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Han S, Xu Q, Du Y, Tang C, Cui H, Xia X, Zheng R, Sun Y, Shang H. Single-cell spatial transcriptomics in cardiovascular development, disease, and medicine. Genes Dis 2024; 11:101163. [PMID: 39224111 PMCID: PMC11367031 DOI: 10.1016/j.gendis.2023.101163] [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: 03/27/2023] [Revised: 10/17/2023] [Accepted: 10/29/2023] [Indexed: 09/04/2024] Open
Abstract
Cardiovascular diseases (CVDs) impose a significant burden worldwide. Despite the elucidation of the etiology and underlying molecular mechanisms of CVDs by numerous studies and recent discovery of effective drugs, their morbidity, disability, and mortality are still high. Therefore, precise risk stratification and effective targeted therapies for CVDs are warranted. Recent improvements in single-cell RNA sequencing and spatial transcriptomics have improved our understanding of the mechanisms and cells involved in cardiovascular phylogeny and CVDs. Single-cell RNA sequencing can facilitate the study of the human heart at remarkably high resolution and cellular and molecular heterogeneity. However, this technique does not provide spatial information, which is essential for understanding homeostasis and disease. Spatial transcriptomics can elucidate intracellular interactions, transcription factor distribution, cell spatial localization, and molecular profiles of mRNA and identify cell populations causing the disease and their underlying mechanisms, including cell crosstalk. Herein, we introduce the main methods of RNA-seq and spatial transcriptomics analysis and highlight the latest advances in cardiovascular research. We conclude that single-cell RNA sequencing interprets disease progression in multiple dimensions, levels, perspectives, and dynamics by combining spatial and temporal characterization of the clinical phenome with multidisciplinary techniques such as spatial transcriptomics. This aligns with the dynamic evolution of CVDs (e.g., "angina-myocardial infarction-heart failure" in coronary artery disease). The study of pathways for disease onset and mechanisms (e.g., age, sex, comorbidities) in different patient subgroups should improve disease diagnosis and risk stratification. This can facilitate precise individualized treatment of CVDs.
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Affiliation(s)
- Songjie Han
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Qianqian Xu
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Yawen Du
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Chuwei Tang
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Herong Cui
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xiaofeng Xia
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Rui Zheng
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Yang Sun
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Hongcai Shang
- Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
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Han Z, Quan Z, Zeng S, Wen L, Wang H. Utilizing omics technologies in the investigation of sepsis-induced cardiomyopathy. IJC HEART & VASCULATURE 2024; 54:101477. [PMID: 39171080 PMCID: PMC11334652 DOI: 10.1016/j.ijcha.2024.101477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/23/2024]
Abstract
Sepsis-induced cardiomyopathy (SIC) is a common and high-mortality complication among critically ill patients. Uncertainties persist regarding the pathogenesis, pathophysiology, and diagnosis of SIC, underscoring the necessity to investigate potential biological mechanisms. With the rise of omics technologies, leveraging their high throughput and big data advantages, a systems biology perspective is employed to study the biological processes of SIC. This approach aids in gaining a better understanding of the disease's onset, progression, and outcomes, ultimately providing improved guidance for clinical practices. This review summarizes the currently applied omics technologies, omics studies related to SIC, and relevant omics databases.
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Affiliation(s)
- Zheng Han
- Harbin Medical University Graduate School, Harbin Medical University, Heilongjiang Province, Harbin 150086, China
| | - Zhen Quan
- Harbin Medical University Graduate School, Harbin Medical University, Heilongjiang Province, Harbin 150086, China
| | - Siyao Zeng
- Harbin Medical University Graduate School, Harbin Medical University, Heilongjiang Province, Harbin 150086, China
| | - Lianghe Wen
- Department of Critical Care Medicine, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin 150086, China
| | - Hongliang Wang
- Department of Critical Care Medicine, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin 150086, China
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3
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Jin W, Pei J, Roy JR, Jayaraman S, Ahalliya RM, Kanniappan GV, Mironescu M, Palanisamy CP. Comprehensive review on single-cell RNA sequencing: A new frontier in Alzheimer's disease research. Ageing Res Rev 2024; 100:102454. [PMID: 39142391 DOI: 10.1016/j.arr.2024.102454] [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: 07/08/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
Alzheimer's disease (AD) is a multifaceted neurodegenerative condition marked by gradual cognitive deterioration and the loss of neurons. While conventional bulk RNA sequencing techniques have shed light on AD pathology, they frequently obscure the cellular diversity within brain tissues. The advent of single-cell RNA sequencing (scRNA-seq) has transformed our capability to analyze the cellular composition of AD, allowing for the detection of unique cell populations, rare cell types, and gene expression alterations at an individual cell level. This review examines the use of scRNA-seq in AD research, focusing on its contributions to understanding cellular diversity, disease progression, and potential therapeutic targets. We discuss key technological innovations, data analysis techniques, and challenges associated with scRNA-seq in studying AD. Furthermore, we highlight recent studies that have utilized scRNA-seq to identify novel biomarkers, uncover disease-associated pathways, and elucidate the role of non-neuronal cells, such as microglia and astrocytes, in AD pathogenesis. By providing a comprehensive overview of advancements in scRNA-seq for unraveling cellular heterogeneity in AD, this review highlights the transformative impact of scRNA-seq on our comprehension of disease mechanisms and the creation of targeted treatments.
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Affiliation(s)
- Wengang Jin
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 2011 QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi Province Key Laboratory of Bio-Resources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - JinJin Pei
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, 2011 QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi Province Key Laboratory of Bio-Resources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Jeane Rebecca Roy
- Department of Anatomy, Bhaarath Medical College and hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai, Tamil Nadu 600073, India
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India
| | - Rathi Muthaiyan Ahalliya
- Department of Biochemistry and Cancer Research Centre, FASCM, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu 641021, India
| | - Gopalakrishnan Velliyur Kanniappan
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu 602105, India.
| | - Monica Mironescu
- Faculty of Agricultural Sciences Food Industry and Environmental Protection, Lucian Blaga University of Sibiu, Bv. Victoriei 10, Sibiu 550024, Romania.
| | - Chella Perumal Palanisamy
- Department of Chemical Technology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Theodorakis N, Feretzakis G, Tzelves L, Paxinou E, Hitas C, Vamvakou G, Verykios VS, Nikolaou M. Integrating Machine Learning with Multi-Omics Technologies in Geroscience: Towards Personalized Medicine. J Pers Med 2024; 14:931. [PMID: 39338186 PMCID: PMC11433587 DOI: 10.3390/jpm14090931] [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: 08/10/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Aging is a fundamental biological process characterized by a progressive decline in physiological functions and an increased susceptibility to diseases. Understanding aging at the molecular level is crucial for developing interventions that could delay or reverse its effects. This review explores the integration of machine learning (ML) with multi-omics technologies-including genomics, transcriptomics, epigenomics, proteomics, and metabolomics-in studying the molecular hallmarks of aging to develop personalized medicine interventions. These hallmarks include genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. Using ML to analyze big and complex datasets helps uncover detailed molecular interactions and pathways that play a role in aging. The advances of ML can facilitate the discovery of biomarkers and therapeutic targets, offering insights into personalized anti-aging strategies. With these developments, the future points toward a better understanding of the aging process, aiming ultimately to promote healthy aging and extend life expectancy.
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Affiliation(s)
- Nikolaos Theodorakis
- Department of Cardiology & 65+ Clinic, Amalia Fleming General Hospital, 14, 25th Martiou Str., 15127 Melissia, Greece
- School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527 Athens, Greece
| | - Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, 18 Aristotelous Str., 26335 Patras, Greece
| | - Lazaros Tzelves
- 2nd Department of Urology, Sismanoglio General Hospital, Sismanogliou 37, National and Kapodistrian University of Athens, 15126 Athens, Greece
| | - Evgenia Paxinou
- School of Science and Technology, Hellenic Open University, 18 Aristotelous Str., 26335 Patras, Greece
| | - Christos Hitas
- Department of Cardiology & 65+ Clinic, Amalia Fleming General Hospital, 14, 25th Martiou Str., 15127 Melissia, Greece
| | - Georgia Vamvakou
- Department of Cardiology & 65+ Clinic, Amalia Fleming General Hospital, 14, 25th Martiou Str., 15127 Melissia, Greece
| | - Vassilios S Verykios
- School of Science and Technology, Hellenic Open University, 18 Aristotelous Str., 26335 Patras, Greece
| | - Maria Nikolaou
- Department of Cardiology & 65+ Clinic, Amalia Fleming General Hospital, 14, 25th Martiou Str., 15127 Melissia, Greece
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Guinn MT, Fernandez R, Lau S, Loor G. Transcriptomic Signatures in Lung Allografts and Their Therapeutic Implications. Biomedicines 2024; 12:1793. [PMID: 39200257 PMCID: PMC11351513 DOI: 10.3390/biomedicines12081793] [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: 06/02/2024] [Revised: 07/20/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Ex vivo lung perfusion (EVLP) is a well-established method of lung preservation in clinical transplantation. Transcriptomic analyses of cells and tissues uncover gene expression patterns which reveal granular molecular pathways and cellular programs under various conditions. Coupling EVLP and transcriptomics may provide insights into lung allograft physiology at a molecular level with the potential to develop targeted therapies to enhance or repair the donor lung. This review examines the current landscape of transcriptional analysis of lung allografts in the context of state-of-the-art therapeutics that have been developed to optimize lung allograft function.
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Affiliation(s)
- Michael Tyler Guinn
- Division of Cardiothoracic Transplantation and Circulatory Support, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; (M.T.G.)
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Ramiro Fernandez
- Division of Cardiothoracic Transplantation and Circulatory Support, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; (M.T.G.)
| | - Sean Lau
- Department of Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Gabriel Loor
- Division of Cardiothoracic Transplantation and Circulatory Support, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; (M.T.G.)
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Yin D, Zhan S, Liu Y, Yan L, Shi B, Wang X, Zhang S. Experimental models for peri-implant diseases: a narrative review. Clin Oral Investig 2024; 28:378. [PMID: 38884808 DOI: 10.1007/s00784-024-05755-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024]
Abstract
OBJECTIVES Peri-implant diseases, being the most common implant-related complications, significantly impact the normal functioning and longevity of implants. Experimental models play a crucial role in discovering potential therapeutic approaches and elucidating the mechanisms of disease progression in peri-implant diseases. This narrative review comprehensively examines animal models and common modeling methods employed in peri-implant disease research and innovatively summarizes the in vitro models of peri-implant diseases. MATERIALS AND METHODS Articles published between 2015 and 2023 were retrieved from PubMed/Medline, Web of Science, and Embase. All studies focusing on experimental models of peri-implant diseases were included and carefully evaluated. RESULTS Various experimental models of peri-implantitis have different applications and advantages. The dog model is currently the most widely utilized animal model in peri-implant disease research, while rodent models have unique advantages in gene knockout and systemic disease induction. In vitro models of peri-implant diseases are also continuously evolving to meet different experimental purposes. CONCLUSIONS The utilization of experimental models helps simplify experiments, save time and resources, and promote advances in peri-implant disease research. Animal models have been proven valuable in the early stages of drug development, while technological advancements have brought about more predictive and relevant in vitro models. CLINICAL RELEVANCE This review provides clear and comprehensive model selection strategies for researchers in the field of peri-implant diseases, thereby enhancing understanding of disease pathogenesis and providing possibilities for developing new treatment strategies.
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Affiliation(s)
- Derong Yin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030032, Shanxi, China
| | - Suying Zhan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yanbo Liu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, 030032, Shanxi, China
| | - Lichao Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Binmian Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiayi Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
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7
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Ding Y, Peng YY, Li S, Tang C, Gao J, Wang HY, Long ZY, Lu XM, Wang YT. Single-Cell Sequencing Technology and Its Application in the Study of Central Nervous System Diseases. Cell Biochem Biophys 2024; 82:329-342. [PMID: 38133792 DOI: 10.1007/s12013-023-01207-3] [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: 08/21/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The mammalian central nervous system consists of a large number of cells, which contain not only different types of neurons, but also a large number of glial cells, such as astrocytes, oligodendrocytes, and microglia. These cells are capable of performing highly refined electrophysiological activities and providing the brain with functions such as nutritional support, information transmission and pathogen defense. The diversity of cell types and individual differences between cells have brought inspiration to the study of the mechanism of central nervous system diseases. In order to explore the role of different cells, a new technology, single-cell sequencing technology has emerged to perform specific analysis of high-throughput cell populations, and has been continuously developed. Single-cell sequencing technology can accurately analyze single-cell expression in mixed-cell populations and collect cells from different spatial locations, time stages and types. By using single-cell sequencing technology to compare gene expression profiles of normal and diseased cells, it is possible to discover cell subsets associated with specific diseases and their associated genes. Therefore, scientists can understand the development process, related functions and disease state of the nervous system from an unprecedented depth. In conclusion, single-cell sequencing technology provides a powerful technology for the discovery of novel therapeutic targets for central nervous system diseases.
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Affiliation(s)
- Yang Ding
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yu-Yuan Peng
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Sen Li
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Can Tang
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jie Gao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Zai-Yun Long
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Yong-Tang Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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Casey C, Fullard JF, Sleator RD. Unravelling the genetic basis of Schizophrenia. Gene 2024; 902:148198. [PMID: 38266791 DOI: 10.1016/j.gene.2024.148198] [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: 09/01/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
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Affiliation(s)
- Clara Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
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Yang Y, Yang X, Ren S, Cao Y, Wang Z, Cheng Z. Identification and analysis of prognostic metabolic characteristics in colon adenocarcinoma. Heliyon 2024; 10:e27388. [PMID: 38509965 PMCID: PMC10950572 DOI: 10.1016/j.heliyon.2024.e27388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Colon adenocarcinoma (COAD) is a highly lethal gastrointestinal malignancy. The five-year survival rate of metastatic colorectal cancer remains low, at 14 percent. Numerous publications have suggested a role for peroxisome proliferator-activated receptors (PPARs) in malignancy. Recent studies have shown that PPARs, as nuclear transcription factors, may serve as potential targets for the treatment of metabolic syndrome tumors and their associated complications. However, the molecular mechanism has not been thoroughly investigated. Hence, in order to enhance the prediction of personalized medicine for PPAR-associated modulators in malignancy treatment, a timely review becomes essential. Utilizing TCGA-COAD expression profile data and patient overall survival (OS) information, this study systematically conducted investigations to identify and develop Hub stem cell-related diagnostic and prognostic identification models, aiming to enhance the multi-gene markers for COAD. Utilizing the differential expression profiles of stem cell-related genes, an 11-gene (SLC27A4, CPT1C, CPT1B, CPT2, CYP4A11, FABP3, FABP7, AQP7, MMP1, ACOX1, ANGPTL4) diagnostic and prognostic model was developed. This model demonstrated precise diagnostic and prognostic capabilities and holds the potential to characterize the clinicopathologic features of COAD. Univariate and multivariate Cox proportional hazards regression analyses were conducted to ascertain the independent factors influencing OS outcomes in COAD. The results revealed that CPT1B, SLC27A4, and FABP3 were identified as independent risk prognostic factors for OS in COAD, whereas ACOX1 and CPT2 served as independent protective prognostic factors. The hub genes associated with PPARs were identified through the differential expression of contrast agent COAD and normal tissues. Finally, the investigation of variations in immune infiltration and the analysis of relevant biological pathways validate the prognostic significance of the independent post-factors within this molecular model. This research aims to provide references for comprehending the mechanism of post-transcriptional regulation of COAD and molecular therapy.
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Affiliation(s)
- Yang Yang
- Department of Trauma Center, Affiliated Hospital of Nantong University, Medicial School of Nantong University, No.20 Xisi Road, Chongchuan District, 226001, Nantong City, Jiangsu Province, China
- Department of Emergency Medicine, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, Nantong City, Jiangsu Province, 226001, China
| | - Xinyu Yang
- Department of Trauma Center, Affiliated Hospital of Nantong University, Medicial School of Nantong University, No.20 Xisi Road, Chongchuan District, 226001, Nantong City, Jiangsu Province, China
- Medical School of Nantong University, Qixiu Road, 226001, Nantong City, Jiangsu Province, China
| | - Shiqi Ren
- Department of Hand Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Yang Cao
- Department of Operation Room, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, 226001, Nantong City, Jiangsu Province, China
| | - Ziheng Wang
- MOE Frontier Science Centre for Precision Oncology, University of Macau, Macau SAR, China
- Department of Clinical-Biobank, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, 226001, Nantong City, Jiangsu Province, China
| | - Zhouyang Cheng
- Department of General Surgery, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, 226001, Nantong City, Jiangsu Province, China
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10
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Chen Y, Zhang Y, Jiang M, Ma H, Cai Y. HMOX1 as a therapeutic target associated with diabetic foot ulcers based on single-cell analysis and machine learning. Int Wound J 2024; 21:e14815. [PMID: 38468410 PMCID: PMC10928352 DOI: 10.1111/iwj.14815] [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: 12/23/2023] [Revised: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Diabetic foot ulcers (DFUs) are a serious chronic complication of diabetes mellitus and a leading cause of disability and death in diabetic patients. However, current treatments remain unsatisfactory. Although macrophages are associated with DFU, their exact role in this disease remains uncertain. This study sought to detect macrophage-related genes in DFU and identify possible therapeutic targets. Single-cell datasets (GSE223964) and RNA-seq datasets (GSM68183, GSE80178, GSE134431 and GSE147890) associated with DFU were retrieved from the gene expression omnibus (GEO) database for this study. Analysis of the provided single-cell data revealed the distribution of macrophage subpopulations in the DFU. Four independent RNA-seq datasets were merged into a single DFU cohort and further analysed using bioinformatics. This included differential expression (DEG) analysis, multiple machine learning algorithms to identify biomarkers and enrichment analysis. Finally, key results were validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western bolt. Finally, the findings were validated using RT-qPCR and western blot. We obtained 802 macrophage-related genes in single-cell analysis. Differential expression analysis yielded 743 DEGs. Thirty-seven macrophage-associated DEGs were identified by cross-analysis of marker genes with macrophage-associated DEGs. Thirty-seven intersections were screened and cross-analysed using four machine learning algorithms. Finally, HMOX1 was identified as a potentially valuable biomarker. HMOX1 was significantly associated with biological pathways such as the insulin signalling pathway. The results showed that HMOX1 was significantly overexpressed in DFU samples. In conclusion, the analytical results of this study identified HMOX1 as a potentially valuable biomarker associated with macrophages in DFU. The results of our analysis improve our understanding of the mechanism of macrophage action in this disease and may be useful in developing targeted therapies for DFU.
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Affiliation(s)
- Yiqi Chen
- Department of Burn and Plastic SurgeryAffiliated Hospital of Nantong UniversityNantongChina
| | - Yixin Zhang
- Department of Burn and Plastic SurgeryAffiliated Hospital of Nantong UniversityNantongChina
- Department of Breast SurgeryYantai City Yantai Hill hospitalYantaiChina
| | - Ming Jiang
- Department of Burn and Plastic SurgeryAffiliated Hospital of Nantong UniversityNantongChina
| | - Hong Ma
- Department of Burn and Plastic SurgeryAffiliated Hospital of Nantong UniversityNantongChina
- Department of BurnHanzhong Central HospitalHanZhongChina
| | - Yuhui Cai
- Department of Burn and Plastic SurgeryAffiliated Hospital of Nantong UniversityNantongChina
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Pereira CA, Reis-de-Oliveira G, Pierone BC, Martins-de-Souza D, Kaster MP. Depicting the molecular features of suicidal behavior: a review from an "omics" perspective. Psychiatry Res 2024; 332:115682. [PMID: 38198856 DOI: 10.1016/j.psychres.2023.115682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Background Suicide is one of the leading global causes of death. Behavior patterns from suicide ideation to completion are complex, involving multiple risk factors. Advances in technologies and large-scale bioinformatic tools are changing how we approach biomedical problems. The "omics" field may provide new knowledge about suicidal behavior to improve identification of relevant biological pathways associated with suicidal behavior. Methods We reviewed transcriptomic, proteomic, and metabolomic studies conducted in blood and post-mortem brains from individuals who experienced suicide or suicidal behavior. Omics data were combined using systems biology in silico, aiming at identifying major biological mechanisms and key molecules associated with suicide. Results Post-mortem samples of suicide completers indicate major dysregulations in pathways associated with glial cells (astrocytes and microglia), neurotransmission (GABAergic and glutamatergic systems), neuroplasticity and cell survivor, immune responses and energy homeostasis. In the periphery, studies found alterations in molecules involved in immune responses, polyamines, lipid transport, energy homeostasis, and amino and nucleic acid metabolism. Limitations We included only exploratory, non-hypothesis-driven studies; most studies only included one brain region and whole tissue analysis, and focused on suicide completers who were white males with almost none confounding factors. Conclusions We can highlight the importance of synaptic function, especially the balance between the inhibitory and excitatory synapses, and mechanisms associated with neuroplasticity, common pathways associated with psychiatric disorders. However, some of the pathways highlighted in this review, such as transcriptional factors associated with RNA splicing, formation of cortical connections, and gliogenesis, point to mechanisms that still need to be explored.
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Affiliation(s)
- Caibe Alves Pereira
- Laboratory of Translational Neurosciences, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil
| | - Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Bruna Caroline Pierone
- Laboratory of Translational Neurosciences, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil; Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION) Conselho Nacional de Desenvolvimento Científico E Tecnológico, São Paulo, Brazil; Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil; D'Or Institute for Research and Education (IDOR), São Paulo, Brazil; INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
| | - Manuella Pinto Kaster
- Laboratory of Translational Neurosciences, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianopolis, Santa Catarina, Brazil.
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12
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [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] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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13
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Wang L, Sun T, Liu X, Wang Y, Qiao X, Chen N, Liu F, Zhou X, Wang H, Shen H. Myocarditis: A multi-omics approach. Clin Chim Acta 2024; 554:117752. [PMID: 38184138 DOI: 10.1016/j.cca.2023.117752] [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: 12/14/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Myocarditis, an inflammatory condition of weakened heart muscles often triggered by a variety of causes, that can result in heart failure and sudden death. Novel ways to enhance our understanding of myocarditis pathogenesis is available through newer modalities (omics). In this review, we examine the roles of various biomolecules and associated functional pathways across genomics, transcriptomics, proteomics, and metabolomics in the pathogenesis of myocarditis. Our analysis further explores the reproducibility and variability intrinsic to omics studies, underscoring the necessity and significance of employing a multi-omics approach to gain profound insights into myocarditis pathogenesis. This integrated strategy not only enhances our understanding of the disease, but also confirms the critical importance of a holistic multi-omics approach in disease analysis.
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Affiliation(s)
- Lulu Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Tao Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang 212000, Jiangsu, China
| | - Xiaolan Liu
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Yan Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaorong Qiao
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Nuo Chen
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Fangqian Liu
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xiaoxiang Zhou
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Hua Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Hongxing Shen
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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14
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Wu Z, Li H, Wu J, Lai X, Huang S, Yu M, Liao Q, Zhang C, Zhou L, Chen X, Guo H, Chen L. The profile of genome-wide DNA methylation, transcriptome, and proteome in streptomycin-resistant Mycobacterium tuberculosis. PLoS One 2024; 19:e0297477. [PMID: 38285653 PMCID: PMC10824437 DOI: 10.1371/journal.pone.0297477] [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: 03/23/2023] [Accepted: 01/06/2024] [Indexed: 01/31/2024] Open
Abstract
Streptomycin-resistant (SM-resistant) Mycobacterium tuberculosis (M. tuberculosis) is a major concern in tuberculosis (TB) treatment. However, the mechanisms underlying streptomycin resistance remain unclear. This study primarily aimed to perform preliminary screening of genes associated with streptomycin resistance through conjoint analysis of multiple genomics. Genome-wide methylation, transcriptome, and proteome analyses were used to elucidate the associations between specific genes and streptomycin resistance in M. tuberculosis H37Rv. Methylation analysis revealed that 188 genes were differentially methylated between the SM-resistant and normal groups, with 89 and 99 genes being hypermethylated and hypomethylated, respectively. Furthermore, functional analysis revealed that these 188 differentially methylated genes were enriched in 74 pathways, with most of them being enriched in metabolic pathways. Transcriptome analysis revealed that 516 genes were differentially expressed between the drug-resistant and normal groups, with 263 and 253 genes being significantly upregulated and downregulated, respectively. KEGG analysis indicated that these 516 genes were enriched in 79 pathways, with most of them being enriched in histidine metabolism. The methylation level was negatively related to mRNA abundance. Proteome analysis revealed 56 differentially expressed proteins, including 14 upregulated and 42 downregulated proteins. Moreover, three hub genes (coaE, fadE5, and mprA) were obtained using synthetic analysis. The findings of this study suggest that an integrated DNA methylation, transcriptome, and proteome analysis can provide important resources for epigenetic studies in SM-resistant M. tuberculosis H37Rv.
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Affiliation(s)
- Zhuhua Wu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Haicheng Li
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiawen Wu
- Institute for tuberculosis control of Zhaoqing, Zhaoqing, China
| | - Xiaoyu Lai
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Shanshan Huang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Meiling Yu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Qinghua Liao
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Xunxun Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Huixin Guo
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Liang Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
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15
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Zhan W, Luo W, Zhang Y, Xiang K, Chen X, Shen S, Huang C, Xu T, Ding W, Chen Y, Lin M, Pan X, Lai K. Sputum Transcriptomics Reveals FCN1+ Macrophage Activation in Mild Eosinophilic Asthma Compared to Non-Asthmatic Eosinophilic Bronchitis. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2024; 16:55-70. [PMID: 38262391 PMCID: PMC10823142 DOI: 10.4168/aair.2024.16.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/08/2023] [Accepted: 08/05/2023] [Indexed: 01/25/2024]
Abstract
PURPOSE Eosinophilic asthma (EA) and non-asthmatic eosinophilic bronchitis (EB) share similar eosinophilic airway inflammation. Unlike EA, EB did not present airway hyperresponsiveness or airflow obstruction. We aimed to compare the mechanism underlying the different manifestations between EA and EB via sputum transcriptomics analysis. METHODS Induced-sputum cells from newly physician-diagnosed EA, EB patients, and healthy controls (HCs) were collected for RNA sequencing. RESULTS Bulk RNA sequencing was performed using sputum cells from patients with EA (n = 18), EB (n = 15) and HCs (n = 28). Principal component analysis revealed similar gene expression patterns in EA and EB. The most differentially expressed genes in EB compared with HC were also shared by EA, including IL4, IL5 IL13, CLC, CPA3, and DNASE1L3. However, gene set enrichment analysis showed that the signatures regulating macrophage activation were enriched in EA compared to EB. Sputum cells were profiled using single-cell RNA sequencing. FABP4+ macrophages, SPP1+ macrophages, FCN1+ macrophages, dendritic cells, T cells, B cells, mast cells, and epithelial cells were identified based on gene expression profiling. Analysis of cell-cell communication revealed that interactions between FCN1+ macrophages and other cells were higher in EA than in EB. A wealth of transforming growth factor beta (TGF-β) and vascular endothelial growth factor (VEGF) interactions between FCN1+ macrophages and other cells have been shown in EA. The gene expression levels of EREG, TGFBI, and VEGFA in FCN1+ macrophages of EA were significantly higher than those of EB. Furthermore, signatures associated with the response to TGF-β, cellular response to VEGF stimulus and developmental cell growth were enriched in FCN1+ macrophages of EA compared to those of EB. CONCLUSIONS FCN1+ macrophage activation associated with airway remodeling processes was upregulated in EA compared to that in EB, which may contribute to airway hyperresponsiveness and airflow obstruction.
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Affiliation(s)
- Wenzhi Zhan
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Luo
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yulong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Keheng Xiang
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaomei Chen
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuirong Shen
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chuqing Huang
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tingting Xu
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenbin Ding
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuehan Chen
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mingtong Lin
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Kefang Lai
- Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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16
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Zhu JH, Guan XC, Yi LL, Xu H, Li QY, Cheng WJ, Xie YX, Li WZ, Zhao HY, Wei HJ, Zhao SM. Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs. BMC Genomics 2023; 24:770. [PMID: 38087243 PMCID: PMC10717992 DOI: 10.1186/s12864-023-09765-9] [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: 07/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs. RESULTS The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways. CONCLUSIONS In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds.
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Affiliation(s)
- Jun-Hong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuan-Cheng Guan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Lan-Lan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong Xu
- School of Public Finance and Economics, Yunnan University of Finance and Economics, Kunming, 650221, China
| | - Qiu-Yan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Wen-Jie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Yu-Xiao Xie
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, 563006, China
| | - Wei-Zhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Ye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Jiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
| | - Su-Mei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China.
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
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Su N, Lin Z, Liu X, Sun X, Jin X, Feng H, Zhan C, Hu X, Gu C, Zhang W, Cheng G. Pathological observation and transcriptomic analysis of thymus injury in PRRSV-infected piglets. Vet Res Commun 2023; 47:1949-1962. [PMID: 37266866 DOI: 10.1007/s11259-023-10133-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: 02/19/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
The thymus, the central immune organ in mammals, plays an important role in immune defense. Porcine reproductive and respiratory syndrome virus (PRRSV) infection in piglets can cause thymus injury and immunosuppression. However, the mechanisms of thymus injury remain unknown. This study was aimed at investigating the specific manifestations of thymus injury through the construction of a PRRSV-infected piglet model and histopathological observation. In this study, fourteen 40-day-old PRRSV-free piglets were randomly divided into two groups, eleven of which were intramuscularly injected with 3 mL of PRRSV WUH3 virus suspension (106 PFU /mL) in the infection group, and three of which were sham-inoculated with 3 mL of RPMI-1640 medium in the control group. Clinical necropsy and samples collection were performed on day 8 after artificial infection. With the Illumina platform, the transcriptomes of piglet thymus tissues from infected and control piglets were sequenced to explore the relationships of differentially expressed genes (DEGs) and signaling pathways with thymus injury. The immune organs of PRRSV-infected piglets were severely damaged. The histopathological findings in the thymus indicated that PRRSV infection was associated with a large decrease in lymphocytes, cell necrosis and cell apoptosis; an increase in blood vessels and macrophages; thymic corpuscle hyperplasia; and interstitial widening of the thymic lobules. The transcriptomic analysis results revealed that the Gene Ontology functions of DEGs were enriched primarily in biological processes such as angiogenesis, regulation of angiogenesis and positive regulation of cell migration. Moreover, greater numbers of blood vessels and macrophages were observed in the thymus in PRRSV-infected than control piglets. KEGG pathway enrichment analysis revealed that the DEGs were significantly enriched in the Toll-like receptor signaling pathway, chemokine signaling pathway, IL-17 signaling pathway and TNF signaling pathway. The expression of TLR8, IRF5, the chemokines CCL2, CCL3L1 and CCL5; and their receptors CCR1, CCR2 and CCR5 was significantly up-regulated in PRRSV infection, thus suggesting that these cytokines were associated with the pathological processes of thymus injury.
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Affiliation(s)
- Naying Su
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
- Shanghai InnoStar Bio-tech Co., Ltd., Shanghai, China
| | - Zhengdan Lin
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Xi Liu
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Xiuxiu Sun
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Xinxin Jin
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Helong Feng
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
- Hubei Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Cunlin Zhan
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Xueying Hu
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Changqin Gu
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Wanpo Zhang
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Guofu Cheng
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, Hubei Province, China.
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Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
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Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
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Pan Z, Guo J, Zhong Y, Fan L, Su Y. Gentamicin resistance to Escherichia coli related to fatty acid metabolism based on transcriptome analysis. Can J Microbiol 2023; 69:328-338. [PMID: 37224563 DOI: 10.1139/cjm-2023-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Antibiotic overuse and misuse have promoted the emergence and spread of antibiotic-resistant bacteria. Increasing bacterial resistance to antibiotics is a major healthcare problem, necessitating elucidation of antibiotic resistance mechanisms. In this study, we explored the mechanism of gentamicin resistance by comparing the transcriptomes of antibiotic-sensitive and -resistant Escherichia coli. A total of 410 differentially expressed genes were identified, of which 233 (56.83%) were up-regulated and 177 (43.17%) were down-regulated in the resistant strain compared with the sensitive strain. Gene Ontology (GO) analysis classifies differential gene expression into three main categories: biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the up-regulated genes were enriched in eight metabolic pathways, including fatty acid metabolism, which suggests that fatty acid metabolism may be involved in the development of gentamicin resistance in E. coli. This was demonstrated by measuring the acetyl-CoA carboxylase activity, plays a fundamental role in fatty acid metabolism, was increased in gentamicin-resistant E. coli. Treatment of fatty acid synthesis inhibitor, triclosan, promoted gentamicin-mediated killing efficacy to antibiotic-resistant bacteria. We also found that exogenous addition of oleic acid, which involved in fatty acid metabolism, reduced E. coli sensitivity to gentamicin. Overall, our results provide insight into the molecular mechanism of gentamicin resistance development in E. coli.
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Affiliation(s)
- Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
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20
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He XL, Chen JY, Feng YL, Song P, Wong YK, Xie LL, Wang C, Zhang Q, Bai YM, Gao P, Luo P, Liu Q, Liao FL, Li ZJ, Jiang Y, Wang JG. Single-cell RNA sequencing deciphers the mechanism of sepsis-induced liver injury and the therapeutic effects of artesunate. Acta Pharmacol Sin 2023; 44:1801-1814. [PMID: 37041228 PMCID: PMC10462669 DOI: 10.1038/s41401-023-01065-y] [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: 11/16/2022] [Accepted: 02/16/2023] [Indexed: 04/13/2023] Open
Abstract
Liver, as an immune and detoxification organ, represents an important line of defense against bacteria and infection and a vulnerable organ that is easily injured during sepsis. Artesunate (ART) is an anti-malaria agent, that also exhibits broad pharmacological activities including anti-inflammatory, immune-regulation and liver protection. In this study, we investigated the cellular responses in liver to sepsis infection and ART hepatic-protective mechanisms against sepsis. Cecal ligation and puncture (CLP)-induced sepsis model was established in mice. The mice were administered ART (10 mg/kg, i.p.) at 4 h, and sacrificed at 12 h after the surgery. Liver samples were collected for preparing single-cell RNA transcriptome sequencing (scRNA-seq). The scRNA-seq analysis revealed that sepsis-induced a dramatic reduction of hepatic endothelial cells, especially the subtypes characterized with proliferation and differentiation. Macrophages were recruited during sepsis and released inflammatory cytokines (Tnf, Il1b, Il6), chemokines (Ccl6, Cd14), and transcription factor (Nfkb1), resulting in liver inflammatory responses. Massive apoptosis of lymphocytes and abnormal recruitment of neutrophils caused immune dysfunction. ART treatment significantly improved the survival of CLP mice within 96 h, and partially relieved or reversed the above-mentioned pathological features, mitigating the impact of sepsis on liver injury, inflammation, and dysfunction. This study provides comprehensive fundamental proof for the liver protective efficacy of ART against sepsis infection, which would potentially contribute to its clinical translation for sepsis therapy. Single cell transcriptome reveals the changes of various hepatocyte subtypes of CLP-induced liver injury and the potential pharmacological effects of artesunate on sepsis.
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Affiliation(s)
- Xue-Ling He
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Jia-Yun Chen
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Yu-Lin Feng
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Ping Song
- China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Lu-Lin Xie
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Chen Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qian Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yun-Meng Bai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Peng Gao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Piao Luo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiang Liu
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, and Cardiovascular Pharmacology Division of Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, 94304, USA
| | - Fu-Long Liao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhi-Jie Li
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China.
| | - Yong Jiang
- Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Ji-Gang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China.
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China.
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Zhang Z, Wang Z, Dong C, Sun C, Zheng W, Wang K, Zhang W, Song Z, Zhao S, Si Z, Gao W, Shen Z. Serum CXCL8 Concentration Can Be Used as a Noninvasive Marker of Subclinical Rejection After Pediatric Liver Transplantation. Transplantation 2023; 107:1999-2008. [PMID: 37607014 DOI: 10.1097/tp.0000000000004601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND This study aimed to explore whether serum CXCL8 concentration can be used as a noninvasive marker of subclinical rejection (SCR) after pediatric liver transplantation (pLT). METHODS Firstly, RNA sequencing (RNA-seq) was performed on 22 protocol liver biopsy samples. Secondly, several experimental methods were used to verify the RNA-seq results. Finally, the clinical data and serum samples of 520 LT patients in the Department of Pediatric Transplantation of Tianjin First Central Hospital from January 2018 to December 2019 were collected. RESULTS RNA-seq results indicated that CXCL8 was significantly increased in the SCR group. The results of the 3 experimental methods were consistent with RNA-seq results. According to the 1:2 propensity score matching, 138 patients were divided into the SCR (n = 46) and non-SCR (n = 92) groups. Serological test results indicated that there was no difference in preoperative CXCL8 concentration between the SCR and non-SCR groups ( P > 0.05). However, during protocol biopsy, CXCL8 in the SCR group was significantly higher than in the non-SCR group ( P < 0.001). In diagnosing SCR, receiver operating characteristic curve analysis showed that the area under the curve of CXCL8 was 0.966 (95% confidence interval, 0.938-0.995), sensitivity was 95%, and specificity was 94.6%. In differentiating nonborderline from borderline rejection, the area under the curve of CXCL8 was 0.853 (95% confidence interval, 0.718-0.988), sensitivity was 86.7%, and specificity was 94.6%. CONCLUSIONS This study demonstrates that serum CXCL8 concentration has high accuracy for the diagnosis and disease stratification of SCR after pLT.
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Affiliation(s)
- Zhixin Zhang
- First Central Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Zhenglu Wang
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Chong Dong
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Chao Sun
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Weiping Zheng
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Kai Wang
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Wei Zhang
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Zhuolun Song
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - Shengqiao Zhao
- First Central Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Zhuyuan Si
- First Central Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Wei Gao
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
| | - ZhongYang Shen
- Department of Pediatric Transplantation, Organ Transplantation Center, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Tianjin, China
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Yang S, Xie BL, Dong XP, Wang LX, Zhu GH, Wang T, Wu WJ, Lai RS, Tao R, Guan MX, Chen FY, Tan DH, Deng Z, Xie HP, Zeng Y, Xiao ZA, Xie DH. cdh23 affects congenital hearing loss through regulating purine metabolism. Front Mol Neurosci 2023; 16:1079529. [PMID: 37575969 PMCID: PMC10416109 DOI: 10.3389/fnmol.2023.1079529] [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: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction The pathogenic gene CDH23 plays a pivotal role in tip links, which is indispensable for mechanoelectrical transduction in the hair cells. However, the underlying molecular mechanism and signal regulatory networks that influence deafness is still largely unknown. Methods In this study, a congenital deafness family, whole exome sequencing revealed a new mutation in the pathogenic gene CDH23, subsequently; the mutation has been validated using Sanger sequencing method. Then CRISPR/Cas9 technology was employed to knockout zebrafish cdh23 gene. Startle response experiment was used to compare with wide-type, the response to sound stimulation between wide-type and cdh23-/-. To further illustrate the molecular mechanisms underlying congenital deafness, comparative transcriptomic profiling and multiple bioinformatics analyses were performed. Results The YO-PRO-1 assay result showed that in cdh23 deficient embryos, the YO-PRO-1 signal in inner ear and lateral line neuromast hair cells were completely lost. Startle response experiment showed that compared with wide-type, the response to sound stimulation decreased significantly in cdh23 mutant larvae. Comparative transcriptomic showed that the candidate genes such as atp1b2b and myof could affect hearing by regulating ATP production and purine metabolism in a synergetic way with cdh23. RT-qPCR results further confirmed the transcriptomics results. Further compensatory experiment showed that ATP treated cdh23-/- embryos can partially recover the mutant phenotype. Conclusion In conclusion, our study may shed light on deciphering the principal mechanism and provide a potential therapeutic method for congenital hearing loss under the condition of CDH23 mutation.
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Affiliation(s)
- Shu Yang
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Bing-Lin Xie
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Xiao-ping Dong
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Ling-xiang Wang
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Gang-hua Zhu
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Tian Wang
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei-jing Wu
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ruo-sha Lai
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Rong Tao
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Min-xin Guan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Human Genetics, Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Fang-yi Chen
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dong-hui Tan
- Department of Otolaryngology—Head and Neck Surgery, The Affiliated Hospital of Xiang Nan College, Chenzhou, China
| | - Zhong Deng
- Department of Otolaryngology—Head and Neck Surgery, The Affiliated Hospital of Xiang Nan College, Chenzhou, China
| | - Hua-ping Xie
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Yong Zeng
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Zi-an Xiao
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ding-hua Xie
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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23
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Zheng Y, Lin C, Chu Y, Gu S, Deng H, Shen Z. Spatial metabolomics in head and neck tumors: a review. Front Oncol 2023; 13:1213273. [PMID: 37519782 PMCID: PMC10374363 DOI: 10.3389/fonc.2023.1213273] [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: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
The joint analysis of single-cell transcriptomics, proteomics, lipidomics, metabolomics and spatial metabolomics is continually transforming our understanding of the mechanisms of metabolic reprogramming in tumor cells. Since head and neck tumor is the sixth most common tumor in the world, the study of the metabolic mechanism of its occurrence, development and prognosis is still undeveloped. In the past decade, this field has witnessed tremendous technological revolutions and considerable development that enables major breakthroughs to be made in the study of human tumor metabolism. In this review, a comprehensive comparison of traditional metabolomics and spatial metabolomics has been concluded, and the recent progress and challenges of the application of spatial metabolomics combined multi-omics in the research of metabolic reprogramming in tumors are reviewed. Furthermore, we also highlight the advances of spatial metabolomics in the study of metabolic mechanisms of head and neck tumors, and provide an outlook of its application prospects.
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Affiliation(s)
- Ye Zheng
- Health Science Center, Ningbo University, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Chen Lin
- Health Science Center, Ningbo University, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Yidian Chu
- Health Science Center, Ningbo University, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Shanshan Gu
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Hongxia Deng
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Zhisen Shen
- Health Science Center, Ningbo University, Ningbo, China
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
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24
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Dudchenko O, Ordovas-Montanes J, Bingle CD. Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing. Biochem J 2023; 480:921-939. [PMID: 37410389 PMCID: PMC10422933 DOI: 10.1042/bcj20220572] [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: 11/19/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Standalone and consortia-led single-cell atlases of healthy and diseased human airways generated with single-cell RNA-sequencing (scRNA-seq) have ushered in a new era in respiratory research. Numerous discoveries, including the pulmonary ionocyte, potentially novel cell fates, and a diversity of cell states among common and rare epithelial cell types have highlighted the extent of cellular heterogeneity and plasticity in the respiratory tract. scRNA-seq has also played a pivotal role in our understanding of host-virus interactions in coronavirus disease 2019 (COVID-19). However, as our ability to generate large quantities of scRNA-seq data increases, along with a growing number of scRNA-seq protocols and data analysis methods, new challenges related to the contextualisation and downstream applications of insights are arising. Here, we review the fundamental concept of cellular identity from the perspective of single-cell transcriptomics in the respiratory context, drawing attention to the need to generate reference annotations and to standardise the terminology used in literature. Findings about airway epithelial cell types, states and fates obtained from scRNA-seq experiments are compared and contrasted with information accumulated through the use of conventional methods. This review attempts to discuss major opportunities and to outline some of the key limitations of the modern-day scRNA-seq that need to be addressed to enable efficient and meaningful integration of scRNA-seq data from different platforms and studies, with each other as well as with data from other high-throughput sequencing-based genomic, transcriptomic and epigenetic analyses.
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Affiliation(s)
- Oleksandr Dudchenko
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, South Yorkshire, U.K
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, U.S.A
- Programme in Immunology, Harvard Medical School, Boston, MA, U.S.A
| | - Colin D. Bingle
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, South Yorkshire, U.K
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Xie J, Yang MR, Hu X, Hong ZS, Bai YY, Sheng J, Tian Y, Shi CY. Moringa oleifera Lam. Isothiocyanate Quinazolinone Derivatives Inhibit U251 Glioma Cell Proliferation through Cell Cycle Regulation and Apoptosis Induction. Int J Mol Sci 2023; 24:11376. [PMID: 37511135 PMCID: PMC10379366 DOI: 10.3390/ijms241411376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
A major active constituent of Moringa oleifera Lam. is 4-[(α-L-rhamnose oxy) benzyl] isothiocyanate (MITC). To broaden MITC's application and improve its biological activity, we synthesized a series of MITC quinazolinone derivatives and evaluated their anticancer activity. The anticancer effects and mechanisms of the compound with the most potent anticancer activity were investigated further. Among 16 MITC quinazolinone derivatives which were analyzed, MITC-12 significantly inhibited the growth of U251, A375, A431, HCT-116, HeLa, and MDA-MB-231 cells. MITC-12 significantly inhibited U251 cell proliferation in a time- and dose-dependent manner and decreased the number of EdU-positive cells, but was not toxic to normal human gastric mucosal cells (GES-1). Further, MITC-12 induced apoptosis of U251 cells, and increased caspase-3 expression levels and the Bax:Bcl-2 ratio. In addition, MITC-12 significantly decreased the proportion of U251 cells in the G1 phase and increased it in S and G2 phases. Transcriptome sequencing showed that MITC-12 had a significant regulatory effect on pathways regulating the cell cycle. Further, MITC-12 significantly decreased the expression levels of the cell cycle-related proteins CDK2, cyclinD1, and cyclinE, and increased those of cyclinA2, as well as the p-JNK:JNK ratio. These results indicate that MITC-12 inhibits U251 cell proliferation by inducing apoptosis and cell cycle arrest, activating JNK, and regulating cell cycle-associated proteins. MITC-12 has potential for use in the prevention and treatment of glioma.
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Affiliation(s)
- Jing Xie
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- National Research and Development Professional Center for Moringa Processing Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ming-Rong Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Rural Science and Technology Service Center, Kunming 650021, China
| | - Xia Hu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
| | - Zi-Shan Hong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
| | - Yu-Ying Bai
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming 650201, China
| | - Jun Sheng
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yang Tian
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- National Research and Development Professional Center for Moringa Processing Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
| | - Chong-Ying Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Key Laboratory of Precision Nutrition and Personalized Food Manufacturing, Yunnan Agricultural University, Kunming 650201, China
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Li L, Liu J, Wang W, Fu Y, Deng Y, Li X, Liu Z, Pang Y, Xu Y, Yan M, Li Z. Cancer stem cells promote lymph nodes metastasis of breast cancer by reprogramming tumor microenvironment. Transl Oncol 2023; 35:101733. [PMID: 37421907 DOI: 10.1016/j.tranon.2023.101733] [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] [Revised: 06/01/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Breast cancer progression and metastasis are governed by a complex interplay within the tumor immune microenvironment (TIME), involving numerous cell types. Lymph node metastasis (LNM) is a key prognostic marker associated with distant organ metastasis and reduced patient survival, but the mechanisms underlying its promotion by breast cancer stem cells (CSCs) remain unclear. Our study sought to unravel how CSCs reprogram TIME to facilitate LNM. Utilizing single-cell RNA sequencing, we profiled TIME in primary cancer and corresponding metastatic lymph node samples from patients at our institution. To verify the derived data, we cultured CSCs and performed validation assays employing flow cytometry and CyTOF. Our analysis revealed distinct differences in cellular infiltration patterns between tumor and LNM samples. Importantly, RAC2 and PTTG1 double-positive CSCs, which exhibit the highest stem-like attributes, were markedly enriched in metastatic lymph nodes. These CSCs are hypothesized to foster metastasis via activation of specific metastasis-related transcription factors and signaling pathways. Additionally, our data suggest that CSCs might modulate adaptive and innate immune cell evolution, thereby further contributing to metastasis. In summary, this study illuminates a critical role of CSCs in modifying TIME to facilitate LNM. The enrichment of highly stem-like CSCs in metastatic lymph nodes offers novel therapeutic targeting opportunities and deepens our understanding of breast cancer metastasis.
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Affiliation(s)
- Lin Li
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Jianyu Liu
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Wenzheng Wang
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Yingqiang Fu
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Yuhan Deng
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Xin Li
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Zhuolin Liu
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Yuheng Pang
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Yangyang Xu
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China
| | - Meisi Yan
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Zhigao Li
- Harbin Medical University Cancer Hospital, Harbin Medical University, No.150 Haping Rd, Nangang District, Harbin 150081, China.
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27
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Su X, Wang L, Ma N, Yang X, Liu C, Yang F, Li J, Yi X, Xing Y. Immune heterogeneity in cardiovascular diseases from a single-cell perspective. Front Cardiovasc Med 2023; 10:1057870. [PMID: 37180791 PMCID: PMC10167030 DOI: 10.3389/fcvm.2023.1057870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
A variety of immune cell subsets occupy different niches in the cardiovascular system, causing changes in the structure and function of the heart and vascular system, and driving the progress of cardiovascular diseases (CVDs). The immune cells infiltrating the injury site are highly diverse and integrate into a broad dynamic immune network that controls the dynamic changes of CVDs. Due to technical limitations, the effects and molecular mechanisms of these dynamic immune networks on CVDs have not been fully revealed. With recent advances in single-cell technologies such as single-cell RNA sequencing, systematic interrogation of the immune cell subsets is feasible and will provide insights into the way we understand the integrative behavior of immune populations. We no longer lightly ignore the role of individual cells, especially certain highly heterogeneous or rare subpopulations. We summarize the phenotypic diversity of immune cell subsets and their significance in three CVDs of atherosclerosis, myocardial ischemia and heart failure. We believe that such a review could enhance our understanding of how immune heterogeneity drives the progression of CVDs, help to elucidate the regulatory roles of immune cell subsets in disease, and thus guide the development of new immunotherapies.
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Affiliation(s)
- Xin Su
- China Academy of Chinese Medical Sciences, Guang’anmen Hospital, Beijing, China
| | - Li Wang
- Department of Breast Surgery, Xingtai People’s Hospital, Xingtai, China
| | - Ning Ma
- Department of Breast Surgery, Dezhou Second People’s Hospital, Dezhou, China
| | - Xinyu Yang
- Fangshan Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Can Liu
- China Academy of Chinese Medical Sciences, Guang’anmen Hospital, Beijing, China
| | - Fan Yang
- China Academy of Chinese Medical Sciences, Guang’anmen Hospital, Beijing, China
| | - Jun Li
- China Academy of Chinese Medical Sciences, Guang’anmen Hospital, Beijing, China
| | - Xin Yi
- Department of Cardiology, Beijing Huimin Hospital, Beijing, China
| | - Yanwei Xing
- China Academy of Chinese Medical Sciences, Guang’anmen Hospital, Beijing, China
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Zhao M, Liu J, Xin M, Yang K, Huang H, Zhang W, Zhang J, He S. Pulmonary arterial hypertension associated with congenital heart disease: An omics study. Front Cardiovasc Med 2023; 10:1037357. [PMID: 36970344 PMCID: PMC10036813 DOI: 10.3389/fcvm.2023.1037357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Pulmonary arterial hypertension associated with congenital heart disease (PAH-CHD) is a severely progressive condition with uncertain physiological course. Hence, it has become increasingly relevant to clarify the specific mechanisms of molecular modification, which is crucial to identify more treatment strategies. With the rapid development of high-throughput sequencing, omics technology gives access to massive experimental data and advanced techniques for systems biology, permitting comprehensive assessment of disease occurrence and progression. In recent years, significant progress has been made in the study of PAH-CHD and omics. To provide a comprehensive description and promote further in-depth investigation of PAH-CHD, this review attempts to summarize the latest developments in genomics, transcriptomics, epigenomics, proteomics, metabolomics, and multi-omics integration.
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Affiliation(s)
- Maolin Zhao
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Jian Liu
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Mei Xin
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Ke Yang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Honghao Huang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Wenxin Zhang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Jinbao Zhang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Siyi He
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
- Correspondence: Siyi He
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Balagannavar G, Basavaraju K, Bajpai AK, Davuluri S, Kannan S, S Srini V, S Chandrashekar D, Chitturi N, K Acharya K. Transcriptomic analysis of the Non-Obstructive Azoospermia (NOA) to address gene expression regulation in human testis. Syst Biol Reprod Med 2023; 69:196-214. [PMID: 36883778 DOI: 10.1080/19396368.2023.2176268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
There is a need to understand the molecular basis of testes under Non-Obstructive Azoospermia (NOA), a state of failed spermatogenesis. There has been a lack of attention to the transcriptome at the level of alternatively spliced mRNAs (iso-mRNAs) and the mechanism of gene expression regulation. Hence, we aimed to establish a reliable iso-mRNA profile of NOA-testes, and explore molecular mechanisms - especially those related to gene expression regulation. We sequenced mRNAs from testicular samples of donors with complete spermatogenesis (control samples) and a failure of spermatogenesis (NOA samples). We identified differentially expressed genes and their iso-mRNAs via standard NGS data analyses. We then listed these iso-mRNAs hierarchically based on the extent of consistency of differential quantities across samples and groups, and validated the lists via RT-qPCRs (for 80 iso-mRNAs). In addition, we performed extensive bioinformatic analysis of the splicing features, domains, interactions, and functions of differentially expressed genes and iso-mRNAs. Many top-ranking down-regulated genes and iso-mRNAs, i.e., those down-regulated more consistently across the NOA samples, are associated with mitosis, replication, meiosis, cilium, RNA regulation, and post-translational modifications such as ubiquitination and phosphorylation. Most down-regulated iso-mRNAs correspond to full-length proteins that include all expected domains. The predominance of alternative promoters and termination sites in these iso-mRNAs indicate their gene expression regulation via promoters and UTRs. We compiled a new, comprehensive list of human transcription factors (TFs) and used it to identify TF-'TF gene' interactions with potential significance in down-regulating genes under the NOA condition. The results indicate that RAD51 suppression by HSF4 prevents SP1-activation, and SP1, in turn, could regulate multiple TF genes. This potential regulatory axis and other TF interactions identified in this study could explain the down-regulation of multiple genes in NOA-testes. Such molecular interactions may also have key regulatory roles during normal human spermatogenesis.
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Affiliation(s)
- Govindkumar Balagannavar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,Research Scholar, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavyashree Basavaraju
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Akhilesh Kumar Bajpai
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Sravanthi Davuluri
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Shruthi Kannan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Vasan S Srini
- Manipal Fertility, Manipal Hospital, Bengaluru, Karnataka, India
| | | | - Neelima Chitturi
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Kshitish K Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
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30
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Using Artificial Intelligence to Better Predict and Develop Biomarkers. Clin Lab Med 2023; 43:99-114. [PMID: 36764811 DOI: 10.1016/j.cll.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Advancements in technology have improved biomarker discovery in the field of heart failure (HF). What was once a slow and laborious process has gained efficiency through use of high-throughput omics platforms to phenotype HF at the level of genes, transcripts, proteins, and metabolites. Furthermore, improvements in artificial intelligence (AI) have made the interpretation of large omics data sets easier and improved analysis. Use of omics and AI in biomarker discovery can aid clinicians by identifying markers of risk for developing HF, monitoring care, determining prognosis, and developing druggable targets. Combined, AI has the power to improve HF patient care.
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31
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Wang JQ, Gao MY, Gao R, Zhao KH, Zhang Y, Li X. Oligodendrocyte lineage cells: Advances in development, disease, and heterogeneity. J Neurochem 2023; 164:468-480. [PMID: 36415921 DOI: 10.1111/jnc.15728] [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: 07/01/2022] [Revised: 11/03/2022] [Accepted: 11/13/2022] [Indexed: 11/24/2022]
Abstract
Oligodendrocyte progenitor cells (OPCs) originate in the ventricular zone (VZ) of the brain and spinal cord, and their primary function is to differentiate into oligodendrocytes (OLs). Studies have shown that OPCs and OLs are pathologically and physiologically heterogeneous. Previous transcriptome analyses used Bulk RNA-seq, which compares average gene expression in cells and does not allow for heterogeneity. In recent years, the development of single-cell sequencing (scRNA-seq) and single-cell nuclear sequencing (snRNA-seq) has allowed us to study an individual cell. In this review, sc/snRNA-seq was used to study the different subpopulations of OL lineage cells, their developmental trajectories, and their applications in related diseases. These techniques can distinguish different subpopulations of cells, and identify differentially expressed genes in particular cell types under certain conditions, such as treatment or disease. It is of great significance to the study of the occurrence, prevention, and treatment of various diseases.
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Affiliation(s)
- Jia-Qi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Meng-Yuan Gao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rui Gao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ke-Han Zhao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xing Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
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32
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Kaplan L, Drexler C, Pfaller AM, Brenna S, Wunderlich KA, Dimitracopoulos A, Merl-Pham J, Perez MT, Schlötzer-Schrehardt U, Enzmann V, Samardzija M, Puig B, Fuchs P, Franze K, Hauck SM, Grosche A. Retinal regions shape human and murine Müller cell proteome profile and functionality. Glia 2023; 71:391-414. [PMID: 36334068 DOI: 10.1002/glia.24283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022]
Abstract
The human macula is a highly specialized retinal region with pit-like morphology and rich in cones. How Müller cells, the principal glial cell type in the retina, are adapted to this environment is still poorly understood. We compared proteomic data from cone- and rod-rich retinae from human and mice and identified different expression profiles of cone- and rod-associated Müller cells that converged on pathways representing extracellular matrix and cell adhesion. In particular, epiplakin (EPPK1), which is thought to play a role in intermediate filament organization, was highly expressed in macular Müller cells. Furthermore, EPPK1 knockout in a human Müller cell-derived cell line led to a decrease in traction forces as well as to changes in cell size, shape, and filopodia characteristics. We here identified EPPK1 as a central molecular player in the region-specific architecture of the human retina, which likely enables specific functions under the immense mechanical loads in vivo.
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Affiliation(s)
- Lew Kaplan
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Corinne Drexler
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.,Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anna M Pfaller
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Santra Brenna
- Neurology Department, Experimental Research in Stroke and Inflammation (ERSI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten A Wunderlich
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Dimitracopoulos
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Maria-Theresa Perez
- Department of Clinical Sciences, Division of Ophthalmology, Lund University, Lund, Sweden.,NanoLund, Nanometer Structure Consortium, Lund University, Lund, Sweden
| | | | - Volker Enzmann
- Department of Ophthalmology, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Marijana Samardzija
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Berta Puig
- Neurology Department, Experimental Research in Stroke and Inflammation (ERSI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Fuchs
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.,Institute of Medical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Antje Grosche
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
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Glenn LM, Troy LK, Corte TJ. Novel diagnostic techniques in interstitial lung disease. Front Med (Lausanne) 2023; 10:1174443. [PMID: 37188089 PMCID: PMC10175799 DOI: 10.3389/fmed.2023.1174443] [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: 02/26/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Research into novel diagnostic techniques and targeted therapeutics in interstitial lung disease (ILD) is moving the field toward increased precision and improved patient outcomes. An array of molecular techniques, machine learning approaches and other innovative methods including electronic nose technology and endobronchial optical coherence tomography are promising tools with potential to increase diagnostic accuracy. This review provides a comprehensive overview of the current evidence regarding evolving diagnostic methods in ILD and to consider their future role in routine clinical care.
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Affiliation(s)
- Laura M. Glenn
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
- *Correspondence: Laura M. Glenn,
| | - Lauren K. Troy
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
| | - Tamera J. Corte
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney School of Medicine, Sydney, NSW, Australia
- NHMRC Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, NSW, Australia
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34
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Gong X, Zhang Y, Ai J, Li K. Application of Single-Cell RNA Sequencing in Ovarian Development. Biomolecules 2022; 13:47. [PMID: 36671432 PMCID: PMC9855652 DOI: 10.3390/biom13010047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
The ovary is a female reproductive organ that plays a key role in fertility and the maintenance of endocrine homeostasis, which is of great importance to women's health. It is characterized by a high heterogeneity, with different cellular subpopulations primarily containing oocytes, granulosa cells, stromal cells, endothelial cells, vascular smooth muscle cells, and diverse immune cell types. Each has unique and important functions. From the fetal period to old age, the ovary experiences continuous structural and functional changes, with the gene expression of each cell type undergoing dramatic changes. In addition, ovarian development strongly relies on the communication between germ and somatic cells. Compared to traditional bulk RNA sequencing techniques, the single-cell RNA sequencing (scRNA-seq) approach has substantial advantages in analyzing individual cells within an ever-changing and complicated tissue, classifying them into cell types, characterizing single cells, delineating the cellular developmental trajectory, and studying cell-to-cell interactions. In this review, we present single-cell transcriptome mapping of the ovary, summarize the characteristics of the important constituent cells of the ovary and the critical cellular developmental processes, and describe key signaling pathways for cell-to-cell communication in the ovary, as revealed by scRNA-seq. This review will undoubtedly improve our understanding of the characteristics of ovarian cells and development, thus enabling the identification of novel therapeutic targets for ovarian-related diseases.
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Affiliation(s)
| | | | - Jihui Ai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kezhen Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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35
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Zhou L, Feng W, Mao Y, Chen Y, Zhang X. Nanoengineered sonosensitive platelets for synergistically augmented sonodynamic tumor therapy by glutamine deprivation and cascading thrombosis. Bioact Mater 2022; 24:26-36. [PMID: 36582345 PMCID: PMC9761609 DOI: 10.1016/j.bioactmat.2022.11.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/06/2022] [Accepted: 11/27/2022] [Indexed: 12/14/2022] Open
Abstract
Ultrasound (US)-activated sonodynamic therapy (SDT) stands for a distinct antitumor modality because of its attractive characteristics including intriguing noninvasiveness, desirable safety, and high tissue penetration depth, which, unfortunately, suffers from compromised therapeutic efficacy due to cancer cell-inherent adaptive mechanisms, such as glutathione (GSH) neutralization response to reactive oxygen species (ROS), and glutamine addictive properties of tumors. In this work, we developed a biological sonosensitive platelet (PLT) pharmacytes for favoring US/GSH-responsive combinational therapeutic of glutamine deprivation and augmented SDT. The amino acid transporter SLC6A14 blockade agent α-methyl-DL-tryptophan (α-MT)-loaded and MnO2-coated porphyrinic metal-organic framework (MOF) nanoparticles were encapsulated in the PLTs through the physical adsorption of electrostatic attraction and the intrinsic endocytosis of PLTs. When the sonosensitive PLT pharmacytes reached tumor sites through their natural tendencies to TME, US stimulated the PLTs-loaded porphyrinic MOF to generate ROS, resulting in morphological changes of the PLTs and the release of nanoparticles. Subsequently, intracellular high concentration of GSH and extracellular spatio-temporal controlled US irradiation programmatically triggered the release of α-MT, which enabled the synergistically amplified SDT by inducing amino acid starvation, inhibiting mTOR, and mediating ferroptosis. In addition, US stimulation achieved the targeted activation of PLTs at tumor vascular site, which evolved from circulating PLTs to dendritic PLTs, effectively blocking the blood supply of tumors through thrombus formation, and revealing the encouraging potential to facilitate tumor therapeutics.
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Affiliation(s)
- Liqiang Zhou
- MOE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
| | - Wei Feng
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yuhang Mao
- School of Medical Technology, Xi'an Medical College, Xi'an, 710021, Shanxi, China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, China,Corresponding author.
| | - Xuanjun Zhang
- MOE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China,Corresponding author.
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36
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Transcriptomics and Metabolomics Analysis of Sclerotium rolfsii Fermented with Differential Carbon Sources. Foods 2022; 11:foods11223706. [PMID: 36429298 PMCID: PMC9689419 DOI: 10.3390/foods11223706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/22/2022] Open
Abstract
Scleroglucan is obtained from Sclerotium rolfsii and is widely used in many fields. In this study, transcriptomics combined with metabolomics were used to study the global metabolites and gene changes. The results of the joint analysis showed that the DEGs (differentially expressed genes) and DEMs (differentially expressed metabolites) of SEPS_48 (fermented with sucrose as a carbon source for 48 h) and GEPS_48 (fermented with glucose as a carbon source for 48 h) comparison groups were mainly related to cell metabolism, focusing on carbohydrate metabolism, amino acid metabolism, and amino sugar and nucleoside sugar metabolism. We therefore hypothesized that the significant differences in these metabolic processes were responsible for the differences in properties. Moreover, the joint analysis provides a scientific theoretical basis for fungal polysaccharides biosynthesis and provides new insights into the effects of carbon sources on the production. As an excellent bioenergy and biological product, scleroglucan can be better applied in different fields, such as the food industry.
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37
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Kalchev Y, Murdjeva M. Current methods for microbiological diagnosis of acute central nervous system infections. Folia Med (Plovdiv) 2022; 64:709-715. [PMID: 36876544 DOI: 10.3897/folmed.64.e72257] [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: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 11/06/2022] Open
Abstract
The incidence of infections affecting the central nervous system has increased in recent years, making neuroinfections a current global health problem. The central nervous system is quite well protected from the external and internal environments, although it is susceptible to infection by a wide variety of pathogens. The etiological diversity further complicates the management of such infections because it is important to identify correctly the specific cause in order to choose the most appropriate antimicrobial therapy. Diagnosis is made not only based on clinical and epidemiological data but also on the results of clinical laboratory and microbiological examination of cerebrospinal fluid. This article aims to review current microbiological methods in the diagnosis of acute central nervous system infections and help healthcare providers to recognize their advantages and limitations in order to manage their patients appropriately.
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38
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Zhang F, Li X, Wu Q, Lu P, Kang Q, Zhao M, Wang A, Dong Q, Sun M, Yang Z, Gao Z. Selenium Application Enhances the Accumulation of Flavones and Anthocyanins in Bread Wheat ( Triticum aestivum L.) Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13431-13444. [PMID: 36198089 DOI: 10.1021/acs.jafc.2c04868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Selenium (Se) biofortification in wheat reduces the risk of Se deficiency in humans. Se biofortification increases the concentration of Se and anthocyanins in wheat grains. However, it is unknown whether Se biofortification can enhance flavonoids other than anthocyanins and the mechanism underlying flavonoid accumulation in wheat grains. Here, foliar application of selenite solution in wheat was conducted 10 days after flowering. Metabolite profiling and transcriptome sequencing were performed in Se-treated grains. A significant increase in the total contents of Se, anthocyanins, and flavonoids was observed in Se-treated mature grains. Twenty-seven significantly increased flavonoids were identified in Se-treated immature grains. The significant accumulation of flavones (tricin, tricin derivatives, and chrysoeriol derivatives) was detected, and six anthocyanins, dihydroquercetin (the precursor for anthocyanin biosynthesis) and catechins were also increased. Integrated analysis of metabolites and transcriptome revealed that Se application enhanced the biosynthesis of flavones, dihydroquercetin, anthocyanins, and catechins by increasing the expression levels of seven key structural genes in flavonoid biosynthesis (two TaF3Hs, two TaDFRs, one TaF3'5'H, one TaOMT, and one TaANR). Our findings shed new light on the molecular mechanism underlying the enhancement in flavonoid accumulation by Se supplementation and pave the way for further enhancing the nutritional value of wheat grains.
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Affiliation(s)
- Fengjie Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Xueyin Li
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Qiangqiang Wu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Ping Lu
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Qingfang Kang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Mengyao Zhao
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
| | - Aiping Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Qi Dong
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Min Sun
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhenping Yang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhiqiang Gao
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
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39
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Wang C, Zhou Q, Wu ST. Scopolin obtained from Smilax china L. against hepatocellular carcinoma by inhibiting glycolysis: A network pharmacology and experimental study. JOURNAL OF ETHNOPHARMACOLOGY 2022; 296:115469. [PMID: 35718053 DOI: 10.1016/j.jep.2022.115469] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Smilax china L. is a well-known traditional medicinal plant. In China, it is a common anti-cancer drug that has been inherited for thousands of years. Some in vitro and in vivo studies have confirmed its potential lipid-lowering, anti-inflammatory and anti-ovarian cancer effects. However, there is no research on the material basis and mechanism of the rhizome of Smilax china L. against hepatocellular carcinoma. AIM OF THE STUDY To explore the material basis and mechanism of scopolin from Smilax china L. against hepatocellular carcinoma. METHODS The potential targets and active components of Smilax china L. against hepatocellular carcinoma were screened by transcriptomics, network pharmacology and molecular docking. Microscale Thermophoresis (MST) detection was used to verify the affinity of small molecule compounds with potential proteins and protein-protein interaction. The Extract from HepG2 cells was used to measure the expression of glycolysis-related proteins, glucose consumption and lactate production. The expression of apoptosis-related factors and glycolysis-related proteins in vivo was detected by immunohistochemistry. RESULTS The glycolysis-related proteins glucose-6-phosphate isomerase (GPI), glycerol-3-phosphate dehydrogenase, mitochondrial (GPD2) and phosphoglycerate kinase 2 (PGK2) screened by transcriptomics, network pharmacology showed strongly binding with scopolin by molecular docking. MST detection has also verified the affinity of scopolin with GPI and GPD2. It was the first time found that Heat shock protein HSP 90-alpha (Hsp90α) bound strongly to GPI and GPD2 in the worldwide, while scopolin was able to affect the interaction between Hsp90α and GPD2. In vitro and in vivo experiments further demonstrated that scopolin may play an anti-cancer role by affecting the stability of tumor-associated proteins. The results showed that scopolin obtained from Smilax china L. could regulate the expression of GPI, GPD2 and PGK2 and inhibit the interaction of protein-protein, reduce the energy metabolism of tumor tissue, thereby inhibit tumor growth. CONCLUSION Scopolin obtained from Smilax china L. plays the role of anti-hepatocellular carcinoma by regulating the expression of glycolysis proteins GPI, GPD2 and PGK2. Scopolin could affect the interaction between Hsp90α and GPD2 may provide a novel potential treatment direction for hepatocellular carcinoma.
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Affiliation(s)
- Chen Wang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, 430065, China.
| | - Qin Zhou
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Song-Tao Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
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40
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Geraldes I, Fernandes M, Fraga AG, Osório NS. The impact of single-cell genomics on the field of mycobacterial infection. Front Microbiol 2022; 13:989464. [PMID: 36246265 PMCID: PMC9562642 DOI: 10.3389/fmicb.2022.989464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing projects of humans and other organisms reinforced that the complexity of biological systems is largely attributed to the tight regulation of gene expression at the epigenome and RNA levels. As a consequence, plenty of technological developments arose to increase the sequencing resolution to the cell dimension creating the single-cell genomics research field. Single-cell RNA sequencing (scRNA-seq) is leading the advances in this topic and comprises a vast array of different methodologies. scRNA-seq and its variants are more and more used in life science and biomedical research since they provide unbiased transcriptomic sequencing of large populations of individual cells. These methods go beyond the previous “bulk” methodologies and sculpt the biological understanding of cellular heterogeneity and dynamic transcriptomic states of cellular populations in immunology, oncology, and developmental biology fields. Despite the large burden caused by mycobacterial infections, advances in this field obtained via single-cell genomics had been comparatively modest. Nonetheless, seminal research publications using single-cell transcriptomics to study host cells infected by mycobacteria have become recently available. Here, we review these works summarizing the most impactful findings and emphasizing the different and recent single-cell methodologies used, potential issues, and problems. In addition, we aim at providing insights into current research gaps and potential future developments related to the use of single-cell genomics to study mycobacterial infection.
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Affiliation(s)
- Inês Geraldes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Mónica Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Alexandra G. Fraga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
- *Correspondence: Nuno S. Osório
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Cimbalo A, Frangiamone M, Font G, Manyes L. The importance of transcriptomics and proteomics for studying molecular mechanisms of mycotoxin exposure: A review. Food Chem Toxicol 2022; 169:113396. [PMID: 36087620 DOI: 10.1016/j.fct.2022.113396] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022]
Abstract
This review aims to highlight recent advances where transcriptomics and proteomics have been used as a key tool to understand molecular toxicity of mycotoxins. The most studied mycotoxin by using transcriptomic approach is deoxynivalenol (DON), followed by aflatoxins (AFs) and zearalenone (ZEA). Instead, proteomics mostly focuses on AFs but also in this case, mildly to ZEA and DON. However, in both omics approaches, fewer studies investigated the toxicological effect of emerging mycotoxins, patulin, ochratoxin A, T-2 toxin, alternariol and amino-14,16-dimethyloctadecan-3-ol. The study of changes in the expression of genes involved in immune system are the most common purposes for transcriptomics whereas cellular processes in proteomics field. Concerning the techniques used to perform the experiments, RT-qPCR is the most employed in gene expression analysis whereas liquid chromatography coupled with mass spectrometry is the master technique for proteomics assays. The gathered data have reported that the interest in using these omic approaches has increased in the last five years. However, in vitro models take precedence over the in vivo and ex vivo ones. Therefore, there is a need to enhance the use of in vivo models and alternative methods to better understand mycotoxins mode of action on animal and human health.
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Affiliation(s)
- A Cimbalo
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n, 46100, Burjassot, Spain
| | - M Frangiamone
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n, 46100, Burjassot, Spain.
| | - G Font
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n, 46100, Burjassot, Spain
| | - L Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n, 46100, Burjassot, Spain
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Keathley J, de Toro-Martín J, Kearney M, Garneau V, Pilon G, Couture P, Marette A, Vohl MC, Couillard C. Gene expression signatures and cardiometabolic outcomes following 8-week mango consumption in individuals with overweight/obesity. Front Nutr 2022; 9:918844. [PMID: 36034894 PMCID: PMC9407242 DOI: 10.3389/fnut.2022.918844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Background Little is known about the impact of mango consumption on metabolic pathways assessed by changes in gene expression. Methods In this single-arm clinical trial, cardiometabolic outcomes and gene expression levels in whole blood samples from 26 men and women were examined at baseline and after 8 weeks of mango consumption and differential gene expression changes were determined. Based on changes in gene expression profiles, partial least squares discriminant analysis followed by hierarchical clustering were used to classify participants into subgroups of response and differences in gene expression changes and in cardiometabolic clinical outcomes following the intervention were tested. Results Two subgroups of participants were separated based on the resemblance of gene expression profiles in response to the intervention and as responders (n = 8) and non-responders (n = 18). A total of 280 transcripts were significantly up-regulated and 603 transcripts down-regulated following the intervention in responders, as compared to non-responders. Several metabolic pathways, mainly related to oxygen and carbon dioxide transport as well as oxidative stress, were found to be significantly enriched with differentially expressed genes. In addition, significantly beneficial changes in hip and waist circumference, c-reactive protein, HOMA-IR and QUICKI indices were observed in responders vs. non-responders, following the intervention. Conclusion The impact of mango consumption on cardiometabolic health appears to largely rely on interindividual variability. The novel transcriptomic-based clustering analysis used herein can provide insights for future research focused on unveiling the origins of heterogeneous responses to dietary interventions. Clinical Trial Registration [clinicaltrials.gov], identifier [NCT03825276].
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Affiliation(s)
- Justine Keathley
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,School of Nutrition, Université Laval, Québec, QC, Canada
| | - Juan de Toro-Martín
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,School of Nutrition, Université Laval, Québec, QC, Canada
| | - Michèle Kearney
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,School of Nutrition, Université Laval, Québec, QC, Canada
| | - Véronique Garneau
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,School of Nutrition, Université Laval, Québec, QC, Canada
| | - Geneviève Pilon
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,Quebec Heart and Lung Institute (IUCPQ) Research Center, Québec, QC, Canada
| | - Patrick Couture
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,Endocrinology and Nephrology Unit, CHU de Quebec Research Center, Québec, QC, Canada
| | - André Marette
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,Quebec Heart and Lung Institute (IUCPQ) Research Center, Québec, QC, Canada
| | - Marie-Claude Vohl
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,School of Nutrition, Université Laval, Québec, QC, Canada
| | - Charles Couillard
- Center Nutrition, Santé et Société (NUTRISS)-Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, QC, Canada.,School of Nutrition, Université Laval, Québec, QC, Canada
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Sandell M, Chireh A, Spyrou A, Grankvist R, Al-Saadi J, Jonsson S, van der Wijngaart W, Stemme G, Holmin S, Roxhed N. Endovascular Device for Endothelial Cell Sampling. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202200023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Mikael Sandell
- Division of Micro and Nanosystems KTH Royal Institute of Technology Malvinas väg 10 114 28 Stockholm Sweden
- Department of Clinical Neuroscience Karolinska Institutet Tomtebodavägen 18A 171 77 Stockholm Sweden
- MedTechLabs Bioclinicum Karolinska University Hospital 171 64 Solna Sweden
| | - Arvin Chireh
- Department of Clinical Neuroscience Karolinska Institutet Tomtebodavägen 18A 171 77 Stockholm Sweden
| | - Argyris Spyrou
- Division of Micro and Nanosystems KTH Royal Institute of Technology Malvinas väg 10 114 28 Stockholm Sweden
- MedTechLabs Bioclinicum Karolinska University Hospital 171 64 Solna Sweden
| | - Rikard Grankvist
- Department of Clinical Neuroscience Karolinska Institutet Tomtebodavägen 18A 171 77 Stockholm Sweden
| | - Jonathan Al-Saadi
- Department of Clinical Neuroscience Karolinska Institutet Tomtebodavägen 18A 171 77 Stockholm Sweden
| | - Stefan Jonsson
- Department of Materials Science and Engineering KTH Royal Institute of Technology Brinellvägen 23 100 44 Stockholm Sweden
| | - Wouter van der Wijngaart
- Division of Micro and Nanosystems KTH Royal Institute of Technology Malvinas väg 10 114 28 Stockholm Sweden
| | - Göran Stemme
- Division of Micro and Nanosystems KTH Royal Institute of Technology Malvinas väg 10 114 28 Stockholm Sweden
| | - Staffan Holmin
- Department of Clinical Neuroscience Karolinska Institutet Tomtebodavägen 18A 171 77 Stockholm Sweden
- MedTechLabs Bioclinicum Karolinska University Hospital 171 64 Solna Sweden
| | - Niclas Roxhed
- Division of Micro and Nanosystems KTH Royal Institute of Technology Malvinas väg 10 114 28 Stockholm Sweden
- MedTechLabs Bioclinicum Karolinska University Hospital 171 64 Solna Sweden
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Cao D, Fan Q, Li Z, Chen M, Jiang Y, Lin R, Li J, Zhao C. Transcriptomic profiling revealed the role of apigenin-4'-O-α-L-rhamnoside in inhibiting the activation of rheumatoid arthritis fibroblast-like synoviocytes via MAPK signaling pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 102:154201. [PMID: 35660352 DOI: 10.1016/j.phymed.2022.154201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/18/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Activated fibroblast-like synoviocyte (FLS) played a significant role in the pathogenesis and progression of rheumatoid arthritis (RA). Apigenin-4'-O-α-L-rhamnoside showed remarkable effects against RA, however, no relevant studies on pharmacology of apigenin-4'-O-α-L-rhamnoside yet, the effects and underlying molecular mechanism of apigenin-4'-O-α-L-rhamnoside on RA are still unclear. PURPOSE This study aimed to investigate the therapeutic effects and mechanisms of apigenin-4'-O-α-L-rhamnoside on RA-FLS cells by transcriptomic analysis. METHODS In vitro, RA-FLS cell viability and migration were measured by CCK-8 and scratch assays, respectively. The effects of apigenin-4'-O-α-L-rhamnoside on inflammatory levels of MMP-1, MMP-3, RANKL and TNF-α in RA-FLS cells were detected using ELISA kits. High-throughput transcriptome analysis was performed to screen the key genes and related pathways of apigenin-4'-O-α-L-rhamnoside inhibit RA-FLSs, and the result of which were validated by RT-qPCR and western blot. Furthermore, in vivo, we also evaluated the effects of apigenin-4'-O-α-L-rhamnoside in rat with CIA. RESULTS Apigenin-4'-O-α-L-rhamnoside significantly suppressed RA-FLS migration, exerted remarkable inhibiting effects on the expression levels on MMP-1, MMP3, RANKL and TNF-α in RA-FLS cells. It seemed that MAPK signaling pathway might be closely related to the pathogenesis of RA by down-regulated relevant core targets (MAPK1, HRAS, ATF-2, p38 and JNK). Moreover, apigenin-4'-O-α-L-rhamnoside attenuated the severity of arthritis in CIA rat. CONCLUSION Apigenin-4'-O-α-L-rhamnoside inhibited pro-inflammatory cytokine, chemokine and MMPs factors production of RA-FLS by targeting the MAPK signaling pathway, which provided a scientific basis for potential application in the treatment of RA.
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Affiliation(s)
- Dan Cao
- Beijing University of Chinese Medicine, Beijing 102488, China; Beijing key lab for quality evaluation of Chinese Materia Medica, Beijing 102488, China; Department of Histology and Embryology, School of Traditional Chinese Medicine, Beijing 102488, China
| | - Qiqi Fan
- Beijing University of Chinese Medicine, Beijing 102488, China; Beijing key lab for quality evaluation of Chinese Materia Medica, Beijing 102488, China
| | - Zhiqi Li
- Beijing University of Chinese Medicine, Beijing 102488, China; Beijing key lab for quality evaluation of Chinese Materia Medica, Beijing 102488, China
| | - Meilin Chen
- Beijing University of Chinese Medicine, Beijing 102488, China; Beijing key lab for quality evaluation of Chinese Materia Medica, Beijing 102488, China
| | - Yangyu Jiang
- Beijing University of Chinese Medicine, Beijing 102488, China; Department of Histology and Embryology, School of Traditional Chinese Medicine, Beijing 102488, China
| | - Ruichao Lin
- Beijing University of Chinese Medicine, Beijing 102488, China; Beijing key lab for quality evaluation of Chinese Materia Medica, Beijing 102488, China.
| | - Jian Li
- Beijing University of Chinese Medicine, Beijing 102488, China; Department of Histology and Embryology, School of Traditional Chinese Medicine, Beijing 102488, China.
| | - Chongjun Zhao
- Beijing University of Chinese Medicine, Beijing 102488, China; Beijing key lab for quality evaluation of Chinese Materia Medica, Beijing 102488, China.
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
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Wang L, Yin D, Fan Y, Min T, Yi Y, Wang H. Molecular mechanism of the anti-gastric cancer activity of 1,2,3,6-tetra-O-galloyl-β-D-glucose isolated from Trapa bispinosa Roxb. shell in vitro. PLoS One 2022; 17:e0269013. [PMID: 35653387 PMCID: PMC9162355 DOI: 10.1371/journal.pone.0269013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/12/2022] [Indexed: 12/03/2022] Open
Abstract
Trapa bispinosa Roxb. is a traditional Chinese food which is well known for its medicinal properties. The shell of Trapa bispinosa has anticancer activity, maybe due to its high content of polyphenols. There are few studies on the chemical composition of Trapa bispinosa shells, then we isolated the active components from Trapa bispinosa shell and clarified the mechanism of its anticancer activity. One monomer compound was separated from the ethanol extract of the Trapa bispinosa shell by fractional extraction, silica gel, Sephadex LH-20 gel column chromatography and liquid phase separation. The structure, identified by NMR was 1,2,3,6-tetra-O-galloyl-β-D-glucose. The results of the CCK-8 assay showed that 1,2,3,6-tetra-O-galloyl-β-D-glucose could significantly inhibit the proliferation of gastric cancer SGC7901 cells, and the effect was close to that of 5-fluorouracil. Here, 1,2,3,6-tetra-O-galloyl-β-D-glucose could affect the cell cycle of SGC7901 cells. At the dose of 200 μg/mL and an incubation time of 48 h, SGC7901 cells remained in the G1 phase, apoptosis occurred, the intracellular calcium ion concentration increased and the mitochondrial membrane potential decreased. Transcriptome sequencing analysis showed that the differentially expressed genes were mainly enriched in the P53 signalling pathway associated with apoptosis. The results of qPCR and Western blot showed that 1,2,3,6-tetra-O-galloyl-β-D-glucose could induce apoptosis of SGC7901 cells by up-regulating the expression levels of P21, PUMA, PERP and IGF-BP3 genes, down-regulating the CyclinD gene, increasing the expression levels of cytochrome C, caspase-3, caspase-9 protein and decreasing that of the protein BCL-2.
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Affiliation(s)
- Limei Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Dongjie Yin
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Yanhui Fan
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Ting Min
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Yang Yi
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Hongxun Wang
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- * E-mail:
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Borm PJA, Lison D, Driscoll K, Duffin R, Harkema J, Weber K, Elder A. Inflammation as a Key Outcome Pathway in Particle Induced Effects in the Lung. Front Public Health 2022; 10:869041. [PMID: 35692318 PMCID: PMC9174653 DOI: 10.3389/fpubh.2022.869041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Inflammation is considered a key event in the pathology of many chronic diseases, including pulmonary and systemic particle induced effects. In addition, inflammation is now considered as the key response in standard setting for poorly-soluble low toxicity (PSLT) particles and also the critical endpoint to screen for in OECD based sub-chronic animal inhalation testing protocols. During Particles & Health 2021, an afternoon session was dedicated to the subject and a brief summary of the most important messages are summarized in this paper. In the first part of this session, two speakers (Prof. Lison and Dr Duffin) provided state of the art insight into different aspects and sequels to (persistent) inflammation as a protective or adverse response. Most recent insights on the role of different macrophage cell types were presented as well as perspectives and data provided by inflammatory pathways in humans, such as in asthma and COPD. A brief review of the expert workshop on PSLT particles focusing on the regulatory impact of using persistent inflammation as a key outcome was provided by Kevin Driscoll. The second part of the session focused on the outcomes that are associated with inflammation in animal studies, with an emphasis by Drs. Harkema (Michigan State) and Weber (Anapath) on cell proliferation and other pathologies that need to be considered when comparing human and animal responses, such as outcomes from 14- or 28 day inhalation studies used for specific target organ toxicity classification.
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Affiliation(s)
- Paul J. A. Borm
- Heinrich Heine University of Dusseldorf, Dusseldorf, Germany
- Nanoconsult Holding BV, Meerssen, Netherlands
- *Correspondence: Paul J. A. Borm
| | - Dominique Lison
- Louvain Centre for Toxicology and Applied Pharmacology, Universite Catholique Louvain, Brussels, Belgium
| | - Kevin Driscoll
- School of Pharmacy, Rutgers University, New York, NY, United States
| | - Rodger Duffin
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Jack Harkema
- Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | | | - Alison Elder
- Department of Environmental Medicine, University of Rochester, Rochester, NY, United States
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Silva DNDA, Monajemzadeh S, Pirih FQ. Systems Biology in Periodontitis. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2022.853133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Systems biology is a promising scientific discipline that allows an integrated investigation of host factors, microbial composition, biomarkers, immune response and inflammatory mediators in many conditions such as chronic diseases, cancer, neurological disorders, and periodontitis. This concept utilizes genetic decoding, bioinformatic, flux-balance analysis in a comprehensive approach. The aim of this review is to better understand the current literature on systems biology and identify a clear applicability of it to periodontitis. We will mostly focus on the association between this condition and topics such as genomics, transcriptomics, proteomics, metabolomics, as well as contextualize delivery systems for periodontitis treatment, biomarker detection in oral fluids and associated systemic conditions.
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Zhao D, Wang Q, Meng F, Lu F, Bie X, Lu Z, Lu Y. TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4362-4372. [PMID: 35311254 DOI: 10.1021/acs.jafc.2c00206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plantaricin EF biosynthesis and enhanced plantaricin EF production. Its production was 17.30 mg/L in 163 (Lp_2642), which was 1.29-fold higher than that of the original strain. The regulation mechanism demonstrated that Lp_2642 can bind to three sites of plnA promoter, which enhances its transcription and expression, thereby increasing plantaricin EF production. Amino acids Asn-100, Asn-64, and Thr-69 may play a key role in the binding of Lp_2642. These results provide a novel strategy for mass production of plantaricin EF, which facilitates its large-scale production and application in the agriculture and food industries as a preservative.
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Affiliation(s)
- Deyin Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fanqiang Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingjian Lu
- College of Food Science & Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
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50
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Liu J, Gu L, Li W. The Prognostic Value of Integrated Analysis of Inflammation and Hypoxia-Related Genes in Idiopathic Pulmonary Fibrosis. Front Immunol 2022; 13:730186. [PMID: 35309336 PMCID: PMC8929415 DOI: 10.3389/fimmu.2022.730186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
Currently, the aetiology and pathogenesis of idiopathic pulmonary fibrosis (IPF) are still largely unclear. Moreover, patients with IPF exhibit a considerable difference in clinical presentation, treatment, and prognosis. Optimal biomarkers or models for IPF prognosis are lacking. Therefore, this study quantified the levels of various hallmarks using a single-sample gene set enrichment analysis algorithm. The hazard ration was calculated using Univariate Cox regression analysis based on the transcriptomic profile of bronchoalveolar lavage cells and clinical survival information. Afterwards, weighted Gene Co-expression Network Analysis was performed to construct a network between gene expression, inflammation response, and hypoxia. Subsequently, univariate Cox, random forest, and multivariate Cox regressions were applied to develop a robust inflammation and hypoxia-related gene signature for predicting clinical outcomes in patients with IPF. Furthermore, a nomogram was constructed to calculate risk assessment. The inflammation response and hypoxia were identified as latent risk factors for patients with IPF. Five genes, including HS3ST1, WFDC2, SPP1, TFPI, and CDC42EP2, were identified that formed the inflammation-hypoxia-related gene signature. Kaplan-Meier plotter showed that the patients with high-risk scores had a worse prognosis than those with low-risk scores in training and validation cohorts. The time-dependent concordance index and the receiver operating characteristic analysis revealed that the risk model could accurately predict the clinical outcome of patients with IPF. Therefore, this study contributes to elucidating the role of inflammation and hypoxia in IPF, which can aid in assessing individual prognosis and personalised treatment decisions.
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Affiliation(s)
- Jun Liu
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Liming Gu
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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