang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huiqin Feng
- Department of Clinical Research Center, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kaichen Song
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xun Zeng
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Zhu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xinyang Hu
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China.
| | - Weiwei Yin
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Wei Chen
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Department of Cell Biology, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China.
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China.
- The MOE Frontier Science Center for Brain Science & Brain-machine Integration, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jian'an Wang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, Zhejiang, China.
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, Zhejiang, China.
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6
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Debreceni IL, Barr JY, Upton EM, Chen YG, Lieberman SM. IL-27 promotes pathogenic T cells in a mouse model of Sjögren's disease. Clin Immunol 2024; 264:110260. [PMID: 38788885 DOI: 10.1016/j.clim.2024.110260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/25/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Sjögren's disease (SjD) is a chronic autoimmune disease characterized by focal lymphocytic inflammation in lacrimal and salivary glands. We recently identified IL-27 as a requisite signal for the spontaneous SjD-like manifestations in nonobese diabetic (NOD) mice. Here, we define T cell-intrinsic effects of IL-27 in lacrimal gland disease in NOD mice. IL-27 receptor was required by both CD4 T effector (Te) cells and CD8 T cells to mediate focal inflammation. Intrinsic IL-27 signaling was associated with PD-1 and ICOS expressing T follicular helper (Tfh)-like CD4 Te cells within lacrimal glands, including subsets defined by CD73 or CD39 expression. CD8 T cells capable of IL-27 signaling also expressed PD-1 with subsets expressing ICOS and CD73 demonstrating a T follicular cytotoxic (Tfc)-like cell phenotype and others expressing a CD39hi exhausted-like phenotype. These findings suggest IL-27 is a key early signal driving a follicular-type response in lacrimal gland inflammation in NOD mice.
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Affiliation(s)
- Ivy L Debreceni
- Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, 500 Newton Road, 2191 Medical Laboratories, Iowa City, IA 52242, USA; Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, 500 Newton Road, 2191 Medical Laboratories, Iowa City, IA 52242, USA.
| | - Jennifer Y Barr
- Scientific Editing and Research Communication Core, Carver College of Medicine, University of Iowa, 451 Newton Road, 130 Medicine Administration Building, Iowa City, IA 52242, USA.
| | - Ellen M Upton
- Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, 500 Newton Road, 2191 Medical Laboratories, Iowa City, IA 52242, USA; Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 451 Newton Road, 200 Medicine Administration Building, Iowa City, IA 52242, USA.
| | - Yi-Guang Chen
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Scott M Lieberman
- Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, 500 Newton Road, 2191 Medical Laboratories, Iowa City, IA 52242, USA; Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, 500 Newton Road, 2191 Medical Laboratories, Iowa City, IA 52242, USA.
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7
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Zeng X, Meng FF, Wen ML, Li SJ, Li Y. GNNGL-PPI: multi-category prediction of protein-protein interactions using graph neural networks based on global graphs and local subgraphs. BMC Genomics 2024; 25:406. [PMID: 38724906 PMCID: PMC11080243 DOI: 10.1186/s12864-024-10299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/10/2024] [Indexed: 05/13/2024] Open
Abstract
Most proteins exert their functions by interacting with other proteins, making the identification of protein-protein interactions (PPI) crucial for understanding biological activities, pathological mechanisms, and clinical therapies. Developing effective and reliable computational methods for predicting PPI can significantly reduce the time-consuming and labor-intensive associated traditional biological experiments. However, accurately identifying the specific categories of protein-protein interactions and improving the prediction accuracy of the computational methods remain dual challenges. To tackle these challenges, we proposed a novel graph neural network method called GNNGL-PPI for multi-category prediction of PPI based on global graphs and local subgraphs. GNNGL-PPI consisted of two main components: using Graph Isomorphism Network (GIN) to extract global graph features from PPI network graph, and employing GIN As Kernel (GIN-AK) to extract local subgraph features from the subgraphs of protein vertices. Additionally, considering the imbalanced distribution of samples in each category within the benchmark datasets, we introduced an Asymmetric Loss (ASL) function to further enhance the predictive performance of the method. Through evaluations on six benchmark test sets formed by three different dataset partitioning algorithms (Random, BFS, DFS), GNNGL-PPI outperformed the state-of-the-art multi-category prediction methods of PPI, as measured by the comprehensive performance evaluation metric F1-measure. Furthermore, interpretability analysis confirmed the effectiveness of GNNGL-PPI as a reliable multi-category prediction method for predicting protein-protein interactions.
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Affiliation(s)
- Xin Zeng
- College of Mathematics and Computer Science, Dali University, 671003, Dali, China
| | - Fan-Fang Meng
- College of Mathematics and Computer Science, Dali University, 671003, Dali, China
| | - Meng-Liang Wen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650000, Kunming, China
| | - Shu-Juan Li
- Yunnan Institute of Endemic Diseases Control & Prevention, 671000, Dali, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, 671003, Dali, China.
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8
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Shu C, Street K, Breton CV, Bastain TM, Wilson ML. A review of single-cell transcriptomics and epigenomics studies in maternal and child health. Epigenomics 2024:1-20. [PMID: 38709139 DOI: 10.1080/17501911.2024.2343276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
Single-cell sequencing technologies enhance our understanding of cellular dynamics throughout pregnancy. We outlined the workflow of single-cell sequencing techniques and reviewed single-cell studies in maternal and child health. We conducted a literature review of single cell studies on maternal and child health using PubMed. We summarized the findings from 16 single-cell atlases of the human and mammalian placenta across gestational stages and 31 single-cell studies on maternal exposures and complications including infection, obesity, diet, gestational diabetes, pre-eclampsia, environmental exposure and preterm birth. Single-cell studies provides insights on novel cell types in placenta and cell type-specific marks associated with maternal exposures and complications.
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Affiliation(s)
- Chang Shu
- Center for Genetic Epidemiology, Division of Epidemiology & Genetics, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Kelly Street
- Division of Biostatistics, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Carrie V Breton
- Division of Environmental Health, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Theresa M Bastain
- Division of Environmental Health, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Melissa L Wilson
- Division of Disease Prevention, Policy, & Global Health, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles,CA USA
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9
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Qayoom A, Khuhro MA, Kumar K, Waqas M, Saeed U, ur Rehman S, Wu Y, Wang S. A novel approach for credit card fraud transaction detection using deep reinforcement learning scheme. PeerJ Comput Sci 2024; 10:e1998. [PMID: 38699207 PMCID: PMC11065415 DOI: 10.7717/peerj-cs.1998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/27/2024] [Indexed: 05/05/2024]
Abstract
Online transactions are still the backbone of the financial industry worldwide today. Millions of consumers use credit cards for their daily transactions, which has led to an exponential rise in credit card fraud. Over time, many variations and schemes of fraudulent transactions have been reported. Nevertheless, it remains a difficult task to detect credit card fraud in real-time. It can be assumed that each person has a unique transaction pattern that may change over time. The work in this article aims to (1) understand how deep reinforcement learning can play an important role in detecting credit card fraud with changing human patterns, and (2) develop a solution architecture for real-time fraud detection. Our proposed model utilizes the Deep Q network for real-time detection. The Kaggle dataset available online was used to train and test the model. As a result, a validation performance of 97.10% was achieved with the proposed deep learning component. In addition, the reinforcement learning component has a learning rate of 80%. The proposed model was able to learn patterns autonomously based on previous events. It adapts to the pattern changes over time and can take them into account without further manual training.
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Affiliation(s)
- Abdul Qayoom
- School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Department of Computer Science, Lasbela University of Agriculture, Water and Marine Science, Uthal, Lasbela, Balochistan, Pakistan
| | - Mansoor Ahmed Khuhro
- Department of Artificial Intelligence and Mathematical Sciences, Sindh Madressa-tul-Islam University, Aiwan-e-Tijarat Road, Karachi, Sindh, Pakistan
| | - Kamlesh Kumar
- Department of Software Engineering, Sindh Madressa-tul-Islam University, Aiwan-e-Tijarat Road, Karachi, Sindh, Pakistan
| | - Muhammad Waqas
- School of Software Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Umair Saeed
- Department of Computer Science, Bahria University, Islamabad, Pakistan
| | - Shafiq ur Rehman
- Department of Computing and Information Technology, Mir Chakar Khan Rind University of Technology, Dera Ghazi Khan, Punjab, Pakistan
| | - Yadong Wu
- School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, China
- School of Computer Science and Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan, China
| | - Song Wang
- School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan, China
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10
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Amarin JZ, Dulek DE, Simmons J, Hayek H, Chappell JD, Nochowicz CH, Kitko CL, Schuster JE, Muñoz FM, Bocchini CE, Moulton EA, Coffin SE, Freedman JL, Ardura MI, Wattier RL, Maron G, Grimley M, Paulsen G, Danziger-Isakov L, Carpenter PA, Englund JA, Halasa NB, Spieker AJ, Kalams SA. Immunophenotypic predictors of influenza vaccine immunogenicity in pediatric hematopoietic cell transplant recipients. Blood Adv 2024; 8:1880-1892. [PMID: 38386973 PMCID: PMC11007439 DOI: 10.1182/bloodadvances.2023012118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
ABSTRACT Pediatric hematopoietic cell transplant (HCT) recipients exhibit poor serologic responses to influenza vaccination early after transplant. To facilitate the optimization of influenza vaccination timing, we sought to identify B- and T-cell subpopulations associated with influenza vaccine immunogenicity in this population. We used mass cytometry to phenotype peripheral blood mononuclear cells collected from pediatric HCT recipients enrolled in a multicenter influenza vaccine trial comparing high- and standard-dose formulations over 3 influenza seasons (2016-2019). We fit linear regression models to estimate relationships between immune cell subpopulation numbers before vaccination and prevaccination to postvaccination geometric mean fold rises in antigen-specific (A/H3N2, A/H1N1, and B/Victoria) serum hemagglutination inhibition antibody titers (28-42 days, and ∼6 months after 2 doses). For cell subpopulations identified as predictive of a response to all 3 antigens, we conducted a sensitivity analysis including time after transplant as an additional covariate. Among 156 HCT recipients, we identified 33 distinct immune cell subpopulations; 7 significantly predicted responses to all 3 antigens 28 to 42 days after a 2-dose vaccine series, irrespective of vaccine dose. We also found evidence that baseline absolute numbers of naïve B cells, naïve CD4+ T cells, and circulating T follicular helper cells predicted peak and sustained vaccine-induced titers irrespective of dose or timing of posttransplant vaccine administration. In conclusion, several B- and T-cell subpopulations predicted influenza vaccine immunogenicity in pediatric HCT recipients. This study provides insights into the immune determinants of vaccine responses and may help guide the development of tailored vaccination strategies for this vulnerable population.
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Affiliation(s)
- Justin Z. Amarin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
- Epidemiology Doctoral Program, School of Medicine, Vanderbilt University, Nashville, TN
| | - Daniel E. Dulek
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Joshua Simmons
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Haya Hayek
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - James D. Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Carrie L. Kitko
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Flor M. Muñoz
- Division of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
- Department of Molecular Virology and Microbiology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Claire E. Bocchini
- Division of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Elizabeth A. Moulton
- Division of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Susan E. Coffin
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L. Freedman
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Monica I. Ardura
- Division of Infectious Diseases and Host Defense Program, Nationwide Children’s Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Rachel L. Wattier
- Department of Pediatrics, University of California San Francisco and Benioff Children’s Hospital, San Francisco, CA
| | - Gabriela Maron
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN
| | - Michael Grimley
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Grant Paulsen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Lara Danziger-Isakov
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Paul A. Carpenter
- Department of Pediatrics, University of Washington and Seattle Children’s Research Institute, Seattle, WA
| | - Janet A. Englund
- Department of Pediatrics, University of Washington and Seattle Children’s Research Institute, Seattle, WA
| | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew J. Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Spyros A. Kalams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
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11
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Pedace L, Pizzi S, Abballe L, Vinci M, Antonacci C, Patrizi S, Nardini C, Del Bufalo F, Rossi S, Pericoli G, Gianno F, Besharat ZM, Tiberi L, Mastronuzzi A, Ferretti E, Tartaglia M, Locatelli F, Ciolfi A, Miele E. Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling. NPJ Precis Oncol 2024; 8:92. [PMID: 38637626 PMCID: PMC11026496 DOI: 10.1038/s41698-024-00578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/13/2024] [Indexed: 04/20/2024] Open
Abstract
In vitro models of pediatric brain tumors (pBT) are instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; thus, ideally, they should recapitulate the original tumor. We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). We performed a t-SNE classification and identified differentially methylated regions in tumors compared to cell models. Early cell cultures recapitulate the original tumor, but serum media and 2D culturing were demonstrated to significantly contribute to the divergence of DNAm profiles from the parental ones. All divergent cells clustered together acquiring a common deregulated epigenetic signature suggesting a shared selective pressure. We identified a set of hypomethylated genes shared among unfaithful cells converging on response to growth factors and migration pathways, such as signaling cascade activation, tissue organization, and cellular migration. In conclusion, DNAm and CNV are informative tools that should be used to assess the recapitulation of pBT-cells from parental tumors.
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Affiliation(s)
- Lucia Pedace
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Luana Abballe
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Vinci
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Celeste Antonacci
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Patrizi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Nardini
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Del Bufalo
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giulia Pericoli
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomic Pathology, Sapienza University, Rome, Italy
| | | | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Angela Mastronuzzi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, "Sapienza" University, 00161, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Franco Locatelli
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.
| | - Evelina Miele
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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12
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Feng DC, Zhu WZ, Wang J, Li DX, Shi X, Xiong Q, You J, Han P, Qiu S, Wei Q, Yang L. The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapy. Mil Med Res 2024; 11:21. [PMID: 38605399 PMCID: PMC11007901 DOI: 10.1186/s40779-024-00526-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
In recent years, advancements in single-cell and spatial transcriptomics, which are highly regarded developments in the current era, particularly the emerging integration of single-cell and spatiotemporal transcriptomics, have enabled a detailed molecular comprehension of the complex regulation of cell fate. The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine. Currently, single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors. Starting from the perspective of RNA sequencing technology, this review outlined the significance of single-cell RNA sequencing (scRNA-seq) in prostate cancer research, encompassing preclinical medicine and clinical applications. We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies, as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis, treatment, and drug resistance characteristics of prostate cancer. These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer. Furthermore, we explore the potential clinical applications stemming from other single-cell technologies in this review, paving the way for future research in precision medicine.
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Affiliation(s)
- De-Chao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Division of Surgery & Interventional Science, University College London, London, WC1E 6BT, UK.
| | - Wei-Zhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Deng-Xiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xu Shi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiao Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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13
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Zhao Q, Zheng Y, Qiu Y, Yu Y, Huang M, Wu Y, Chen X, Huang Y, Cui S, Zhuang S. Graph Convolutional Network-Enhanced Model for Screening Persistent, Mobile, and Toxic and Very Persistent and Very Mobile Substances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6149-6157. [PMID: 38556993 DOI: 10.1021/acs.est.4c01201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The global management for persistent, mobile, and toxic (PMT) and very persistent and very mobile (vPvM) substances has been further strengthened with the rapid increase of emerging contaminants. The development of a ready-to-use and publicly available tool for the high-throughput screening of PMT/vPvM substances is thus urgently needed. However, the current model building with the coupling of conventional algorithms, small-scale data set, and simplistic features hinders the development of a robust model for screening PMT/vPvM with wide application domains. Here, we construct a graph convolutional network (GCN)-enhanced model with feature fusion of a molecular graph and molecular descriptors to effectively utilize the significant correlation between critical descriptors and PMT/vPvM substances. The model is built with 213,084 substances following the latest PMT classification criteria. The application domains of the GCN-enhanced model assessed by kernel density estimation demonstrate the high suitability for high-throughput screening PMT/vPvM substances with both a high accuracy rate (86.6%) and a low false-negative rate (6.8%). An online server named PMT/vPvM profiler is further developed with a user-friendly web interface (http://www.pmt.zj.cn/). Our study facilitates a more efficient evaluation of PMT/vPvM substances with a globally accessible screening platform.
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Affiliation(s)
- Qiming Zhao
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yuting Zheng
- Solid Waste and Chemicals Management Center, Ministry of Ecology and Environment of the People's Republic of China, Beijing 100029, China
| | - Yu Qiu
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yang Yu
- Solid Waste and Chemicals Management Center, Ministry of Ecology and Environment of the People's Republic of China, Beijing 100029, China
| | - Meiling Huang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yiqu Wu
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiyu Chen
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Huang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shixuan Cui
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shulin Zhuang
- College of Environmental and Resource Sciences, and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
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14
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Putri GH, Howitt G, Marsh-Wakefield F, Ashhurst TM, Phipson B. SuperCellCyto: enabling efficient analysis of large scale cytometry datasets. Genome Biol 2024; 25:89. [PMID: 38589921 PMCID: PMC11003185 DOI: 10.1186/s13059-024-03229-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Advancements in cytometry technologies have enabled quantification of up to 50 proteins across millions of cells at single cell resolution. Analysis of cytometry data routinely involves tasks such as data integration, clustering, and dimensionality reduction. While numerous tools exist, many require extensive run times when processing large cytometry data containing millions of cells. Existing solutions, such as random subsampling, are inadequate as they risk excluding rare cell subsets. To address this, we propose SuperCellCyto, an R package that builds on the SuperCell tool which groups highly similar cells into supercells. SuperCellCyto is available on GitHub ( https://github.com/phipsonlab/SuperCellCyto ) and Zenodo ( https://doi.org/10.5281/zenodo.10521294 ).
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Affiliation(s)
- Givanna H Putri
- The Walter and Eliza Hall Institute of Medical Research and The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
| | - George Howitt
- Peter MacCallum Cancer Centre and The Sir Peter MacCallum, Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Felix Marsh-Wakefield
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia
| | - Thomas M Ashhurst
- Sydney Cytometry Core Research Facility and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Belinda Phipson
- The Walter and Eliza Hall Institute of Medical Research and The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
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15
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Cui C, Tang X, Xing J, Sheng X, Chi H, Zhan W. Single-cell RNA-seq revealed heterogeneous responses and functional differentiation of hemocytes against white spot syndrome virus infection in Litopenaeus vannamei. J Virol 2024; 98:e0180523. [PMID: 38323810 PMCID: PMC10949519 DOI: 10.1128/jvi.01805-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Shrimp hemocytes are the vital immune cells participating in innate immune response to defend against viruses. However, the lack of specific molecular markers for shrimp hemocyte hindered the insightful understanding of their functional clusters and differential roles in combating microbial infections. In this study, we used single-cell RNA sequencing to map the transcriptomic landscape of hemocytes from the white spot syndrome virus (WSSV)-infected Litopenaeus vannamei and conjointly analyzed with our previous published single-cell RNA sequencing technology data from the healthy hemocytes. A total of 16 transcriptionally distinct cell clusters were identified, which occupied different proportions in healthy and WSSV-infected hemocytes and exerted differential roles in antiviral immune response. Following mapping of the sequencing data to the WSSV genome, we found that all types of hemocytes could be invaded by WSSV virions, especially the cluster 8, which showed the highest transcriptional levels of WSSV genes and exhibited a cell type-specific antiviral response to the viral infection. Further evaluation of the cell clusters revealed the delicate dynamic balance between hemocyte immune response and viral infestation. Unsupervised pseudo-time analysis of hemocytes showed that the hemocytes in immune-resting state could be significantly activated upon WSSV infection and then functionally differentiated to different hemocyte subsets. Collectively, our results revealed the differential responses of shrimp hemocytes and the process of immune-functional differentiation post-WSSV infection, providing essential resource for the systematic insight into the synergistic immune response mechanism against viral infection among hemocyte subtypes. IMPORTANCE Current knowledge of shrimp hemocyte classification mainly comes from morphology, which hinder in-depth characterization of cell lineage development, functional differentiation, and different immune response of hemocyte types during pathogenic infections. Here, single-cell RNA sequencing was used for mapping hemocytes during white spot syndrome virus (WSSV) infection in Litopenaeus vannamei, identifying 16 cell clusters and evaluating their potential antiviral functional characteristics. We have described the dynamic balance between viral infestation and hemocyte immunity. And the functional differentiation of hemocytes under WSSV stimulation was further characterized. Our results provided a comprehensive transcriptional landscape and revealed the heterogeneous immune response in shrimp hemocytes during WSSV infection.
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Affiliation(s)
- Chuang Cui
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China
| | - Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Heng Chi
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Huang C, Wang X, Wang Y, Feng Y, Wang X, Chen S, Yan P, Liao J, Zhang Q, Mao C, Li Y, Wang L, Wang X, Yi W, Cai W, Chen S, Hong N, He W, Chen J, Jin W. Sirpα on tumor-associated myeloid cells restrains antitumor immunity in colorectal cancer independent of its interaction with CD47. NATURE CANCER 2024; 5:500-516. [PMID: 38200243 DOI: 10.1038/s43018-023-00691-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/15/2023] [Indexed: 01/12/2024]
Abstract
Immunosuppressive myeloid cells hinder immunotherapeutic efficacy in tumors, but the precise mechanisms remain undefined. Here, by performing single-cell RNA sequencing in colorectal cancer tissues, we found tumor-associated macrophages and granulocytic myeloid-derived suppressor cells increased most compared to their counterparts in normal tissue and displayed the highest immune-inhibitory signatures among all immunocytes. These cells exhibited significantly increased expression of immunoreceptor tyrosine-based inhibitory motif-bearing receptors, including SIRPA. Notably, Sirpa-/- mice were more resistant to tumor progression than wild-type mice. Moreover, Sirpα deficiency reprogramed the tumor microenvironment through expansion of TAM_Ccl8hi and gMDSC_H2-Q10hi subsets showing strong antitumor activity. Sirpa-/- macrophages presented strong phagocytosis and antigen presentation to enhance T cell activation and proliferation. Furthermore, Sirpa-/- macrophages facilitated T cell recruitment via Syk/Btk-dependent Ccl8 secretion. Therefore, Sirpα deficiency enhances innate and adaptive immune activation independent of expression of CD47 and Sirpα blockade could be a promising strategy to improve cancer immunotherapy efficacy.
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Affiliation(s)
- Chunliu Huang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xuefei Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yingzhao Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yongyi Feng
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shan Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Peidong Yan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jing Liao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qi Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chengzhou Mao
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, China
| | - Yang Li
- Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wei Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Weibin Cai
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Gastrointestinal Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Wenfei Jin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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17
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Jiang J, Liu H, He L, Pei M, Lin T, Yang H, Yang J, Gong J, Wei X, Zhu M, Wu G, Li Z. HM_ADET: a hybrid model for automatic detection of eyelid tumors based on photographic images. Biomed Eng Online 2024; 23:25. [PMID: 38419078 PMCID: PMC10903075 DOI: 10.1186/s12938-024-01221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The accurate detection of eyelid tumors is essential for effective treatment, but it can be challenging due to small and unevenly distributed lesions surrounded by irrelevant noise. Moreover, early symptoms of eyelid tumors are atypical, and some categories of eyelid tumors exhibit similar color and texture features, making it difficult to distinguish between benign and malignant eyelid tumors, particularly for ophthalmologists with limited clinical experience. METHODS We propose a hybrid model, HM_ADET, for automatic detection of eyelid tumors, including YOLOv7_CNFG to locate eyelid tumors and vision transformer (ViT) to classify benign and malignant eyelid tumors. First, the ConvNeXt module with an inverted bottleneck layer in the backbone of YOLOv7_CNFG is employed to prevent information loss of small eyelid tumors. Then, the flexible rectified linear unit (FReLU) is applied to capture multi-scale features such as texture, edge, and shape, thereby improving the localization accuracy of eyelid tumors. In addition, considering the geometric center and area difference between the predicted box (PB) and the ground truth box (GT), the GIoU_loss was utilized to handle cases of eyelid tumors with varying shapes and irregular boundaries. Finally, the multi-head attention (MHA) module is applied in ViT to extract discriminative features of eyelid tumors for benign and malignant classification. RESULTS Experimental results demonstrate that the HM_ADET model achieves excellent performance in the detection of eyelid tumors. In specific, YOLOv7_CNFG outperforms YOLOv7, with AP increasing from 0.763 to 0.893 on the internal test set and from 0.647 to 0.765 on the external test set. ViT achieves AUCs of 0.945 (95% CI 0.894-0.981) and 0.915 (95% CI 0.860-0.955) for the classification of benign and malignant tumors on the internal and external test sets, respectively. CONCLUSIONS Our study provides a promising strategy for the automatic diagnosis of eyelid tumors, which could potentially improve patient outcomes and reduce healthcare costs.
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Affiliation(s)
- Jiewei Jiang
- School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Haiyang Liu
- School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Lang He
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Mengjie Pei
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Tongtong Lin
- School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Hailong Yang
- School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Junhua Yang
- School of Electronic Engineering, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Jiamin Gong
- School of Modern Post, Xi'an University of Posts and Telecommunications, Xi'an, 710061, China
| | - Xumeng Wei
- School of Communications and Information Engineering, Xi'an University of Posts and Telecommunications, Xi'an, 710121, China
| | - Mingmin Zhu
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, China.
| | - Guohai Wu
- Ningbo Eye Hospital, Wenzhou Medical University, Ningbo, 315000, China.
| | - Zhongwen Li
- Ningbo Eye Hospital, Wenzhou Medical University, Ningbo, 315000, China.
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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18
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Xia L, Lee C, Li JJ. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun 2024; 15:1753. [PMID: 38409103 PMCID: PMC10897166 DOI: 10.1038/s41467-024-45891-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP's 2D embeddings might not reliably inform the similarities among cell clusters. Motivated by this challenge, we present a statistical method, scDEED, for detecting dubious cell embeddings output by a 2D-embedding method. By calculating a reliability score for every cell embedding based on the similarity between the cell's 2D-embedding neighbors and pre-embedding neighbors, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. We show the effectiveness of scDEED on multiple datasets for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP.
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Affiliation(s)
- Lucy Xia
- Department of ISOM, School of Business and Management, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Christy Lee
- Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Radcliffe Institute of Advanced Study, Harvard University, Cambridge, MA, USA.
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19
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Burke Schinkel SC, Barros PO, Berthoud T, Byrareddy SN, McGuinty M, Cameron DW, Angel JB. Comparative analysis of human gut- and blood-derived mononuclear cells: contrasts in function and phenotype. Front Immunol 2024; 15:1336480. [PMID: 38444848 PMCID: PMC10912472 DOI: 10.3389/fimmu.2024.1336480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Alterations in the gut immune system have been implicated in various diseases.The challenge of obtaining gut tissues from healthy individuals, commonly performed via surgical explants, has limited the number of studies describing the phenotype and function of gut-derived immune cells in health. Methods Here, by means of recto-sigmoid colon biopsies obtained during routine care (colon cancer screening in healthy adults), the phenotype and function of immune cells present in the gut were described and compared to those found in blood. Results The proportion of CD4+, CD8+, MAIT, γδ+ T, and NK cells phenotype, expression of integrins, and ability to produce cytokine in response to stimulation with PMA and ionomycin. T cells in the gut were found to predominantly have a memory phenotype as compared to T cells in blood where a naïve phenotype predominates. Recto-sigmoid mononuclear cells also had higher PD-1 and Ki67 expression. Furthermore, integrin expression and cytokine production varied by cell type and location in blood vs. gut. Discussion These findings demonstrate the differences in functionality of these cells when compared to their blood counterparts and validate previous studies on phenotype within gut-derived immune cells in humans (where cells have been obtained through surgical means). This study suggests that recto-sigmoid biopsies collected during colonoscopy can be a reliable yet more accessible sampling method for follow up of alterations of gut derived immune cells in clinical settings.
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Affiliation(s)
| | - Priscila O Barros
- Chronic Diseases Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Tamara Berthoud
- Chronic Diseases Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, United States
| | - Michaeline McGuinty
- Department of Medicine, Division of Infectious Diseases, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - D William Cameron
- Department of Medicine, Division of Infectious Diseases, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Jonathan B Angel
- Chronic Diseases Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Medicine, Division of Infectious Diseases, The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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20
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Ren H, Zhang Y, Huang W, Xu H, He W, Hao N, Zhang C. Tumor-targeted nanodrug FSGG/siGal-9 for transdermal photothermal immunotherapy of melanoma. Commun Biol 2024; 7:188. [PMID: 38366083 PMCID: PMC10873409 DOI: 10.1038/s42003-024-05891-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Photothermal therapy (PTT) is a cancer-targeted treatment approach.The occurrence of tumors may be related to microbial infections (Viruses, bacteria, fungi, etc.), which probably provokes anti-tumor immunity. However, T cells in the context of cancer become exhausted and dysfunctional. Galectin-9 (Gal-9) is highly expressed in normal tissues and associates with body immune tolerance, and was firstly evidenced with much higher expression on the primary solid tumors than CD80/86 (B7) and CD274 (PD-L1) here, which suggests that Gal-9 may be a key factor in inhibiting the anti-tumor immunity, and its receptor T cell immunoglobulin and mucin domain 3 (TIM-3) was discovered on the cytotoxic T lymphocytes (CTL) with high expression as well based on the single cell analysis. The immune checkpoint communications showed that the Gal-9/TIM-3 axis played the most vital role on negatively regulating the anti-tumor immunity of CTL for melanoma. Then, we used a novel transdermal photothermal nanosensitizer (FSGG) loading Gal-9 siRNA (FSGG/siGal-9) for knocking the tumor cells down Gal-9 to block the Gal-9/TIM-3 axis and prohibit CTL exhaustion synergizing PTT against melanoma, which evidenced good effects on inhibiting tumor growth and enhancing anti-tumor immunity, named "photothermal immunotherapy". This paper provides a new perspective for tumor prevention and treatment.
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Affiliation(s)
- Huihong Ren
- School of Pharmacy and School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
- Drug Dispensing Department, Zibo Central Hospital, Zibo, 255000, China
| | - Yujuan Zhang
- Department of Otolaryngology, The First Dongguan Affiliated Hospital, and Nursing College, Guangdong Medical University, Dongguan, 523808, China.
| | - Wei Huang
- School of Pharmacy and School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Haiyan Xu
- School of Pharmacy and School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Weixiong He
- School of Pharmacy and School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Nan Hao
- School of Pharmacy and School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
| | - Cong Zhang
- School of Pharmacy and School of Basic Medical Sciences, Nanchang University, Nanchang, 330006, China
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21
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Sun T, Vander Heiden JA, Gao X, Yin J, Uttarwar S, Liang WC, Jia G, Yadav R, Huang Z, Mitra M, Halpern W, Bender HS, Brightbill HD, Wu Y, Lupardus P, Ramalingam T, Arron JR. Isoform-selective TGF-β3 inhibition for systemic sclerosis. MED 2024; 5:132-147.e7. [PMID: 38272035 DOI: 10.1016/j.medj.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Transforming growth factor β (TGF-β) is implicated as a key mediator of pathological fibrosis, but its pleiotropic activity in a range of homeostatic functions presents challenges to its safe and effective therapeutic targeting. There are three isoforms of TGF-β, TGF-β1, TGF-β2, and TGF-β3, which bind to a common receptor complex composed of TGF-βR1 and TGF-βR2 to induce similar intracellular signals in vitro. We have recently shown that the cellular expression patterns and activation thresholds of TGF-β2 and TGF-β3 are distinct from those of TGF-β1 and that selective short-term TGF-β2 and TGF-β3 inhibition can attenuate fibrosis in vivo without promoting excessive inflammation. Isoform-selective inhibition of TGF-β may therefore provide a therapeutic opportunity for patients with chronic fibrotic disorders. METHODS Transcriptomic profiling of skin biopsies from patients with systemic sclerosis (SSc) from multiple clinical trials was performed to evaluate the role of TGF-β3 in this disease. Antibody humanization, biochemical characterization, crystallization, and pre-clinical experiments were performed to further characterize an anti-TGF-β3 antibody. FINDINGS In the skin of patients with SSc, TGF-β3 expression is uniquely correlated with biomarkers of TGF-β signaling and disease severity. Crystallographic studies establish a structural basis for selective TGF-β3 inhibition with a potent and selective monoclonal antibody that attenuates fibrosis effectively in vivo at clinically translatable exposures. Toxicology studies suggest that, as opposed to pan-TGF-β inhibitors, this anti-TGF-β3 antibody has a favorable safety profile for chronic administration. CONCLUSION We establish a rationale for targeting TGF-β3 in SSc with a favorable therapeutic index. FUNDING This study was funded by Genentech, Inc.
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Affiliation(s)
- Tianhe Sun
- Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Jason A Vander Heiden
- Department of OMNI Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xia Gao
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jianping Yin
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Salil Uttarwar
- Department of OMNI Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei-Ching Liang
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Guiquan Jia
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rajbharan Yadav
- Department of Preclinical and Translational Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zhiyu Huang
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mayurranjan Mitra
- Department of DevSci Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wendy Halpern
- Department of DevSci SA Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hannah S Bender
- Department of Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Lupardus
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Thirumalai Ramalingam
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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22
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Murakami M, Hara K, Ikeda K, Horino M, Okazaki R, Niitsu Y, Takeuchi A, Aoki J, Shiba K, Tsujimoto K, Komiya C, Nakamura Y, Kurata M, Akashi T, Fujii Y, Yamada T. Single-Nucleus Analysis Reveals Tumor Heterogeneity of Aldosterone-Producing Adenoma. Hypertension 2024; 81:361-371. [PMID: 38095094 DOI: 10.1161/hypertensionaha.123.21446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/03/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Recent advances in omics techniques have allowed detailed genetic characterization of aldosterone-producing adenoma (APA). The pathogenesis of APA is characterized by tumorigenesis-associated aldosterone synthesis. The pathophysiological intricacies of APAs have not yet been elucidated at the level of individual cells. Therefore, a single-cell level analysis is speculated to be valuable in studying the differentiation process of APA. METHODS We conducted single-nucleus RNA sequencing of APAs with KCNJ5 mutation and nonfunctional adenomas obtained from 3 and 2 patients, respectively. RESULTS The single-nucleus RNA sequencing revealed the intratumoral heterogeneity of APA and identified cell populations consisting of a shared cluster of nonfunctional adenoma and APA. In addition, we extracted 2 cell fates in APA and obtained a cell population specialized in aldosterone synthesis. Genes related to ribosomes and neurodegenerative diseases were upregulated in 1 of these fates, whereas those related to the regulation of glycolysis were upregulated in the other fate. Furthermore, the total RNA reads in the nucleus were higher in hormonally activated clusters, indicating a marked activation of transcription per cell. CONCLUSIONS The single-nucleus RNA sequencing revealed intratumoral heterogeneity of APA with KCNJ5 mutation. The observation of 2 cell fates in KCNJ5-mutated APAs provides the postulation that a heterogeneous process of cellular differentiation was implicated in the pathophysiological mechanisms underlying APA tumors.
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Affiliation(s)
- Masanori Murakami
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Kazunari Hara
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Kenji Ikeda
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Masato Horino
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Rei Okazaki
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Yoshihiro Niitsu
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Akira Takeuchi
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Jun Aoki
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Kumiko Shiba
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
- Center for Personalized Medicine for Healthy Aging (K.S.), Tokyo Medical and Dental University, Japan
| | - Kazutaka Tsujimoto
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Chikara Komiya
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
| | - Yuki Nakamura
- Department of Urology, Graduate School of Medical and Dental Sciences (Y.N., Y.F.), Tokyo Medical and Dental University, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences (M.K.), Tokyo Medical and Dental University, Japan
| | - Takumi Akashi
- Department of Diagnostic Pathology, Graduate School of Medical and Dental Sciences (T.A.), Tokyo Medical and Dental University, Japan
- Division of Surgical Pathology, Tokyo Medical and Dental University Hospital, Japan (T.A.)
| | - Yasuhisa Fujii
- Department of Urology, Graduate School of Medical and Dental Sciences (Y.N., Y.F.), Tokyo Medical and Dental University, Japan
| | - Tetsuya Yamada
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences (M.M., K.H., K.I., M.H., R.O., Y.N., A.T., J.A., K.S., K.T., C.K., T.Y.), Tokyo Medical and Dental University, Japan
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23
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Motomura K, Matsuzaka T, Shichino S, Ogawa T, Pan H, Nakajima T, Asano Y, Okayama T, Takeuchi T, Ohno H, Han SI, Miyamoto T, Takeuchi Y, Sekiya M, Sone H, Yahagi N, Nakagawa Y, Oda T, Ueha S, Ikeo K, Ogura A, Matsushima K, Shimano H. Single-Cell Transcriptome Profiling of Pancreatic Islets From Early Diabetic Mice Identifies Anxa10 for Ca2+ Allostasis Toward β-Cell Failure. Diabetes 2024; 73:75-92. [PMID: 37871012 PMCID: PMC10784657 DOI: 10.2337/db23-0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023]
Abstract
Type 2 diabetes is a progressive disorder denoted by hyperglycemia and impaired insulin secretion. Although a decrease in β-cell function and mass is a well-known trigger for diabetes, the comprehensive mechanism is still unidentified. Here, we performed single-cell RNA sequencing of pancreatic islets from prediabetic and diabetic db/db mice, an animal model of type 2 diabetes. We discovered a diabetes-specific transcriptome landscape of endocrine and nonendocrine cell types with subpopulations of β- and α-cells. We recognized a new prediabetic gene, Anxa10, that was induced by and regulated Ca2+ influx from metabolic stresses. Anxa10-overexpressed β-cells displayed suppression of glucose-stimulated intracellular Ca2+ elevation and potassium-induced insulin secretion. Pseudotime analysis of β-cells predicted that this Ca2+-surge responder cluster would proceed to mitochondria dysfunction and endoplasmic reticulum stress. Other trajectories comprised dedifferentiation and transdifferentiation, emphasizing acinar-like cells in diabetic islets. Altogether, our data provide a new insight into Ca2+ allostasis and β-cell failure processes. ARTICLE HIGHLIGHTS The transcriptome of single-islet cells from healthy, prediabetic, and diabetic mice was studied. Distinct β-cell heterogeneity and islet cell-cell network in prediabetes and diabetes were found. A new prediabetic β-cell marker, Anxa10, regulates intracellular Ca2+ and insulin secretion. Diabetes triggers β-cell to acinar cell transdifferentiation.
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Affiliation(s)
- Kaori Motomura
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Takashi Matsuzaka
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Tatsuro Ogawa
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Hao Pan
- Department of Bio-Science, Nagahama Institute of BioScience and Technology, Nagahama, Shiga, Japan
| | - Takuya Nakajima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Yasuhito Asano
- Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan
| | - Toshitsugu Okayama
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Tomoyo Takeuchi
- Tsukuba Human Tissue Biobank Center, University of Tsukuba Hospital, Ibaraki, Japan
| | - Hiroshi Ohno
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Song-iee Han
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshinori Takeuchi
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Motohiro Sekiya
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hirohito Sone
- Department of Hematology, Endocrinology and Metabolism, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Naoya Yahagi
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshimi Nakagawa
- Division of Complex Biosystem Research, Department of Research and Development, Institute of Natural Medicine, University of Toyama, Toyama, Japan
| | - Tatsuya Oda
- Department of Gastrointestinal and Hepatobiliary Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | - Atsushi Ogura
- Department of Bio-Science, Nagahama Institute of BioScience and Technology, Nagahama, Shiga, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Hitoshi Shimano
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki, Japan
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
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24
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Zeng X, Meng FF, Li X, Zhong KY, Jiang B, Li Y. GHGPR-PPIS: A graph convolutional network for identifying protein-protein interaction site using heat kernel with Generalized PageRank techniques and edge self-attention feature processing block. Comput Biol Med 2024; 168:107683. [PMID: 37984202 DOI: 10.1016/j.compbiomed.2023.107683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/10/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Accurately pinpointing protein-protein interaction site (PPIS) on the molecular level is of utmost significance for annotating protein function and comprehending the mechanisms underpinning various diseases. While numerous computational methods for predicting PPIS have emerged, they have indeed mitigated the labor and time constraints associated with traditional experimental methods. However, the predictive accuracy of these methods has yet to reach the desired threshold. In this context, we proposed a groundbreaking graph-based computational model called GHGPR-PPIS. This innovative model leveraged a graph convolutional network using heat kernel (GraphHeat) in conjunction with Generalized PageRank techniques (GHGPR) to predict PPIS. Additionally, building upon the GHGPR framework, we devised an edge self-attention feature processing block, further augmenting the performance of the model. Experimental findings conclusively demonstrated that GHGPR-PPIS surpassed all competing state-of-the-art models when evaluated on the benchmark test set. Impressively, on two distinct independent test sets and a specific protein chain, GHGPR-PPIS consistently demonstrated superior generalization performance and practical applicability compared to the comparative model, AGAT-PPIS. Lastly, leveraging the t-SNE dimensionality reduction algorithm and clustering visualization technique, we delved into an interpretability analysis of the effectiveness of GHGPR-PPIS by meticulously comparing the outputs from different stages of the model.
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Affiliation(s)
- Xin Zeng
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China
| | - Fan-Fang Meng
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China
| | - Xin Li
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China
| | - Kai-Yang Zhong
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China
| | - Bei Jiang
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan, Dali University, Dali, 671000, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali, 671003, China.
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25
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Hunter B, Nicorescu I, Foster E, McDonald D, Hulme G, Fuller A, Thomson A, Goldsborough T, Hilkens CMU, Majo J, Milross L, Fisher A, Bankhead P, Wills J, Rees P, Filby A, Merces G. OPTIMAL: An OPTimized Imaging Mass cytometry AnaLysis framework for benchmarking segmentation and data exploration. Cytometry A 2024; 105:36-53. [PMID: 37750225 PMCID: PMC10952805 DOI: 10.1002/cyto.a.24803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Analysis of imaging mass cytometry (IMC) data and other low-resolution multiplexed tissue imaging technologies is often confounded by poor single-cell segmentation and suboptimal approaches for data visualization and exploration. This can lead to inaccurate identification of cell phenotypes, states, or spatial relationships compared to reference data from single-cell suspension technologies. To this end we have developed the "OPTimized Imaging Mass cytometry AnaLysis (OPTIMAL)" framework to benchmark any approaches for cell segmentation, parameter transformation, batch effect correction, data visualization/clustering, and spatial neighborhood analysis. Using a panel of 27 metal-tagged antibodies recognizing well-characterized phenotypic and functional markers to stain the same Formalin-Fixed Paraffin Embedded (FFPE) human tonsil sample tissue microarray over 12 temporally distinct batches we tested several cell segmentation models, a range of different arcsinh cofactor parameter transformation values, 5 different dimensionality reduction algorithms, and 2 clustering methods. Finally, we assessed the optimal approach for performing neighborhood analysis. We found that single-cell segmentation was improved by the use of an Ilastik-derived probability map but that issues with poor segmentation were only really evident after clustering and cell type/state identification and not always evident when using "classical" bivariate data display techniques. The optimal arcsinh cofactor for parameter transformation was 1 as it maximized the statistical separation between negative and positive signal distributions and a simple Z-score normalization step after arcsinh transformation eliminated batch effects. Of the five different dimensionality reduction approaches tested, PacMap gave the best data structure with FLOWSOM clustering out-performing phenograph in terms of cell type identification. We also found that neighborhood analysis was influenced by the method used for finding neighboring cells with a "disc" pixel expansion outperforming a "bounding box" approach combined with the need for filtering objects based on size and image-edge location. Importantly, OPTIMAL can be used to assess and integrate with any existing approach to IMC data analysis and, as it creates .FCS files from the segmentation output and allows for single-cell exploration to be conducted using a wide variety of accessible software and algorithms familiar to conventional flow cytometrists.
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Affiliation(s)
- Bethany Hunter
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Ioana Nicorescu
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Emma Foster
- Image Analysis Unit, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - David McDonald
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Gillian Hulme
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew Fuller
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Amanda Thomson
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | | | - Catharien M. U. Hilkens
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Joaquim Majo
- Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Luke Milross
- Transplantation and Regenerative Medicine, Newcastle University Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew Fisher
- Transplantation and Regenerative Medicine, Newcastle University Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Peter Bankhead
- Centre for Genomic and Experimental Medicine, CRUK Scotland Centre, and Edinburgh PathologyUniversity of EdinburghEdinburghUK
| | - John Wills
- Department of Veterinary MedicineCambridge UniversityCambridgeUK
- Department of Biomedical EngineeringSwansea UniversitySwansea, WalesUK
| | - Paul Rees
- Department of Biomedical EngineeringSwansea UniversitySwansea, WalesUK
- Imaging PlatformBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Andrew Filby
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - George Merces
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Image Analysis Unit, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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26
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Schmassmann P, Roux J, Dettling S, Hogan S, Shekarian T, Martins TA, Ritz MF, Herter S, Bacac M, Hutter G. Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation. eLife 2023; 12:RP92678. [PMID: 38127790 PMCID: PMC10735226 DOI: 10.7554/elife.92678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Glioblastoma (GBM) harbors a highly immunosuppressive tumor microenvironment (TME) which influences glioma growth. Major efforts have been undertaken to describe the TME on a single-cell level. However, human data on regional differences within the TME remain scarce. Here, we performed high-depth single-cell RNA sequencing (scRNAseq) on paired biopsies from the tumor center, peripheral infiltration zone and blood of five primary GBM patients. Through analysis of >45,000 cells, we revealed a regionally distinct transcription profile of microglia (MG) and monocyte-derived macrophages (MdMs) and an impaired activation signature in the tumor-peripheral cytotoxic-cell compartment. Comparing tumor-infiltrating CD8+ T cells with circulating cells identified CX3CR1high and CX3CR1int CD8+ T cells with effector and memory phenotype, respectively, enriched in blood but absent in the TME. Tumor CD8+ T cells displayed a tissue-resident memory phenotype with dysfunctional features. Our analysis provides a regionally resolved mapping of transcriptional states in GBM-associated leukocytes, serving as an additional asset in the effort towards novel therapeutic strategies to combat this fatal disease.
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Affiliation(s)
- Philip Schmassmann
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Julien Roux
- Bioinformatics Core Facility, Department of Biomedicine, University of BaselBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Steffen Dettling
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center MunichPenzbergGermany
| | - Sabrina Hogan
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Tala Shekarian
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Tomás A Martins
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Marie-Françoise Ritz
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Sylvia Herter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center ZürichSchlierenSwitzerland
| | - Marina Bacac
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center ZürichSchlierenSwitzerland
| | - Gregor Hutter
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
- Department of Neurosurgery, University Hospital BaselBaselSwitzerland
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27
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Mo Y, Yue M, Yim LY, Zhou R, Yu C, Peng Q, Zhou Y, Luk TY, Lui GCY, Huang H, Lim CYH, Wang H, Liu L, Sun H, Wang J, Song Y, Chen Z. Nicotinamide mononucleotide impacts HIV-1 infection by modulating immune activation in T lymphocytes and humanized mice. EBioMedicine 2023; 98:104877. [PMID: 37980794 PMCID: PMC10694053 DOI: 10.1016/j.ebiom.2023.104877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND HIV-1-associated immune activation drives CD4+ T cell depletion and the development of acquired immunodeficiency syndrome. We aimed to determine the role of nicotinamide mononucleotide (NMN), the direct precursor of nicotinamide adenine dinucleotide (NAD) co-enzyme, in CD4+ T cell modulation during HIV-1 infection. METHODS We examined HIV-1 integrated DNA or transcribed RNA, intracellular p24 protein, and T cell activation markers in CD4+ T cells including in vitro HIV-1-infected cells, reactivated patient-derived cells, and in HIV-1-infected humanized mice, under NMN treatment. RNA-seq and CyTOF analyses were used for investigating the effect of NMN on CD4+ T cells. FINDINGS We found that NMN increased the intracellular NAD amount, resulting in suppressed HIV-1 p24 production and proliferation in infected CD4+ T cells, especially in activated CD25+CD4+ T cells. NMN also inhibited CD25 expression on reactivated resting CD4+ T cells derived from cART-treated people living with HIV-1 (PLWH). In HIV-1-infected humanized mice, the frequency of CD4+ T cells was reconstituted significantly by combined cART and NMN treatment as compared with cART or NMN alone, which correlated with suppressed hyperactivation of CD4+ T cells. INTERPRETATION Our results highlight the suppressive role of NMN in CD4+ T cell activation during HIV-1 infection. It warrants future clinical investigation of NMN as a potential treatment in combination with cART in PLWH. FUNDING This work was supported by the Hong Kong Research Grants Council Theme-Based Research Scheme (T11-706/18-N), University Research Committee of The University of Hong Kong, the Collaborative Research with GeneHarbor (Hong Kong) Biotechnologies Limited and National Key R&D Program of China (Grant2021YFC2301900).
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Affiliation(s)
- Yufei Mo
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Ming Yue
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Lok Yan Yim
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Runhong Zhou
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Chunhao Yu
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Qiaoli Peng
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China; HKU-AIDS Institute Shenzhen Research Laboratory and AIDS Clinical Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, People's Republic of China
| | - Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Tsz-Yat Luk
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Grace Chung-Yan Lui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, People's Republic of China
| | - Huarong Huang
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Chun Yu Hubert Lim
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Hui Wang
- HKU-AIDS Institute Shenzhen Research Laboratory and AIDS Clinical Research Laboratory, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Shenzhen, 518112, People's Republic of China
| | - Li Liu
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Jun Wang
- GeneHarbor (Hong Kong) Biotechnologies Ltd., Hong Kong Science Park, Hong Kong SAR, People's Republic of China
| | - Youqiang Song
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China; Center for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, 518053, People's Republic of China.
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28
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Ting KK, Coleman P, Kim HJ, Zhao Y, Mulangala J, Cheng NC, Li W, Gunatilake D, Johnstone DM, Loo L, Neely GG, Yang P, Götz J, Vadas MA, Gamble JR. Vascular senescence and leak are features of the early breakdown of the blood-brain barrier in Alzheimer's disease models. GeroScience 2023; 45:3307-3331. [PMID: 37782439 PMCID: PMC10643714 DOI: 10.1007/s11357-023-00927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/27/2023] [Indexed: 10/03/2023] Open
Abstract
Alzheimer's disease (AD) is an age-related disease, with loss of integrity of the blood-brain barrier (BBB) being an early feature. Cellular senescence is one of the reported nine hallmarks of aging. Here, we show for the first time the presence of senescent cells in the vasculature in AD patients and mouse models of AD. Senescent endothelial cells and pericytes are present in APP/PS1 transgenic mice but not in wild-type littermates at the time of amyloid deposition. In vitro, senescent endothelial cells display altered VE-cadherin expression and loss of cell junction formation and increased permeability. Consistent with this, senescent endothelial cells in APP/PS1 mice are present at areas of vascular leak that have decreased claudin-5 and VE-cadherin expression confirming BBB breakdown. Furthermore, single cell sequencing of endothelial cells from APP/PS1 transgenic mice confirms that adhesion molecule pathways are among the most highly altered pathways in these cells. At the pre-plaque stage, the vasculature shows significant signs of breakdown, with a general loss of VE-cadherin, leakage within the microcirculation, and obvious pericyte perturbation. Although senescent vascular cells were not directly observed at sites of vascular leak, senescent cells were close to the leak area. Thus, we would suggest in AD that there is a progressive induction of senescence in constituents of the neurovascular unit contributing to an increasing loss of vascular integrity. Targeting the vasculature early in AD, either with senolytics or with drugs that improve the integrity of the BBB may be valid therapeutic strategies.
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Affiliation(s)
- Ka Ka Ting
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia.
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
| | - Paul Coleman
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Hani Jieun Kim
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Yang Zhao
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jocelyne Mulangala
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
| | - Ngan Ching Cheng
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
| | - Wan Li
- Department of General Surgery, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Dilini Gunatilake
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
| | - Daniel M Johnstone
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, & School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - G Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, & School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, 2145, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Mathew A Vadas
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia
- Heart Research Institute, Sydney, NSW, Australia
| | - Jennifer R Gamble
- Vascular Biology Program, Centenary Institute, Camperdown, NSW, Australia.
- School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
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29
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Wu DM, Liu JP, Liu J, Ge WH, Wu SZ, Zeng CJ, Liang J, Liu K, Lin Q, Hong XW, Sun YE, Lu J. Immune pathway activation in neurons triggers neural damage after stroke. Cell Rep 2023; 42:113368. [PMID: 37917581 DOI: 10.1016/j.celrep.2023.113368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Ischemic brain injury is a severe medical condition with high incidences in elderly people without effective treatment for the resulting neural damages. Using a unilateral mouse stroke model, we analyze single-cell transcriptomes of ipsilateral and contralateral cortical penumbra regions to objectively reveal molecular events with single-cell resolution at 4 h and 1, 3, and 7 days post-injury. Here, we report that neurons are among the first cells that sense the lack of blood supplies by elevated expression of CCAAT/enhancer-binding protein β (C/EBPβ). To our surprise, the canonical inflammatory cytokine gene targets for C/EBPβ, including interleukin-1β (IL-1β) and tumor necrosis factor α (TNF-α), are subsequently induced also in neuronal cells. Neuronal-specific silencing of C/EBPβ or IL-1β and TNF-α substantially alleviates downstream inflammatory injury responses and is profoundly neural protective. Taken together, our findings reveal a neuronal inflammatory mechanism underlying early pathological triggers of ischemic brain injury.
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Affiliation(s)
- Dong-Mei Wu
- Clinical Medicine Center, Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Guangdong 528000, China
| | - Ji-Ping Liu
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Jie Liu
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; Clinical Medicine Center, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China
| | - Wei-Hong Ge
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Su-Zhen Wu
- Clinical Medicine Center, Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Guangdong 528000, China
| | - Chi-Jia Zeng
- Clinical Medicine Center, Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Guangdong 528000, China
| | - Jia Liang
- Life Science Institution, Jinzhou Medical University, Jinzhou 121000, China
| | - KeJian Liu
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Quan Lin
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiao-Wu Hong
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Research Institute of Fudan University in Ningbo, Zhejiang 315336, China.
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Jun Lu
- Clinical Medicine Center, Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Guangdong 528000, China.
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30
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Atitey K, Motsinger-Reif AA, Anchang B. Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics. Brief Bioinform 2023; 25:bbad455. [PMID: 38113074 PMCID: PMC10729792 DOI: 10.1093/bib/bbad455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Optimizing and benchmarking data reduction methods for dynamic or spatial visualization and interpretation (DSVI) face challenges due to many factors, including data complexity, lack of ground truth, time-dependent metrics, dimensionality bias and different visual mappings of the same data. Current studies often focus on independent static visualization or interpretability metrics that require ground truth. To overcome this limitation, we propose the MIBCOVIS framework, a comprehensive and interpretable benchmarking and computational approach. MIBCOVIS enhances the visualization and interpretability of high-dimensional data without relying on ground truth by integrating five robust metrics, including a novel time-ordered Markov-based structural metric, into a semi-supervised hierarchical Bayesian model. The framework assesses method accuracy and considers interaction effects among metric features. We apply MIBCOVIS using linear and nonlinear dimensionality reduction methods to evaluate optimal DSVI for four distinct dynamic and spatial biological processes captured by three single-cell data modalities: CyTOF, scRNA-seq and CODEX. These data vary in complexity based on feature dimensionality, unknown cell types and dynamic or spatial differences. Unlike traditional single-summary score approaches, MIBCOVIS compares accuracy distributions across methods. Our findings underscore the joint evaluation of visualization and interpretability, rather than relying on separate metrics. We reveal that prioritizing average performance can obscure method feature performance. Additionally, we explore the impact of data complexity on visualization and interpretability. Specifically, we provide optimal parameters and features and recommend methods, like the optimized variational contractive autoencoder, for targeted DSVI for various data complexities. MIBCOVIS shows promise for evaluating dynamic single-cell atlases and spatiotemporal data reduction models.
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Affiliation(s)
- Komlan Atitey
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 T W Alexander Dr, David P Rall Building, Research Triangle Park, NC 27709, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 T W Alexander Dr, David P Rall Building, Research Triangle Park, NC 27709, USA
| | - Benedict Anchang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 T W Alexander Dr, David P Rall Building, Research Triangle Park, NC 27709, USA
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Trinh XT, Chien PN, Long NV, Van Anh LT, Giang NN, Nam SY, Myung Y. Development of predictive models for lymphedema by using blood tests and therapy data. Sci Rep 2023; 13:19720. [PMID: 37957217 PMCID: PMC10643602 DOI: 10.1038/s41598-023-46567-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Lymphedema is a disease that refers to tissue swelling caused by an accumulation of protein-rich fluid that is usually drained through the lymphatic system. Detection of lymphedema is often based on expensive diagnoses such as bioimpedance spectroscopy, shear wave elastography, computed tomography, etc. In current machine learning models for lymphedema prediction, reliance on observable symptoms reported by patients introduces the possibility of errors in patient-input data. Moreover, these symptoms are often absent during the initial stages of lymphedema, creating challenges in its early detection. Identifying lymphedema before these observable symptoms manifest would greatly benefit patients by potentially minimizing the discomfort caused by these symptoms. In this study, we propose to use new data, such as complete blood count, serum, and therapy data, to develop predictive models for lymphedema. This approach aims to compensate for the limitations of using only observable symptoms data. We collected data from 2137 patients, including 356 patients with lymphedema and 1781 patients without lymphedema, with the lymphedema status of each patient confirmed by clinicians. The data for each patient included: (1) a complete blood count (CBC) test, (2) a serum test, and (3) therapy information. We used various machine learning algorithms (i.e. random forest, gradient boosting, decision tree, logistic regression, and artificial neural network) to develop predictive models on the training dataset (i.e. 80% of the data) and evaluated the models on the external validation dataset (i.e. 20% of the data). After selecting the best predictive models, we created a web application to aid medical doctors and clinicians in the rapid screening of lymphedema patients. A dataset of 2137 patients was assembled from Seoul National University Bundang Hospital. Predictive models based on the random forest algorithm exhibited satisfactory performance (balanced accuracy = 87.0 ± 0.7%, sensitivity = 84.3 ± 0.6%, specificity = 89.1 ± 1.5%, precision = 97.4 ± 0.7%, F1 score = 90.4 ± 0.4%, and AUC = 0.931 ± 0.007). We developed a web application to facilitate the swift screening of lymphedema among medical practitioners: https://snubhtxt.shinyapps.io/SNUBH_Lymphedema . Our study introduces a novel tool for the early detection of lymphedema and establishes the foundation for future investigations into predicting different stages of the condition.
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Affiliation(s)
- Xuan-Tung Trinh
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Pham Ngoc Chien
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Nguyen-Van Long
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Le Thi Van Anh
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
| | - Nguyen Ngan Giang
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea
- Department of Medical Device Development, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Sun-Young Nam
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea.
| | - Yujin Myung
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea.
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Guo Y, Bao Q, Hu P, Shi J. Nanomedicine-based co-delivery of a calcium channel inhibitor and a small molecule targeting CD47 for lung cancer immunotherapy. Nat Commun 2023; 14:7306. [PMID: 37951973 PMCID: PMC10640620 DOI: 10.1038/s41467-023-42972-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023] Open
Abstract
Pro-tumoral macrophages in lung tumors present a significant challenge in immunotherapy. Here, we introduce a pH-responsive nanomedicine approach for activating anti-tumoral macrophages and dendritic cells. Using a layered double hydroxide nanosheet carrier, we co-deliver a T-type calcium channel inhibitor (TTA-Q6) and a CD47 inhibitor (RRX-001) into lung tumors. In the tumor acidic environment, TTA-Q6 is released, disrupting cancer cell calcium uptake, causing endoplasmic reticulum stress and inducing calreticulin transfer to the cell surface. Surface calreticulin activates macrophages and triggers dendritic cell maturation, promoting effective antigen presentation and therefore activating antitumor T cells. Simultaneously, RRX-001 reduces CD47 protein levels, aiding in preventing immune escape by calreticulin-rich cancer cells. In lung tumor models in male mice, this combined approach shows anti-tumor effects and immunity against tumor re-exposure, highlighting its potential for lung cancer immunotherapy.
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Affiliation(s)
- Yuedong Guo
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), 200050, Shanghai, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Qunqun Bao
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, 200331, Shanghai, P. R. China
| | - Ping Hu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), 200050, Shanghai, P. R. China.
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, 200331, Shanghai, P. R. China.
| | - Jianlin Shi
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), 200050, Shanghai, P. R. China.
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, 200331, Shanghai, P. R. China.
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Vladyka O, Vrabcova P, Reiterova M, Parackova Z, Haesler R, Sediva A, Kalina T, Klocperk A. Th1/interferon-γ bias in 22q11.2 deletion syndrome is driven by memory T cells and exacerbated by IL-7. Clin Immunol 2023; 256:109793. [PMID: 37776967 DOI: 10.1016/j.clim.2023.109793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
The aim of this study was to investigate the impact of thymic dysplasia on the phenotypic and functional characteristics of T cells in patients with 22q11.2 deletion syndrome, including T-cell phenotype, transcriptional profile, cytokine production, as well as the possibility of utilizing IL-7 to recover their numbers and function. We found a strong bias towards Th1 response in pediatric and young adult 22q11.2DS patients, expansion of CXCR5+ follicular helper cells and CXCR3+CCR6- Th1 cells, increased production of cytokines IFN-γ, IL-10, IL-2, IL-21 and TNF-α. This Th1 skew was primarily driven by expanded terminally differentiated T cells. IL-7 further reduced naive T cells, increased cytokine production and caused an upregulation of exhaustion markers. Thus, Th1 bias in T cell populations persists from infancy into adolescence and is accompanied by accelerated maturation of T cells into memory stages. This phenotype is exacerbated by IL-7 which causes further decrease in naïve T cells in vitro.
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Affiliation(s)
- Ondrej Vladyka
- Department of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic
| | - Petra Vrabcova
- Department of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic
| | - Michaela Reiterova
- CLIP - Childhood Leukaemia Investigation Prague, Czech Republic; Department of Pediatric Hematology, Charles University and Univ. Hospital Motol, Prague, Czech Republic
| | - Zuzana Parackova
- Department of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic
| | - Robert Haesler
- Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anna Sediva
- Department of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic
| | - Tomas Kalina
- CLIP - Childhood Leukaemia Investigation Prague, Czech Republic; Department of Pediatric Hematology, Charles University and Univ. Hospital Motol, Prague, Czech Republic
| | - Adam Klocperk
- Department of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic.
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Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biol 2023; 24:236. [PMID: 37858253 PMCID: PMC10588049 DOI: 10.1186/s13059-023-03067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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Affiliation(s)
- Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Research Computing Center, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Vesalius Therapeutics, Cambridge, MA, USA
| | - Anthony Hung
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Statistics, University of Chicago, Chicago, IL, USA.
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Hindle MS, Cheah LT, Yates DM, Naseem KM. Preanalytical conditions for multiparameter platelet flow cytometry. Res Pract Thromb Haemost 2023; 7:102205. [PMID: 37854456 PMCID: PMC10579537 DOI: 10.1016/j.rpth.2023.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 10/20/2023] Open
Abstract
Background Flow cytometry is an important technique for understanding multiple aspects of blood platelet biology. Despite the widespread use of the platform for assessing platelet function, the optimization and careful consideration of preanalytical conditions, sample processing techniques, and data analysis strategies should be regularly assessed. When set up and designed with optimal conditions, it can ensure the acquisition of robust and reproducible flow cytometry data. However, these parameters are rarely described despite their importance. Objectives We aimed to characterize the effects of several preanalytical variables on the analysis of blood platelets by multiparameter fluorescent flow cytometry. Methods We assessed anticoagulant choice, sample material, sample processing, and storage times on 4 distinct and commonly used markers of platelet activation, including fibrinogen binding, expression of CD62P and CD42b, and phosphatidylserine exposure. Results The use of suboptimal conditions led to increases in basal platelet activity and reduced sensitivities to stimulation; however, the use of optimal conditions protected the platelets from artifactual stimulation and preserved basal activity and sensitivity to activation. Conclusion The optimal preanalytical conditions identified here for the measurement of platelet phenotype by flow cytometry suggest a framework for future development of multiparameter platelet assays for high-quality data sets and advanced analysis.
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Affiliation(s)
- Matthew S. Hindle
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, UK
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, UK
| | - Lih T. Cheah
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, UK
| | - Daisie M. Yates
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, UK
| | - Khalid M. Naseem
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, UK
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Dai M, Zhu S, An Z, You B, Li Z, Yao Y, Nair V, Liao M. Dissection of key factors correlating with H5N1 avian influenza virus driven inflammatory lung injury of chicken identified by single-cell analysis. PLoS Pathog 2023; 19:e1011685. [PMID: 37819993 PMCID: PMC10593216 DOI: 10.1371/journal.ppat.1011685] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 10/23/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023] Open
Abstract
Chicken lung is an important target organ of avian influenza virus (AIV) infection, and different pathogenic virus strains lead to opposite prognosis. Using a single-cell RNA sequencing (scRNA-seq) assay, we systematically and sequentially analyzed the transcriptome of 16 cell types (19 clusters) in the lung tissue of chickens infected with H5N1 highly pathogenic avian influenza virus (HPAIV) and H9N2 low pathogenic avian influenza virus (LPAIV), respectively. Notably, we developed a valuable catalog of marker genes for these cell types. Compared to H9N2 AIV infection, H5N1 AIV infection induced extensive virus replication and the immune reaction across most cell types simultaneously. More importantly, we propose that infiltrating inflammatory macrophages (clusters 0, 1, and 14) with massive viral replication, pro-inflammatory cytokines (IFN-β, IL1β, IL6 and IL8), and emerging interaction of various cell populations through CCL4, CCL19 and CXCL13, potentially contributed to the H5N1 AIV driven inflammatory lung injury. Our data revealed complex but distinct immune response landscapes in the lung tissue of chickens after H5N1 and H9N2 AIV infection, and deciphered the potential mechanisms underlying AIV-driven inflammatory reactions in chicken. Furthermore, this article provides a rich database for the molecular basis of different cell-type responses to AIV infection.
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Affiliation(s)
- Manman Dai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Sufang Zhu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhihao An
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bowen You
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ziwei Li
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Akiba H, Fujita J, Ise T, Nishiyama K, Miyata T, Kato T, Namba K, Ohno H, Kamada H, Nagata S, Tsumoto K. Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection. Commun Biol 2023; 6:987. [PMID: 37758868 PMCID: PMC10533564 DOI: 10.1038/s42003-023-05326-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Conventional bivalent antibodies against cell surface receptors often initiate unwanted signal transduction by crosslinking two antigen molecules. Biparatopic antibodies (BpAbs) bind to two different epitopes on the same antigen, thus altering crosslinking ability. In this study, we develop BpAbs against tumor necrosis factor receptor 2 (TNFR2), which is an attractive immune checkpoint target. Using different pairs of antibody variable regions specific to topographically distinct TNFR2 epitopes, we successfully regulate the size of BpAb-TNFR2 immunocomplexes to result in controlled agonistic activities. Our series of results indicate that the relative positions of the two epitopes recognized by the BpAb are critical for controlling its signaling activity. One particular antagonist, Bp109-92, binds TNFR2 in a 1:1 manner without unwanted signal transduction, and its structural basis is determined using cryo-electron microscopy. This antagonist suppresses the proliferation of regulatory T cells expressing TNFR2. Therefore, the BpAb format would be useful in designing specific and distinct antibody functions.
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Affiliation(s)
- Hiroki Akiba
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan.
| | - Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tomoko Ise
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan
| | - Kentaro Nishiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takayuki Kato
- Institute of Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan
- RIKEN SPring-8 Center, Suita, Osaka, 565-0871, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan
| | - Haruhiko Kamada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan
| | - Satoshi Nagata
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan.
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 562-0011, Japan.
- School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Institute of Medical Sciences, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
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Hausmann F, Ergen C, Khatri R, Marouf M, Hänzelmann S, Gagliani N, Huber S, Machart P, Bonn S. DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection. Genome Biol 2023; 24:212. [PMID: 37730638 PMCID: PMC10510283 DOI: 10.1186/s13059-023-03049-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constraints, most notably a limited number of expressed genes per cell, which leads to suboptimal clustering and cell type identification. RESULTS Here, we present DISCERN, a novel deep generative network that precisely reconstructs missing single-cell gene expression using a reference dataset. DISCERN outperforms competing algorithms in expression inference resulting in greatly improved cell clustering, cell type and activity detection, and insights into the cellular regulation of disease. We show that DISCERN is robust against differences between batches and is able to keep biological differences between batches, which is a common problem for imputation and batch correction algorithms. We use DISCERN to detect two unseen COVID-19-associated T cell types, cytotoxic CD4+ and CD8+ Tc2 T helper cells, with a potential role in adverse disease outcome. We utilize T cell fraction information of patient blood to classify mild or severe COVID-19 with an AUROC of 80% that can serve as a biomarker of disease stage. DISCERN can be easily integrated into existing single-cell sequencing workflow. CONCLUSIONS Thus, DISCERN is a flexible tool for reconstructing missing single-cell gene expression using a reference dataset and can easily be applied to a variety of data sets yielding novel insights, e.g., into disease mechanisms.
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Affiliation(s)
- Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Can Ergen
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Mohamed Marouf
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Nicola Gagliani
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Pierre Machart
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Hamburg Center for Translational Immunology (HCTI), I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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Que W, Ueta H, Hu X, Morita-Nakagawa M, Fujino M, Ueda D, Tokuda N, Huang W, Guo WZ, Zhong L, Li XK. Temporal and spatial dynamics of immune cells in spontaneous liver transplant tolerance. iScience 2023; 26:107691. [PMID: 37694154 PMCID: PMC10485166 DOI: 10.1016/j.isci.2023.107691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/11/2023] [Accepted: 08/17/2023] [Indexed: 09/12/2023] Open
Abstract
The liver has long been deemed a tolerogenic organ. We employed high-dimensional mass cytometry and immunohistochemistry to depict the temporal and spatial dynamics of immune cells in the spleen and liver in a murine model of spontaneous liver allograft acceptance. We depicted the immune landscape of spontaneous liver tolerance throughout the rejection and acceptance stages after liver transplantation and highlighted several points of importance. Of note, the CD4+/CD8+ T cell ratio remained low, even in the tolerance phase. Furthermore, a PhenoGraph clustering analysis revealed that exhausted CD8+ T cells were the most dominant metacluster in graft-infiltrating lymphocytes (GILs), which highly expressed the costimulatory molecule CD86. The temporal and spatial dynamics of immune cells revealed by high-dimensional analyses enable a fine-grained analysis of GIL subsets, contribute to new insights for the discovery of immunological mechanisms of liver tolerance, and provide potential ways to achieve clinical operational tolerance after liver transplantation.
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Affiliation(s)
- Weitao Que
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Division of Transplantation Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hisashi Ueta
- Department of Anatomy, Dokkyo Medical University, Tochigi 321-0293, Japan
| | - Xin Hu
- Division of Transplantation Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Miwa Morita-Nakagawa
- Division of Transplantation Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka 814-0175, Japan
| | - Masayuki Fujino
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Daisuke Ueda
- Division of Hepato-Pancreato-Biliary Surgery and Transplantation, Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto 606-8303, Japan
| | - Nobuko Tokuda
- Department of Anatomy, Dokkyo Medical University, Tochigi 321-0293, Japan
| | - Wenxin Huang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Wen-Zhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lin Zhong
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Xiao-Kang Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Division of Transplantation Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
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Xia L, Lee C, Li JJ. scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537839. [PMID: 37163087 PMCID: PMC10168265 DOI: 10.1101/2023.04.21.537839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-SNE and UMAP are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP's 2D embedding might not reliably inform the similarities among cell clusters. Motivated by this challenge, we developed a statistical method, scDEED, for detecting dubious cell embeddings output by any 2D-embedding method. By calculating a reliability score for every cell embedding, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. Applied to multiple scRNA-seq datasets, scDEED demonstrates its effectiveness for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP.
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Adamo A, Frusteri C, Pilotto S, Caligola S, Belluomini L, Poffe O, Giacobazzi L, Dusi S, Musiu C, Hu Y, Wang T, Rizzini D, Vella A, Canè S, Sartori G, Insolda J, Sposito M, Incani UC, Carbone C, Piro G, Pettinella F, Qi F, Wang D, Sartoris S, De Sanctis F, Scapini P, Dusi S, Cassatella MA, Bria E, Milella M, Bronte V, Ugel S. Immune checkpoint blockade therapy mitigates systemic inflammation and affects cellular FLIP-expressing monocytic myeloid-derived suppressor cells in non-progressor non-small cell lung cancer patients. Oncoimmunology 2023; 12:2253644. [PMID: 37720688 PMCID: PMC10503454 DOI: 10.1080/2162402x.2023.2253644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/10/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023] Open
Abstract
Cancer cells favor the generation of myeloid cells with immunosuppressive and inflammatory features, including myeloid-derived suppressor cells (MDSCs), which support tumor progression. The anti-apoptotic molecule, cellular FLICE (FADD-like interleukin-1β-converting enzyme)-inhibitory protein (c-FLIP), which acts as an important modulator of caspase-8, is required for the development and function of monocytic (M)-MDSCs. Here, we assessed the effect of immune checkpoint inhibitor (ICI) therapy on systemic immunological landscape, including FLIP-expressing MDSCs, in non-small cell lung cancer (NSCLC) patients. Longitudinal changes in peripheral immunological parameters were correlated with patients' outcome. In detail, 34 NSCLC patients were enrolled and classified as progressors (P) or non-progressors (NP), according to the RECIST evaluation. We demonstrated a reduction in pro-inflammatory cytokines such as IL-8, IL-6, and IL-1β in only NP patients after ICI treatment. Moreover, using t-distributed stochastic neighbor embedding (t-SNE) and cluster analysis, we characterized in NP patients a significant increase in the amount of lymphocytes and a slight contraction of myeloid cells such as neutrophils and monocytes. Despite this moderate ICI-associated alteration in myeloid cells, we identified a distinctive reduction of c-FLIP expression in M-MDSCs from NP patients concurrently with the first clinical evaluation (T1), even though NP and P patients showed the same level of expression at baseline (T0). In agreement with the c-FLIP expression, monocytes isolated from both P and NP patients displayed similar immunosuppressive functions at T0; however, this pro-tumor activity was negatively influenced at T1 in the NP patient cohort exclusively. Hence, ICI therapy can mitigate systemic inflammation and impair MDSC-dependent immunosuppression.
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Affiliation(s)
- Annalisa Adamo
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Cristina Frusteri
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Sara Pilotto
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Simone Caligola
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IOV-IRCCS), Padova, Italy
| | - Lorenzo Belluomini
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Ornella Poffe
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Luca Giacobazzi
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Silvia Dusi
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IOV-IRCCS), Padova, Italy
| | - Chiara Musiu
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Yushu Hu
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Tian Wang
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Davide Rizzini
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Antonio Vella
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Stefania Canè
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IOV-IRCCS), Padova, Italy
| | - Giulia Sartori
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Jessica Insolda
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Marco Sposito
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Ursula Cesta Incani
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Carmine Carbone
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Geny Piro
- Medical Oncology, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Francesca Pettinella
- General Pathology section, Department of Medicine University of Verona, Verona, Italy
| | - Fang Qi
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Dali Wang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Silvia Sartoris
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Francesco De Sanctis
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
| | - Patrizia Scapini
- General Pathology section, Department of Medicine University of Verona, Verona, Italy
| | - Stefano Dusi
- General Pathology section, Department of Medicine University of Verona, Verona, Italy
| | | | - Emilio Bria
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IOV-IRCCS), Padova, Italy
| | - Michele Milella
- Oncology section, Department of Engineering for Innovative Medicine and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Bronte
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IOV-IRCCS), Padova, Italy
| | - Stefano Ugel
- Immunology section, Department of Medicine University and Hospital Trust of Verona, Verona, Italy
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Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.03.531029. [PMID: 36945441 PMCID: PMC10028846 DOI: 10.1101/2023.03.03.531029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.
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Affiliation(s)
- Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Research Computing Center, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Vesalius Therapeutics, Cambridge, MA, USA
| | - Anthony Hung
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Statistics, University of Chicago, Chicago, IL, USA
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43
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Puccio S, Grillo G, Alvisi G, Scirgolea C, Galletti G, Mazza EMC, Consiglio A, De Simone G, Licciulli F, Lugli E. CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data. Nat Commun 2023; 14:5102. [PMID: 37666818 PMCID: PMC10477295 DOI: 10.1038/s41467-023-40790-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 08/10/2023] [Indexed: 09/06/2023] Open
Abstract
Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/ .
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Affiliation(s)
- Simone Puccio
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy.
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, via Manzoni 56, 20089, Rozzano, Milan, Italy.
| | - Giorgio Grillo
- Institute for Biomedical Technologies, National Research Council, via Amendola 122/D, 70126, Bari, Italy
| | - Giorgia Alvisi
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Caterina Scirgolea
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
- School of Biological Sciences, Department of Molecular Biology, University of California San Diego, San Diego, CA, USA
| | - Emilia Maria Cristina Mazza
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Arianna Consiglio
- Institute for Biomedical Technologies, National Research Council, via Amendola 122/D, 70126, Bari, Italy
| | - Gabriele De Simone
- Flow Cytometry Core, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Flavio Licciulli
- Institute for Biomedical Technologies, National Research Council, via Amendola 122/D, 70126, Bari, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy.
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Tu W, Ling G, Liu F, Hu F, Song X. GCSTI: A Single-Cell Pseudotemporal Trajectory Inference Method Based on Graph Compression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2945-2958. [PMID: 37037234 DOI: 10.1109/tcbb.2023.3266109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The single-cell pseudotemporal trajectory inference is an important way to explore the process of developmental changes within a cell. Due to the uneven rate of cell growth, changes in gene expression depend less on the time of data collection and more on a cell's "internal clock". To overcome the challenges of gene analysis, and replicate biological developmental processes, several strategies have been put forth. However, due to the size of single-cell datasets, locating relevant signposts usually necessitate clustering analysis or a sizable amount of priori information. To this end, we propose a novel single-cell pseudotemporal trajectory inference technique: GCSTI method, which is based on graph compression and doesn't rely on a priori knowledge or clustering procedures, can handle the trajectory inference problem for a large network in a stable and efficient manner. Additionally, we simultaneously improve the pseudotime defining method currently employed in this study in order to obtain more trustworthy and beneficial outcomes for trajectory inference. Finally, we validate the efficacy and stability of the GCSTI method using datasets from human skeletal muscle myogenic cells and four simulated datasets.
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45
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Arredondo-Alonso S, Gladstone R, Pöntinen A, Gama J, Schürch A, Lanza V, Johnsen P, Samuelsen Ø, Tonkin-Hill G, Corander J. Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genom Bioinform 2023; 5:lqad066. [PMID: 37435357 PMCID: PMC10331934 DOI: 10.1093/nargab/lqad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Here, we introduce mge-cluster that can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. Our approach offers a faster runtime than existing algorithms, with moderate memory usage, and enables an intuitive visualization, classification and clustering scheme that users can explore interactively within a single framework. Mge-cluster platform for plasmid analysis can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We underscore the advantages of our approach by analysing a population-wide plasmid data set obtained from the opportunistic pathogen Escherichia coli, studying the prevalence of the colistin resistance gene mcr-1.1 within the plasmid population, and describing an instance of resistance plasmid transmission within a hospital environment.
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Affiliation(s)
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - João A Gama
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anita C Schürch
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Val F Lanza
- CIBERINFEC, Madrid, Spain
- Bioinformatics Unit, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Pål Jarle Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Helsinki, Finland
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46
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Ahor HS, Schulte R, Adankwah E, Harelimana JDD, Minadzi D, Acheampong I, Vivekanandan MM, Aniagyei W, Yeboah A, Arthur JF, Lamptey M, Abass MK, Kumbel F, Osei-Yeboah F, Gawusu A, Debrah LB, Owusu DO, Debrah A, Mayatepek E, Seyfarth J, Phillips RO, Jacobsen M. Monocyte pathology in human tuberculosis is due to plasma milieu changes and aberrant STAT signalling. Immunology 2023; 170:154-166. [PMID: 37219921 DOI: 10.1111/imm.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/29/2023] [Indexed: 05/24/2023] Open
Abstract
Monocyte-derived macrophages contribute centrally to immune protection in Mycobacterium tuberculosis infection and changes in monocyte phenotype characterize immunopathology in tuberculosis patients. Recent studies highlighted an important role of the plasma milieu in tuberculosis immunopathology. Here, we investigated monocyte pathology in patients with acute tuberculosis and determined tuberculosis plasma milieu effects on phenotype as well as cytokine signalling of reference monocytes. Patients with tuberculosis (n = 37) and asymptomatic contacts (controls n = 35) were recruited as part of a hospital-based study in the Ashanti region of Ghana. Multiplex flow cytometry phenotyping of monocyte immunopathology was performed and effects of individual blood plasma samples on reference monocytes prior to and during treatment were characterized. Concomitantly, cell signalling pathways were analysed to elucidate underlying mechanisms of plasma effects on monocytes. Multiplex flow cytometry visualization characterized changes in monocyte subpopulations and detected higher expression of CD40, CD64 and PD-L1 in monocytes from tuberculosis patients as compared to controls. Aberrant expression normalized during anti-mycobacterial treatment and also CD33 expression decreased markedly. Notably, higher CD33, CD40 and CD64 expression was induced in reference monocytes when cultured in the presence of plasma samples from tuberculosis patients as compared to controls. STAT signalling pathways were affected by the aberrant plasma milieu and higher levels of STAT3 and STAT5 phosphorylation was found in tuberculosis plasma-treated reference monocytes. Importantly, high pSTAT3 levels were associated with high CD33 expression and pSTAT5 correlated with CD40 as well as CD64 expression. These results suggested plasma milieu effects with potential implications on monocyte phenotype and function in acute tuberculosis.
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Affiliation(s)
- Hubert Senanu Ahor
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine University, Duesseldorf, Germany
| | - Rebecca Schulte
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine University, Duesseldorf, Germany
| | - Ernest Adankwah
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Jean De Dieu Harelimana
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine University, Duesseldorf, Germany
| | - Difery Minadzi
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Isaac Acheampong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | | | - Wilfred Aniagyei
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Augustine Yeboah
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Joseph F Arthur
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Millicent Lamptey
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | | | | | | | - Amidu Gawusu
- Sene West Health Directorate, Kwame Danso, Ghana
| | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Dorcas O Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Alexander Debrah
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine University, Duesseldorf, Germany
| | - Julia Seyfarth
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine University, Duesseldorf, Germany
| | - Richard O Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
- School of Medicine and Dentistry, College of Health Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Marc Jacobsen
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Duesseldorf, Heinrich-Heine University, Duesseldorf, Germany
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Baird S, Ashley CL, Marsh‐Wakefield F, Alca S, Ashhurst TM, Ferguson AL, Lukeman H, Counoupas C, Post JJ, Konecny P, Bartlett A, Martinello M, Bull RA, Lloyd A, Grey A, Hutchings O, Palendira U, Britton WJ, Steain M, Triccas JA. A unique cytotoxic CD4 + T cell-signature defines critical COVID-19. Clin Transl Immunology 2023; 12:e1463. [PMID: 37645435 PMCID: PMC10461786 DOI: 10.1002/cti2.1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/04/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Objectives SARS-CoV-2 infection causes a spectrum of clinical disease presentation, ranging from asymptomatic to fatal. While neutralising antibody (NAb) responses correlate with protection against symptomatic and severe infection, the contribution of the T-cell response to disease resolution or progression is still unclear. As newly emerging variants of concern have the capacity to partially escape NAb responses, defining the contribution of individual T-cell subsets to disease outcome is imperative to inform the development of next-generation COVID-19 vaccines. Methods Immunophenotyping of T-cell responses in unvaccinated individuals was performed, representing the full spectrum of COVID-19 clinical presentation. Computational and manual analyses were used to identify T-cell populations associated with distinct disease states. Results Critical SARS-CoV-2 infection was characterised by an increase in activated and cytotoxic CD4+ lymphocytes (CTL). These CD4+ CTLs were largely absent in asymptomatic to severe disease states. In contrast, non-critical COVID-19 was associated with high frequencies of naïve T cells and lack of activation marker expression. Conclusion Highly activated and cytotoxic CD4+ T-cell responses may contribute to cell-mediated host tissue damage and progression of COVID-19. Induction of these potentially detrimental T-cell responses should be considered when developing and implementing effective COVID-19 control strategies.
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Affiliation(s)
- Sarah Baird
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Caroline L Ashley
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Felix Marsh‐Wakefield
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
- Human Cancer and Viral Immunology LaboratoryThe University of SydneyCamperdownNSWAustralia
| | - Sibel Alca
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Thomas M Ashhurst
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Sydney Cytometry Core Research FacilityCharles Perkins Centre, Centenary Institute and The University of SydneyCamperdownNSWAustralia
| | - Angela L Ferguson
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
| | - Hannah Lukeman
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Claudio Counoupas
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Tuberculosis Research ProgramCentenary InstituteSydneyNSWAustralia
| | - Jeffrey J Post
- Prince of Wales Clinical SchoolUNSWSydneyNSWAustralia
- School of Clinical Medicine, Medicine & HealthUNSWSydneyNSWAustralia
| | - Pamela Konecny
- Prince of Wales Clinical SchoolUNSWSydneyNSWAustralia
- St George HospitalSydneyNSWAustralia
| | - Adam Bartlett
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
- Sydney Children's HospitalSydneyNSWAustralia
| | | | - Rowena A Bull
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
| | - Andrew Lloyd
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
| | - Alice Grey
- RPA Virtual Hospital, Sydney Local Health DistrictSydneyNSWAustralia
| | - Owen Hutchings
- RPA Virtual Hospital, Sydney Local Health DistrictSydneyNSWAustralia
| | - Umaimainthan Palendira
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
| | - Warwick J Britton
- Tuberculosis Research ProgramCentenary InstituteSydneyNSWAustralia
- Department of Clinical ImmunologyRoyal Prince Alfred HospitalCamperdownNSWAustralia
| | - Megan Steain
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - James A Triccas
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
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48
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Han W, Pu H, Li S, Liu Y, Zhao Y, Xu M, Chen C, Wu Y, Yang T, Ye Q, Wang H, Stetler RA, Chen J, Shi Y. Targeted ablation of signal transducer and activator of transduction 1 alleviates inflammation by microglia/macrophages and promotes long-term recovery after ischemic stroke. J Neuroinflammation 2023; 20:178. [PMID: 37516843 PMCID: PMC10385956 DOI: 10.1186/s12974-023-02860-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND Brain microglia and macrophages (Mi/MΦ) can shift to a harmful or advantageous phenotype following an ischemic stroke. Identification of key molecules that regulate the transformation of resting Mi/MΦ could aid in the development of innovative therapies for ischemic stroke. The transcription factor signal transducer and activator of transduction 1 (STAT1) has been found to contribute to acute neuronal death (in the first 24 h) following ischemic stroke, but its effects on Mi/MΦ and influence on long-term stroke outcomes have yet to be determined. METHODS We generated mice with tamoxifen-induced, Mi/MΦ-specific knockout (mKO) of STAT1 driven by Cx3cr1CreER. Expression of STAT1 was examined in the brain by flow cytometry and RNA sequencing after ischemic stroke induced by transient middle cerebral artery occlusion (MCAO). The impact of STAT1 mKO on neuronal cell death, Mi/MΦ phenotype, and brain inflammation profiles were examined 3-5 days after MCAO. Neurological deficits and the integrity of gray and white matter were assessed for 5 weeks after MCAO by various neurobehavioral tests and immunohistochemistry. RESULTS STAT1 was activated in Mi/MΦ at the subacute stage (3 days) after MCAO. Selective deletion of STAT1 in Mi/MΦ did not alter neuronal cell death or infarct size at 24 h after MCAO, but attenuated Mi/MΦ release of high mobility group box 1 and increased arginase 1-producing Mi/MΦ 3d after MCAO, suggesting boosted inflammation-resolving responses of Mi/MΦ. As a result, STAT1 mKO mice had mitigated brain inflammation at the subacute stage after MCAO and less white matter injury in the long term. Importantly, STAT1 mKO was sufficient to improve functional recovery for at least 5 weeks after MCAO in both male and female mice. CONCLUSIONS Mi/MΦ-targeted STAT1 KO does not provide immediate neuroprotection but augments inflammation-resolving actions of Mi/MΦ, thereby facilitating long-term functional recovery after stroke. STAT1 is, therefore, a promising therapeutic target to harness beneficial Mi/MΦ responses and improve long-term outcomes after ischemic stroke.
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Affiliation(s)
- Wenxuan Han
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Hongjian Pu
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Sicheng Li
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Yaan Liu
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Yongfang Zhao
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Mingyue Xu
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Caixia Chen
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Yun Wu
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Tuo Yang
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Qing Ye
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
| | - Hong Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - R Anne Stetler
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, 15261, USA
| | - Jun Chen
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, 15261, USA
| | - Yejie Shi
- Pittsburgh Institute of Brain Disorders and Recovery and Department of Neurology, University of Pittsburgh, 3500 Terrace Street, S-510 BST, Pittsburgh, PA, 15213, USA.
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, 15261, USA.
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49
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Lee S, Deng L, Wang Y, Wang K, Sartor MA, Wang XS. IndepthPathway: an integrated tool for in-depth pathway enrichment analysis based on single-cell sequencing data. Bioinformatics 2023; 39:btad325. [PMID: 37243667 PMCID: PMC10275909 DOI: 10.1093/bioinformatics/btad325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/29/2023] [Accepted: 05/26/2023] [Indexed: 05/29/2023] Open
Abstract
MOTIVATION Single-cell sequencing enables exploring the pathways and processes of cells, and cell populations. However, there is a paucity of pathway enrichment methods designed to tolerate the high noise and low gene coverage of this technology. When gene expression data are noisy and signals are sparse, testing pathway enrichment based on the genes expression may not yield statistically significant results, which is particularly problematic when detecting the pathways enriched in less abundant cells that are vulnerable to disturbances. RESULTS In this project, we developed a Weighted Concept Signature Enrichment Analysis specialized for pathway enrichment analysis from single-cell transcriptomics (scRNA-seq). Weighted Concept Signature Enrichment Analysis took a broader approach for assessing the functional relations of pathway gene sets to differentially expressed genes, and leverage the cumulative signature of molecular concepts characteristic of the highly differentially expressed genes, which we termed as the universal concept signature, to tolerate the high noise and low coverage of this technology. We then incorporated Weighted Concept Signature Enrichment Analysis into an R package called "IndepthPathway" for biologists to broadly leverage this method for pathway analysis based on bulk and single-cell sequencing data. Through simulating technical variability and dropouts in gene expression characteristic of scRNA-seq as well as benchmarking on a real dataset of matched single-cell and bulk RNAseq data, we demonstrate that IndepthPathway presents outstanding stability and depth in pathway enrichment results under stochasticity of the data, thus will substantially improve the scientific rigor of the pathway analysis for single-cell sequencing data. AVAILABILITY AND IMPLEMENTATION The IndepthPathway R package is available through: https://github.com/wangxlab/IndepthPathway.
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Affiliation(s)
- Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, United States
| | - Letian Deng
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Yue Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Kai Wang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Maureen A Sartor
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, United States
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, United States
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50
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Wu SY, Zhang SW, Ma D, Xiao Y, Liu Y, Chen L, Song XQ, Ma XY, Xu Y, Chai WJ, Jin X, Shao ZM, Jiang YZ. CCL19 + dendritic cells potentiate clinical benefit of anti-PD-(L)1 immunotherapy in triple-negative breast cancer. MED 2023:S2666-6340(23)00140-X. [PMID: 37201522 DOI: 10.1016/j.medj.2023.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/23/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND The extensive involvement of dendritic cells (DCs) in immune contexture indicates their potent value in cancer immunotherapy. Understanding DC diversity in patient cohorts may strengthen the clinical benefit of immune checkpoint inhibitors (ICIs). METHODS Single-cell profiling of breast tumors from two clinical trials was performed to investigate DC heterogeneity. Multiomics, tissue characterization, and pre-clinical experiments were used to evaluate the role of the identified DCs in the tumor microenvironment. Four independent clinical trials were leveraged to explore biomarkers to predict ICI and chemotherapy outcomes. FINDINGS We identified a distinct CCL19-expressing functional state of DCs associated with favorable responses to anti-programmed death (ligand)-1 (PD-(L)1), which displayed migratory and immunomodulatory phenotypes. These cells were correlated with antitumor T cell immunity and the presence of tertiary lymphoid structures and lymphoid aggregates, defining immunogenic microenvironments in triple-negative breast cancer. In vivo, CCL19+ DC deletion by Ccl19 gene ablation dampened CCR7+CD8+ T cells and tumor elimination in response to anti-PD-1. Notably, high circulating and intratumoral CCL19 levels were associated with superior response and survival in patients receiving anti-PD-1 but not chemotherapy. CONCLUSIONS We uncovered a critical role of DC subsets in immunotherapy, which has implications for designing novel therapies and patient stratification strategies. FUNDING This study was funded by the National Key Research and Development Project of China, the National Natural Science Foundation of China, the Program of Shanghai Academic/Technology Research Leader, the Natural Science Foundation of Shanghai, the Shanghai Key Laboratory of Breast Cancer, the Shanghai Hospital Development Center (SHDC), and the Shanghai Health Commission.
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Affiliation(s)
- Song-Yang Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Si-Wei Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yin Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiao-Qing Song
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiao-Yan Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ying Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wen-Jun Chai
- Laboratory Animal Center, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Precision Cancer Medical Center, Fudan University Shanghai Cancer Center, Shanghai 201315, China.
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