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He X, Zhang Z, Hu M, Lin X, Weng X, Lu J, Fang L, Chen X. Liquiritin Alleviates Inflammation in Lipopolysaccharide-Induced Human Corneal Epithelial Cells. Curr Eye Res 2024; 49:930-941. [PMID: 38767463 DOI: 10.1080/02713683.2024.2353263] [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: 01/02/2024] [Revised: 04/09/2024] [Accepted: 05/04/2024] [Indexed: 05/22/2024]
Abstract
PURPOSE This research was designed to elucidate the anti-inflammatory impacts of liquiritin on lipopolysaccharide (LPS)-activated human corneal epithelial cells (HCECs). METHODS The Cell Counting kit-8 (CCK-8) assay was adopted to assess cell viability. The enzyme-linked immunosorbent assay (ELISA) was used to detect the secretion levels of the proinflammatory cytokines IL-6, IL-8, and TNF-α. Transcriptome analysis was conducted to identify the genes that exhibited differential expression between different treatment. The model group included cells treated with LPS (10 µg/mL), the treatment group comprised cells treated with liquiritin (80 µM) and LPS (10 µg/mL), and the control group consisted of untreated cells. To further validate the expression levels of the selected genes, including CSF2, CXCL1, CXCL2, CXCL8, IL1A, IL1B, IL24, IL6, and LTB, quantitative real-time PCR was performed. The expression of proteins related to the Akt/NF-κB signaling pathway was assessed through western blot analysis. NF-κB nuclear translocation was evaluated through immunofluorescence staining. RESULTS The secretion of IL-6, IL-8, and TNF-α in LPS-induced HCECs was significantly downregulated by liquiritin. Based on the transcriptome analysis, the mRNA expression of pro-inflammatory cytokines, namely IL-6, IL-8, IL-1β, IL-24, TNF-α, and IL-1α was overproduced by LPS stimulation, and suppressed after liquiritin treatment. Furthermore, the Western blot results revealed a remarkable reduction in the phosphorylation degrees of NF-κB p65, IκB, and Akt upon treatment with liquiritin. Additionally, immunofluorescence analysis confirmed liquiritin's inhibition of LPS-induced p65 nuclear translocation. CONCLUSIONS Collectively, these findings imply that liquiritin suppresses the expression of proinflammatory cytokines, and the anti-inflammatory impacts of liquiritin may be caused by its repression of the Akt/NF-κB signaling pathway in LPS-induced HCECs. These data indicate that liquiritin could provide a potential therapeutic application for inflammation-associated corneal diseases.
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Affiliation(s)
- Xian He
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
- Key Laboratory of Safety Evaluation of Medical Devices of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Ziyang Zhang
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
| | - Meili Hu
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
| | - Xinyi Lin
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
| | - Xu Weng
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
| | - Jiajun Lu
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
| | - Li Fang
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
- Key Laboratory of Safety Evaluation of Medical Devices of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Xianhua Chen
- Zhejiang Institute of Medical Device Supervision and Testing, Hangzhou, Zhejiang Province, China
- Key Laboratory of Safety Evaluation of Medical Devices of Zhejiang Province, Hangzhou, Zhejiang Province, China
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Zeng Z, Ma Y, Hu L, Tan B, Liu P, Wang Y, Xing C, Xiong Y, Du H. OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing. Nat Commun 2024; 15:5983. [PMID: 39013860 PMCID: PMC11252408 DOI: 10.1038/s41467-024-50194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Single-cell sequencing is frequently affected by "omission" due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly "omitted" cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of "omitted" cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.
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Affiliation(s)
- Zehua Zeng
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, China.
| | - Yuqing Ma
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province, China
- Institute of Biopharmaceutics and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong Province, China
| | - Lei Hu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Bowen Tan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, China
| | - Peng Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yixuan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Cencan Xing
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, China.
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun-Yat-Sen University, Guangzhou, Guangdong, China.
| | - Hongwu Du
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China.
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, China.
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Xu Y, Yu F, Feng W, Wei J, Su S, Li J, Hua G, Li W, Tang Y. Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases. Brief Funct Genomics 2024:elae030. [PMID: 38984674 DOI: 10.1093/bfgp/elae030] [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: 04/11/2024] [Revised: 06/02/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024] Open
Abstract
At present, public databases house an extensive repository of transcriptome data, with the volume continuing to grow at an accelerated pace. Utilizing these data effectively is a shared interest within the scientific community. In this study, we introduced a novel strategy that harnesses SNPs and InDels identified from transcriptome data, combined with sample metadata from databases, to effectively screen for molecular markers correlated with traits. We utilized 228 transcriptome datasets of Eriocheir sinensis from the NCBI database and employed the Genome Analysis Toolkit software to identify 96 388 SNPs and 20 645 InDels. Employing the genome-wide association study analysis, in conjunction with the gender information from databases, we identified 3456 sex-biased SNPs and 639 sex-biased InDels. The KOG and KEGG annotations of the sex-biased SNPs and InDels revealed that these genes were primarily involved in the metabolic processes of E. sinensis. Combined with SnpEff annotation and PCR experimental validation, a highly sex-biased SNP located in the Kelch domain containing 4 (Klhdc4) gene, CHR67-6415071, was found to alter the splicing sites of Klhdc4, generating two splice variants, Klhdc4_a and Klhdc4_b. Additionally, Klhdc4 exhibited robust expression across the ovaries, testes, and accessory glands. The sex-biased SNPs and InDels identified in this study are conducive to the development of unisexual cultivation methods for E. sinensis, and the alternative splicing event caused by the sex-biased SNP in Klhdc4 may serve as a potential mechanism for sex regulation in E. sinensis. The analysis strategy employed in this study represents a new direction for the rational exploitation and utilization of transcriptome data in public databases.
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Affiliation(s)
- Yuanfeng Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Fan Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenrong Feng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jia Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianlin Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guoan Hua
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou 225309, China
| | - Wenjing Li
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou 225309, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214128, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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Nguyen LD, Sengupta S, Cho K, Floru A, George RE, Krichevsky AM. Novel miRNA-inducing drugs enable differentiation of retinoic acid-resistant neuroblastoma cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597584. [PMID: 38895399 PMCID: PMC11185630 DOI: 10.1101/2024.06.05.597584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tumor cell heterogeneity in neuroblastoma, a pediatric cancer arising from neural crest-derived progenitor cells, poses a significant clinical challenge. In particular, unlike adrenergic (ADRN) neuroblastoma cells, mesenchymal (MES) cells are resistant to chemotherapy and retinoid therapy and thereby significantly contribute to relapses and treatment failures. Previous research suggested that overexpression or activation of miR-124, a neurogenic microRNA with tumor suppressor activity, can induce the differentiation of retinoic acid-resistant neuroblastoma cells. Leveraging our established screen for miRNA modulatory small molecules, we validated PP121, a dual inhibitor of tyrosine and phosphoinositide kinases, as a robust inducer of miR-124. A combination of PP121 and miR-132-inducing bufalin synergistically arrests proliferation, induces differentiation, and prolongs the survival of differentiated MES SK-N-AS cells for 8 weeks. RNA- seq and deconvolution analyses revealed a collapse of the ADRN core regulatory circuitry (CRC) and the emergence of novel CRCs associated with chromaffin cells and Schwann cell precursors. Using a similar protocol, we differentiated and maintained other MES neuroblastoma, as well as glioblastoma cells, over 16 weeks. In conclusion, our novel protocol suggests a promising treatment for therapy-resistant cancers of the nervous system. Moreover, these long-lived, differentiated cells provide valuable models for studying mechanisms underlying differentiation, maturation, and senescence.
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Luo YM, Liu SS, Zhao M, Wei W, Yao JX, Sun JH, Cao Y, Li H. Crosstalk among Oxidative Stress, Autophagy, and Apoptosis in the Protective Effects of Ginsenoside Rb1 on Brain Microvascular Endothelial Cells: A Mixed Computational and Experimental Study. Curr Med Sci 2024; 44:578-588. [PMID: 38853191 DOI: 10.1007/s11596-024-2858-2] [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: 08/29/2023] [Accepted: 02/28/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE Brain microvascular endothelial cells (BMECs) were found to shift from their usually inactive state to an active state in ischemic stroke (IS) and cause neuronal damage. Ginsenoside Rb1 (GRb1), a component derived from medicinal plants, is known for its pharmacological benefits in IS, but its protective effects on BMECs have yet to be explored. This study aimed to investigate the potential protective effects of GRb1 on BMECs. METHODS An in vitro oxygen-glucose deprivation/reperfusion (OGD/R) model was established to mimic ischemia-reperfusion (I/R) injury. Bulk RNA-sequencing data were analyzed by using the Human Autophagy Database and various bioinformatic tools, including gene set enrichment analysis (GSEA), Gene Ontology (GO) classification and enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction network analysis, and molecular docking. Experimental validation was also performed to ensure the reliability of our findings. RESULTS Rb1 had a protective effect on BMECs subjected to OGD/R injury. Specifically, GRb1 was found to modulate the interplay between oxidative stress, apoptosis, and autophagy in BMECs. Key targets such as sequestosome 1 (SQSTM1/p62), autophagy related 5 (ATG5), and hypoxia-inducible factor 1-alpha (HIF-1α) were identified, highlighting their potential roles in mediating the protective effects of GRb1 against IS-induced damage. CONCLUSION GRbl protects BMECs against OGD/R injury by influencing oxidative stress, apoptosis, and autophagy. The identification of SQSTM1/p62, ATG5, and HIF-1α as promising targets further supports the potential of GRb1 as a therapeutic agent for IS, providing a foundation for future research into its mechanisms and applications in IS treatment.
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Affiliation(s)
- Yi-Miao Luo
- Department of Geriatrics, Peking University Traditional Chinese Medicine Clinical Medical School (Xiyuan), Beijing, 100901, China
- Department of Integration of Chinese and Western Medicine, Peking University Health Science Center, Beijing, 100191, China
| | - Shu-Sen Liu
- School of Pharmacy, Harbin University of Commerce, Harbin, 150028, China
| | - Ming Zhao
- Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, 100901, China
| | - Wei Wei
- Wangjing Hospital, China Academy of Chinese Medical Science, Beijing, 100102, China
| | - Jiu-Xiu Yao
- Wangjing Hospital, China Academy of Chinese Medical Science, Beijing, 100102, China
| | - Jia-Hui Sun
- Wangjing Hospital, China Academy of Chinese Medical Science, Beijing, 100102, China
| | - Yu Cao
- Xiyuan Hospital, China Academy of Chinese Medical Science, Beijing, 100901, China.
| | - Hao Li
- Department of Geriatrics, Peking University Traditional Chinese Medicine Clinical Medical School (Xiyuan), Beijing, 100901, China.
- Department of Integration of Chinese and Western Medicine, Peking University Health Science Center, Beijing, 100191, China.
- Wangjing Hospital, China Academy of Chinese Medical Science, Beijing, 100102, China.
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Kumari P, Kaur M, Dindhoria K, Ashford B, Amarasinghe SL, Thind AS. Advances in long-read single-cell transcriptomics. Hum Genet 2024:10.1007/s00439-024-02678-x. [PMID: 38787419 DOI: 10.1007/s00439-024-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The scRNA-Seq protocols developed for long-read sequencing platforms overcome these limitations by enabling the characterization of full-length transcripts. Long-read scRNA-Seq techniques initially suffered from comparatively poor accuracy compared to short read scRNA-Seq. However, with improvements in accuracy, accessibility, and cost efficiency, long-reads are gaining popularity in the field of scRNA-Seq. This review details the advances in long-read scRNA-Seq, with an emphasis on library preparation protocols and downstream bioinformatics analysis tools.
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Affiliation(s)
- Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Manmeet Kaur
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Bruce Ashford
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia
| | - Shanika L Amarasinghe
- Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G, Royal Parade, Parkville, VIC, 3025, Australia
| | - Amarinder Singh Thind
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia.
- The School of Chemistry and Molecular Bioscience (SCMB), University of Wollongong, Loftus St, Wollongong, NSW, 2500, Australia.
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Li S, Zhang T, Sun X, Li X. Construction of an Immunogenic Cell Death-Related Gene Signature and Genetic Subtypes for Predicting Prognosis, Immune Microenvironments, and Drug Sensitivity in Hepatocellular Carcinoma. J Inflamm Res 2024; 17:2427-2444. [PMID: 38681068 PMCID: PMC11049185 DOI: 10.2147/jir.s451800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/29/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Immunogenic cell death (ICD) is a type of regulated cell death that modifies the immune response by releasing DAMPs or danger signals. Herein, we aimed to develop an ICD-related predictive model for patients with hepatocellular carcinoma (HCC) and investigate its applicability for predicting prognostic outcomes and immunotherapeutic responses. Methods Differentially expressed genes of ICD were identified in the HCC and normal liver samples. A prognostic risk model and a nomogram containing clinicopathological features were created. To validate the effectiveness of the model, an external dataset was used. Clinical characteristics, prognosis, tumor mutation burden, immune microenvironments, biological function and chemotherapeutic drug sensitivity were evaluated for different genetic subtypes and risk groups. Results A total of 35 ICD-related genes (ICDRGs) were identified between HCC and normal samples, 11 of which were significantly associated with overall survival (OS) in HCC patients. Four different genetic subtypes were formed and eight ICDRGs were selected to develop a risk prognostic model. The risk scores were shown to be an independent prognostic factor for HCC and positively correlated with pathological severity. Patients in the high-risk group had a higher frequency of TP53 mutations, increased expression of immune checkpoints and human leukocyte antigen genes. The inhibitory concentrations of chemotherapeutic drugs differed in different populations. Conclusion In this study, we developed an ICDRG risk model and demonstrated its applicability in predicting survival outcomes, immune and chemotherapeutic responses in HCC patients. ICDRGs are expected to be used as novel biomarkers in the medical decision-making of HCC.
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Affiliation(s)
- Shuo Li
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
- Institute of Liver Diseases, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Tingyu Zhang
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
- Institute of Liver Diseases, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Xin Sun
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
- Institute of Liver Diseases, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Xiaoke Li
- Department of Gastroenterology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
- Institute of Liver Diseases, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
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Mao S, Wang Y, Chao N, Zeng L, Zhang L. Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals immune suppression subtypes and establishes a novel signature for determining the prognosis in lung adenocarcinoma. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00948-4. [PMID: 38616208 DOI: 10.1007/s13402-024-00948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer with lower survival rates. Recent advancements in targeted therapies and immunotherapies targeting immune checkpoints have achieved remarkable success, there is still a large percentage of LUAD that lacks available therapeutic options. Due to tumor heterogeneity, the diagnosis and treatment of LUAD are challenging. Exploring the biology of LUAD and identifying new biomarker and therapeutic targets options are essential. METHOD We performed single-cell RNA sequencing (scRNA-seq) of 6 paired primary and adjacent LUAD tissues, and integrative omics analysis of the scRNA-seq, bulk RNA-seq and whole-exome sequencing data revealed molecular subtype characteristics. Our experimental results confirm that CDC25C gene can serve as a potential marker for poor prognosis in LUAD. RESULTS We investigated aberrant gene expression in diverse cell types in LUAD via the scRNA-seq data. Moreover, multi-omics clustering revealed four subgroups defined by transcriptional profile and molecular subtype 4 (MS4) with poor survival probability, and immune cell infiltration signatures revealed that MS4 tended to be the immunosuppressive subtype. Our study revealed that the CDC25C gene can be a distinct prognostic biomarker that indicates immune infiltration levels and response to immunotherapy in LUAD patients. Our experimental results concluded that CDC25C expression affects lung cancer cell invasion and migration, might play a key role in regulating Epithelial-Mesenchymal Transition (EMT) pathways. CONCLUSIONS Our multi-omics result revealed a comprehensive set of molecular attributes associated with prognosis-related genes in LUAD at the cellular and tissue level. Identification of a subtype of immunosuppressive TME and prognostic signature for LUAD. We identified the cell cycle regulation gene CDC25C affects lung cancer cell invasion and migration, which can be used as a potential biomarker for LUAD.
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Affiliation(s)
- Shengqiang Mao
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yilong Wang
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ningning Chao
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Lingyan Zeng
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Li Zhang
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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Bühring S, Brunner A, Heeb K, Mergard MP, Schmauck G, Jacob S. An array of signal-specific MoYpd1 isoforms determines full virulence in the pathogenic fungus Magnaporthe oryzae. Commun Biol 2024; 7:265. [PMID: 38438487 PMCID: PMC10912366 DOI: 10.1038/s42003-024-05941-z] [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: 10/04/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Magnaporthe oryzae is placed first on a list of the world's top ten plant pathogens with the highest scientific and economic importance. The locus MGG_07173 occurs only once in the genome of M. oryzae and encodes the phosphotransfer protein MoYpd1p, which plays an important role in the high osmolarity glycerol (HOG) signaling pathway for osmoregulation. Originating from this locus, at least three MoYPD1 isoforms are produced in a signal-specific manner. The transcript levels of these MoYPD1-isoforms were individually affected by external stress. Salt (KCI) stress raised MoYPD1_T0 abundance, whereas osmotic stress by sorbitol elevates MoYPD1_T1 levels. In line with this, signal-specific nuclear translocation of green fluorescent protein-fused MoYpd1p isoforms in response to stress was observed. Mutant strains that produce only one of the MoYpd1p isoforms are less virulent, suggesting a combination thereof is required to invade the host successfully. In summary, we demonstrate signal-specific production of MoYpd1p isoforms that individually increase signal diversity and orchestrate virulence in M. oryzae.
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Affiliation(s)
- Sri Bühring
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Antonia Brunner
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Klemens Heeb
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Marius-Peter Mergard
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Greta Schmauck
- Johannes Gutenberg-University Mainz, Microbiology and Biotechnology at the Institute of Molecular Physiology, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Stefan Jacob
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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Li Y, Wang B, Sun W, Kong C, Ding J, Hu F, Li J, Chen X, Lu S. Construction of circ_0071922-miR-15a-5p-mRNA network in intervertebral disc degeneration by RNA-sequencing. JOR Spine 2024; 7:e1275. [PMID: 38222808 PMCID: PMC10782064 DOI: 10.1002/jsp2.1275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/25/2023] [Accepted: 07/19/2023] [Indexed: 01/16/2024] Open
Abstract
Background Low back pain (LBP) is the main factor of global disease burden. Intervertebral disc degeneration (IVDD) has long been known as the leading reason of LBP. Increasing studies have verified that circular RNAs (circRNAs)-microRNAs (miRNAs)-mRNAs network is widely involved in the pathological processes of IVDD. However, no study was made to demonstrate the circRNAs-mediated ferroptosis, oxidative stress, extracellular matrix metabolism, and immune response in IVDD. Methods We collected 3 normal and 3 degenerative nucleus pulposus tissues to conduct RNA-sequencing to identify the key circRNAs and miRNAs in IVDD. Bioinformatics analysis was then conducted to construct circRNAs-miRNAs-mRNAs interaction network associated with ferroptosis, oxidative stress, extracellular matrix metabolism, and immune response. We also performed animal experiments to validate the therapeutic effects of key circRNAs in IVDD. Results We found that circ_0015435 was most obviously upregulated and circ_0071922 was most obviously downregulated in IVDD using RNA-sequencing. Then we observed that hsa-miR-15a-5p was the key downstream of circ_0071922, and hsa-miR-15a-5p was the top upregulated miRNA in IVDD. Bioinformatics analysis was conducted to predict that 56 immunity-related genes, 29 ferroptosis-related genes, 23 oxidative stress-related genes and 8 ECM-related genes are the targets mRNAs of hsa-miR-15a-5p. Then we constructed a ceRNA network encompassing 24 circRNAs, 6 miRNAs, and 101 mRNAs. Additionally, we demonstrated that overexpression of circ_0071922 can alleviate IVDD progression in a rat model. Conclusions The findings of this study suggested that circ_0071922-miR-15a-5p-mRNA signaling network might affect IVDD by modulating the nucleus pulposus cells ferroptosis, oxidative stress, ECM metabolism, and immune response, which is an effective therapeutic targets of IVDD.
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Affiliation(s)
- Yongjin Li
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Baobao Wang
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Wenzhi Sun
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Chao Kong
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Junzhe Ding
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Feng Hu
- Spine Center, Department of Orthopaedics, The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Jianhua Li
- Department of OrthopedicsTianjin Haihe HospitalTianjinChina
| | - Xiaolong Chen
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Shibao Lu
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
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11
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Zhou B, Zhou N, Liu Y, Dong E, Peng L, Wang Y, Yang L, Suo H, Tao J. Identification and validation of CCR5 linking keloid with atopic dermatitis through comprehensive bioinformatics analysis and machine learning. Front Immunol 2024; 15:1309992. [PMID: 38476235 PMCID: PMC10927814 DOI: 10.3389/fimmu.2024.1309992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
There is sufficient evidence indicating that keloid is strongly associated with atopic dermatitis (AD) across ethnic groups. However, the molecular mechanism underlying the association is not fully understood. The aim of this study is to discover the underlying mechanism of the association between keloid and AD by integrating comprehensive bioinformatics techniques and machine learning methods. The gene expression profiles of keloid and AD were downloaded from the Gene Expression Omnibus (GEO) database. A total of 449 differentially expressed genes (DEGs) were found to be shared in keloid and AD using the training datasets of GEO (GSE158395 and GSE121212). The hub genes were identified using the protein-protein interaction network and Cytoscape software. 20 of the most significant hub genes were selected, which were mainly involved in the regulation of the inflammatory and immune response. Through two machine learning algorithms of LASSO and SVM-RFE, CCR5 was identified as the most important key gene. Subsequently, upregulated CCR5 gene expression was confirmed in validation GEO datasets (GSE188952 and GSE32924) and clinical samples of keloid and AD. Immune infiltration analysis showed that T helper (Th) 1, 2 and 17 cells were significantly enriched in the microenvironment of both keloid and AD. Positive correlations were found between CCR5 and Th1, Th2 and Th17 cells. Finally, two TFs of CCR5, NR3C2 and YY1, were identified, both of which were downregulated in keloid and AD tissues. Our study firstly reveals that keloid and AD shared common inflammatory and immune pathways. Moreover, CCR5 plays a key role in the pathogenesis association between keloid and AD. The common pathways and key genes may shed light on further mechanism research and targeted therapy, and may provide therapeutic interventions of keloid with AD.
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Affiliation(s)
- Bin Zhou
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Nuoya Zhou
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Yan Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Enzhu Dong
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Lianqi Peng
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Yifei Wang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Liu Yang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Huinan Suo
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
| | - Juan Tao
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, China
- Hubei Engineering Research Center for Skin Repair and Theranostics, Wuhan, Hubei, China
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12
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Westrin KJ, Kretzschmar WW, Emanuelsson O. ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs. BMC Bioinformatics 2024; 25:54. [PMID: 38302873 PMCID: PMC10836024 DOI: 10.1186/s12859-024-05663-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstruct transcript isoforms. We address this issue by constructing an assembly pipeline whose main purpose is to produce a comprehensive set of transcript isoforms. RESULTS We present the de novo transcript isoform assembler ClusTrast, which takes short read RNA-seq data as input, assembles a primary assembly, clusters a set of guiding contigs, aligns the short reads to the guiding contigs, assembles each clustered set of short reads individually, and merges the primary and clusterwise assemblies into the final assembly. We tested ClusTrast on real datasets from six eukaryotic species, and showed that ClusTrast reconstructed more expressed known isoforms than any of the other tested de novo assemblers, at a moderate reduction in precision. For recall, ClusTrast was on top in the lower end of expression levels (<15% percentile) for all tested datasets, and over the entire range for almost all datasets. Reference transcripts were often (35-69% for the six datasets) reconstructed to at least 95% of their length by ClusTrast, and more than half of reference transcripts (58-81%) were reconstructed with contigs that exhibited polymorphism, measuring on a subset of reliably predicted contigs. ClusTrast recall increased when using a union of assembled transcripts from more than one assembly tool as primary assembly. CONCLUSION We suggest that ClusTrast can be a useful tool for studying isoforms in species without a reliable reference genome, in particular when the goal is to produce a comprehensive transcriptome set with polymorphic variants.
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Affiliation(s)
- Karl Johan Westrin
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65, Solna, Sweden
| | - Warren W Kretzschmar
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65, Solna, Sweden
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine (HERM), Karolinska Institute, 141 52, Flemingsberg, Sweden
| | - Olof Emanuelsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65, Solna, Sweden.
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Zhu KL, Su F, Yang JR, Xiao RW, Wu RY, Cao MY, Ling XL, Zhang T. TP53 to mediate immune escape in tumor microenvironment: an overview of the research progress. Mol Biol Rep 2024; 51:205. [PMID: 38270700 PMCID: PMC10811008 DOI: 10.1007/s11033-023-09097-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Increasing evidence suggests that key cancer-causing driver genes continue to exert a sustained influence on the tumor microenvironment (TME), highlighting the importance of immunotherapeutic targeting of gene mutations in governing tumor progression. TP53 is a prominent tumor suppressor that encodes the p53 protein, which controls the initiation and progression of different tumor types. Wild-type p53 maintains cell homeostasis and genomic instability through complex pathways, and mutant p53 (Mut p53) promotes tumor occurrence and development by regulating the TME. To date, it has been wildly considered that TP53 is able to mediate tumor immune escape. Herein, we summarized the relationship between TP53 gene and tumors, discussed the mechanism of Mut p53 mediated tumor immune escape, and summarized the progress of applying p53 protein in immunotherapy. This study will provide a basic basis for further exploration of therapeutic strategies targeting p53 protein.
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Affiliation(s)
- Kai-Li Zhu
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Fei Su
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Jing-Ru Yang
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Ruo-Wen Xiao
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Rui-Yue Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Meng-Yue Cao
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Xiao-Ling Ling
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Tao Zhang
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
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14
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Lin H, Zhang M, Hu M, Zhang Y, Jiang W, Tang W, Ouyang Y, Jiang L, Mi Y, Chen Z, He P, Zhao G, Ouyang X. Emerging applications of single-cell profiling in precision medicine of atherosclerosis. J Transl Med 2024; 22:97. [PMID: 38263066 PMCID: PMC10804726 DOI: 10.1186/s12967-023-04629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/14/2023] [Indexed: 01/25/2024] Open
Abstract
Atherosclerosis is a chronic, progressive, inflammatory disease that occurs in the arterial wall. Despite recent advancements in treatment aimed at improving efficacy and prolonging survival, atherosclerosis remains largely incurable. In this review, we discuss emerging single-cell sequencing techniques and their novel insights into atherosclerosis. We provide examples of single-cell profiling studies that reveal phenotypic characteristics of atherosclerosis plaques, blood, liver, and the intestinal tract. Additionally, we highlight the potential clinical applications of single-cell analysis and propose that combining this approach with other techniques can facilitate early diagnosis and treatment, leading to more accurate medical interventions.
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Affiliation(s)
- Huiling Lin
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
- Department of Physiology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Ming Zhang
- Affiliated Qingyuan Hospital, Guangzhou Medical University (Qingyuan People's Hospital), Qingyuan, 511518, Guangdong, China
| | - Mi Hu
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - Yangkai Zhang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - WeiWei Jiang
- Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wanying Tang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - Yuxin Ouyang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China
| | - Liping Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yali Mi
- Affiliated Qingyuan Hospital, Guangzhou Medical University (Qingyuan People's Hospital), Qingyuan, 511518, Guangdong, China
| | - Zhi Chen
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Pingping He
- Department of Nursing, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Guojun Zhao
- Affiliated Qingyuan Hospital, Guangzhou Medical University (Qingyuan People's Hospital), Qingyuan, 511518, Guangdong, China.
| | - Xinping Ouyang
- Department of Physiology, Medical College, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, University of South China, Hengyang, 421001, Hunan, China.
- Department of Physiology, School of Medicine, Hunan Normal University, Changsha, 410081, Hunan, China.
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, 410081, Hunan, Changsha, China.
- The Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, 410081, Hunan, Changsha, China.
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15
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Su Z, Yao C, Tipper J, Yang L, Xu X, Chen X, Bao G, He B, Xu X, Zheng Y. Nanostrategy of Targeting at Embryonic Trophoblast Cells Using CuO Nanoparticles for Female Contraception. ACS NANO 2023; 17:25185-25204. [PMID: 38088330 DOI: 10.1021/acsnano.3c08267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Effective contraceptives have been comprehensively adopted by women to prevent the negative consequences of unintended pregnancy for women, families, and societies. With great contributions of traditional hormonal drugs and intrauterine devices (IUDs) to effective female contraception by inhibiting ovulation and deactivating sperm, their long-standing side effects on hormonal homeostasis and reproductive organs for females remain concerns. Herein, we proposed a nanostrategy for female contraceptives, inducing embryonic trophoblast cell death using nanoparticles to prevent embryo implantation. Cupric oxide nanoparticles (CuO NPs) were adopted in this work to verify the feasibility of the nanostrategy and its contraceptive efficacy. We carried out the in vitro assessment on the interaction of CuO NPs with trophoblast cells using the HTR8/SVneo cell line. The results showed that the CuO NPs were able to be preferably uptaken into cells and induced cell damage via a variety of pathways including oxidative stress, mitochondrial damage, DNA damage, and cell cycle arrest to induce cell death of apoptosis, ferroptosis, and cuproptosis. Moreover, the key regulatory processes and the key genes for cell damage and cell death caused by CuO NPs were revealed by RNA-Seq. We also conducted in vivo experiments using a rat model to examine the contraceptive efficacy of both the bare CuO NPs and the CuO/thermosensitive hydrogel nanocomposite. The results demonstrated that the CuO NPs were highly effective for contraception. There was no sign of disrupting the homeostasis of copper and hormone, or causing inflammation and organ damage in vivo. In all, this nanostrategy exhibited huge potential for contraceptive development with high biosafety, efficacy, clinical translation, nonhormonal style, and on-demand for women.
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Affiliation(s)
- Zhenning Su
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Cancan Yao
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Joanne Tipper
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Lijun Yang
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Xiangbo Xu
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
| | - Xihua Chen
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
| | - Guo Bao
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
| | - Bin He
- NHC Key Laboratory of Reproductive Health Engineering Technology Research, Department of Reproduction Physiology, National Research Institute for Family Planning, Beijing 100081, China
| | - Xiaoxue Xu
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, New South Wales 2007, Australia
- School of Science, Western Sydney University, Sydney, New South Wales 2751, Australia
| | - Yufeng Zheng
- School of Materials Science and Engineering, Peking University, Beijing 100871, China
- International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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16
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Qin Y, Yan G, Qiao Y, Wang D, Tang C. Identification of hub genes based on integrated analysis of single-cell and microarray transcriptome in patients with pulmonary arterial hypertension. BMC Genomics 2023; 24:788. [PMID: 38110868 PMCID: PMC10729354 DOI: 10.1186/s12864-023-09892-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a devastating chronic cardiopulmonary disease without an effective therapeutic approach. The underlying molecular mechanism of PAH remains largely unexplored at single-cell resolution. METHODS Single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database (GSE210248) was included and analyzed comprehensively. Additionally, microarray transcriptome data including 15 lung tissue from PAH patients and 11 normal samples (GSE113439) was also obtained. Seurat R package was applied to process scRNA-seq data. Uniform manifold approximation and projection (UMAP) was utilized for dimensionality reduction and cluster identification, and the SingleR package was performed for cell annotation. FindAllMarkers analysis and ClusterProfiler package were applied to identify differentially expressed genes (DEGs) for each cluster in GSE210248 and GSE113439, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) were used for functional enrichment analysis of DEGs. Microenvironment Cell Populations counter (MCP counter) was applied to evaluate the immune cell infiltration. STRING was used to construct a protein-protein interaction (PPI) network of DEGs, followed by hub genes selection through Cytoscape software and Veen Diagram. RESULTS Nineteen thousand five hundred seventy-six cells from 3 donors and 21,896 cells from 3 PAH patients remained for subsequent analysis after filtration. A total of 42 cell clusters were identified through UMAP and annotated by the SingleR package. 10 cell clusters with the top 10 cell amounts were selected for consequent analysis. Compared with the control group, the proportion of adipocytes and fibroblasts was significantly reduced, while CD8+ T cells and macrophages were notably increased in the PAH group. MCP counter revealed decreased distribution of CD8+ T cells, cytotoxic lymphocytes, and NK cells, as well as increased infiltration of monocytic lineage in PAH lung samples. Among 997 DEGs in GSE113439, module 1 with 68 critical genes was screened out through the MCODE plug-in in Cytoscape software. The top 20 DEGs in each cluster of GSE210248 were filtered out by the Cytohubba plug-in using the MCC method. Eventually, WDR43 and GNL2 were found significantly increased in PAH and identified as the hub genes after overlapping these DEGs from GSE210248 and GSE113439. CONCLUSION WDR43 and GNL2 might provide novel insight into revealing the new molecular mechanisms and potential therapeutic targets for PAH.
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Affiliation(s)
- Yuhan Qin
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Gaoliang Yan
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People's Republic of China.
| | - Yong Qiao
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Dong Wang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Chengchun Tang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, People's Republic of China.
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17
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Zhang Y, Hu L, Ren G, Zeng Y, Zhao X, Zhong C. Distinct regulatory machineries underlying divergent chromatin landscapes distinguish innate lymphoid cells from T helper cells. Front Immunol 2023; 14:1271879. [PMID: 38106414 PMCID: PMC10722145 DOI: 10.3389/fimmu.2023.1271879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Innate lymphoid cells (ILCs), as the innate counterpart of CD4+ T helper (Th) cells, play crucial roles in maintaining tissue homeostasis. While the ILC subsets and their corresponding Th subsets demonstrate significant similarities in core programming related to effector function and regulatory mechanisms, their principal distinctions, given their innate and adaptive lymphocyte nature, remain largely unknown. In this study, we have employed an integrative analysis of 294 bulk RNA-sequencing results across all ILC and Th subsets, using scRNA-seq algorithms. Consequently, we identify two genesets that predominantly differentiate ILCs from Th cells, as well as three genesets that distinguish various immune responses. Furthermore, through chromatin accessibility analysis, we find that the ILC geneset tends to rely on specific transcriptional regulation at promoter regions compared with the Th geneset. Additionally, we observe that ILCs and Th cells are under differential transcriptional regulation. For example, ILCs are under stronger regulation by multiple transcription factors, including RORα, GATA3, and NF-κB. Otherwise, Th cells are under stronger regulation by AP-1. Thus, our findings suggest that, despite the acknowledged similarities in effector functions between ILC subsets and corresponding Th subsets, the underlying regulatory machineries still exhibit substantial distinctions. These insights provide a comprehensive understanding of the unique roles played by each cell type during immune responses.
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Affiliation(s)
- Yime Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Luni Hu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
| | - Guanqun Ren
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
| | - Yanyu Zeng
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xingyu Zhao
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Chao Zhong
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
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18
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Beňačka R, Szabóová D, Guľašová Z, Hertelyová Z, Radoňak J. Non-Coding RNAs in Human Cancer and Other Diseases: Overview of the Diagnostic Potential. Int J Mol Sci 2023; 24:16213. [PMID: 38003403 PMCID: PMC10671391 DOI: 10.3390/ijms242216213] [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: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are abundant single-stranded RNA molecules in human cells, involved in various cellular processes ranging from DNA replication and mRNA translation regulation to genome stability defense. MicroRNAs are multifunctional ncRNA molecules of 18-24 nt in length, involved in gene silencing through base-pair complementary binding to target mRNA transcripts. piwi-interacting RNAs are an animal-specific class of small ncRNAs sized 26-31 nt, responsible for the defense of genome stability via the epigenetic and post-transcriptional silencing of transposable elements. Long non-coding RNAs are ncRNA molecules defined as transcripts of more than 200 nucleotides, their function depending on localization, and varying from the regulation of cell differentiation and development to the regulation of telomere-specific heterochromatin modifications. The current review provides recent data on the several forms of small and long non-coding RNA's potential to act as diagnostic, prognostic or therapeutic target for various human diseases.
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Affiliation(s)
- Roman Beňačka
- Department of Pathophysiology, Medical Faculty, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (R.B.); (D.S.)
| | - Daniela Szabóová
- Department of Pathophysiology, Medical Faculty, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (R.B.); (D.S.)
| | - Zuzana Guľašová
- Center of Clinical and Preclinical Research MEDIPARK, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (Z.G.); (Z.H.)
| | - Zdenka Hertelyová
- Center of Clinical and Preclinical Research MEDIPARK, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (Z.G.); (Z.H.)
| | - Jozef Radoňak
- 1st Department of Surgery, Faculty of Medicine, Louis Pasteur University Hospital (UNLP) and Pavol Jozef Šafarik University, 04011 Košice, Slovakia
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Wang C, Bai Y, Li T, Liu J, Wang Y, Ju S, Yao W, Xiong B, Zhou G. Beneficial effects of ginkgetin on improving nonalcoholic steatohepatitis characterized by bulk and single-cell RNA sequencing analysis. Front Pharmacol 2023; 14:1267445. [PMID: 37860111 PMCID: PMC10582714 DOI: 10.3389/fphar.2023.1267445] [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: 07/26/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Background and aims: Nonalcoholic steatohepatitis (NASH) has become one of the major causes of cirrhosis and liver failure. However, there are currently no approved medications for managing NASH. Our study was designed to assess the effects of ginkgetin on NASH and the involved mechanisms. Methods: We constructed a mouse model of NASH by high-fat diet for 24 weeks. The effects of ginkgetin on NASH were evaluated by histological study, Western blot, and biochemical analysis. RNA Sequencing (RNA-Seq) analysis was used to investigate the alteration in gene expression and signaling pathways at bulk and single-cell levels. Results: Administration of ginkgetin resulted in a marked improvement in hepatic lipid accumulation, inflammation, and fibrosis in the NASH model. And these results were supported by bulk RNA-Seq analysis, in which the related signaling pathways and gene expression were markedly downregulated. Furthermore, single-cell RNA-Seq (scRNA-Seq) analysis revealed that the effects of ginkgetin on NASH were associated with the reprogramming of macrophages, hepatic stellate cells, and endothelial cells. Especially, ginkgetin induced a marked decrease in macrophages and a shift from pro-inflammatory to anti-inflammatory phenotype in NASH mice. And the NASH-associated macrophages (NAMs), which emerge during NASH, were also significantly downregulated by ginkgetin. Conclusion: Ginkgetin exhibits beneficial effects on improving NASH, supported by bulk and single-cell RNA-Seq. Our study may promote pharmacological therapy for NASH and raise the existent understanding of NASH.
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Affiliation(s)
- Chaoyang Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaowei Bai
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongqiang Li
- Department of Interventional Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiacheng Liu
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingliang Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuguang Ju
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yao
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Xiong
- Department of Interventional Radiology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guofeng Zhou
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Cheng D, Zhang Z, Mi Z, Tao W, Liu D, Fu J, Fan H. Deciphering the heterogeneity and immunosuppressive function of regulatory T cells in osteosarcoma using single-cell RNA transcriptome. Comput Biol Med 2023; 165:107417. [PMID: 37669584 DOI: 10.1016/j.compbiomed.2023.107417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/03/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
Osteosarcoma (OS) is a highly invasive malignant neoplasm with poor prognosis. The tumor microenvironment (TME) plays an essential role in the occurrence and development of OS. Regulatory T cells (Tregs) are known to facilitate immunosuppression, tumor progression, invasion, and metastasis. However, the effect of Tregs in the TME of OS remains unclear. In this study, single-cell RNA sequencing (scRNA-seq) data was used to identify Tregs and various other cell clusters in the TME of OS. Gene set variation analysis (GSVA) was used to investigate the signaling pathways in Tregs from OS and adjacent tissues. The CellChat and iTALK packages were used to analyze cellular communication. In addition, a prognostic model was established based on the Tregs-specific genes using bulk RNA-seq from the TARGET database, and it was verified using a Gene Expression Omnibus dataset. The pRRophetic package was used to predict drug sensitivity. Immunohistochemistry was used to verify the expression of candidate genes in OS. Based on the above methods, we showed that the OS samples were highly infiltrated with Tregs. GSVA revealed that oxidative phosphorylation, angiogenesis and mammalian target of rapamycin complex 1 (mTORC1) were highly activated in Tregs from OS compared with those from adjacent tissues. Using cellular communication analysis, we found that Tregs interacted with osteoblastic, endothelial, and myeloid cells via C-X-C motif chemokine ligand (CXCL) signaling; particularly, they strongly affected the expression of C-X-C motif chemokine receptor 4 (CXCR4) and interacted with other cell clusters through CXCL12/transforming growth factor β1 (TGFB1) to collectively enable tumor growth and progression. Subsequently, two Tregs-specific genes-CD320 and MAF-were screened through univariate, least absolute shrinkage and selection operator regression (LASSO) and multivariate analysis to construct a prognostic model, which showed excellent prognostic accuracy in two independent cohorts. In addition, drug sensitivity analysis demonstrated that OS patients at high Tregs risk were sensitive to sunitinib, sorafenib, and axitinib. We also used immunohistochemistry to validate that CD320 and MAF were significantly upregulated in OS tissues compared with adjacent tissues. Overall, this study reveals the heterogeneity of Tregs in the OS TME, providing new insights into the invasion and treatment of this cancer.
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Affiliation(s)
- Debin Cheng
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Zhao Zhang
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Zhenzhou Mi
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Weidong Tao
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Dong Liu
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Jun Fu
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Hongbin Fan
- Department of Orthopaedic Surgery, Xi Jing Hospital, The Fourth Military Medical University, Xi'an, China.
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21
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Shi X, Li J, Liu T, Zhao H, Leng H, Sun K, Feng J. Divergence of cochlear transcriptomics between reference‑based and reference‑free transcriptome analyses among Rhinolophus ferrumequinum populations. PLoS One 2023; 18:e0288404. [PMID: 37432940 DOI: 10.1371/journal.pone.0288404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Differences in gene expression within tissues can lead to differences in tissue function. Understanding the transcriptome of a species helps elucidate the molecular mechanisms underlying phenotypic divergence. According to the presence or absence of a reference genome of for a studied species, transcriptome analyses can be divided into reference‑based and reference‑free methods, respectively. Presently, comparisons of complete transcriptome analysis results between those two methods are still rare. In this study, we compared the cochlear transcriptome analysis results of greater horseshoe bats (Rhinolophus ferrumequinum) from three lineages in China with different acoustic phenotypes using reference‑based and reference‑free methods to explore their differences in subsequent analysis. The results gained by reference-based results had lower false-positive rates and were more accurate because differentially expressed genes among the three populations obtained by this method had greater reliability and a higher annotation rate. Some phenotype-related enrichment terms, including those related to inorganic molecules and proton transmembrane channels, were also obtained only by the reference-based method. However, the reference‑based method might have the limitation of incomplete information acquisition. Thus, we believe that a combination of reference‑free and reference‑based methods is ideal for transcriptome analyses. The results of our study provided a reference for the selection of transcriptome analysis methods in the future.
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Affiliation(s)
- Xiaoxiao Shi
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Tong Liu
- Department of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Hanbo Zhao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural, Shenzhen, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, Jilin, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
- Department of Life Science, Jilin Agricultural University, Changchun, Jilin, China
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22
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 164] [Impact Index Per Article: 164.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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23
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Li Y, Deng W, Wu L, Chen S, Zheng Z, Song H. Anti-Inflammatory Effects of Polyphenols from Plum ( Prunus salicina Lindl) on RAW264.7 Macrophages Induced by Monosodium Urate and Potential Mechanisms. Foods 2023; 12:254. [PMID: 36673346 PMCID: PMC9858531 DOI: 10.3390/foods12020254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/09/2023] Open
Abstract
Acute gouty arthritis is an acute inflammatory reaction caused by the deposition of monosodium urate (MSU) crystals in joints and surrounding soft tissues. Controlling inflammation is the key to preventing acute gouty arthritis. Anti-inflammatory activities and the possible molecular mechanisms of plum (Prunus salicina Lindl cv. "furong") polyphenols (PSLP) on RAW264.7 macrophage cells induced by monosodium urate were investigated. PPSF significantly inhibited the activity of inflammatory factors such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-18 (IL-18). In addition, PPSF exhibited excellent activation of superoxide dismutase (SOD) activity and reduction of intracellular reactive oxygen species (ROS) and malondialdehyde (MDA) levels in RAW264.7 macrophages. The results of global screening of all transcripts by RNA-seq revealed 8585 differentially expressed genes between the PSLP-treated group and the MUS group. From GO analysis, PSLP could affect the occurrence and development of RAW264.7 macrophage inflammation through biological processes, such as organic substance metabolism, intracellular organelles, and binding function. The regulation mechanism of PSLP on MSU-induced RAW264.7 macrophage inflammation may be achieved through the HIF-1 signaling pathway, renal cell carcinoma, the ErbB signaling pathway, and the FoxO signaling pathway. Therefore, PSLP has great prospects in the prevention of gout and similar inflammatory diseases.
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Affiliation(s)
- Yibin Li
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Research Institute of Agri-Engineering and Technology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- Key Laboratory of Subtropical Characteristic Fruits, Vegetables and Edible Fungi Processing, Ministry of Agriculture and Rural Affairs, Fuzhou 350003, China
| | - Wei Deng
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Wu
- Research Institute of Agri-Engineering and Technology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- Key Laboratory of Subtropical Characteristic Fruits, Vegetables and Edible Fungi Processing, Ministry of Agriculture and Rural Affairs, Fuzhou 350003, China
| | - Shouhui Chen
- Research Institute of Agri-Engineering and Technology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Zhipeng Zheng
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongbo Song
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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24
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O’Shaughnessy KL, McMichael BD, Sasser AL, Bell KS, Riutta C, Ford JL, Stoker TE, Grindstaff RD, Pandiri AR, Gilbert ME. Thyroid hormone action controls multiple components of cell junctions at the ventricular zone in the newborn rat brain. Front Endocrinol (Lausanne) 2023; 14:1090081. [PMID: 36843608 PMCID: PMC9950412 DOI: 10.3389/fendo.2023.1090081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/09/2023] [Indexed: 02/12/2023] Open
Abstract
Thyroid hormone (TH) action controls brain development in a spatiotemporal manner. Previously, we demonstrated that perinatal hypothyroidism led to formation of a periventricular heterotopia in developing rats. This heterotopia occurs in the posterior telencephalon, and its formation was preceded by loss of radial glia cell polarity. As radial glia mediate cell migration and originate in a progenitor cell niche called the ventricular zone (VZ), we hypothesized that TH action may control cell signaling in this region. Here we addressed this hypothesis by employing laser capture microdissection and RNA-Seq to evaluate the VZ during a known period of TH sensitivity. Pregnant rats were exposed to a low dose of propylthiouracil (PTU, 0.0003%) through the drinking water during pregnancy and lactation. Dam and pup THs were quantified postnatally and RNA-Seq of the VZ performed in neonates. The PTU exposure resulted in a modest increase in maternal thyroid stimulating hormone and reduced thyroxine (T4). Exposed neonates exhibited hypothyroidism and T4 and triiodothyronine (T3) were also reduced in the telencephalon. RNA-Seq identified 358 differentially expressed genes in microdissected VZ cells of hypothyroid neonates as compared to controls (q-values ≤0.05). Pathway analyses showed processes like maintenance of the extracellular matrix and cytoskeleton, cell adhesion, and cell migration were significantly affected by hypothyroidism. Immunofluorescence also demonstrated that collagen IV, F-actin, radial glia, and adhesion proteins were reduced in the VZ. Immunohistochemistry of integrin αvβ3 and isoforms of both thyroid receptors (TRα/TRβ) showed highly overlapping expression patterns, including enrichment in the VZ. Taken together, our results show that TH action targets multiple components of cell junctions in the VZ, and this may be mediated by both genomic and nongenomic mechanisms. Surprisingly, this work also suggests that the blood-brain and blood-cerebrospinal fluid barriers may also be affected in hypothyroid newborns.
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Affiliation(s)
- Katherine L. O’Shaughnessy
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
- *Correspondence: Katherine L. O’Shaughnessy,
| | - Benjamin D. McMichael
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
- Oak Ridge Institute for Science Education, Oak Ridge, TN, United States
| | - Aubrey L. Sasser
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
- Oak Ridge Institute for Science Education, Oak Ridge, TN, United States
| | - Kiersten S. Bell
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
- Oak Ridge Institute for Science Education, Oak Ridge, TN, United States
| | - Cal Riutta
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
- Oak Ridge Institute for Science Education, Oak Ridge, TN, United States
| | - Jermaine L. Ford
- Chemical Characterization and Exposure Division, Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Tammy E. Stoker
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
| | - Rachel D. Grindstaff
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
| | - Arun R. Pandiri
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Mary E. Gilbert
- United States Environmental Protection Agency, Public Health Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, United States
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25
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A Framework for Comparison and Assessment of Synthetic RNA-Seq Data. Genes (Basel) 2022; 13:genes13122362. [PMID: 36553629 PMCID: PMC9778097 DOI: 10.3390/genes13122362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/16/2022] Open
Abstract
The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, differential expression analysis, correlation and network studies and the optimization of data integration and normalization techniques. Here, we propose a general framework to compare synthetically generated RNA-seq data and select a data-generating tool that is suitable for a set of specific study goals. As there are multiple methods for synthetic RNA-seq data generation, researchers can use the proposed framework to make an informed choice of an RNA-seq data simulation algorithm and software that are best suited for their specific scientific questions of interest.
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26
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Holman AR, Chi NC. Fishing Out the Role of RBPMS2 in Cardiac Splicing. Circ Res 2022; 131:1001-1003. [PMID: 36454855 DOI: 10.1161/circresaha.122.321922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alyssa R Holman
- Department of Medicine (A.R.H., N.C.C.).,Biomedical Sciences Graduate Program (A.R.H.), University of California, San Diego, La Jolla, CA
| | - Neil C Chi
- Department of Medicine (A.R.H., N.C.C.).,Institute of Genomic Medicine, School of Medicine (N.C.C.), University of California, San Diego, La Jolla, CA
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27
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Dindhoria K, Monga I, Thind AS. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Funct Integr Genomics 2022; 22:1105-1112. [DOI: 10.1007/s10142-022-00915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022]
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28
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Han H, Zhuang K, Qiu Z. CLE peptides join the plant longevity club. TRENDS IN PLANT SCIENCE 2022; 27:961-963. [PMID: 35843831 DOI: 10.1016/j.tplants.2022.07.001] [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: 05/20/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Leaf senescence, the final step of leaf development, is an essential adaptive process that involves intricate regulatory networks mediated by various developmental and environmental clues. Two recent reports, by Zhang Z. et al. and Zhang Y. et al., shed light on how CLE peptides recruit reactive oxygen species (ROS) and ethylene signaling to promote plant leaf longevity.
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Affiliation(s)
- Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China.
| | - Keqing Zhuang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Ziwen Qiu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
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29
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Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect. Biomedicines 2022; 10:biomedicines10092318. [PMID: 36140419 PMCID: PMC9496268 DOI: 10.3390/biomedicines10092318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Emergence of methods interrogating gene expression at high throughput gave birth to quantitative transcriptomics, but also posed a question of inter-comparison of expression profiles obtained using different equipment and protocols and/or in different series of experiments. Addressing this issue is challenging, because all of the above variables can dramatically influence gene expression signals and, therefore, cause a plethora of peculiar features in the transcriptomic profiles. Millions of transcriptomic profiles were obtained and deposited in public databases of which the usefulness is however strongly limited due to the inter-comparison issues; (2) Methods: Dozens of methods and software packages that can be generally classified as either flexible or predefined format harmonizers have been proposed, but none has become to the date the gold standard for unification of this type of Big Data; (3) Results: However, recent developments evidence that platform/protocol/batch bias can be efficiently reduced not only for the comparisons of limited transcriptomic datasets. Instead, instruments were proposed for transforming gene expression profiles into the universal, uniformly shaped format that can support multiple inter-comparisons for reasonable calculation costs. This forms a basement for universal indexing of all or most of all types of RNA sequencing and microarray hybridization profiles; (4) Conclusions: In this paper, we attempted to overview the landscape of modern approaches and methods in transcriptomic harmonization and focused on the practical aspects of their application.
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30
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OUP accepted manuscript. Brief Funct Genomics 2022; 21:159-176. [DOI: 10.1093/bfgp/elac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
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