201
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Ma XB, Yue CX, Liu Y, Yang Y, Wang J, Yang XN, Huang LD, Zhu MX, Hattori M, Li CZ, Yu Y, Guo CR. A shared mechanism for TNP-ATP recognition by members of the P2X receptor family. Comput Struct Biotechnol J 2024; 23:295-308. [PMID: 38173879 PMCID: PMC10762375 DOI: 10.1016/j.csbj.2023.12.005] [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: 05/02/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show that a common mechanism of TNP-ATP recognition exists for the P2X family members by combining enhanced conformation sampling, engineered disulfide bond analysis, and covalent occupancy. In this model, the polar triphosphate moiety of TNP-ATP interacts with the orthosteric site, while its TNP-moiety is deeply embedded in the head and dorsal fin (DF) interface, creating a restrictive allostery in these two domains that results in a partly enlarged yet ion-impermeable pore. Similar results were obtained from multiple P2X subtypes of different species, including ckP2X7, hP2X3, rat P2X2 (rP2X2), and human P2X1 (hP2X1). Thus, TNP-ATP uses a common mechanism for P2X recognition and modulation by restricting the movements of the head and DF domains which are essential for P2X activation. This knowledge is applicable to the development of new P2X inhibitors.
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Affiliation(s)
- Xiao-Bo Ma
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chen-Xi Yue
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Na Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Dong Huang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Michael X. Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chang-Zhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Ye Yu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Chang-Run Guo
- School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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202
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Hou CX, Chen Y, Liu SH, Jiang YZ, Huang DP, Chen SN. Effective treatment with Gilteritinib-based regimens for FLT3-mutant extramedullary relapse in acute promyelocytic leukemia. Hematology 2024; 29:2293496. [PMID: 38095349 DOI: 10.1080/16078454.2023.2293496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVE Extramedullary relapse (EMR) is rare in acute promyelocytic leukemia (APL) and, there is a lack of information on its management. Current practices for EMR in APL are always to adopt strategies from other subtypes of Acute lymphoblastic leukemia (ALL) and Acute myeloid leukemia (AML). Gilteritinib, a highly selective FLT3 inhibitor, has demonstrated a remarkable effect on EMR in FLT3-mutant AML. Therefore, it is worthwhile exploring if FLT3 mutation can be a therapeutic target and assessing the efficacy of Gilteritinib on FLT3-mutant EMR in APL. METHODS We described three cases of FLT3-mutant EMR in APL, comprising two isolated EMR cases and one systemic relapse. The patients underwent treatment with Gilteritinib-based regimens based on FLT3 mutation. RESULTS All three patients achieved complete regression of EMR, and no signs of tumor lysis syndrome during Gilteritinib-based therapy, only patient 1 showed mild granulocytopenia. They all maintained molecular complete remission (mCR) during the follow-up period. CONCLUSIONS The Gilteritinib-based regimen shows a high and sustained therapeutic effect with minimal adverse effects, and provides a valuable experience for further evaluation in EMR APL patients.
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Affiliation(s)
- Chun-Xiao Hou
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yu Chen
- Department of Hematology, the Second Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Shan-Hao Liu
- Department of Hematology, the First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Yi-Zhi Jiang
- Department of Hematology, the First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Dong-Ping Huang
- Department of Hematology, the First Affiliated Hospital of Wannan Medical College, Wuhu, People's Republic of China
| | - Su-Ning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, People's Republic of China
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203
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Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [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: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
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Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
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204
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Shi A, Yun F, Shi L, Liu X, Jia Y. Research progress on the mechanism of common inflammatory pathways in the pathogenesis and development of lymphoma. Ann Med 2024; 56:2329130. [PMID: 38489405 PMCID: PMC10946270 DOI: 10.1080/07853890.2024.2329130] [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: 08/22/2023] [Accepted: 02/25/2024] [Indexed: 03/17/2024] Open
Abstract
In recent years, the incidence and mortality rates of lymphoma have gradually increased worldwide. Tumorigenesis and drug resistance are closely related to intracellular inflammatory pathways in lymphoma. Therefore, understanding the biological role of inflammatory pathways and their abnormal activation in relation to the development of lymphoma and their selective modulation may open new avenues for targeted therapy of lymphoma. The biological functions of inflammatory pathways are extensive, and they are central hubs for regulating inflammatory responses, immune responses, and the tumour immune microenvironment. However, limited studies have investigated the role of inflammatory pathways in lymphoma development. This review summarizes the relationship between abnormal activation of common inflammatory pathways and lymphoma development to identify precise and efficient targeted therapeutic options for patients with advanced, drug-resistant lymphoma.
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Affiliation(s)
- Aorong Shi
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
| | - Fen Yun
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Lin Shi
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Xia Liu
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Yongfeng Jia
- Department of Pathology, Basic Medical Sciences College, Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Huhhot, China
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205
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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [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: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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206
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Liu T, Cao Y, Weng J, Gao S, Jin Z, Zhang Y, Yang Y, Zhang H, Xia C, Yin X, Luo Y, He Q, Jiang H, Wang L, Zhang Z. Hepatitis E virus infects human testicular tissue and Sertoli cells. Emerg Microbes Infect 2024; 13:2332657. [PMID: 38517709 PMCID: PMC11057402 DOI: 10.1080/22221751.2024.2332657] [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: 02/15/2024] [Accepted: 03/14/2024] [Indexed: 03/24/2024]
Abstract
Globally, hepatitis E virus (HEV) infections are prevalent. The finding of high viral loads and persistent viral shedding in ejaculate suggests that HEV replicates within the human male genital tract, but its target organ is unknown and appropriate models are lacking. We aimed to determine the HEV tropism in the human testis and its potential influence on male reproductive health. We conducted an ex vivo culture of human testis explants and in vitro culture of primary human Sertoli cells. Clinically derived HEV genotype 1 (HEV1) and HEV3 virions, as well as rat-derived HEV-C1, were used for inoculation. Transcriptomic analysis was performed on testis tissues collected from tacrolimus-treated rabbits with chronic HEV3 infection. Our findings reveal that HEV3, but not HEV1 or HEV-C1, can replicate in human testis explants and primary human Sertoli cells. Tacrolimus treatment significantly enhanced the replication efficiency of HEV3 in testis explants and enabled successful HEV1 infection in Sertoli cells. HEV3 infection disrupted the secretion of several soluble factors and altered the cytokine microenvironment within primary human Sertoli cells. Finally, intratesticular transcriptomic analysis of immunocompromised rabbits with chronic HEV infection indicated downregulation of genes associated with spermatogenesis. HEV can infect the human testicular tissues and Sertoli cells, with increased replication efficiency when exposed to tacrolimus treatment. These findings shed light on how HEV may persist in the ejaculate of patients with chronic hepatitis E and provide valuable ex vivo tools for studying countermeasures.
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Affiliation(s)
- Tianxu Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Yalei Cao
- Department of Urology, Peking University Third Hospital, Beijing, People’s Republic of China
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, People’s Republic of China
| | - Jiaming Weng
- Department of Urology, Peking University Third Hospital, Beijing, People’s Republic of China
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, People’s Republic of China
| | - Songzhan Gao
- Department of Andrology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Zirun Jin
- Department of Urology, Peking University Third Hospital, Beijing, People’s Republic of China
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, People’s Republic of China
| | - Yun Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Yuzhuo Yang
- Department of Urology, Peking University First Hospital, Beijing, People’s Republic of China
| | - He Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xin Yin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yong Luo
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Qiyu He
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Hui Jiang
- Department of Urology, Peking University First Hospital, Beijing, People’s Republic of China
| | - Lin Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Zhe Zhang
- Department of Urology, Peking University Third Hospital, Beijing, People’s Republic of China
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, People’s Republic of China
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207
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Zhou X, Zhou L, Qian F, Chen J, Zhang Y, Yu Z, Zhang J, Yang Y, Li Y, Song C, Wang Y, Shang D, Dong L, Zhu J, Li C, Wang Q. TFTG: A comprehensive database for human transcription factors and their targets. Comput Struct Biotechnol J 2024; 23:1877-1885. [PMID: 38707542 PMCID: PMC11068477 DOI: 10.1016/j.csbj.2024.04.036] [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: 01/27/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Transcription factors (TFs) are major contributors to gene transcription, especially in controlling cell-specific gene expression and disease occurrence and development. Uncovering the relationship between TFs and their target genes is critical to understanding the mechanism of action of TFs. With the development of high-throughput sequencing techniques, a large amount of TF-related data has accumulated, which can be used to identify their target genes. In this study, we developed TFTG (Transcription Factor and Target Genes) database (http://tf.liclab.net/TFTG), which aimed to provide a large number of available human TF-target gene resources by multiple strategies, besides performing a comprehensive functional and epigenetic annotations and regulatory analyses of TFs. We identified extensive available TF-target genes by collecting and processing TF-associated ChIP-seq datasets, perturbation RNA-seq datasets and motifs. We also obtained experimentally confirmed relationships between TF and target genes from available resources. Overall, the target genes of TFs were obtained through integrating the relevant data of various TFs as well as fourteen identification strategies. Meanwhile, TFTG was embedded with user-friendly search, analysis, browsing, downloading and visualization functions. TFTG is designed to be a convenient resource for exploring human TF-target gene regulations, which will be useful for most users in the TF and gene expression regulation research.
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Affiliation(s)
- Xinyuan Zhou
- The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- College of Artificial Intelligence and Big Data For Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Liwei Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fengcui Qian
- The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jiaxin Chen
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yuexin Zhang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhengmin Yu
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yongsan Yang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chao Song
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Desi Shang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Longlong Dong
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chunquan Li
- The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Maternal and Child Health Care Hospital, National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
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208
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Lin Y, Liang Y, Wang D, Chang Y, Ma Q, Wang Y, He F, Xu D. A contrastive learning approach to integrate spatial transcriptomics and histological images. Comput Struct Biotechnol J 2024; 23:1786-1795. [PMID: 38707535 PMCID: PMC11068546 DOI: 10.1016/j.csbj.2024.04.039] [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: 12/31/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, we present ConGcR, a contrastive learning-based model for integrating gene expression, spatial location, and tissue morphology for data representation and spatial tissue architecture identification. Graph convolution and ResNet were used as encoders for gene expression with spatial location and histological image inputs, respectively. We further enhanced ConGcR with a graph auto-encoder as ConGaR to better model spatially embedded representations. We validated our models using 16 human brains, four chicken hearts, eight breast tumors, and 30 human lung spatial transcriptomics samples. The results showed that our models generated more effective embeddings for obtaining tissue architectures closer to the ground truth than other methods. Overall, our models not only can improve tissue architecture identification's accuracy but also may provide valuable insights and effective data representation for other tasks in spatial transcriptome analyses.
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Affiliation(s)
- Yu Lin
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yanchun Liang
- School of Computer Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yuzhou Chang
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, United States
| | - Qin Ma
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, United States
| | - Yan Wang
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Fei He
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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209
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Barrett J, Leysen S, Galmiche C, Al-Mossawi H, Bowness P, Edwards TE, Lawson AD. Chimeric antigens displaying GPR65 extra cellular loops on a soluble scaffold enabled the discovery of antibodies, which recognized native receptor. Bioengineered 2024; 15:2299522. [PMID: 38184821 PMCID: PMC10773626 DOI: 10.1080/21655979.2023.2299522] [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: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024] Open
Abstract
GPR65 is a proton-sensing G-protein coupled receptor associated with multiple immune-mediated inflammatory diseases, whose function is relatively poorly understood. With few reagents commercially available to probe the biology of receptor, generation of an anti-GPR65 monoclonal antibody was desired. Using soluble chimeric scaffolds, such as ApoE3, displaying the extracellular loops of GPR65, together with established phage display technology, native GPR65 loop-specific antibodies were identified. Phage-derived loop-binding antibodies recognized the wild-type native receptor to which they had not previously been exposed, generating confidence in the use of chimeric soluble proteins to act as efficient surrogates for membrane protein extracellular loop antigens. This technique provides promise for the rational design of chimeric antigens in facilitating the discovery of specific antibodies to GPCRs.
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Affiliation(s)
- Janine Barrett
- UK Research Department, UCB Pharma, Slough, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | | | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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210
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Ding R, Yu J, Ke W, Du L, Cheng G, Hu S, Xu Y, Liu Y. TLR2 regulates Moraxella catarrhalis adhesion to and invasion into alveolar epithelial cells and mediates inflammatory responses. Virulence 2024; 15:2298548. [PMID: 38169345 PMCID: PMC10772937 DOI: 10.1080/21505594.2023.2298548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Moraxella catarrhalis is a major cause of chronic obstructive pulmonary disease. Toll-like receptor 2 (TLR2) plays an important role in the inflammatory response in host respiratory epithelial cells. M. catarrhalis induces an inflammatory immune response in respiratory epithelial cells that is mostly dependent on TLR2. However, the mechanisms by which this pathogen adheres to and invades the respiratory epithelium are not well understood. The present study aimed to reveal the role of TLR2 in M. catarrhalis adhesion to and invasion into alveolar epithelial cells, using molecular techniques. Pretreatment with the TLR2 inhibitor TLR2-IN-C29 enhanced M. catarrhalis adhesion to A549 cells but reduced its invasion, whereas the agonist Pam3CSK4 reduced both M. catarrhalis adhesion and invasion into A549 cells. Similarly, M. catarrhalis 73-OR strain adhesion and invasion were significantly reduced in TLR2-/- A549 cells. Moreover, the lung clearance rate of the 73-OR strain was significantly higher in TLR2-/- C57/BL6J mice than in wild-type (WT) mice. Histological analysis showed that inflammatory responses were milder in TLR2-/- C57/BL6J mice than in WT mice, which was confirmed by a decrease in cytokine levels in TLR2-/- C57/BL6J mice. Overall, these results indicate that TLR2 promoted M. catarrhalis adhesion and invasion of A549 cells and lung tissues and mediated inflammatory responses in infected lungs. This study provides important insights into the development of potential therapeutic strategies against M. catarrhalis and TLR2-induced inflammatory responses.
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Affiliation(s)
- Rui Ding
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jinhan Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weixin Ke
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lijun Du
- Department of Clinical Laboratory, Nanchong Central Hospital, the Second Clinical Medical College, North Sichuan Medical College, Nanchong, China
| | - Guixue Cheng
- Department of Clinical Laboratory, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Siqi Hu
- Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yali Liu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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211
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Milcamps R, Michiels T. Involvement of paraspeckle components in viral infections. Nucleus 2024; 15:2350178. [PMID: 38717150 PMCID: PMC11086011 DOI: 10.1080/19491034.2024.2350178] [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: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Paraspeckles are non-membranous subnuclear bodies, formed through the interaction between the architectural long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) and specific RNA-binding proteins, including the three Drosophila Behavior/Human Splicing (DBHS) family members (PSPC1 (Paraspeckle Component 1), SFPQ (Splicing Factor Proline and Glutamine Rich) and NONO (Non-POU domain-containing octamer-binding protein)). Paraspeckle components were found to impact viral infections through various mechanisms, such as induction of antiviral gene expression, IRES-mediated translation, or viral mRNA polyadenylation. A complex involving NEAT1 RNA and paraspeckle proteins was also found to modulate interferon gene transcription after nuclear DNA sensing, through the activation of the cGAS-STING axis. This review aims to provide an overview on how these elements actively contribute to the dynamics of viral infections.
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Affiliation(s)
- Romane Milcamps
- Université catholique de Louvain, de Duve Institute, Brussels, Belgium
| | - Thomas Michiels
- Université catholique de Louvain, de Duve Institute, Brussels, Belgium
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212
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Hu X, Bai X, Tian F, Xing Y, Shi Y, Tong Y, Zhong J. A novel BSL-2 Lassa virus reverse genetics system modelling the complete viral life cycle. Emerg Microbes Infect 2024; 13:2356149. [PMID: 38747061 PMCID: PMC11168227 DOI: 10.1080/22221751.2024.2356149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/11/2024] [Indexed: 06/11/2024]
Abstract
Lassa virus (LASV), a risk-group 4 pathogen, must be handled in biosafety level-4 (BSL-4) conditions, thereby limiting its research and antiviral development. Here, we developed a novel LASV reverse genetics system which, to our knowledge, is the first to study the complete LASV life cycle under BSL-2 conditions. Viral particles can be produced efficiently when LASV minigenomic RNA harbouring minimal viral cis-elements and reporter genes is transfected into a helper cell line stably expressing viral NP, GP, Z and L proteins. The resulting defective virions, named LASVmg, can propagate only in the helper cell line, providing a BSL-2 model to study the complete LASV life cycle. Using this model, we found that a previously reported cellular receptor α-dystroglycan is dispensable for LASVmg infection. Furthermore, we showed that ribavirin can inhibit LASVmg infection by inducing viral mutations. This new BSL-2 system should facilitate studying the LASV life cycle and screening antivirals.
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Affiliation(s)
- Xiaoyou Hu
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xu Bai
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Fangling Tian
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yifan Xing
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yi Shi
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yimin Tong
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Jin Zhong
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, People's Republic of China
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213
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Cao T, Wang Y, Huimin S. Causal effects between gut microbiota and endometriosis: a two-sample Mendelian randomisation study. J OBSTET GYNAECOL 2024; 44:2362415. [PMID: 38885114 DOI: 10.1080/01443615.2024.2362415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/26/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Previous observational evidence has indicated the potential involvement of the gut microbiota (GM) in the development of endometriosis. However, the causal relationship of the association remains to be investigated. METHOD Genome-wide association study (GWAS) data of GM was obtained from the MiBioGen consortium, and GWAS for endometriosis data was from the FinnGen consortium. Initially, a two-sample Mendelian randomisation (MR) analysis was performed to identify specific bacteria associated with endometriosis. Inverse variance-weighted (IVW) was used as the main MR analysis to infer causal relationships. The other four popular MR methods including MR-Egger regression, weighted mode, weighted median, and simple mode were used for secondary confirmation. Subsequently, these selected bacteria were employed as exposure to investigate their causal effects on six sub-types of endometriosis. Furthermore, reverse MR analysis was implemented to evaluate the reverse causal effects. Cochran's Q statistics was used to test the heterogeneity of instrumental variables (IVs); MR-Egger regression was used to test horizontal pleiotropy; MR-PRESSO and leave-one-out sensitivity analysis were applied to find significant outliers. RESULT A total of 1131 single nucleotide polymorphisms (SNPs) were collected as IVs for 196 GM taxa with endometriosis as the outcome. We identified 12 causal relationships between endometriosis and GM taxa including 1 phylum, 3 families, 2 orders, and 6 genera (Rikenellaceae RC9 gut group, Eubacterium ruminantium group, Faecalibacterium, Peptococcus, Clostridium sensu stricto 1, and Ruminococcaceae UCG005). Utilizing the Bonferroni method, we identified phylum Cyanobacteria as the strongest associated GM taxa. Subsequently, 6 significant causal effects were uncovered between the 12 selected specific GM and 6 sub-types of endometriosis. Meanwhile, no reverse causal relationship was found. Further, no horizontal pleiotropy and no significant outliers were detected in the sensitive analysis. CONCLUSIONS This MR analysis revealed significant causal effects between GM and endometriosis and phylum Cyanobacteria had the strongest association.
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Affiliation(s)
- Tiefeng Cao
- Department of Gynaecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P.R. China
| | - Yunfei Wang
- Department of Oncology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P.R. China
| | - Shen Huimin
- Department of Gynaecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P.R. China
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214
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Mars JC, Culjkovic-Kraljacic B, Borden KL. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 PMCID: PMC11185188 DOI: 10.1080/19491034.2024.2360196] [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: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.
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Affiliation(s)
- Jean-Clément Mars
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Katherine L.B. Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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215
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Eldeeb D, Ikeda Y, Hojo H, Ohba S. Unraveling the hidden complexity: Exploring dental tissues through single- cell transcriptional profiling. Regen Ther 2024; 27:218-229. [PMID: 38596822 PMCID: PMC11002530 DOI: 10.1016/j.reth.2024.03.023] [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: 02/09/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/11/2024] Open
Abstract
Understanding the composition and function of cells constituting tissues and organs is vital for unraveling biological processes. Single-cell analysis has allowed us to move beyond traditional methods of categorizing cell types. This innovative technology allows the transcriptional and epigenetic profiling of numerous individual cells, leading to significant insights into the development, homeostasis, and pathology of various organs and tissues in both animal models and human samples. In this review, we delve into the outcomes of major investigations using single-cell transcriptomics to decipher the cellular composition of mammalian teeth and periodontal tissues. The recent single-cell transcriptome-based studies have traced in detail the dental epithelium-ameloblast lineage and dental mesenchyme lineages in the mouse incisors and the tooth germ of both mice and humans; unraveled the microenvironment, the identity of niche cells, and cellular intricacies in the dental pulp; shed light on the molecular mechanisms orchestrating root formation; and characterized cellular dynamics of the periodontal ligament. Additionally, cellular components in dental pulps were compared between healthy and carious teeth at a single-cell level. Each section of this review contributes to a comprehensive understanding of tooth biology, offering valuable insights into developmental processes, niche cell identification, and the molecular secrets of the dental environment.
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Affiliation(s)
- Dahlia Eldeeb
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Physiology, Division of Biomedical Sciences, Nihon University School of Medicine, Japan
- Department of Oral Biology, Faculty of Dentistry, Cairo University, Egypt
| | - Yuki Ikeda
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, Japan
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, Japan
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216
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Mach N. The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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217
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Jin Q, Ren F, Song P. Innovate therapeutic targets for autoimmune diseases: insights from proteome-wide mendelian randomization and Bayesian colocalization. Autoimmunity 2024; 57:2330392. [PMID: 38515381 DOI: 10.1080/08916934.2024.2330392] [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: 11/23/2023] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Despite growing knowledge regarding the pathogenesis of autoimmune diseases (ADs) onset, the current treatment remains unsatisfactory. This study aimed to identify innovative therapeutic targets for ADs through various analytical approaches. RESEARCH DESIGN AND METHODS Utilizing Mendelian randomization, Bayesian co-localization, phenotype scanning, and protein-protein interaction network, we explored potential therapeutic targets for 14 ADs and externally validated our preliminary findings. RESULTS This study identified 12 circulating proteins as potential therapeutic targets for six ADs. Specifically, IL12B was judged to be a risk factor for ankylosing spondylitis (p = 1.61E - 07). TYMP (p = 6.28E - 06) was identified as a protective factor for ulcerative colitis. For Crohn's disease, ERAP2 (p = 4.47E - 14), HP (p = 2.08E - 05), and RSPO3 (p = 6.52E - 07), were identified as facilitators, whereas FLRT3 (p = 3.42E - 07) had a protective effect. In rheumatoid arthritis, SWAP70 (p = 3.26E - 10), SIGLEC6 (p = 2.47E - 05), ISG15 (p = 3.69E - 05), and FCRL3 (p = 1.10E - 10) were identified as risk factors. B4GALT1 (p = 6.59E - 05) was associated with a lower risk of Type 1 diabetes (T1D). Interestingly, CTSH was identified as a protective factor for narcolepsy (p = 1.58E - 09) but a risk factor for T1D (p = 7.36E - 11), respectively. External validation supported the associations of eight of these proteins with three ADs. CONCLUSIONS Our integrated study identified 12 potential therapeutic targets for ADs and provided novel insights into future drug development for ADs.
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Affiliation(s)
- Qiubai Jin
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Feihong Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate school, Beijing University of Chinese Medicine, Beijing, China
| | - Ping Song
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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218
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Liao W, Liu T, Li Y, Liang H, Deng J, Shen F. The bioinfomatics analysis of the M1 macrophage-related gene CXCL9 signature in cervical cancer. J OBSTET GYNAECOL 2024; 44:2373951. [PMID: 38963237 DOI: 10.1080/01443615.2024.2373951] [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: 07/05/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND The expression and function of coexpression genes of M1 macrophage in cervical cancer have not been identified. And the CXCL9-expressing tumour-associated macrophage has been poorly reported in cervical cancer. METHODS To clarify the regulatory gene network of M1 macrophage in cervical cancer, we downloaded gene expression profiles of cervical cancer patients in TCGA database to identify M1 macrophage coexpression genes. Then we constructed the protein-protein interaction networks by STRING database and performed functional enrichment analysis to investigate the biological effects of the coexpression genes. Next, we used multiple bioinformatics databases and experiments to overall investigate coexpression gene CXCL9, including western blot assay and immunohistochemistry assay, GeneMANIA, Kaplan-Meier Plotter, Xenashiny, TISCH2, ACLBI, HPA, TISIDB, GSCA and cBioPortal databases. RESULTS There were 77 positive coexpression genes and 5 negative coexpression genes in M1 macrophage. The coexpression genes in M1 macrophage participated in the production and function of chemokines and chemokine receptors. Especially, CXCL9 was positively correlated with M1 macrophage infiltration levels in cervical cancer. CXCL9 expression would significantly decrease and high CXCL9 levels were linked to good prognosis in the cervical cancer tumour patients, it manifestly expressed in blood immune cells, and was positively related to immune checkpoints. CXCL9 amplification was the most common type of mutation. The CXCL9 gene interaction network could regulate immune-related signalling pathways, and CXCL9 amplification was the most common mutation type in cervical cancer. Meanwhile, CXCL9 may had clinical significance for the drug response in cervical cancer, possibly mediating resistance to chemotherapy and targeted drug therapy. CONCLUSION Our findings may provide new insight into the M1 macrophage coexpression gene network and molecular mechanisms in cervical cancer, and indicated that M1 macrophage association gene CXCL9 may serve as a good prognostic gene and a potential therapeutic target for cervical cancer therapies.
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Affiliation(s)
- Wenxin Liao
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Tingting Liu
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Yang Li
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Hua Liang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Juexiao Deng
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Fujin Shen
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
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219
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Schwardmann LS, Benninghaus L, Lindner SN, Wendisch VF. Prospects of formamide as nitrogen source in biotechnological production processes. Appl Microbiol Biotechnol 2024; 108:105. [PMID: 38204134 PMCID: PMC10781810 DOI: 10.1007/s00253-023-12962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 01/12/2024]
Abstract
This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.
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Affiliation(s)
- Lynn S Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- , Aminoverse B.V., Daelderweg 9, 6361 HK, Nuth, Beekdaelen, The Netherlands
| | - Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Steffen N Lindner
- Department of Biochemistry, Charite Universitatsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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220
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Mondal S, Becskei A. Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication. Comput Struct Biotechnol J 2024; 23:2534-2547. [PMID: 38974885 PMCID: PMC11226983 DOI: 10.1016/j.csbj.2024.06.004] [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: 02/29/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
Cancers share common cellular and physiological features. Little is known about whether distinctive gene expression patterns can be displayed at the single-cell level by gene families in cancer cells. The expression of gene homologs within a family can exhibit concurrence and exclusivity. Concurrence can promote all-or-none expression patterns of related genes and underlie alternative physiological states. Conversely, exclusive gene families express the same or similar number of homologs in each cell, allowing a broad repertoire of cell identities to be generated. We show that gene families involved in the cell-cycle and antigen presentation are expressed concurrently. Concurrence in the DNA replication complex MCM reflects the replicative status of cells, including cell lines and cancer-derived organoids. Exclusive expression requires precise regulatory mechanism, but cancer cells retain this form of control for ion homeostasis and extend it to gene families involved in cell migration. Thus, the cell adhesion-based identity of healthy cells is transformed to an identity based on migration in the population of cancer cells, reminiscent of epithelial-mesenchymal transition.
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Affiliation(s)
- Samuel Mondal
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
| | - Attila Becskei
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
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221
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Tian Y, Liu M, Sun JY, Wang Y, Chen L, Sun W, Zhou L. Diagnosis of preeclampsia using metabolomic biomarkers. Hypertens Pregnancy 2024; 43:2379386. [PMID: 39039822 DOI: 10.1080/10641955.2024.2379386] [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: 04/19/2024] [Accepted: 06/30/2024] [Indexed: 07/24/2024]
Abstract
The diagnostic criteria for preeclampsia do not accurately reflect the pathophysiological characteristics of patients with preeclampsia. Conventional biomarkers and diagnostic approaches have proven insufficient to fully comprehend the intricacies of preeclampsia. This study aimed to screen differentially abundant metabolites as candidate biomarkers for preeclampsia. A propensity score matching method was used to perform a 1:1 match between preeclampsia patients (n = 70) and healthy control individuals (n = 70). Based on univariate and multivariate statistical analysis methods, the different characteristic metabolites were screened and identified. Least absolute shrinkage and selection operator (LASSO) regression analysis was subsequently used to further screen for differentially abundant metabolites. A receiver operating characteristic (ROC) curve was drawn to evaluate the diagnostic efficacy of the metabolites. A total of 1,630 metabolites were identified and quantified in maternal serum samples. Fifty-three metabolites were significantly increased, and two were significantly decreased in preeclampsia patients. The area under the curve (AUC) of the model composed of isobutyryl-L-carnitine and acetyl-leucine was 0.878, and the sensitivity and specificity in detecting preeclampsia were 81.4% and 87.1%, respectively. There are significant differences in metabolism between preeclampsia patients and healthy pregnant women, and a range of novel biomarkers have been identified. These findings lay the foundation for the use of metabolomic biomarkers for the diagnosis of preeclampsia.
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Affiliation(s)
- Yunfan Tian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingwei Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin-Yu Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yifeng Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ling Zhou
- Department of Obstetrics and Gynecology, Liyang People's Hospital, Liyang, Jiangsu, China
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222
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Abedimanesh S, Safaralizadeh R, Jahanafrooz Z, Najafi S, Amini M, Nazarloo SS, Bahojb Mahdavi SZ, Baradaran B, Jebelli A, Mokhtarzadeh AA. Interaction of noncoding RNAs with hippo signaling pathway in cancer cells and cancer stem cells. Noncoding RNA Res 2024; 9:1292-1307. [PMID: 39045083 PMCID: PMC11263728 DOI: 10.1016/j.ncrna.2024.06.006] [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: 01/13/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 07/25/2024] Open
Abstract
The Hippo signaling pathway has a regulatory function in the organogenesis process and cellular homeostasis, switching the cascade reactions of crucial kinases acts to turn off/on the Hippo pathway, altering the downstream gene expression and thereby regulating proliferation, apoptosis, or stemness. Disruption of this pathway can lead to the occurrence of various disorders and different types of cancer. Recent findings highlight the importance of ncRNAs, such as microRNA, circular RNA, and lncRNAs, in modulating the Hippo pathway. Defects in ncRNAs can disrupt Hippo pathway balance, increasing tumor cells, tumorigenesis, and chemotherapeutic resistance. This review summarizes ncRNAs' inhibitory or stimulatory role in - Hippo pathway regulation in cancer and stem cells. Identifying the relation between ncRNAs and the components of this pathway could pave the way for developing new biomarkers in the treatment and diagnosis of cancers.
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Affiliation(s)
- Saba Abedimanesh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Zohreh Jahanafrooz
- Department of Biology, Faculty of Sciences, University of Maragheh, Maragheh, Iran
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shabnam Soltani Nazarloo
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asiyeh Jebelli
- Department of Biological Sciences, Faculty of Basic Sciences, Higher Education Institute of Rab-Rashid, Tabriz, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
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223
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Wang L, Yin N, Shi W, Xie Y, Yi J, Tang Z, Tang J, Xiang J. Splicing inhibition mediated by reduced splicing factors and helicases is associated with the cellular response of lung cancer cells to cisplatin. Comput Struct Biotechnol J 2024; 23:648-658. [PMID: 38283853 PMCID: PMC10819863 DOI: 10.1016/j.csbj.2023.12.039] [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: 09/13/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
Lung cancer's mortality is predominantly linked to post-chemotherapy recurrence, driven by the reactivation of dormant cancer cells. Despite the critical role of these reactivated cells in cancer recurrence and metastasis, the molecular mechanisms governing their therapeutic selection remain poorly understood. In this study, we conducted an integrative analysis by combining PacBio single molecule real-time (SMRT) sequencing with short reads Illumina RNA-seq. Our study revealed that cisplatin-induced dormant and reactivated cancer cells exhibited a noteworthy reduction in gene transcripts and alternative splicing events. Particularly, the differential alternative splicing events were found to be overlapping with the differentially expression genes and enriched in genes related to cell cycle and cell division. Utilizing ENCORI database and correlation analysis, we identified key splicing factors, including SRSF7, SRSF3, PRPF8, and HNRNPC, as well as RNA helicase such as EIF4A3, DDX39A, DDX11, and BRIP1, which were associated with the observed reduction in alternative splicing and subsequent decrease in gene expression. Our study demonstrated that lung cancer cells reduce gene transcripts through diminished alternative splicing events mediated by specific splicing factors and RNA helicase in response to the chemotherapeutic stress. These findings provide insights into the molecular mechanisms underlying the therapeutic selection and reactivation of dormant cancer cells. This discovery opens a potential avenue for the development of therapeutic strategies aimed at preventing cancer recurrence following chemotherapy.
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Affiliation(s)
- Lujuan Wang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Na Yin
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Wenhua Shi
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yaohuan Xie
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Junqi Yi
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ziying Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingqun Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Juanjuan Xiang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Changsha, Hunan 410011, China
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410011, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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224
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Wang KL, Yeh TY, Hsu PC, Wong TH, Liu JR, Chern JW, Lin MH, Yu CW. Discovery of novel anaplastic lymphoma kinase (ALK) and histone deacetylase (HDAC) dual inhibitors exhibiting antiproliferative activity against non-small cell lung cancer. J Enzyme Inhib Med Chem 2024; 39:2318645. [PMID: 38465731 DOI: 10.1080/14756366.2024.2318645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024] Open
Abstract
A series of novel benzimidazole derivatives were designed and synthesised based on the structures of reported oral available ALK inhibitor and HDAC inhibitor, pracinostat. In enzymatic assays, compound 3b, containing a 2-acyliminobenzimidazole moiety and hydroxamic acid side chain, could inhibit both ALK and HDAC6 (IC50 = 16 nM and 1.03 µM, respectively). Compound 3b also inhibited various ALK mutants known to be involved in crizotinib resistance, including mutant L1196M (IC50, 4.9 nM). Moreover, 3b inhibited the proliferation of several cancer cell lines, including ALK-addicted H2228 cells. To evaluate its potential for treating cancers in vivo, 3b was used in a human A549 xenograft model with BALB/c nude mice. At 20 mg/kg, 3b inhibited tumour growth by 85% yet had a negligible effect on mean body weight. These results suggest a attracting route for the further research and optimisation of dual ALK/HDAC inhibitors.
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Affiliation(s)
- Kang-Li Wang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Yu Yeh
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Chen Hsu
- Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hsuan Wong
- Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jia-Rong Liu
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ji-Wang Chern
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Miao-Hsia Lin
- Department and Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chao-Wu Yu
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
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225
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Nguyen PT, Harris BJ, Mateos DL, González AH, Murray AM, Yarov-Yarovoy V. Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold. Channels (Austin) 2024; 18:2325032. [PMID: 38445990 PMCID: PMC10936637 DOI: 10.1080/19336950.2024.2325032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/14/2024] [Indexed: 03/07/2024] Open
Abstract
Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8, human voltage-gated calcium (CaV) channel - CaV1.1, and human voltage-gated potassium (KV) channel - KV1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.
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Affiliation(s)
- Phuong Tran Nguyen
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
| | - Brandon John Harris
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Diego Lopez Mateos
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Adriana Hernández González
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Department of Anesthesiology and Pain Medicine, University of California School of Medicine, Davis, CA, USA
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226
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Li X, Liang Q, Liu L, Chen S, Li Y, Pu Y. FTO attenuates TNF-α-induced damage of proximal tubular epithelial cells in acute pancreatitis-induced acute kidney injury via targeting AQP3 in an N6-methyladenosine-dependent manner. Ren Fail 2024; 46:2322037. [PMID: 38445367 PMCID: PMC10919303 DOI: 10.1080/0886022x.2024.2322037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is a frequent complication of severe acute pancreatitis (SAP). Previous investigations have revealed the involvement of FTO alpha-ketoglutarate-dependent dioxygenase (FTO) and aquaporin 3 (AQP3) in AKI. Therefore, the aim of this study is to explore the association of FTO and AQP3 on proximal tubular epithelial cell damage in SAP-induced AKI. METHODS An in-vitro AKI model was established in human proximal tubular epithelial cells (PTECs) HK-2 via tumor necrosis factor-α (TNF-α) induction (20 ng/mL), after which FTO and AQP3 expression was manipulated and quantified by quantitative real-time PCR and Western blotting. The viability and apoptosis of PTECs under various conditions, and reactive oxygen species (ROS), superoxide dismutase (SOD), and malonaldehyde (MDA) levels within these cells were measured using commercial assay kits and flow cytometry. Methylated RNA immunoprecipitation and mRNA stability assays were performed to elucidate the mechanism of FTO-mediated N6-methyladenosine (m6A) modification. Western blotting was performed to quantify β-catenin protein levels in the PTECs. RESULTS FTO overexpression attenuated the TNF-α-induced decrease in viability and SOD levels, elevated apoptosis, increased levels of ROS and MDA, and diminished TNF-α-induced AQP3 expression and reduced β-catenin expression, but its silencing led to contradictory results. FTO negatively modulates AQP3 levels in RTECs in an m6A-depednent manner and compromises AQP3 stability. In addition, all FTO overexpression-induced effects in TNF-α-induced PTECs were neutralized following AQP3 upregulation. CONCLUSION FTO alleviates TNF-α-induced damage to PTECs in vitro by targeting AQP3 in an m6A-dependent manner.
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Affiliation(s)
- Xinghui Li
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Qi Liang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Lu Liu
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Shujun Chen
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Yong Li
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
| | - Yu Pu
- Department of Radiology, Affiliated Hospital of North Sichuan Medical College, Medical Imaging Key Laboratory of Sichuan Province, Nanchong, Sichuan Province, China
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227
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Onuzulu CD, Lee S, Basu S, Comte J, Hai Y, Hizon N, Chadha S, Fauni MS, Halayko AJ, Pascoe CD, Jones MJ. Novel DNA methylation changes in mouse lungs associated with chronic smoking. Epigenetics 2024; 19:2322386. [PMID: 38436597 PMCID: PMC10913724 DOI: 10.1080/15592294.2024.2322386] [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: 11/14/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Smoking is a potent cause of asthma exacerbations, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most studies of smoking and DNAm have been done using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is lacking. Here, we identified DNAm patterns in the lungs that are altered by smoking. We used an established mouse model to measure the effects of chronic smoke exposure first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model recapitulates previous DNAm patterns observed in smoking humans, specifically measuring DNAm at a candidate gene responsive to cigarette smoke, Cyp1a1. Finally, we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are associated with nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, to fully understand mechanisms underlying CS-mediated health outcomes.
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Affiliation(s)
- Chinonye Doris Onuzulu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Samantha Lee
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sujata Basu
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeannette Comte
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Yan Hai
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nikho Hizon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Shivam Chadha
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maria Shenna Fauni
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew J. Halayko
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Christopher D. Pascoe
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Meaghan J. Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Biology of Breathing Theme, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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228
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Sun J, Li J, He Y, Kang W, Ye X. Identification and validation of protein biomarkers for predicting gastrointestinal stromal tumor recurrence. Comput Struct Biotechnol J 2024; 23:1065-1075. [PMID: 38455069 PMCID: PMC10918489 DOI: 10.1016/j.csbj.2024.02.017] [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: 10/16/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
We conducted a proteomic analysis using mass spectrometry to identify and validate protein biomarkers for accurately predicting recurrence risk in gastrointestinal stromal tumors (GIST) patients, focusing on differentially expressed proteins in metastatic versus primary GIST tissues. We selected five biomarkers-GPX4, RBM4, TPM3, PFKFB2, and PGAM5-and validated their expressions in primary tumors of recurrent and non-recurrent GIST patients via immunohistochemistry. Our analysis of the association between these biomarkers with recurrence-free survival (RFS) and overall survival (OS), along with their interrelationships, revealed that immunohistochemistry confirmed significantly higher expressions of these biomarkers in primary GIST tissues of recurrent patients. Kaplan-Meier survival analysis showed that high expressions of GPX4, RBM4, TPM3, PFKFB2, and PGAM5 correlated with lower RFS, and GPX4 and RBM4 with lower OS. All biomarker pairs showed positive associations, with high expressions correlating with increased recurrence rates, and GPX4 and RBM4 with higher mortality rates. In conclusion, the biomarkers GPX4, RBM4, TPM3, PFKFB2, and PGAM5 are clinically relevant for predicting GIST recurrence, with their high expressions in primary tumors linked to poorer RFS and OS. They serve as potential prognostic indicators, enabling early treatment and improved outcomes. The observed interrelationships among these biomarkers further validate their accuracy in predicting GIST recurrence.
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Affiliation(s)
| | | | - Yixuan He
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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229
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Marasco M, Kirkpatrick J, Carlomagno T, Hub JS, Anselmi M. Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet. Comput Struct Biotechnol J 2024; 23:1169-1180. [PMID: 38510972 PMCID: PMC10951427 DOI: 10.1016/j.csbj.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations. As an orthogonal method to X-ray crystallography, we use a combination of NMR spectroscopy and MD simulations to accurately determine the conformation of apo N-SH2 in solution. In contrast to earlier reports based on crystallographic data, our results indicate that apo N-SH2 in solution primarily adopts a conformation with a fully zipped central β-sheet, and that partial unzipping of this β-sheet is promoted by binding of either phosphopeptides or even phosphate/sulfate ions.
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Affiliation(s)
- Michelangelo Marasco
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Kirkpatrick
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Teresa Carlomagno
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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230
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Das Adhikari S, Yang J, Wang J, Cui Y. Recent advances in spatially variable gene detection in spatial transcriptomics. Comput Struct Biotechnol J 2024; 23:883-891. [PMID: 38370977 PMCID: PMC10869304 DOI: 10.1016/j.csbj.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered on identifying spatially variable genes (SVGs) or genes expressed with specific spatial patterns across the tissue. SVG detection is an important task since many downstream analyses depend on these selected SVGs. Over the past few years, a plethora of new methods have been proposed for the detection of SVGs, accompanied by numerous innovative concepts and discussions. This article provides a selective review of methods and their practical implementations, offering valuable insights into the current literature in this field.
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Affiliation(s)
- Sikta Das Adhikari
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA
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231
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Mehdipour chari K, Enderami SE, Mansour RN, Hasanzadeh E, Amini Mahabadi J, Abazari M, Asadi P, Hojjat A. Applications of blood plasma derivatives for cutaneous wound healing: A mini-review of clinical studies. Regen Ther 2024; 27:251-258. [PMID: 38596823 PMCID: PMC11002853 DOI: 10.1016/j.reth.2024.02.011] [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: 09/16/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
Skin injuries are a global healthcare problem. Chronic ulcers do not heal in a timely fashion, so it is essential to help the body with skin repair. There are some treatments that have been applied to chronic ulcers. One of these treatments is growth factor (GF) therapy. Platelet-rich plasma (PRP) and Platelet-poor plasma (PPP) are two types of plasma derivatives containing many GFs important for wound healing. Several works have reported their application in wound healing and tissue regeneration. The use of autologous PRP is now an adequate alternative in regenerative medicine. It was also demonstrated that PPP is a hemostatic agent for wounds. This review has studied the latest clinical studies, which have applied PRP and PPP to patients with chronic wounds.
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Affiliation(s)
- Kayvan Mehdipour chari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Ehsan Enderami
- Immunogenetics Research Center, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reyhaneh Nassiri Mansour
- Immunogenetics Research Center, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Tissue Engineering & Regenerative Medicine, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Elham Hasanzadeh
- Department of Tissue Engineering & Regenerative Medicine, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Mohamadfoad Abazari
- Division of Medical Sciences, Island Medical Program, University of British Columbia, Victoria, BC, Canada
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, Canada
| | - Peyman Asadi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Atefeh Hojjat
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Uehara K, Oshiro E, Ochiai A, Takagi R, Yamato M, Kato A. Lessons learned from contamination with endotoxin originated from the supplement in the cell culture medium. Regen Ther 2024; 27:230-233. [PMID: 38596824 PMCID: PMC11002528 DOI: 10.1016/j.reth.2024.03.022] [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: 01/16/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Endotoxin is a typical pyrogen derived from the outer membrane of Gram-negative bacteria. In fabricating cell-based medicinal products, it is necessary to control endotoxin in the process and the products. In the quality control tests of our clinical study, endotoxin concentration in the culture supernatant of autologous oral mucosal epithelial cell sheets exceeded the criterion value. Therefore, endotoxin measurements were conducted to clarify the cause of the endotoxin contamination. Methods The reagents used to prepare the culture medium, the unused culture medium, and the culture supernatants were diluted with pure water. Endotoxin concentrations in the diluted samples were measured. Results Endotoxin was detected in both the unused culture medium and the culture supernatant of the epithelial cell sheets at higher concentrations than the criterion value. Therefore, endotoxin concentrations in the reagents used to prepare the culture medium were measured and were found to be below the criterion value, except for cholera toxin. On the other hand, three lots of cholera toxin products were used for the measurement, and the endotoxin concentrations were higher than the criterion value. The results indicate that the endotoxin contamination is caused by the cholera toxin product. Conclusions To prevent endotoxin contamination in cell-based medicinal products, endotoxin concentrations in reagents used for the fabrication should be measured in the facility conducting clinical research or confirmed by an adequate certificate of analysis from the manufacturers of the reagents.
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Affiliation(s)
- Koaki Uehara
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
| | - Eriko Oshiro
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
| | - Atsushi Ochiai
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
| | - Ryo Takagi
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Masayuki Yamato
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, TWIns, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Atsunaga Kato
- Social Medical Corporation Yuuaikai, Yuuai Medical Center, Advanced Medical Research Center, 50-5, Yone, Tomigusuku-shi, Okinawa 901-0224, Japan
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233
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Zhuang Y, Jiang W, Zhao Z, Li W, Deng Z, Liu J. Ion channel-mediated mitochondrial volume regulation and its relationship with mitochondrial dynamics. Channels (Austin) 2024; 18:2335467. [PMID: 38546173 PMCID: PMC10984129 DOI: 10.1080/19336950.2024.2335467] [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: 12/11/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
The mitochondrion, one of the important cellular organelles, has the major function of generating adenosine triphosphate and plays an important role in maintaining cellular homeostasis, governing signal transduction, regulating membrane potential, controlling programmed cell death and modulating cell proliferation. The dynamic balance of mitochondrial volume is an important factor required for maintaining the structural integrity of the organelle and exerting corresponding functions. Changes in the mitochondrial volume are closely reflected in a series of biological functions and pathological changes. The mitochondrial volume is controlled by the osmotic balance between the cytoplasm and the mitochondrial matrix. Thus, any disruption in the influx of the main ion, potassium, into the cells can disturb the osmotic balance between the cytoplasm and the matrix, leading to water movement between these compartments and subsequent alterations in mitochondrial volume. Recent studies have shown that mitochondrial volume homeostasis is closely implicated in a variety of diseases. In this review, we provide an overview of the main influencing factors and research progress in the field of mitochondrial volume homeostasis.
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Affiliation(s)
- Yujia Zhuang
- Hand and Foot Surgery Department, Shenzhen Second People’s Hospital/the First Hospital Affiliated to Shenzhen University, Shenzhen, China
- Clinical College of Shantou University Medical College, Shantou, China
| | - Wenting Jiang
- Operating room, Shenzhen Second People’s Hospital/the First Hospital Affiliated to Shenzhen University, Shenzhen, China
| | - Zhe Zhao
- Hand and Foot Surgery Department, Shenzhen Second People’s Hospital/the First Hospital Affiliated to Shenzhen University, Shenzhen, China
| | - Wencui Li
- Hand and Foot Surgery Department, Shenzhen Second People’s Hospital/the First Hospital Affiliated to Shenzhen University, Shenzhen, China
| | - Zhiqin Deng
- Hand and Foot Surgery Department, Shenzhen Second People’s Hospital/the First Hospital Affiliated to Shenzhen University, Shenzhen, China
| | - Jianquan Liu
- Hand and Foot Surgery Department, Shenzhen Second People’s Hospital/the First Hospital Affiliated to Shenzhen University, Shenzhen, China
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Aydillo T, Balsera-Manzanero M, Rojo-Fernandez A, Escalera A, Salamanca-Rivera C, Pachón J, Del Mar Muñoz-García M, Sánchez-Cordero MJ, Sánchez-Céspedes J, García-Sastre A, Cordero E. Concomitant administration of seasonal influenza and COVID-19 mRNA vaccines. Emerg Microbes Infect 2024; 13:2292068. [PMID: 38054302 PMCID: PMC10798284 DOI: 10.1080/22221751.2023.2292068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Current clinical guidelines support the concomitant administration of seasonal influenza vaccines and COVID-19 mRNA boosters vaccine. Whether dual vaccination may impact vaccine immunogenicity due to an interference between influenza or SARS-CoV-2 antigens is unknown. We aimed to understand the impact of mRNA COVID-19 vaccines administered concomitantly on the immune response to influenza vaccines. For this, 128 volunteers were vaccinated during the 22-23 influenza season. Three groups of vaccination were assembled: FLU vaccine only (46, 35%) versus volunteers that received the mRNA bivalent COVID-19 vaccines concomitantly to seasonal influenza vaccines, FluCOVID vaccine in the same arm (42, 33%) or different arm (40, 31%), respectively. Sera and whole blood were obtained the day of vaccination, +7, and +28 days after for antibody and T cells response quantification. As expected, side effects were increased in individuals who received the FluCOVID vaccine as compared to FLU vaccine only based on the known reactogenicity of mRNA vaccines. In general, antibody levels were high at 4 weeks post-vaccination and differences were found only for the H3N2 virus when administered in different arms compared to the other groups at day 28 post-vaccination. Additionally, our data showed that subjects that received the FluCOVID vaccine in different arm tended to have better antibody induction than those receiving FLU vaccines for H3N2 virus in the absence of pre-existing immunity. Furthermore, no notable differences in the influenza-specific cellular immune response were found for any of the vaccination groups. Our data supports the concomitant administration of seasonal influenza and mRNA COVID-19 vaccines.
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Affiliation(s)
- Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, USA
| | - Maria Balsera-Manzanero
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Amaya Rojo-Fernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, USA
| | - Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Celia Salamanca-Rivera
- Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Sevilla, Spain
- Department of Preventive Medicine, University of Seville, Spain
| | - Jerónimo Pachón
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
- Department of Medicine, School of Medicine, University of Sevilla, Sevilla, Spain
| | | | | | - Javier Sánchez-Céspedes
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
- Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Sevilla, Spain
- CIBERINFEC, CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, USA
| | - Elisa Cordero
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
- Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Sevilla, Spain
- CIBERINFEC, CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, School of Medicine, University of Sevilla, Sevilla, Spain
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235
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Gong H, Zhang S, Zhang X, Chen Y. A method for chromatin domain partitioning based on hypergraph clustering. Comput Struct Biotechnol J 2024; 23:1584-1593. [PMID: 38655013 PMCID: PMC11035048 DOI: 10.1016/j.csbj.2024.04.008] [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: 01/28/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
For many years, multi-scale models of chromatin domains, such as A/B compartments, sub-compartments, topologically associated domains (TADs), sub-TADs, and loops have been popular. However, existing methods can only identify structures at a single scale and cannot partition multi-scale structures. In this paper, we proposed a method (TORNADOES) for chromatin domain partitioning based on hypergraph clustering. First, we use a density clustering algorithm to identify TADs at different scales based on Hi-C data with different resolutions. Then, by combining ChIP-seq data features and TAD results at different scales, we generate a hypergraph based on these TADs. Finally, we partition the chromatin domain structure at different scales, including A/B, A1, A2, B1, B2, and B3 based on the Laplacian matrix feature of the hypergraph. Similarity comparison experiments and ChIP-seq signal enrichment analysis are performed on the A/B region and sub-TAD levels, respectively, demonstrating that our method can identify chromatin domains with distinct features and provide a deeper understanding of the organizational patterns and functional differences in TADs at the genomic hierarchical structure. Comparative analysis of multiple cell line data shows that TORNADOES can better classify different numbers and types of compartments by changing the factors ChIP-seq data and clustering number used to characterize TAD compared to other methods. Source code for the TORNADOES method can be found at https://github.com/ghaiyan/TORNADOES.
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Affiliation(s)
- Haiyan Gong
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
- Shunde Innovation School, University of Science and Technology Beijing, Foshan, 528399, Guangdong, China
| | - Sichen Zhang
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiaotong Zhang
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Shunde Innovation School, University of Science and Technology Beijing, Foshan, 528399, Guangdong, China
| | - Yang Chen
- The State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
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236
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Guan J, Chen X, Li Z, Deng S, Wumaier A, Ma Y, Xie L, Huang S, Zhu Y, Zhuo Y. Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma. Epigenetics 2024; 19:2348840. [PMID: 38716769 PMCID: PMC11086004 DOI: 10.1080/15592294.2024.2348840] [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: 12/03/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
To explore the role of lncRNA m6A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05-0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m6A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m6A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m6A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m6A peaks, with statistically significant differences (| Fold Change (FC) |≥2, p < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m6A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m6A methylation.
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Affiliation(s)
- Jieying Guan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Shuifeng Deng
- The Department of Ophthalmology, Huizhou Hospital Affiliated to Guangzhou Medical University (Huizhou Third People’s Hospital), Huizhou, China
| | - Aizezi Wumaier
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Yuncheng Ma
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Lingling Xie
- The Affiliated Kashi Hospital, Sun Yat-sen University, Kashi, Xinjiang, China
- The First Department of Ophthalmology, The First People’s Hospital of Kashi Prefecture, Kashi, Xinjiang, China
| | - Shengsong Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, World Health Organization Collaborating Center for Eye Care and Vision, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
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237
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Li W, Yu L. Role and therapeutic perspectives of extra cellular vesicles derived from liver and adipose tissue in metabolic dysfunction-associated steatotic liver disease. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:355-369. [PMID: 38833340 DOI: 10.1080/21691401.2024.2360008] [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: 10/13/2023] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
The global epidemic of metabolic diseases has led to the emergence of metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH), which pose a significant threat to human health. Despite recent advances in research on the pathogenesis and treatment of MASLD/MASH, there is still a lack of more effective and targeted therapies. Extracellular vesicles (EVs) discovered in a wide range of tissues and body fluids encapsulate different activated biomolecules and mediate intercellular communication. Recent studies have shown that EVs derived from the liver and adipose tissue (AT) play vital roles in MASLD/MASH pathogenesis and therapeutics, depending on their sources and intervention types. Besides, adipose-derived stem cell (ADSC)-derived EVs appear to be more effective in mitigating MASLD/MASH. This review presents an overview of the definition, extraction strategies, and characterisation of EVs, with a particular focus on the biogenesis and release of exosomes. It also reviews the effects and potential molecular mechanisms of liver- and AT-derived EVs on MASLD/MASH, and emphasises the contribution and clinical therapeutic potential of ADSC-derived EVs. Furthermore, the future perspective of EV therapy in a clinical setting is discussed.
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Affiliation(s)
- Wandi Li
- Senior Department of Burns and Plastic Surgery, the Fourth Medical Center of PLA General Hospital, Haidian District, Beijing, P.R. China
| | - Lili Yu
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, P.R. China
- Endocrine Department, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang Medical University, Henan, P.R. China
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238
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Xu Y, Das P, McCord RP, Shen T. Node features of chromosome structure networks and their connections to genome annotation. Comput Struct Biotechnol J 2024; 23:2240-2250. [PMID: 38827231 PMCID: PMC11140560 DOI: 10.1016/j.csbj.2024.05.026] [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: 12/13/2023] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/04/2024] Open
Abstract
The 3D conformations of chromosomes can encode biological significance, and the implications of such structures have been increasingly appreciated recently. Certain chromosome structural features, such as A/B compartmentalization, are frequently extracted from Hi-C pairwise genome contact information (physical association between different regions of the genome) and compared with linear annotations of the genome, such as histone modifications and lamina association. We investigate how additional properties of chromosome structure can be deduced using an abstract graph representation of the contact heatmap, and describe specific network properties that can have a strong connection with some of these biological annotations. We constructed chromosome structure networks (CSNs) from bulk Hi-C data and calculated a set of site-resolved (node-based) network properties. These properties are useful for characterizing certain aspects of chromosomal structure. We examined the ability of network properties to differentiate several scenarios, such as haploid vs diploid cells, partially inverted nuclei vs conventional architecture, depletion of chromosome architectural proteins, and structural changes during cell development. We also examined the connection between network properties and a series of other linear annotations, such as histone modifications and chromatin states including poised promoter and enhancer labels. We found that semi-local network properties exhibit greater capability in characterizing genome annotations compared to diffusive or ultra-local node features. For example, the local square clustering coefficient can be a strong classifier of lamina-associated domains. We demonstrated that network properties can be useful for highlighting large-scale chromosome structure differences that emerge in different biological situations.
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Affiliation(s)
- Yingjie Xu
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Priyojit Das
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel Patton McCord
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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239
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Losurdo NA, Bibo A, Bedke J, Link N. A novel adipose loss-of-function mutant in Drosophila. Fly (Austin) 2024; 18:2352938. [PMID: 38741287 PMCID: PMC11095658 DOI: 10.1080/19336934.2024.2352938] [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: 08/23/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
To identify genes required for brain growth, we took an RNAi knockdown reverse genetic approach in Drosophila. One potential candidate isolated from this effort is the anti-lipogenic gene adipose (adp). Adp has an established role in the negative regulation of lipogenesis in the fat body of the fly and adipose tissue in mammals. While fat is key to proper development in general, adp has not been investigated during brain development. Here, we found that RNAi knockdown of adp in neuronal stem cells and neurons results in reduced brain lobe volume and sought to replicate this with a mutant fly. We generated a novel adp mutant that acts as a loss-of-function mutant based on buoyancy assay results. We found that despite a change in fat content in the body overall and a decrease in the number of larger (>5 µm) brain lipid droplets, there was no change in the brain lobe volume of mutant larvae. Overall, our work describes a novel adp mutant that can functionally replace the long-standing adp60 mutant and shows that the adp gene has no obvious involvement in brain growth.
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Affiliation(s)
| | - Adriana Bibo
- Department of Neurobiology, University of Utah, Salt Lake, UT, USA
| | - Jacob Bedke
- Department of Neurobiology, University of Utah, Salt Lake, UT, USA
| | - Nichole Link
- Department of Neurobiology, University of Utah, Salt Lake, UT, USA
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240
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Victorio CBL, Ganasarajah A, Novera W, Ong J, Msallam R, Chacko AM. Translocator protein (TSPO) is a biomarker of Zika virus (ZIKV) infection-associated neuroinflammation. Emerg Microbes Infect 2024; 13:2348528. [PMID: 38662785 PMCID: PMC11132733 DOI: 10.1080/22221751.2024.2348528] [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: 01/31/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
Zika is a systemic inflammatory disease caused by infection with Zika virus (ZIKV). ZIKV infection in adults is associated with encephalitis marked by elevated expression of pro-inflammatory cytokines and chemokines, as well as increased brain infiltration of immune cells. In this study, we demonstrate that ZIKV encephalitis in a mouse infection model exhibits increased brain TSPO expression. TSPO expression on brain-resident and infiltrating immune cells in ZIKV infection correlates with disease and inflammation status in the brain. Brain TSPO expression can also be sensitively detected ex vivo and in vitro using radioactive small molecule probes that specifically bind to TSPO, such as [3H]PK11195. TSPO expression on brain-resident and infiltrating immune cells is a biomarker of ZIKV neuroinflammation, which can also be a general biomarker of acute viral neuroinflammatory disease.
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Affiliation(s)
- Carla Bianca Luena Victorio
- Laboratory for Translational and Molecular Imaging (LTMI), Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Arun Ganasarajah
- Laboratory for Translational and Molecular Imaging (LTMI), Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Wisna Novera
- Laboratory for Translational and Molecular Imaging (LTMI), Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Joanne Ong
- Laboratory for Translational and Molecular Imaging (LTMI), Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Rasha Msallam
- Laboratory for Translational and Molecular Imaging (LTMI), Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Ann-Marie Chacko
- Laboratory for Translational and Molecular Imaging (LTMI), Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Singapore
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241
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Kwon T, Trujillo JD, Carossino M, Lyoo EL, McDowell CD, Cool K, Matias-Ferreyra FS, Jeevan T, Morozov I, Gaudreault NN, Balasuriya UB, Webby RJ, Osterrieder N, Richt JA. Pigs are highly susceptible to but do not transmit mink-derived highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b. Emerg Microbes Infect 2024; 13:2353292. [PMID: 38712345 PMCID: PMC11132737 DOI: 10.1080/22221751.2024.2353292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
ABSTRACTRapid evolution of highly pathogenic avian influenza viruses (HPAIVs) is driven by antigenic drift but also by reassortment, which might result in robust replication in and transmission to mammals. Recently, spillover of clade 2.3.4.4b HPAIV to mammals including humans, and their transmission between mammalian species has been reported. This study aimed to evaluate the pathogenicity and transmissibility of a mink-derived clade 2.3.4.4b H5N1 HPAIV isolate from Spain in pigs. Experimental infection caused interstitial pneumonia with necrotizing bronchiolitis with high titers of virus present in the lower respiratory tract and 100% seroconversion. Infected pigs shed limited amount of virus, and importantly, there was no transmission to contact pigs. Notably, critical mammalian-like adaptations such as PB2-E627 K and HA-Q222L emerged at low frequencies in principal-infected pigs. It is concluded that pigs are highly susceptible to infection with the mink-derived clade 2.3.4.4b H5N1 HPAIV and provide a favorable environment for HPAIV to acquire mammalian-like adaptations.
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Affiliation(s)
- Taeyong Kwon
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Eu Lim Lyoo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chester D. McDowell
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Konner Cool
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Franco S. Matias-Ferreyra
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Udeni B.R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Nikolaus Osterrieder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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Zhang Z, Zhou L, Liu Q, Zheng Y, Tan X, Huang Z, Guo M, Wang X, Chen X, Liang S, Li W, Song K, Yan K, Li J, Li Q, Zhang Y, Yang S, Cai Z, Dai M, Xian Q, Shi ZL, Xu K, Lan K, Chen Y. The lethal K18-hACE2 knock-in mouse model mimicking the severe pneumonia of COVID-19 is practicable for antiviral development. Emerg Microbes Infect 2024; 13:2353302. [PMID: 38753462 PMCID: PMC11132709 DOI: 10.1080/22221751.2024.2353302] [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: 01/09/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Animal models of COVID-19 facilitate the development of vaccines and antivirals against SARS-CoV-2. The efficacy of antivirals or vaccines may differ in different animal models with varied degrees of disease. Here, we introduce a mouse model expressing human angiotensin-converting enzyme 2 (ACE2). In this model, ACE2 with the human cytokeratin 18 promoter was knocked into the Hipp11 locus of C57BL/6J mouse by CRISPR - Cas9 (K18-hACE2 KI). Upon intranasal inoculation with high (3 × 105 PFU) or low (2.5 × 102 PFU) dose of SARS-CoV-2 wildtype (WT), Delta, Omicron BA.1, or Omicron BA.2 variants, all mice showed obvious infection symptoms, including weight loss, high viral loads in the lung, and interstitial pneumonia. 100% lethality was observed in K18-hACE2 KI mice infected by variants with a delay of endpoint for Delta and BA.1, and a significantly attenuated pathogenicity was observed for BA.2. The pneumonia of infected mice was accompanied by the infiltration of neutrophils and pulmonary fibrosis in the lung. Compared with K18-hACE2 Tg mice and HFH4-hACE2 Tg mice, K18-hACE2 KI mice are more susceptible to SARS-CoV-2. In the antivirals test, REGN10933 and Remdesivir had limited antiviral efficacies in K18-hACE2 KI mice upon the challenge of SARS-CoV-2 infections, while Nirmatrelvir, monoclonal antibody 4G4, and mRNA vaccines potently protected the mice from death. Our results suggest that the K18-hACE2 KI mouse model is lethal and stable for SARS-CoV-2 infection, and is practicable and stringent to antiviral development.
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Affiliation(s)
- Zhen Zhang
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Qianyun Liu
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Yucheng Zheng
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Xue Tan
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Zhixiang Huang
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Ming Guo
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Xin Wang
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Xianying Chen
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Simeng Liang
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Wenkang Li
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Kun Song
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Kun Yan
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Jiali Li
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Qiaohong Li
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Yuzhen Zhang
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Shimin Yang
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
| | - Zeng Cai
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Ming Dai
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Qiaoyang Xian
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ke Xu
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Ke Lan
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
| | - Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center and RNA Institute, College of Life Sciences and Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, People’s Republic of China
- Institute for Vaccine Research, Animal Bio-Safety Level III Laboratory / Center for Animal Experiment, Wuhan University School of Medicine, Wuhan, People’s Republic of China
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Cao J, Huang Z, Zeng J, Liu J, Zuo W, Su Z, Chen Y, Yu W, Ye H. Maternal and neonatal outcomes and clinical laboratory testing of pregnant women with COVID-19 during the BA.5.2/BF.7 surge. Virulence 2024; 15:2360130. [PMID: 38803076 DOI: 10.1080/21505594.2024.2360130] [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: 02/27/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024] Open
Abstract
The impact of COVID-19 on pregnant women and newborns continues to be a critical societal concern. However, the majority of research focuses on the disease resulting from the early pandemic variants, without sufficient study on the more recent BA.5.2/BF.7. We retrospectively recruited pregnant women giving birth during the surge of the BA.5.2/BF.7 and analysed the risk impact of COVID-19 on maternal and neonatal outcomes. Furthermore, subjects matched through propensity scores were used for the analysis of clinical laboratory tests. A total of 818 pregnant women were enrolled, among 276 (33.7%) were diagnosed with SARS-CoV-2 during childbirth. COVID-19 significantly increased the risk of a hospital length of stay equal to or greater than seven days and neonatal admission to the neonatal intensive care unit, with an aHR of 2.03 (95% CI, 1.22-3.38) and 1.51 (95% CI, 1.12-2.03), respectively. In the analysis of 462 matched subjects, it was found that subjects infected with SARS-CoV-2 tended slight leucopenia and coagulation abnormalities. We found that during the surge of the BA.5.2/BF.7, COVID-19 increased the risk of maternal and neonatal outcomes among Chinese pregnant women. This finding offers significant insights to guide clinical practices involving pregnant women infected with the recently emerged Omicron subvariants.
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Affiliation(s)
- Jiali Cao
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zehong Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen, China
| | - Jing Zeng
- School of Pharmacy, Xiamen University, Xiamen, China
| | - Jumei Liu
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Weilun Zuo
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhiying Su
- Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yujuan Chen
- Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Weiwei Yu
- Department of Obstetrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Huiming Ye
- Department of Laboratory Medicine, Fujian Key Clinical Specialty of Laboratory Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
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244
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Das Mahapatra PP, Roy C, Agarwal K, Sharma SD, Chowdhury SR, Sharma S, Rajagopal H, Meher D. Non-invasive hemoglobin screening device: a promising digital method for reducing anemia prevalence through routine screening and timely intervention. Hematology 2024; 29:2365078. [PMID: 38864489 DOI: 10.1080/16078454.2024.2365078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Several non-invasive technologies are nowadays available in the market which claim to determine the hemoglobin levels instantly without the requirement of the blood sample. But no study has shown the significance of such non-invasive devices on a routine basis for determining their impact on anemia reduction programs. This study is conducted to determine the impact of regular hemoglobin screening on the women population to determine its potential in reducing anemia, using a digitalized non-invasive device. METHOD A cross-sectional study was conducted on 203 women of reproductive age group, residing in the Moradabad district. Repetitive readings were taken after a time interval of a minimum of 1 month for determining the impact of regular screening. The entire data collection process was carried out using the EzeCheck mobile app. RESULTS It was observed that the prevalence of anemia was reduced upon the second time screening and was accepted by the women population. Repetitive testing has a significant impact on reducing anemia prevalence. Also, the simplified non-invasive technology for estimating the hemoglobin values, makes the user more comfortable to take the test. CONCLUSION Non-invasive devices should be used regularly to keep track of hemoglobin levels which will help in the effective treatment of anemia. The mobile app-based testing could help to easily evaluate the reports of the patients from any remote location with instant result interpretation and health assistance.
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Affiliation(s)
| | - Chaitali Roy
- EzeRx Health Tech Private Limited, Bhubaneswar, India
| | - Komal Agarwal
- EzeRx Health Tech Private Limited, Bhubaneswar, India
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245
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Ooi SL, Micalos PS, Kim J, Pak SC. Rice bran arabinoxylan compound as a natural product for cancer treatment - an evidence-based assessment of the effects and mechanisms. PHARMACEUTICAL BIOLOGY 2024; 62:367-393. [PMID: 38745507 PMCID: PMC11097709 DOI: 10.1080/13880209.2024.2349042] [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: 11/10/2023] [Accepted: 04/14/2024] [Indexed: 05/16/2024]
Abstract
CONTEXT Rice bran arabinoxylan compound (RBAC) is a natural immunomodulator with anticancer properties. OBJECTIVE This study critically evaluates the available evidence on the biological pathways of RBAC and its effects on cancer treatment. METHODS This secondary analysis of a scoping review includes studies evaluating the mechanisms of RBAC on healthy or malignant cells, animal models, or humans for cancer prevention or treatment. Data from randomized controlled trials on survival and quality of life outcomes were subjectd to meta analysis. RESULTS The evidence synthesis was based on 38 articles. RBAC exhibited antitumor properties by promoting apoptosis and restoring immune function in cancer patients to enhance inflammatory and cytotoxic responses to block tumorigenesis. RBAC works synergistically with chemotherapeutic agents by upregulating drug transport. In a clinical trial, combining RBAC with chemoembolization in treating liver cancer showed improved response, reduced recurrence rates, and prolonged survival. RBAC also augments the endogenous antioxidant system to prevent oxidative stress and protect against radiation side effects. In addition, RBAC has chemoprotective effects. Animals and humans have exhibited reduced toxicity and side effects from chemotherapy. Meta analysis indicates that RBAC treatment increases the survival odds by 4.02-times (95% CI: 1.67, 9.69) in the first year and 2.89-times (95% CI: 1.56, 5.35) in the second year. CONCLUSION RBAC is a natural product with immense potential in cancer treatment. Additional research is needed to characterize, quantify, and standardize the active ingredients in RBAC responsible for the anticancer effects. More well-designed, large-scale clinical trials are required to substantiate the treatment efficacies further.
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Affiliation(s)
- Soo Liang Ooi
- School of Dentistry and Medical Sciences, Charles Sturt University, Bathurst,Australia
| | - Peter S. Micalos
- School of Dentistry and Medical Sciences, Charles Sturt University, Port Macquarie, Australia
| | - Jeanman Kim
- STR Biotech Co. Ltd, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Sok Cheon Pak
- School of Dentistry and Medical Sciences, Charles Sturt University, Bathurst,Australia
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246
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Longo M, Greco E, Listorti I, Varricchio MT, Litwicka K, Arrivi C, Mencacci C, Greco P. Telomerase activity, telomere length, and the euploidy rate of human embryos. Gynecol Endocrinol 2024; 40:2373742. [PMID: 38946430 DOI: 10.1080/09513590.2024.2373742] [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: 03/20/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND Telomeres maintain chromosome stability, while telomerase counteracts their progressive shortening. Telomere length varies between cell types, with leukocyte telomere length (LTL) decreasing with age. Reduced telomerase activity has been linked to reproductive issues in females, such as low pregnancy rates and premature ovarian failure, with recent studies indicating correlations between telomere length in granulosa cells and IVF outcomes. OBJECTIVES The study aims to explore the relationship between telomere length, telomerase activity, and euploid blastocyst rate in infertile women undergoing IVF/ICSI PGT-A cycles. METHODS This prospective study involves 108 patients undergoing controlled ovarian stimulation and PGT-A. Telomere length and telomerase activity were measured in peripheral mononuclear cells and granulosa cells (GC), respectively. RESULTS The telomere repeat copy number to single gene copy number ratio (T/S) results respectively 0.6 ± 0.8 in leukocytes and 0.7 ± 0.9 in GC. An inverse relationship was found between LTL and the patient's age (p < .01). A higher aneuploid rate was noticed in patients with short LTL, with no differences in ovarian reserve markers (p = .15), number of oocytes retrieved (p = .33), and number of MII (p = 0.42). No significant association was noticed between telomere length in GC and patients' age (p = 0.95), in ovarian reserve markers (p = 0.32), number of oocytes retrieved (p = .58), number of MII (p = .74) and aneuploidy rate (p = .65). CONCLUSION LTL shows a significant inverse correlation with patient age and higher aneuploidy rates. Telomere length in GCs does not correlate with patient age or reproductive outcomes, indicating differential telomere dynamics between leukocytes and granulosa cells.
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Affiliation(s)
- Maria Longo
- Department of Medical and Surgical Sciences of the Mother, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Ermanno Greco
- Center for Reproductive Medicine, Casa di Cura Privata Villa Mafalda, Rome, Italy
- Department of Obstetrician and Gynecology, Saint Camillus International University of Health and Medical Sciences (Unicamillus), Rome, Italy
| | - Ilaria Listorti
- Center for Reproductive Medicine, Casa di Cura Privata Villa Mafalda, Rome, Italy
| | | | - Katerina Litwicka
- Center for Reproductive Medicine, Casa di Cura Privata Villa Mafalda, Rome, Italy
| | - Cristiana Arrivi
- Center for Reproductive Medicine, Casa di Cura Privata Villa Mafalda, Rome, Italy
| | - Cecilia Mencacci
- Center for Reproductive Medicine, Casa di Cura Privata Villa Mafalda, Rome, Italy
| | - Pierfrancesco Greco
- Center for Reproductive Medicine, Casa di Cura Privata Villa Mafalda, Rome, Italy
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Hasan MZ, Claus M, Krüger N, Reusing S, Gall E, Bade-Döding C, Braun A, Watzl C, Uhrberg M, Walter L. SARS-CoV-2 infection induces adaptive NK cell responses by spike protein-mediated induction of HLA-E expression. Emerg Microbes Infect 2024; 13:2361019. [PMID: 38804979 PMCID: PMC11212573 DOI: 10.1080/22221751.2024.2361019] [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: 04/05/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
HLA-E expression plays a central role for modulation of NK cell function by interaction with inhibitory NKG2A and stimulatory NKG2C receptors on canonical and adaptive NK cells, respectively. Here, we demonstrate that infection of human primary lung tissue with SARS-CoV-2 leads to increased HLA-E expression and show that processing of the peptide YLQPRTFLL from the spike protein is primarily responsible for the strong, dose-dependent increase of HLA-E. Targeting the peptide site within the spike protein revealed that a single point mutation was sufficient to abrogate the increase in HLA-E expression. Spike-mediated induction of HLA-E differentially affected NK cell function: whereas degranulation, IFN-γ production, and target cell cytotoxicity were enhanced in NKG2C+ adaptive NK cells, effector functions were inhibited in NKG2A+ canonical NK cells. Analysis of a cohort of COVID-19 patients in the acute phase of infection revealed that adaptive NK cells were induced irrespective of the HCMV status, challenging the paradigm that adaptive NK cells are only generated during HCMV infection. During the first week of hospitalization, patients exhibited a selective increase of early NKG2C+CD57- adaptive NK cells whereas mature NKG2C+CD57+ cells remained unchanged. Further analysis of recovered patients suggested that the adaptive NK cell response is primarily driven by a wave of early adaptive NK cells during acute infection that wanes once the infection is cleared. Together, this study suggests that NK cell responses to SARS-CoV-2 infection are majorly influenced by the balance between canonical and adaptive NK cells via the HLA-E/NKG2A/C axis.
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Affiliation(s)
- Mohammad Zahidul Hasan
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
- PhD Program Molecular Biology of Cells, GGNB, Georg August University, Göttingen, Germany
| | - Maren Claus
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Nadine Krüger
- Platform Infection Models, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Sarah Reusing
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Eline Gall
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | | | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine, Member of the German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hannover, Germany
- Institute of Immunology, Medical School Hannover, Hannover, Germany
| | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund, Dortmund, Germany
| | - Markus Uhrberg
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz-Institute for Primate Research, Göttingen, Germany
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248
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [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: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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249
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Irani D, Tandon D, Bansal V, Patil A, Balasinor N, Singh D. Correlation between sperm DNA fragmentation and methylation in male partners of couples with idiopathic recurrent pregnancy loss. Syst Biol Reprod Med 2024; 70:164-173. [PMID: 38913941 DOI: 10.1080/19396368.2024.2363209] [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: 08/04/2023] [Accepted: 05/24/2024] [Indexed: 06/26/2024]
Abstract
With ∼50% recurrent pregnancy loss cases being termed idiopathic (iRPL), understanding of contribution of male factors to iRPL is still lacking. Higher prevalence of sperm DNA fragmentation index (DFI) and lower sperm 5-methylcytosine (5-mC) levels have been previously reported in male partners of iRPL couples and shed light on importance of the male gamete in maintenance of a successful pregnancy. The present study aimed to determine the serum sex steroid hormone levels, sperm DFI and 5-mC and correlation between them in male partners of fertile and iRPL couples. Further, correlation between sperm DFI and 5-mC with semen parameters and paternal age in both groups were determined. 36 male partners of fertile couples and 45 male partners of women experiencing iRPL were enrolled for this study and semen and blood samples were collected. Serum testosterone and estradiol levels were measured by ELISA; sperm DFI and global 5-mC were determined by TUNEL assay and ELISA respectively. Significantly higher serum testosterone levels were noted in the iRPL group (p = 0.028). Incidence of sperm DNA fragmentation was found to be higher in the iRPL study group but with no significance difference. No significant differences in sperm 5-mC values were noted. Upon correlation analysis within both groups, strong significant negative correlation of sperm DFI % and 5-mC % was observed in the control group (p < 0.001) but not the iRPL group (p = 0.249). Hence, we infer that with lower 5-mC levels in sperm genome, there is a higher incidence of sperm DFI in fertile men. However, this trend is not noted in men of iRPL group which could possibly be due to other underlying epigenetic alterations in genomic regions probably unsusceptible to fragmentation. On the other hand, no significant correlations of semen parameters, testosterone, estradiol and paternal age with sperm DFI and 5-mC were noted in both groups.
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Affiliation(s)
- Delna Irani
- Department of Neuroendocrinology, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Deepti Tandon
- Department of Clinical Research, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Vandana Bansal
- Department of Obstetrics and Gynaecology, Nowrosjee Wadia Maternity Hospital, Mumbai, India
| | - Anushree Patil
- Department of Clinical Research, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Nafisa Balasinor
- Department of Neuroendocrinology, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
| | - Dipty Singh
- Department of Neuroendocrinology, ICMR - National Institute for Research in Reproductive and Child Health, Mumbai, India
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Lai TH, Hwang JS, Ngo QN, Lee DK, Kim HJ, Kim DR. A comparative assessment of reference genes in mouse brown adipocyte differentiation and thermogenesis in vitro. Adipocyte 2024; 13:2330355. [PMID: 38527945 PMCID: PMC10965104 DOI: 10.1080/21623945.2024.2330355] [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: 11/15/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Adipogenic differentiation and thermogenesis in brown adipose tissue (BAT) undergo dynamic processes, altering phenotypes and gene expressions. Proper reference genes in gene expression analysis are crucial to mitigate experimental variances and ensure PCR efficacy. Unreliable reference genes can lead to erroneous gene expression quantification, resulting in data misinterpretation. This study focused on identifying suitable reference genes for mouse brown adipocyte research, utilizing brown adipocytes from the Ucp1-luciferase ThermoMouse model. Comparative analysis of gene expression data under adipogenesis and thermogenesis conditions was conducted, validating 13 housekeeping genes through various algorithms, including DeltaCq, BestKeeper, geNorm, Normfinder, and RefFinder. Tbp and Rer1 emerged as optimal references for Ucp1 and Pparg expression in brown adipogenesis, while Tbp and Ubc were ideal for the expression analysis of these target genes in thermogenesis. Conversely, certain conventional references, including Actb, Tubb5, and Gapdh, proved unstable as reference genes under both conditions. These findings stress the critical consideration of reference gene selection in gene expression analysis within specific biological systems to ensure accurate conclusions.
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Affiliation(s)
- Trang Huyen Lai
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Jin Seok Hwang
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Quang Nhat Ngo
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
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