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Nunes S, Bastos R, Marinho AI, Vieira R, Benício I, de Noronha MA, Lírio S, Brodskyn C, Tavares NM. Recent advances in the development and clinical application of miRNAs in infectious diseases. Noncoding RNA Res 2025; 10:41-54. [PMID: 39296638 PMCID: PMC11406675 DOI: 10.1016/j.ncrna.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/06/2024] [Accepted: 09/01/2024] [Indexed: 09/21/2024] Open
Abstract
In the search for new biomarkers and therapeutic targets for infectious diseases, several molecules have been investigated. Small RNAs, known as microRNAs (miRs), are important regulators of gene expression, and have emerged as promising candidates for these purposes. MiRs are a class of small, endogenous non-coding RNAs that play critical roles in several human diseases, including host-pathogen interaction mechanisms. Recently, miRs signatures have been reported in different infectious diseases, opening new perspectives for molecular diagnosis and therapy. MiR profiles can discriminate between healthy individuals and patients, as well as distinguish different disease stages. Furthermore, the possibility of assessing miRs in biological fluids, such as serum and whole blood, renders these molecules feasible for the development of new non-invasive diagnostic and prognostic tools. In this manuscript, we will comprehensively describe miRs as biomarkers and therapeutic targets in infectious diseases and explore how they can contribute to the advance of existing and new tools. Additionally, we will discuss different miR analysis platforms to understand the obstacles and advances of this molecular approach and propose their potential clinical applications and contributions to public health.
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Affiliation(s)
- Sara Nunes
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Rana Bastos
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
| | - Ananda Isis Marinho
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
| | - Raissa Vieira
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
| | - Ingra Benício
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | | | - Sofia Lírio
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Bahiana School of Medicine and Public Health, Salvador, Brazil
| | - Cláudia Brodskyn
- Federal University of Bahia (UFBA), Salvador, Brazil
- Laboratory of Parasite-Host Interaction and Epidemiology (LaIPHE), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Instituto Nacional de Ciência e Tecnologia (INCT) Iii - Instituto de Investigação Em Imunologia, São Paulo, Brazil
| | - Natalia Machado Tavares
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia (INCT) Iii - Instituto de Investigação Em Imunologia, São Paulo, Brazil
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Zhang J, Li Z, Han J, Tian Z, Meng Q, Niu W. KLF7 enhances the invasion and migration of colorectal cancer cells via the miR-139-5p/TPD52 axis. Cancer Biol Ther 2024; 25:2385172. [PMID: 39097779 PMCID: PMC11299624 DOI: 10.1080/15384047.2024.2385172] [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: 08/22/2023] [Revised: 07/07/2024] [Accepted: 07/23/2024] [Indexed: 08/05/2024] Open
Abstract
In this study, we aimed to investigate the molecular mechanism of Krüppel-like factor 7 (KLF7) in colorectal cancer (CRC) cell invasion and migration. The expression pattern of KLF7 in CRC tissues and the correlation between KLF7 expression and clinical symptoms of CRC were analyzed. CRC cell lines were transfected with si-KLF7, followed by qRT-PCR or western blot detection of KLF7, miR-139-5p, and tumor protein D52 (TPD52) expression, cell counting kit-8 (CCK-8) assay to detect cell viability, and transwell detection of invasion and migration. Chromatin immunoprecipitation (ChIP) analyzed the enrichment KLF7 in the miR-139-5p promoter. The dual-luciferase reporter assay verified the binding relationship between KLF7 and miR-139-5p, and between miR-139-5p and TPD52. In the subcutaneous tumorigenesis experiment, tumor growth was observed and ki67-positive expression was detected. KLF7 is abundantly expressed in CRC cells KLF7 silencing inhibits CRC cell viability, invasion, and migration. KLF7 represses miR-139-5p expression by binding to the miR-139-5p promoter. miR-139-5p targets TPD52 expression. miR-13-5p inhibition or TPD52 overexpression partially counteracted the effect of KLF7 silencing in CRC cells. KLF7 silencing suppresses tumor growth in vivo. In conclusion, KLF7 suppresses miR-139-5p expression by binding to the miR-139-5p promoter, thereby upregulating TPD52 expression and enhancing CRC cell invasion and migration.
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Affiliation(s)
- Juan Zhang
- Department of External Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhihan Li
- Department of External Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jiaxu Han
- Department of External Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhongtao Tian
- Department of External Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qingyu Meng
- Department of External Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenbo Niu
- Department of External Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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Mm Yahya S, Elsayed GH. The role of MiRNA-34 family in different signaling pathways and its therapeutic options. Gene 2024; 931:148829. [PMID: 39154971 DOI: 10.1016/j.gene.2024.148829] [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: 01/19/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024]
Abstract
MiRNAs are short non-coding RNA molecules that have been shown to affect a vast number of genes at the post-transcriptional level, hence regulating several signaling pathways. Because the miRNA-34 family regulates a number of different signaling pathways, including those linked to cancer, the immune system, metabolism, cellular structure, and neurological disorders, it has garnered a great deal of attention from researchers. Members of the miRNA-34 family have been shown to inhibit tumors in a variety of cancer types. This family is also important for obesity, the cardiovascular system, and glycolysis. It's interesting to note that the miRNA-34 family is known to play a role in major depressive disorder, schizophrenia, Parkinson's disease (PD), adverse childhood experiences or trauma, regulation of stress responses, Alzheimer's disease (AD), and stress-related psychatric conditions. In this review, the expected targets of the miRNA-34 family are presented alongside the well-established targets identified by pathway analysis. Furthermore, the therapeutic potential of this miRNA family will be discussed.
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Affiliation(s)
- Shaymaa Mm Yahya
- Hormones Department, Medical Research and Clinical Studies Institute, and Stem Cell Lab, Centre of Excellence for Advanced SciencesNational Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt.
| | - Ghada H Elsayed
- Hormones Department, Medical Research and Clinical Studies Institute, and Stem Cell Lab, Centre of Excellence for Advanced SciencesNational Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
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4
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Picard M, Scott-Boyer MP, Bodein A, Leclercq M, Prunier J, Périn O, Droit A. Target repositioning using multi-layer networks and machine learning: The case of prostate cancer. Comput Struct Biotechnol J 2024; 24:464-475. [PMID: 38983753 PMCID: PMC11231507 DOI: 10.1016/j.csbj.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
The discovery of novel therapeutic targets, defined as proteins which drugs can interact with to induce therapeutic benefits, typically represent the first and most important step of drug discovery. One solution for target discovery is target repositioning, a strategy which relies on the repurposing of known targets for new diseases, leading to new treatments, less side effects and potential drug synergies. Biological networks have emerged as powerful tools for integrating heterogeneous data and facilitating the prediction of biological or therapeutic properties. Consequently, they are widely employed to predict new therapeutic targets by characterizing potential candidates, often based on their interactions within a Protein-Protein Interaction (PPI) network, and their proximity to genes associated with the disease. However, over-reliance on PPI networks and the assumption that potential targets are necessarily near known genes can introduce biases that may limit the effectiveness of these methods. This study addresses these limitations in two ways. First, by exploiting a multi-layer network which incorporates additional information such as gene regulation, metabolite interactions, metabolic pathways, and several disease signatures such as Differentially Expressed Genes, mutated genes, Copy Number Alteration, and structural variants. Second, by extracting relevant features from the network using several approaches including proximity to disease-associated genes, but also unbiased approaches such as propagation-based methods, topological metrics, and module detection algorithms. Using prostate cancer as a case study, the best features were identified and utilized to train machine learning algorithms to predict 5 novel promising therapeutic targets for prostate cancer: IGF2R, C5AR, RAB7, SETD2 and NPBWR1.
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Affiliation(s)
- Milan Picard
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Julien Prunier
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Transformation and Innovation Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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Luna-Cerralbo D, Blasco-Machín I, Adame-Pérez S, Lampaya V, Larraga A, Alejo T, Martínez-Oliván J, Broset E, Bruscolini P. A statistical-physics approach for codon usage optimisation. Comput Struct Biotechnol J 2024; 23:3050-3064. [PMID: 39188969 PMCID: PMC11345917 DOI: 10.1016/j.csbj.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024] Open
Abstract
The concept of "codon optimisation" involves adjusting the coding sequence of a target protein to account for the inherent codon preferences of a host species and maximise protein expression in that species. However, there is still a lack of consensus on the most effective approach to achieve optimal results. Existing methods typically depend on heuristic combinations of different variables, leaving the user with the final choice of the sequence hit. In this study, we propose a new statistical-physics model for codon optimisation. This model, called the Nearest-Neighbour interaction (NN) model, links the probability of any given codon sequence to the "interactions" between neighbouring codons. We used the model to design codon sequences for different proteins of interest, and we compared our sequences with the predictions of some commercial tools. In order to assess the importance of the pair interactions, we additionally compared the NN model with a simpler method (Ind) that disregards interactions. It was observed that the NN method yielded similar Codon Adaptation Index (CAI) values to those obtained by other commercial algorithms, despite the fact that CAI was not explicitly considered in the algorithm. By utilising both the NN and Ind methods to optimise the reporter protein luciferase, and then analysing the translation performance in human cell lines and in a mouse model, we found that the NN approach yielded the highest protein expression in vivo. Consequently, we propose that the NN model may prove advantageous in biotechnological applications, such as heterologous protein expression or mRNA-based therapies.
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Affiliation(s)
- David Luna-Cerralbo
- Department of Theoretical Physics, Faculty of Science, University of Zaragoza, c/ Pedro Cerbuna s/n, Zaragoza, 50009, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, c/ Mariano Esquillor s/n, Zaragoza, 50018, Spain
| | - Irene Blasco-Machín
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Susana Adame-Pérez
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Verónica Lampaya
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Ana Larraga
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Teresa Alejo
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Juan Martínez-Oliván
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Esther Broset
- Certest Pharma, Certest Biotec S.L, Polígono Industrial Río Gallego II, Calle J, 1, San Mateo de Gállego, 50840, Spain
| | - Pierpaolo Bruscolini
- Department of Theoretical Physics, Faculty of Science, University of Zaragoza, c/ Pedro Cerbuna s/n, Zaragoza, 50009, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, c/ Mariano Esquillor s/n, Zaragoza, 50018, Spain
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Alshamrani AA, Bin Salman SB, Alsaleh NB, Assiri MA, Almutairi MM, Almudimeegh S, Alwhaibi A, As Sobeai HM. miRNA-driven sensitization of breast cancer cells to Doxorubicin treatment following exposure to low dose of Zinc Oxide nanoparticles. Saudi Pharm J 2024; 32:102169. [PMID: 39318640 PMCID: PMC11421238 DOI: 10.1016/j.jsps.2024.102169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/04/2024] [Indexed: 09/26/2024] Open
Abstract
The impact of Engineered nanomaterials (ENMs) (i.e., Zinc Oxide nanoparticles (ZnO NPs)) on human health has been investigated at high and unrealistic exposure levels, overlooking the potential indirect harm of subtoxic and long exposures. Therefore, this study aimed to investigate the impacts of subtoxic concentrations of zinc oxide (ZnO NPs) on breast cancer cells' response to Doxorubicin. Zinc oxide nanoparticles caused a concentration-dependent reduction of cell viability in multiple breast cancer cell lines. A subtoxic concentration of 1.56 µg/mL (i.e., no observed adverse effect level) was used in subsequent mechanistic studies. Molecularly, miRNA profiling revealed significant downregulation of 13 oncogenic miRNAs (OncomiRs) in cells exposed to the sub-toxic dose of ZnO NPs followed by doxorubicin treatment. Our comprehensive bioinformatic analysis has identified 617 target genes enriched in ten pathways, mainly regulating gene expression and transcription, cell cycle, and apoptotic cell death. Several tumor suppressor genes emerged as validated direct targets of the 13 OncomiRs, including TFDP2, YWHAG, SMAD2, SMAD4, CDKN1A, CDKN1B, BCL2L11, and TGIF2. This study insinuates the importance of miRNAs in regulating the responsiveness of cancer cells to chemotherapy. Our findings further indicate that being exposed to environmental ENMs, even at levels below toxicity, might still modulate cancer cells' response to chemotherapy, which highlights the need to reestablish endpoints of ENM exposure and toxicity in cancer patients receiving chemotherapeutics.
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Affiliation(s)
- Ali A. Alshamrani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sami B. Bin Salman
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Nasser B. Alsaleh
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammed A. Assiri
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammed M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sultan Almudimeegh
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulrahman Alwhaibi
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Homood M. As Sobeai
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Balasubramanian S, Perumal E. Integrated in silico analysis of transcriptomic alterations in nanoparticle toxicity across human and mouse models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174897. [PMID: 39053559 DOI: 10.1016/j.scitotenv.2024.174897] [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: 05/20/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Nanoparticles, due to their exceptional physicochemical properties are used in our day-to-day environment. They are currently not regulated which might lead to increased levels in the biological systems causing adverse effects. However, the overall mechanism behind nanotoxicity remains elusive. Previously, we analysed the transcriptome datasets of copper oxide nanoparticles using in silico tools and identified IL-17, chemokine signaling pathway, and cytokine-cytokine receptor interaction as the key pathways altered. Based on the findings, we hypothesized a common pathway could be involved in transition metal oxide nanoparticles toxicity irrespective of the variables. Further, there could be unique transcriptome changes between metal oxide nanoparticles and other nanoparticles. To accomplish this, the overall transcriptome datasets of nanoparticles consisting of microarray and RNA-Seq were obtained. >90 studies for 17 different nanoparticles, performed in humans, rats, and mice were assessed. After initial screening, 24 mouse studies (with 196 datasets) and 34 human studies (with 200 datasets) were used for further analyses. The common genes that are dysregulated upon NPs exposure were identified for human and mouse datasets separately. Further, an overrepresentation functional enrichment analysis was performed. The common genes, their gene ontology, gene-gene, and protein-protein interactions were assessed. The overall results suggest that IL-17 and its related pathways might be commonly altered in nanoparticle exposure with lung as one of the major organs affected.
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Affiliation(s)
- Satheeswaran Balasubramanian
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Ekambaram Perumal
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
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Han J, Huang J, Hu J, Shi W, Wang H, Zhang W, Wang J, Shao H, Shen H, Bo H, Tao C, Wu F. miR-744-5p promotes T-cell differentiation via inhibiting STK11. Gene 2024; 926:148635. [PMID: 38830518 DOI: 10.1016/j.gene.2024.148635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
T cells utilized in adoptive T cell immunotherapy are typically activated in vitro. Although these cells demonstrate proliferation and anti-tumor activity following activation, they often face difficulties in sustaining long-term survival post-reinfusion. This issue is attributed to the induction of T cells into a terminal differentiation state upon activation, whereas early-stage differentiated T cells exhibit enhanced proliferation potential and survival capabilities. In previous study, we delineated four T cell subsets at varying stages of differentiation: TN, TSCM, TCM, and TEM, and acquired their miRNA expression profiles via high-throughput sequencing. In the current study, we performed a differential analysis of miRNA across these subsets, identifying a distinct miRNA, hsa-miR-744-5p, characterized by progressively increasing expression levels upon T cell activation. This miRNA is not expressed in TSCM but is notably present in TEM. Target genes of miR-744-5p were predicted, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, revealing that these genes predominantly associate with pathways related to the 'Wnt signaling pathway'. We established that miR-744-5p directly targets STK11, influencing its expression. Further, we investigated the implications of miR-744-5p on T cell differentiation and functionality. Overexpression of miR-744-5p in T cells resulted in heightened apoptosis, reduced proliferation, an increased proportion of late-stage differentiated T cells, and elevated secretion of the cytokine TNF-α. Moreover, post-overexpression of miR-744-5p led to a marked decline in the expression of early-stage differentiation-associated genes in T cells (CCR7, CD62L, LEF1, BCL2) and a significant rise in late-stage differentiation-associated genes (KLRG1, PDCD1, GZMB). In conclusion, our findings affirm that miR-744-5p contributes to the progressive differentiation of T cells by downregulating the STK11 gene expression.
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Affiliation(s)
- Jiayi Han
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jianqing Huang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jieming Hu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenkai Shi
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Hongqiong Wang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenfeng Zhang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jinquan Wang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Hongwei Shao
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Han Shen
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Huaben Bo
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Changli Tao
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fenglin Wu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China.
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He T, Yuan Z, Chen Q, Luo J, Mao J, Yang Y, Cao K, Yang Z. Circular RNAs mediate the regulation of maternal placental nutrient transport and fetal development by sugar-sweetened beverages. Food Res Int 2024; 193:114856. [PMID: 39160047 DOI: 10.1016/j.foodres.2024.114856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/22/2024] [Accepted: 07/29/2024] [Indexed: 08/21/2024]
Abstract
Epidemiological and experimental studies have demonstrated a strong association between maternal diet and fetal birth weight, obesity, and metabolic syndrome. We investigated the pathways and modes of action of circular RNAs (circRNAs) that mediate the regulation of maternal reproductive performance and fetal development by sugar-sweetened beverages (20 % sucrose water, SSBs) using C57BL/6J mice as a model. Results showed that SSBs significantly increased the reproductive performance (P<0.05), body weight (P<0.01), fetal birth weight (P<0.05), placental weight (P<0.01), and the expression of nutrient transporter genes in the placenta and fetal liver (P<0.05), mainly by accelerating the maternal energy metabolism during pregnancy. However, maternal serum biochemical indices, antioxidant indices, and pathological damage to the liver and placenta predicted that the mother would be at greater health risks during this period. Moreover, transcriptomics results indicated that the differentially expressed (DE) circRNAs in the placenta regulate the maternal multiple metabolic pathways and the placental nutrient transport efficiency by sponging miRNAs and forming growth factors and proteins, ultimately improving the maternal reproductive performance. In addition, we verified the reliability of the sequencing results using reverse transcription polymerase chain reaction and identified the possibility of DE circRNAs binding to nutrient transporter genes using targeting relationship prediction. Finally, we constructed a correlation network that regulates maternal placental nutrient transport based on DE circRNAs, targeted miRNAs and nutrient transport-related genes. This study will provide scientific dietary guidance for pregnant women and new research ideas for preventing and treating pregnancy complications.
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Affiliation(s)
- Tianle He
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zhidong Yuan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, School of Basic Medicine, Gannan Medical University, Ganzhou 341000, China.
| | - Qingyun Chen
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Ju Luo
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Jiani Mao
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Yulian Yang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Kai Cao
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zhenguo Yang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
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Wu H, Chen H, Ding X, Kuang X, Pang M, Liu S, Zhang Y, Wang Q, Li K, Zhang H. Identification of autophagy-related signatures in doxorubicin-induced cardiotoxicity. Toxicol Appl Pharmacol 2024; 491:117082. [PMID: 39218162 DOI: 10.1016/j.taap.2024.117082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/12/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE Doxorubicin is an antibiotic drug used clinically to treat infectious diseases and tumors. Unfortunately, it is cardiotoxic. Autophagy is a cellular self-decomposition process that is essential for maintaining homeostasis in the internal environment. Accordingly, the present study was proposed to characterize the autophagy-related signatures of doxorubicin-induced cardiotoxicity. METHODS Datasets related to doxorubicin-induced cardiotoxicity were retrieved by searching the GEO database and differentially expressed genes (DEGs) were identified. DEGs were taken to intersect with autophagy-related genes to obtain autophagy-related signatures, and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein-protein interaction (PPI) network were performed on them. Further, construction of miRNA-hub gene networks and identification of target drugs to reveal potential molecular mechanisms and therapeutic strategies. Animal models of doxorubicin-induced cardiotoxicity were constructed to validate differences in gene expression for autophagy-related signatures. RESULTS PBMC and heart samples from the GSE37260 dataset were selected for analysis. There were 995 and 2357 DEGs in PBMC and heart samples, respectively, and they had 23 intersecting genes with autophagy-related genes. RT-qPCR confirmed the differential expression of 23 intersecting genes in doxorubicin-induced cardiotoxicity animal models in general agreement with the bioinformatics results. An autophagy-related signatures consisting of 23 intersecting genes is involved in mediating processes and pathways such as autophagy, oxidative stress, apoptosis, protein ubiquitination and phosphorylation. Moreover, Akt1, Hif1a and Mapk3 are hub genes in autophagy-associated signatures and their upstream miRNAs are mainly rno-miR-1188-5p, rno-miR-150-3p and rno-miR-326-3p, and their drugs are mainly CHEMBL55802, Carboxyamidotriazole and 3-methyladenine. CONCLUSION This study identifies for the first-time autophagy-related signatures in doxorubicin's cardiotoxicity, which could provide potential molecular mechanisms and therapeutic strategies for doxorubicin-induced cardiotoxicity.
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Affiliation(s)
- Haiyan Wu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, No. 727 Jingming South Road, Kunming 650500, P.R.China; Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Haoqiang Chen
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Xiaoxue Ding
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Xiaohui Kuang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Mingjie Pang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Suijuan Liu
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Yan Zhang
- Department of Magnetic Resonance lmaging, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming, 650032, P.R. China
| | - Qian Wang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Kunzhi Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, No. 727 Jingming South Road, Kunming 650500, P.R.China.
| | - Hong Zhang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China.
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11
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Chen Q, Li X, Yang Y, Ni J, Chen J. Combined Analysis of Human and Experimental Rat Samples Identified Biomarkers for Ischemic Stroke. Mol Neurobiol 2024:10.1007/s12035-024-04512-x. [PMID: 39325100 DOI: 10.1007/s12035-024-04512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/18/2024] [Indexed: 09/27/2024]
Abstract
The genetic transcription profile and underlying molecular mechanisms of ischemic stroke (IS) remain elusive. To address this issue, four mRNA and one miRNA expression profile of rats with middle cerebral artery occlusion (MCAO) were acquired from the Gene Expression Omnibus (GEO) database. A total of 780 differentially expressed genes (DEGs) and 56 miRNAs (DEMs) were screened. Gene set and functional enrichment analysis revealed that a substantial number of immune-inflammation-related pathways were abnormally activated in IS. Through weighted gene co-expression network analysis, the turquoise module was identified as meaningful. By taking the intersection of the turquoise module genes, DEM-target genes, and all DEGs, 354 genes were subsequently obtained as key IS-related genes. Among them, six characteristic genes were identified using the least absolute shrinkage and selection operator. After validation with three external datasets, transforming growth factor beta 1 (Tgfb1) was selected as the hub gene. This finding was further confirmed by gene expression pattern analysis in both the MCAO model rats and clinical IS patients. Moreover, the expression of the hub genes exhibited a negative correlation with the modified Rankin scale score (P < 0.05). Collectively, these results expand our knowledge of the genetic profile and molecular mechanisms involved in IS and suggest that the Tgfb1 gene is a potential biomarker of this disease.
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Affiliation(s)
- Qingfa Chen
- Department of Rehabilitation, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Xiaolu Li
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530022, Guangxi, China
| | - Ye Yang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530022, Guangxi, China
| | - Jun Ni
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, Fujian, China.
| | - Jianmin Chen
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, Fujian, China.
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12
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Cuccato M, Divari S, Giannuzzi D, Grange C, Moretti R, Rinaldi A, Leroux C, Sacchi P, Cannizzo FT. Extracellular vesicle miRNome during subclinical mastitis in dairy cows. Vet Res 2024; 55:112. [PMID: 39300590 DOI: 10.1186/s13567-024-01367-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/13/2024] [Indexed: 09/22/2024] Open
Abstract
Bovine mastitis is one of the main inflammatory diseases that can affect the udder during lactation. Somatic cell counts and sometimes microbiological tests are routinely adopted during monitoring diagnostics in dairy herds. However, subclinical mastitis is challenging to identify, reducing the possibility of early treatments. The main aim of this study was to investigate the miRNome profile of extracellular vesicles isolated from milk as potential biomarkers of subclinical mastitis. Milk samples were collected from a total of 60 dairy cows during routine monitoring tests. Small RNA sequencing technology was applied to extracellular vesicles of milk samples collected from cows classified according to the somatic cell count to identify differences in the miRNome between mastitic and healthy cows. A total of 1997 miRNAs were differentially expressed between both groups. Among them, 68 miRNAs whose FDRs were < 0.05 were mostly downregulated, with only one upregulated miRNA (i.e., miR-361). Functional analysis revealed that miR-455-3p, miR-503-3p, miR-1301-3p and miR-361-5p are involved in the regulation of several biological processes related to mastitis, including immune system-related processes. This study suggests the involvement of extracellular vesicle-derived miRNAs in the regulation of mastitis. Moreover, these findings provide evidence that miRNAs from milk extracellular vesicles can be used to identify biomarkers of mastitis. However, further studies must be conducted to validate these miRNAs, especially for subclinical diagnosis.
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Affiliation(s)
- Matteo Cuccato
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Turin, Italy
| | - Sara Divari
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Turin, Italy.
| | - Diana Giannuzzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, 35020, Padua, Italy
| | - Cristina Grange
- Department of Medical Sciences, VEXTRA Facility, University of Turin, 10126, Turin, Italy
| | - Riccardo Moretti
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Turin, Italy
| | - Andrea Rinaldi
- Faculty of Biomedical Sciences, Institute of Oncology Research (IOR), Università della Svizzera Italiana (USI), 6500, Bellinzona, Switzerland
| | - Christine Leroux
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122, Saint-Genès-Champanelle, France
- Department of Food Science and Technology, University of California Davis, Davis, CA, USA
| | - Paola Sacchi
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Turin, Italy
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Bereczki Z, Benczik B, Balogh OM, Marton S, Puhl E, Pétervári M, Váczy-Földi M, Papp ZT, Makkos A, Glass K, Locquet F, Euler G, Schulz R, Ferdinandy P, Ágg B. Mitigating off-target effects of small RNAs: conventional approaches, network theory and artificial intelligence. Br J Pharmacol 2024. [PMID: 39293936 DOI: 10.1111/bph.17302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/07/2024] [Accepted: 06/17/2024] [Indexed: 09/20/2024] Open
Abstract
Three types of highly promising small RNA therapeutics, namely, small interfering RNAs (siRNAs), microRNAs (miRNAs) and the RNA subtype of antisense oligonucleotides (ASOs), offer advantages over small-molecule drugs. These small RNAs can target any gene product, opening up new avenues of effective and safe therapeutic approaches for a wide range of diseases. In preclinical research, synthetic small RNAs play an essential role in the investigation of physiological and pathological pathways as silencers of specific genes, facilitating discovery and validation of drug targets in different conditions. Off-target effects of small RNAs, however, could make it difficult to interpret experimental results in the preclinical phase and may contribute to adverse events of small RNA therapeutics. Out of the two major types of off-target effects we focused on the hybridization-dependent, especially on the miRNA-like off-target effects. Our main aim was to discuss several approaches, including sequence design, chemical modifications and target prediction, to reduce hybridization-dependent off-target effects that should be considered even at the early development phase of small RNA therapy. Because there is no standard way of predicting hybridization-dependent off-target effects, this review provides an overview of all major state-of-the-art computational methods and proposes new approaches, such as the possible inclusion of network theory and artificial intelligence (AI) in the prediction workflows. Case studies and a concise survey of experimental methods for validating in silico predictions are also presented. These methods could contribute to interpret experimental results, to minimize off-target effects and hopefully to avoid off-target-related adverse events of small RNA therapeutics.
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Affiliation(s)
- Zoltán Bereczki
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Bettina Benczik
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Olivér M Balogh
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Szandra Marton
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
| | - Eszter Puhl
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
| | - Mátyás Pétervári
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Sanovigado Kft, Budapest, Hungary
| | - Máté Váczy-Földi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Zsolt Tamás Papp
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - András Makkos
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Fabian Locquet
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gerhild Euler
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Rainer Schulz
- Physiologisches Institut, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Center for Pharmacology and Drug Research & Development, Semmelweis University, Budapest, Hungary
- HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
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Han SW, Park YH, Bice PJ, Bennett DA, Kim S, Saykin AJ, Nho K. miR-133b as a potential regulator of a synaptic NPTX2 protein in Alzheimer's disease. Ann Clin Transl Neurol 2024. [PMID: 39289904 DOI: 10.1002/acn3.52175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 09/19/2024] Open
Abstract
A synaptic protein, Neuronal Pentraxin 2 (NPTX2), has emerged as a pivotal biomarker for Alzheimer's dementia (AD). We identified candidate miRNAs targeting NPTX2 and performed association and mediation analyses using multi-omics data (N = 702). Among 44 candidate miRNAs, miR-133b was significantly associated with AD and Braak positivity. Higher miR-133b expression was also associated with higher NPTX2 gene expression and better cognition. Mediation analysis showed that miR-133b partially influences AD and cognition through the NPTX2 protein. Our integrated approach suggests a potential role of miR-133b in synaptic integrity and offers new insights into AD pathogenesis.
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Affiliation(s)
- Sang-Won Han
- Department of Neurology, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, 77 Sakju-ro, Chuncheon-si, Gangwon-do, 24253, Republic of Korea
| | - Young Ho Park
- Department of Neurology, Seoul National University Bundang Hospital and Seoul National University College of Medicine, 82, Gumi-ro 173 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Paula J Bice
- Department of Radiology and Imaging Sciences, Center for Computational Biology and Bioinformatics, Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Suite 1000, Chicago, Illinois, 60612, USA
| | - SangYun Kim
- Department of Neurology, Seoul National University Bundang Hospital and Seoul National University College of Medicine, 82, Gumi-ro 173 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Center for Computational Biology and Bioinformatics, Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Center for Computational Biology and Bioinformatics, Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
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15
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Sajanti A, Li Y, Hellström S, Cao Y, Girard R, Umemori J, Frantzén J, Koskimäki F, Lyne SB, Falter J, Rantamäki T, Takala R, Posti JP, Roine S, Kolehmainen S, Srinath A, Jänkälä M, Puolitaival J, Rahi M, Rinne J, Castrén E, Koskimäki J. Brain plasticity and neuroinflammatory protein biomarkers with circulating MicroRNAs as predictors of acute brain injury outcome - A prospective cohort study. J Neurol Sci 2024; 464:123169. [PMID: 39126731 DOI: 10.1016/j.jns.2024.123169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/17/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Brain recovery mechanisms after injuries like aneurysmal subarachnoid hemorrhage (aSAH), ischemic stroke (IS), and traumatic brain injury (TBI) involve brain plasticity, synaptic regeneration, and neuroinflammation. We hypothesized that serum levels of the p75 neurotrophic receptor (p75NTR) and associated signaling proteins, as well as differentially expressed (DE) microRNAs, could predict recovery outcomes irrespective of injury type. METHODS A prospective patient cohort with ischemic stroke (IS, n = 30), aneurysmal subarachnoid hemorrhage (aSAH, n = 31), and traumatic brain injury (TBI, n = 13) were evaluated (total n = 74). Serum samples were collected at two post-injury intervals (early: 1-3 days, late: 4-8 days), and outcomes were assessed after three months using the modified Rankin Scale (mRS), categorizing outcomes as favorable (mRS 0-3) or unfavorable (mRS 4-6). Six proteins were measured using ELISAs: p75NTR, NGF, sortilin, IL1β, TNFα, and cyclophilin. DE microRNAs were identified using DESeq2, and their target genes were predicted. Serum molecules between patients with differing outcomes were compared using a Kolmogorov-Smirnov test, 2-tailed t-test and multivariate linear discriminant analysis (LDA). RESULTS Favorable (n = 46) and unfavorable (n = 28) outcome cohorts were balanced with age and sex (p = 0.25 and 0.63). None of the studied proteins correlated with age. Combinatory LDA of the six protein biomarkers indicated strong prognostic value for favorable outcomes (OR 2.09; AUC = 70.3%, p = 0.0058). MicroRNA expression changes over time were identified in the aSAH, TBI, and IS groups (p < 0.05, FDR corrected). Twenty-three microRNAs were commonly DE across all brain injury groups when comparing favorable and unfavorable outcomes (p < 0.05). LDA of four microRNAs targeting the studied proteins showed high prognostic accuracy (OR 11.7; AUC = 94.1%, p = 0.016). CONCLUSIONS The combined prognostic microRNA and protein biomarker models demonstrated accurate outcome prognostication across diverse injury types, implying the presence of a common recovery mechanism. DE microRNAs were found to target the studied molecules, suggesting a potential mechanistic role in recovery. Further investigation is warranted to study these molecules in prognostication, as well as therapeutic targets for enhancing recovery.
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Affiliation(s)
- Antti Sajanti
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland
| | - Yan Li
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, United States of America
| | - Santtu Hellström
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland
| | - Ying Cao
- Department of Radiation Oncology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL 60637, United States of America
| | - Juzoh Umemori
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland; Gene and Cell Technology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland
| | - Janek Frantzén
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland
| | - Fredrika Koskimäki
- Neurocenter, Acute Stroke Unit, Turku University Hospital, P.O. Box 52, FI-20521 Turku, Finland
| | - Seán B Lyne
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Johannes Falter
- Department of Neurosurgery, University Medical Center of Regensburg, Regensburg 93042, Germany
| | - Tomi Rantamäki
- Laboratory of Neurotherapeutics, Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland; SleepWell Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
| | - Riikka Takala
- Perioperative Services, Intensive Care and Pain Medicine and Department of Anaesthesiology and Intensive Care, Turku University Hospital and University of Turku, P.O. Box52, FI-20521 Turku, Finland
| | - Jussi P Posti
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland
| | - Susanna Roine
- Neurocenter, Acute Stroke Unit, Turku University Hospital, P.O. Box 52, FI-20521 Turku, Finland
| | - Sulo Kolehmainen
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
| | - Abhinav Srinath
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL 60637, United States of America
| | - Miro Jänkälä
- Department of Neurosurgery, Oulu University Hospital, Box 25, 90029 OYS, Finland
| | - Jukka Puolitaival
- Department of Neurosurgery, Oulu University Hospital, Box 25, 90029 OYS, Finland
| | - Melissa Rahi
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland
| | - Jaakko Rinne
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland
| | - Eero Castrén
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland
| | - Janne Koskimäki
- Neurocenter, Department of Neurosurgery, Turku University Hospital and University of Turku, P.O. Box 52, FI-20521 Turku, Finland; Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, FI-00014 Helsinki, Finland; Department of Neurosurgery, Oulu University Hospital, Box 25, 90029 OYS, Finland.
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Lin H, Yao T, Ding H, Chu J, Yuan D, Ping F, Chen F, Liu X. Identification and functional characterization of differentially expressed circRNAs in high glucose treated endothelial cells: Construction of circRNA-miRNA-mRNA network. Heliyon 2024; 10:e37028. [PMID: 39281534 PMCID: PMC11399645 DOI: 10.1016/j.heliyon.2024.e37028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/31/2024] [Accepted: 08/26/2024] [Indexed: 09/18/2024] Open
Abstract
Background Endothelial dysfunction is a complication of diabetes mellitus (DM), characterized by impaired endothelial function in both microvessels and macrovessels, closely linked to atherosclerosis (AS). Endothelial dysfunction, characterized by impaired endothelial cell (EC) function, is a pivotal factor in AS and DM. Circular RNAs (circRNAs) are endogenous non-coding RNAs that can act as competing endogenous RNAs (ceRNAs) and regulate gene expression. However, the role of circRNAs in ECs dysfunction and AS under high glucose (HG) condition remains elusive. Methods We performed high-throughput sequencing to identify differentially expressed (DE) circRNAs in human umbilical vein endothelial cells (HUVEC) exposed to HG, one risk factors of endothelial dysfunction and AS. We then validated eight candidate circRNAs by qRT-PCR and functional analysis, directing our attention to hsa_circ_0122319. Moreover, microarray analysis identified the differential expression profiles of miRNAs and mRNAs regulated by hsa_circ_0122319. Subsequently, the construction of the ceRNAs network employed bioinformatic analysis and Cytoscape software. Furthermore, the role of the PI3K-Akt signaling pathway in regulating ceRNAs was evaluated. Results We detected 917 DE circRNAs in HG treated HUVEC. The parental genes of these circRNAs were enriched in cell cycle, cellular senescence and endocytosis related pathways. The differential expression of hsa_circ_0122319 was confirmed to be most obvious at the cellular level and in clinical samples by qPCR experiments. After overexpression of hsa_circ_0122319, 49 DE miRNAs and 459 DE mRNAs were identified using microarray analysis. Subsequently, a ceRNAs network was constructed, comprising hsa_circ_0122319, 8 miRNAs, and 41 mRNAs. Conclusion In summary, our study delves into the role of circRNAs in endothelial dysfunction associated with DM and AS. Through high-throughput sequencing and validation, we identified hsa_circ_0122319 as a pivotal regulator of ECs function under HG conditions. It also showed that hsa_circ_0123319 has the potential to serve as a biomarker for DM and its vascular complications, and provides new evidence for future exploration of the intricate molecular mechanisms of endothelial dysfunction in the progression of DM and AS.
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Affiliation(s)
- Hao Lin
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Tongqing Yao
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Haoran Ding
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Jiapeng Chu
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Deqiang Yuan
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Fan Ping
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Fei Chen
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
| | - Xuebo Liu
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, 200092, Shanghai, China
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Biase FH, Moorey SE, Schnuelle JG, Rodning S, Ortega MS, Spencer TE. Altered microRNA composition in the uterine lumen fluid in cattle (Bos taurus) pregnancies initiated by artificial insemination or transfer of an in vitro produced embryo. J Anim Sci Biotechnol 2024; 15:130. [PMID: 39267128 PMCID: PMC11397056 DOI: 10.1186/s40104-024-01083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/29/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are presented in the uterine lumen of many mammals, and in vitro experiments have determined that several miRNAs are important for the regulation of endometrial and trophoblast functions. Our aim was to identify and contrast the miRNAs present in extracellular vesicles (EVs) in the uterine lumen fluid (ULF) at the onset of attachment in cattle pregnancies (gestation d 18) initiated by artificial insemination (AI) or by the transfer of an in vitro-produced blastocyst (IVP-ET). A third group had no conceptus after the transfer of an IVP embryo. RESULTS The abundance of 263 annotated miRNAs was quantified in the EVs collected from ULF. There was an increase in the transcript abundance of 20 miRNAs in the ULF EVs from the AI pregnant group, while 4 miRNAs had a lower abundance relative to the group not containing a conceptus. Additionally, 4 miRNAs were more abundant in ULF EVs in the AI pregnant group relative to IVP-ET group (bta-mir-17, bta-mir-7-3, MIR7-1, MIR18A). Specific miRNAs in the ULF EVs were co-expressed with messenger RNAs expressed in extra-embryonic tissues and endometrium, including genes that are known to be their targets. CONCLUSIONS The results provide biological insights into the participation of miRNAs in the regulation of trophoblast proliferation and differentiation, as well as in endometrium receptivity. The knowledge that in vitro cultured embryos can contribute to the altered abundance of specific miRNAs in the uterine lumen can lead to the development of corrective approaches to reduce conceptus losses during the first month of pregnancy in cattle.
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Affiliation(s)
- Fernando H Biase
- School of Animal Sciences, Virginia Polytechnic Institute and State University, 175 W Campus Dr, Blacksburg, VA, 24061, USA.
| | - Sarah E Moorey
- Department of Animal Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Julie G Schnuelle
- Department of Clinical Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Soren Rodning
- Department of Animal Science, Auburn University, Auburn, AL, 36849, USA
| | - Martha Sofia Ortega
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
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18
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Helin TA, Lemponen M, Immonen K, Lakkisto P, Joutsi-Korhonen L. Circulating microRNAs targeting coagulation and fibrinolysis in patients with severe COVID-19. Thromb J 2024; 22:80. [PMID: 39237986 PMCID: PMC11375984 DOI: 10.1186/s12959-024-00649-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 08/26/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Coronavirus-19 disease (COVID-19) frequently causes coagulation disturbances. Data remains limited on the effects of microRNAs (miRNAs) on coagulation during COVID-19 infection. We aimed to analyze the comprehensive miRNA profile as well as coagulation markers and blood count in hospitalized COVID-19 patients. METHODS Citrated plasma samples from 40 patients (24 men and 16 women) hospitalized for COVID-19 were analyzed. Basic coagulation tests, von Willebrand factor (VWF), ADAMTS13, blood count, C-reactive protein, and 27 miRNAs known to associate with thrombosis or platelet activation were analyzed. MiRNAs were analyzed using quantitative reverse transcription polymerase chain reaction (RT qPCR), with 10 healthy controls serving as a comparator. RESULTS Among the patients, 15/36 (41%) had platelet count of over 360 × 109/L and 10/36 (28%) had low hemoglobin of < 100 g/L, while 26/37 (72%) had high VWF of over 200 IU/dL. Patients had higher levels of the miRNAs miR-27b-3p, miR-320a-3p, miR-320b-3p, and miR-424-5p, whereas levels of miR-103a-3p and miR-145-5p were lower than those in healthy controls. In total, 11 miRNAs were associated with platelet count. Let-7b-3p was associated with low hemoglobin levels of < 100 g/L. miR-24-3p, miR-27b-3p, miR-126-3p, miR-145-5p and miR-338-5p associated with high VWF. CONCLUSION COVID-19 patients differentially express miRNAs with target genes involved in fibrinolysis inhibition, coagulation activity, and increased inflammatory response. These findings support the notion that COVID-19 widely affects hemostasis, including platelets, coagulation and fibrinolysis.
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Affiliation(s)
- Tuukka A Helin
- HUS Diagnostic Center, Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, POB 720, Helsinki, 00029, Finland.
| | - Marja Lemponen
- HUS Diagnostic Center, Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, POB 720, Helsinki, 00029, Finland
| | - Katariina Immonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Päivi Lakkisto
- HUS Diagnostic Center, Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, POB 720, Helsinki, 00029, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Lotta Joutsi-Korhonen
- HUS Diagnostic Center, Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, POB 720, Helsinki, 00029, Finland
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19
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Koh YW, Han JH, Haam S, Lee HW. Machine learning-driven prediction of brain metastasis in lung adenocarcinoma using miRNA profile and target gene pathway analysis of an mRNA dataset. Clin Transl Oncol 2024; 26:2296-2308. [PMID: 38568412 DOI: 10.1007/s12094-024-03474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/21/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND Brain metastasis (BM) is common in lung adenocarcinoma (LUAD) and has a poor prognosis, necessitating predictive biomarkers. MicroRNAs (MiRNAs) promote cancer cell growth, infiltration, and metastasis. However, the relationship between the miRNA expression profiles and BM occurrence in patients with LUAD remains unclear. METHODS We conducted an analysis to identify miRNAs in tissue samples that exhibited different expression levels between patients with and without BM. Using a machine learning approach, we confirmed whether the miRNA profile could be a predictive tool for BM. We performed pathway analysis of miRNA target genes using a matched mRNA dataset. RESULTS We selected 25 miRNAs that consistently exhibited differential expression between the two groups of 32 samples. The 25-miRNA profile demonstrated a strong predictive potential for BM in both Group 1 and Group 2 and the entire dataset (area under the curve [AUC] = 0.918, accuracy = 0.875 in Group 1; AUC = 0.867, accuracy = 0.781 in Group 2; and AUC = 0.908, accuracy = 0.875 in the entire group). Patients predicted to have BM, based on the 25-miRNA profile, had lower survival rates. Target gene analysis of miRNAs suggested that BM could be induced through the ErbB signaling pathway, proteoglycans in cancer, and the focal adhesion pathway. Furthermore, patients predicted to have BM based on the 25-miRNA profile exhibited higher expression of the epithelial-mesenchymal transition signature, TWIST, and vimentin than those not predicted to have BM. Specifically, there was a correlation between EGFR mRNA levels and BM. CONCLUSIONS This 25-miRNA profile may serve as a biomarker for predicting BM in patients with LUAD.
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Affiliation(s)
- Young Wha Koh
- Department of Pathology, Ajou University School of Medicine, 206 Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea.
| | - Jae-Ho Han
- Department of Pathology, Ajou University School of Medicine, 206 Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Seokjin Haam
- Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon-si, Republic of Korea
| | - Hyun Woo Lee
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon-si, Republic of Korea
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20
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Varik I, Zou R, Bellavia A, Rosenberg K, Sjunnesson Y, Hallberg I, Holte J, Lenters V, Van Duursen M, Pedersen M, Svingen T, Vermeulen R, Salumets A, Damdimopoulou P, Velthut-Meikas A. Reduced ovarian cholesterol and steroid biosynthesis along with increased inflammation are associated with high DEHP metabolite levels in human ovarian follicular fluids. ENVIRONMENT INTERNATIONAL 2024; 191:108960. [PMID: 39173238 DOI: 10.1016/j.envint.2024.108960] [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: 05/28/2024] [Revised: 07/22/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
The plasticizer di(2-ethylhexyl) phthalate (DEHP) is known to have endocrine-disrupting properties mediated by its many metabolites that form upon exposure in biological systems. In a previous study, we reported an inverse association between DEHP metabolites in the human ovarian follicular fluid (FF) and the responsiveness of the follicles to controlled ovarian stimulation during in vitro fertilization (IVF) treatments. Here, we explored this association further through molecular analysis of the ovarian FF samples. Ninety-six IVF patients from Swedish (N = 48) and Estonian (N = 48) infertility clinics were selected from the previous cohort (N = 333) based on the molar sum of DEHP metabolites in their FF samples to arrive at "high" (mean 7.7 ± SD 2.3 nM, N = 48) and "low" (0.8 ± 0.4 nM, N = 48) exposure groups. Extracellular miRNA levels and concentrations of 15 steroid hormones were measured across FF samples. In addition, FF somatic cells, available for the Estonian patients, were used for RNA sequencing. Differential expression (DE) and interactions between miRNA and mRNA networks revealed that the expression levels of genes in the cholesterol biosynthesis and steroidogenesis pathways were significantly decreased in the high compared to the low DEHP group. In addition, the DE miRNAs were predicted to target key enzymes within these pathways (FDR < 0.05). A decreased 17-OH-progesterone to progesterone ratio was observed in the FF of the high DEHP group (p < 0.05). Additionally, the expression levels of genes associated with inflammatory processes were elevated in the FF somatic cells, and a computational cell-type deconvolution analysis suggested an increased immune cell infiltration into the high DEHP follicles (p < 0.05). In conclusion, elevated DEHP levels in FF were associated with a significantly altered follicular milieu within human ovaries, involving a pro-inflammatory environment and reduced cholesterol metabolism, including steroid synthesis. These results contribute to our understanding of the molecular mechanisms of female reprotoxic effects of DEHP.
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Affiliation(s)
- Inge Varik
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Runyu Zou
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Andrea Bellavia
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kristine Rosenberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Nova Vita Clinic, Tallinn, Estonia
| | - Ylva Sjunnesson
- Department of Clinical Sciences, Division of Reproduction, The Center for Reproductive Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ida Hallberg
- Department of Clinical Sciences, Division of Reproduction, The Center for Reproductive Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Animal Biosciences, Division of Reproduction, The Center for Reproductive Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Holte
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden; Carl von Linné Clinic, Uppsala, Sweden
| | - Virissa Lenters
- Amsterdam Institute for Life and Environment, Section Environmental Health and Toxicology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Majorie Van Duursen
- Amsterdam Institute for Life and Environment, Section Environmental Health and Toxicology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Mikael Pedersen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Andres Salumets
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; Competence Center on Health Technologies, Tartu, Estonia; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Sweden; Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pauliina Damdimopoulou
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Sweden
| | - Agne Velthut-Meikas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
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21
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Sokouti B. The identification of biomarkers for Alzheimer's disease using a systems biology approach based on lncRNA-circRNA-miRNA-mRNA ceRNA networks. Comput Biol Med 2024; 179:108860. [PMID: 38996555 DOI: 10.1016/j.compbiomed.2024.108860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/16/2024] [Accepted: 07/06/2024] [Indexed: 07/14/2024]
Abstract
In addition to being the most prevalent form of neurodegeneration among the elderly, AD is a devastating multifactorial disease. Currently, treatments address only its symptoms. Several clinical studies have shown that the disease begins to manifest decades before the first symptoms appear, indicating that studying early changes is crucial to improving early diagnosis and discovering novel treatments. Our study used bioinformatics and systems biology to identify biomarkers in AD that could be used for diagnosis and prognosis. The procedure was performed on data from the GEO database, and GO and KEGG enrichment analysis were performed. Then, we set up a network of interactions between proteins. Several miRNA prediction tools including miRDB, miRWalk, and TargetScan were used. The ceRNA network led to the identification of eight mRNAs, four circRNAs, seven miRNAs, and seven lncRNAs. Multiple mechanisms, including the cell cycle and DNA replication, have been linked to the promotion of AD development by the ceRNA network. By using the ceRNA network, it should be possible to extract prospective biomarkers and therapeutic targets for the treatment of AD. It is possible that the processes involved in DNA cell cycle and the replication of DNA contribute to the development of Alzheimer's disease.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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22
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Yu X, Ge J, Xie H, Qian J, Xia W, Wang Q, Zhou X, Zhou Y. MiR-483-3p promotes dental pulp stem cells osteogenic differentiation via the MAPK signaling pathway by targeting ARRB2. In Vitro Cell Dev Biol Anim 2024; 60:879-887. [PMID: 38833209 DOI: 10.1007/s11626-024-00929-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
Human dental pulp stem cells (DPSCs) have become an important component for bone tissue engineering and regenerative medicine due to their ability to differentiate into osteoblast precursors. Two miRNA chip datasets (GSE138180 and E-MTAB-3077) of DPSCs osteogenic differentiation were analyzed respectively to find the expression of miR-483-3p significantly increased in the differentiated groups. We further confirmed that miR-483-3p continued to overexpress during osteogenic differentiation of DPSCs, especially reaching its peak on the 7th day. Moreover, miR-483-3p could significantly promote the expression of osteogenic markers including RUNX2 and OSX, and activate MAPK signaling pathway by inducing phosphorylation of ERK, p38, and JNK. In addition, as a significant gene within the MAPK signaling pathway, ARRB2 was identified as the target gene of miR-483-3p by bioinformatic prediction and experimental verification. In conclusion, we identified miR-483-3p could promote osteogenic differentiation of DPSCs via the MAPK signaling pathway by targeting ARRB2.
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Affiliation(s)
- Xin Yu
- Department of Orthodontics and Periodontology, Affiliated Nantong Stomatological Hospital of Nantong University, 36 South Yuelong Road, Nantong, 226001, China
| | - Juan Ge
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Huimin Xie
- Department of Orthodontics and Periodontology, Affiliated Nantong Stomatological Hospital of Nantong University, 36 South Yuelong Road, Nantong, 226001, China
| | - Jialu Qian
- Department of Clinical Laboratory, The First People's Hospital of Nantong, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Wenqian Xia
- Department of Orthodontics and Periodontology, Affiliated Nantong Stomatological Hospital of Nantong University, 36 South Yuelong Road, Nantong, 226001, China
| | - Qinghua Wang
- Laboratory Animal Center, Nantong University, Nantong, China
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China.
| | - Yan Zhou
- Department of Orthodontics and Periodontology, Affiliated Nantong Stomatological Hospital of Nantong University, 36 South Yuelong Road, Nantong, 226001, China.
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23
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Wei T, Xu Z. The diagnostic value and associated molecular mechanism study for fibroblast-related mitochondrial genes on keloid. Skin Res Technol 2024; 30:e70024. [PMID: 39221860 PMCID: PMC11367665 DOI: 10.1111/srt.70024] [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: 07/15/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE This study aims to reveal the mechanism of fibroblast-related mitochondrial genes on keloid formation and explore promising signature genes for keloid diagnosis. METHOD The distribution of fibroblasts between the keloid sample and control sample based on three keloid datasets, followed by the differentially expressed genes (DEGs) investigation and associated enrichment analysis. Then, hub genes were explored based on DEGs, mitochondrial genes from an online database, as well as fibroblast-related genes that were revealed by WCGNA. Subsequently, signature genes were screened through machine learning, and their diagnostic value was validated by nomogram. Moreover, the targeted drugs and related transcriptional regulation of these genes were analyzed. Finally, the verification analysis was performed on signature genes using qPCR analysis. RESULT A total of totally 329 DEGs were revealed based on three datasets, followed by enrichment analysis. WGCNA revealed a total of 258 fibroblast-related genes, which were primarily assembled in functions like muscle tissue development. By using machine learning, we screened four signature genes (ACSF2, ALDH1B1, OCIAD2, and SIRT4) based on eight hub genes (fibroblast-related mitochondrial genes). Nomogram and validation analyses confirmed the well-diagnostic performance of these four genes in keloid. Immune infiltration and drug correlation analyses showed that SIRT4 was significantly associated with immune cell type 2 T helper cells and molecular drug cyclosporin. All these findings provided new perspectives for the clinical diagnosis and therapy of keloid. CONCLUSION The fibroblast-related mitochondrial genes including SIRT4, OCIAD2, ALDH1B1, and ACSF2 were novel signature genes for keloid diagnosis, offering novel targets and strategies for diagnosis and therapy of keloid.
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Affiliation(s)
- Ting Wei
- Department of DermatologyTai'an Central HospitalTai'anShandongChina
| | - Zuojiao Xu
- Dermatology and Cosmetic Medicine CenterWeifang People's HospitalWeifangShandongChina
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24
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Vaxevanis C, Bachmann M, Seliger B. Immune modulatory microRNAs in tumors, their clinical relevance in diagnosis and therapy. J Immunother Cancer 2024; 12:e009774. [PMID: 39209767 PMCID: PMC11367391 DOI: 10.1136/jitc-2024-009774] [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] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
The importance of the immune system in regulating tumor growth by inducing immune cell-mediated cytotoxicity associated with patients' outcomes has been highlighted in the past years by an increasing life expectancy in patients with cancer on treatment with different immunotherapeutics. However, tumors often escape immune surveillance, which is accomplished by different mechanisms. Recent studies demonstrated an essential role of small non-coding RNAs, such as microRNAs (miRNAs), in the post-transcriptional control of immune modulatory molecules. Multiple methods have been used to identify miRNAs targeting genes involved in escaping immune recognition including miRNAs targeting CTLA-4, PD-L1, HLA-G, components of the major histocompatibility class I antigen processing machinery (APM) as well as other immune response-relevant genes in tumors. Due to their function, these immune modulatory miRNAs can be used as (1) diagnostic and prognostic biomarkers allowing to discriminate between tumor stages and to predict the patients' outcome as well as response and resistance to (immuno) therapies and as (2) therapeutic targets for the treatment of tumor patients. This review summarizes the role of miRNAs in tumor-mediated immune escape, discuss their potential as diagnostic, prognostic and predictive tools as well as their use as therapeutics including alternative application methods, such as chimeric antigen receptor T cells.
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Affiliation(s)
- Christoforos Vaxevanis
- Institute for Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Germany
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Barbara Seliger
- Institute for Medical Immunology, Martin Luther University Halle Wittenberg, Halle, Germany
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute of Translational Immunology, Faculty of Health Sciences Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
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25
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Arulsamy K, Xia B, Chen H, Zhang L, Chen K. Machine Learning Uncovers Vascular Endothelial Cell Identity Genes by Expression Regulation Features in Single Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609808. [PMID: 39253493 PMCID: PMC11383289 DOI: 10.1101/2024.08.27.609808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and many diseases involving cell identity dysregulation. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes are regulated with unique epigenetic signatures, we found cell identity genes exhibit distinctive genetic sequence signatures, e.g., unique enrichment patterns of cis-regulatory elements. Using these genetic sequence signatures, along with gene expression information from single-cell RNA-seq data, enables SCIG to uncover the identity genes of a cell without a need for comparison to other cells. Cell identity gene score defined by SCIG surpassed expression value in network analysis to uncover master transcription factors regulating cell identity. Applying SCIG to the human endothelial cell atlas revealed that the tissue microenvironment is a critical supplement to master transcription factors for cell identity refinement. SCIG is publicly available at https://github.com/kaifuchenlab/SCIG , offering a valuable tool for advancing cell differentiation, development, and regenerative medicine research.
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26
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Lu Q, Ren N, Chen H, Zhang S, Yan R, Li M, Zheng L, Tan W, Lin D. Polymorphism in the Hsa-miR-4274 seed region influences the expression of PEX5 and enhances radiotherapy resistance in colorectal cancer. Front Med 2024:10.1007/s11684-024-1082-6. [PMID: 39190270 DOI: 10.1007/s11684-024-1082-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/18/2024] [Indexed: 08/28/2024]
Abstract
Identifying biomarkers for predicting radiotherapy efficacy is crucial for optimizing personalized treatments. We previously reported that rs1553867776 in the miR-4274 seed region can predict survival in patients with rectal cancer receiving postoperative chemoradiation therapy. Hence, to investigate the molecular mechanism of the genetic variation and its impact on the radiosensitivity of colorectal cancer (CRC), in this study, bioinformatics analysis is combined with functional experiments to confirm peroxisomal biogenesis factor 5 (PEX5) as a direct target of miR-4274. The miR-4274 rs1553867776 variant influences the binding of miR-4274 and PEX5 mRNA, which subsequently regulates PEX5 protein expression. The interaction between PEX5 and Ku70 was verified by co-immunoprecipitation and immunofluorescence. A xenograft tumor model was established to validate the effects of miR-4274 and PEX5 on CRC progression and radiosensitivity in vivo. The overexpression of PEX5 enhances radiosensitivity by preventing Ku70 from entering the nucleus and reducing the repair of ionizing radiation (IR)-induced DNA damage by the Ku70/Ku80 complex in the nucleus. In addition, the enhanced expression of PEX5 is associated with increased IR-induced ferroptosis. Thus, targeting this mechanism might effectively increase the radiosensitivity of CRC. These findings offer novel insights into the mechanism of cancer radioresistance and have important implications for clinical radiotherapy.
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Affiliation(s)
- Qixuan Lu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ningxin Ren
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hongxia Chen
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shaosen Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ruoqing Yan
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mengjie Li
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Linlin Zheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wen Tan
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Beijing Key Laboratory for Carcinogenesis and Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
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27
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Xu F, Zheng H, Dong X, Zhou A, Emu Q. miRNA expression signatures induced by pasteurella multocida infection in goats lung. Sci Rep 2024; 14:19626. [PMID: 39179681 PMCID: PMC11343864 DOI: 10.1038/s41598-024-69654-3] [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: 01/04/2024] [Accepted: 08/07/2024] [Indexed: 08/26/2024] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and are involved in bacterial pathogenesis and host-pathogen interactions. In this study, we investigated the function of miRNAs in the regulation of host responses to Pasteurella multocida infection. Using next-generation sequencing, we analyzed miRNA expression pattern and identified differentially expressed miRNAs in Pasteurella multocida-infected goat lungs. In addition, we investigated the function of differentially expressed miRNAs andtheir targeted signaling pathways in bacterial infection processes. The results showed that Pasteurella multocida infection led to 69 significantly differentially expressed miRNAs, including 28 known annotated miRNAs with miR-497-3p showing the most significant difference. Gene target prediction and functional enrichment analyses showed that the target genes were mainly involved in cell proliferation, regulation of the cellular metabolic process, positive regulation of cellular process, cellular senescence, PI3K-Akt signaling pathway, FoxO signaling pathway and infection-related pathways. In conclusion, these data provide a new perspective on the roles of miRNAs in Pasteurella multocida infection.
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Affiliation(s)
- Feng Xu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Animal Science Academy of Sichuan Province, Chengdu, China
| | - Hao Zheng
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan, China
| | - Xia Dong
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan, China
| | - Ao Zhou
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, Wuhan, China.
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Animal Science Academy of Sichuan Province, Chengdu, China.
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Lu B, Liu Y, Yao Y, Zhu D, Zhang X, Dong K, Xu X, Lv D, Zhao Z, Zhang H, Yang X, Fu W, Huang R, Cao J, Chu J, Pan X, Cui X. Unveiling the unique role of TSPAN7 across tumors: a pan-cancer study incorporating retrospective clinical research and bioinformatic analysis. Biol Direct 2024; 19:72. [PMID: 39175035 PMCID: PMC11340126 DOI: 10.1186/s13062-024-00516-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 08/08/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND TSPAN7 is an important factor in tumor progression. However, the precise function of TSPAN7 and its role in pan-cancer are not clear. METHODS Based on Xinhua cohort incorporating 370 patients with kidney neoplasm, we conducted differential expression analysis by immunohistochemistry between tumor and normal tissues, and explored correlations of TSPAN7 with patients' survival. Subsequently, we conducted a pan-cancer study, and successively employed differential expression analysis, competing endogenous RNA (ceRNA) analysis, protein-protein interaction (PPI) analysis, correlation analysis of TSPAN7 with clinical characteristics, tumor purity, tumor genomics, tumor immunity, and drug sensitivity. Last but not least, gene set enrichment analysis was applied to identify enriched pathways of TSPAN7. RESULTS In Xinhua cohort, TSPAN7 expression was significantly up-regulated (P-value = 0.0019) in tumor tissues of kidney neoplasm patients. High TSPAN7 expression was associated with decreases in overall survival (OS) (P-value = 0.009) and progression-free survival (P-value = 0.009), and it was further revealed as an independent risk factor for OS (P-value = 0.0326, HR = 5.66, 95%CI = 1.155-27.8). In pan-cancer analysis, TSPAN7 expression was down-regulated in most tumors, and it was associated with patients' survival, tumor purity, tumor genomics, tumor immunity, and drug sensitivity. The ceRNA network and PPI network of TSPAN7 were also constructed. Last but not least, the top five enriched pathways of TSPAN7 in various tumors were identified. CONCLUSION TSPAN7 served as a promising biomarker of various tumors, especially kidney neoplasms, and it was closely associated with tumor purity, tumor genomics, tumor immunology, and drug sensitivity in pan-cancer level.
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Affiliation(s)
- Bingnan Lu
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Yifan Liu
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Yuntao Yao
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Dawei Zhu
- Department of Urology, the Second People's Hospital of Pinghu, Zhejiang, 314200, China
| | - Xiangmin Zhang
- Department of Urology, Shanghai Baoshan Luodian Hospital, Shanghai, 201908, China
| | - Keqin Dong
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Xiao Xu
- Department of Urology, the Second People's Hospital of Pinghu, Zhejiang, 314200, China
| | - Donghao Lv
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Zihui Zhao
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Haoyu Zhang
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Xinyue Yang
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Wenjia Fu
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China
| | - Runzhi Huang
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China.
| | - Jianwei Cao
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
- Department of Urology, the Second People's Hospital of Pinghu, Zhejiang, 314200, China.
| | - Jian Chu
- Department of Urology, Shanghai Baoshan Luodian Hospital, Shanghai, 201908, China.
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
| | - Xingang Cui
- Department of Urology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, No.1665 Kongjiang Road, Shanghai, 200092, China.
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Wei L, Xie Y, Yu P, Zhu Q, Lan X, Xiao J. Bioinformatics analysis and validation of RNA methylation-related genes in osteogenic and adipogenic differentiation of rat bone marrow mesenchymal stem cells. Biochem Biophys Res Commun 2024; 739:150570. [PMID: 39181069 DOI: 10.1016/j.bbrc.2024.150570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND The regulatory mechanisms of RNA methylation during the processes of osteogenic and adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) have yet to be fully understood. The objective of our study was to analyze and validate the contribution of RNA methylation regulators to the mechanisms underlying the osteogenic and adipogenic differentiation of rat BMSCs. METHODS We downloaded the GSE186026 from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were screened using the DESeq2 package in R software (version 3.6.3). A total of 50 RNA methylation genes obtained from literature review and summary were intersected with the previous DEGs to obtain RNA methylation genes, which have different expressions (RM-DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were utilized to reveal the functional enrichment. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate RM-DEGs. Protein-protein interaction network (PPI) analysis and visual analysis were performed using STRING and Cytoscape. RM-DEGs regulatory network was constructed to analyze the top 10 hub genes. The relationship between RM-DEGs, some enriched GO and pathways was also been analyzed. The miRNAs and RM-DEGs regulatory networks were established by using miRWalk and TargetScan. RESULTS As part of our research, we detected varying levels of expression for m6A regulators Mettl3 and Rbm15, as well as m7G regulators Mettl1 and Wdr4, in relation to osteogenic differentiation, along with m6A regulator Fmr1 in adipogenic differentiation. The protein-protein interaction (PPI) networks were constructed for 49 differentially expressed genes (DEGs) related to RNA methylation during the process of osteogenic differentiation, and 13 DEGs for adipogenic differentiation. Moreover, top10 hub genes were calculated. In osteogenic differentiation, Mettl3 regulated the Wnt pathway and Hippo pathway by regulating Smad3, Rbm15 regulated the Notch pathway by Notch1, Mettl1 regulated the PI3K-Akt pathway by Gnb4. In adipogenic differentiation, Fmr1 regulated the PI3K-Akt pathway by Egfr. M6A methylation sites of Smad3, Notch1 and Gnb4 were predicted, and the results showed that all three genes were possibly methylated by m6A, and more than 9 sites per gene were possibly methylated. Finally, we constructed the regulatory networks of Mettl3, Rbm15, Mettl1, and Wdr4 and 109 miRNAs in osteogenic differentiation, Fmr1 and 118 miRNAs in adipogenic differentiation. CONCLUSIONS Mettl3(m6A), Rbm15(m6A), Wdr4 and Mettl1(m7G) were differentially expressed in osteogenic differentiation, while Fmr1(m6A) was differentially expressed in adipogenic differentiation. These findings offered potential candidates for further research on the involvement of RNA methylation in the osteogenic and adipogenic differentiation of BMSCs.
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Affiliation(s)
- Li Wei
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Yuping Xie
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Peiyang Yu
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Qiang Zhu
- Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Xiaorong Lan
- Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Jingang Xiao
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China.
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Almeida RA, Ferreira CG, Matos VUS, Nogueira JM, Braga MP, Caldi Gomes L, Jorge EC, Soriani FM, Michel U, Ribas VT. AAV-Mediated Expression of miR-17 Enhances Neurite and Axon Regeneration In Vitro. Int J Mol Sci 2024; 25:9057. [PMID: 39201743 PMCID: PMC11355044 DOI: 10.3390/ijms25169057] [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: 07/10/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
Neurodegenerative disorders, including traumatic injuries to the central nervous system (CNS) and neurodegenerative diseases, are characterized by early axonal damage, which does not regenerate in the adult mammalian CNS, leading to permanent neurological deficits. One of the primary causes of the loss of regenerative ability is thought to be a developmental decline in neurons' intrinsic capability for axon growth. Different molecules are involved in the developmental loss of the ability for axon regeneration, including many transcription factors. However, the function of microRNAs (miRNAs), which are also modulators of gene expression, in axon re-growth is still unclear. Among the various miRNAs recently identified with roles in the CNS, miR-17, which is highly expressed during early development, emerges as a promising target to promote axon regeneration. Here, we used adeno-associated viral (AAV) vectors to overexpress miR-17 (AAV.miR-17) in primary cortical neurons and evaluate its effects on neurite and axon regeneration in vitro. Although AAV.miR-17 had no significant effect on neurite outgrowth and arborization, it significantly enhances neurite regeneration after scratch lesion and axon regeneration after axotomy of neurons cultured in microfluidic chambers. Target prediction and functional annotation analyses suggest that miR-17 regulates gene expression associated with autophagy and cell metabolism. Our findings suggest that miR-17 promotes regenerative response and thus could mitigate neurodegenerative effects.
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Affiliation(s)
- Raquel Alves Almeida
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31279-901, Brazil (E.C.J.)
| | - Carolina Gomes Ferreira
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31279-901, Brazil (E.C.J.)
| | - Victor Ulysses Souza Matos
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31279-901, Brazil (E.C.J.)
| | - Julia Meireles Nogueira
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31279-901, Brazil (E.C.J.)
| | - Marina Pimenta Braga
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31279-901, Brazil (F.M.S.)
| | - Lucas Caldi Gomes
- Clinical Department of Neurology, TUM School of Medicine, Rechts der Isar Hospital, Technical University of Munich, 81675 Munich, Germany;
| | - Erika Cristina Jorge
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31279-901, Brazil (E.C.J.)
| | - Frederico Marianetti Soriani
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31279-901, Brazil (F.M.S.)
| | - Uwe Michel
- Department of Neurology, University Medicine Göttingen, 37075 Göttingen, Germany
| | - Vinicius Toledo Ribas
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31279-901, Brazil (E.C.J.)
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Li TL, Zhu NN, Yin Z, Sun J, Guo JP, Yuan HT, Shi XM, Guo HY, Li SX, Shan ZL. Transcriptomic analysis of epicardial adipose tissue reveals the potential crosstalk genes and immune relationship between type 2 diabetes mellitus and atrial fibrillation. Gene 2024; 920:148528. [PMID: 38703871 DOI: 10.1016/j.gene.2024.148528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/27/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND The complex relationship between atrial fibrillation (AF) and type 2 diabetes mellitus (T2DM) suggests a potential role for epicardial adipose tissue (EAT) that requires further investigation. This study employs bioinformatics and experimental approaches to clarify EAT's role in linking T2DM and AF, aiming to unravel the biological mechanisms involved. METHOD Bioinformatics analysis initially identified common differentially expressed genes (DEGs) in EAT from T2DM and AF datasets. Pathway enrichment and network analyses were then performed to determine the biological significance and network connections of these DEGs. Hub genes were identified through six CytoHubba algorithms and subsequently validated biologically, with further in-depth analyses confirming their roles and interactions. Experimentally, db/db mice were utilized to establish a T2DM model. AF induction was executed via programmed transesophageal electrical stimulation and burst pacing, focusing on comparing the incidence and duration of AF. Frozen sections and Hematoxylin and Eosin (H&E) staining illuminated the structures of the heart and EAT. Moreover, quantitative PCR (qPCR) measured the expression of hub genes. RESULTS The study identified 106 DEGs in EAT from T2DM and AF datasets, underscoring significant pathways in energy metabolism and immune regulation. Three hub genes, CEBPZ, PAK1IP1, and BCCIP, emerged as pivotal in this context. In db/db mice, a marked predisposition towards AF induction and extended duration was observed, with HE staining verifying the presence of EAT. Additionally, qPCR validated significant changes in hub genes expression in db/db mice EAT. In-depth analysis identified 299 miRNAs and 33 TFs as potential regulators, notably GRHL1 and MYC. GeneMANIA analysis highlighted the hub genes' critical roles in stress responses and leukocyte differentiation, while immune profile correlations highlighted their impact on mast cells and neutrophils, emphasizing the genes' significant influence on immune regulation within the context of T2DM and AF. CONCLUSION This investigation reveals the molecular links between T2DM and AF with a focus on EAT. Targeting these pathways, especially EAT-related ones, may enable personalized treatments and improved outcomes.
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Affiliation(s)
- Tian-Lun Li
- Postgraduate School, Medical School of Chinese PLA, Beijing, China; Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Na-Na Zhu
- Postgraduate School, Medical School of Chinese PLA, Beijing, China; Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhao Yin
- Postgraduate School, Medical School of Chinese PLA, Beijing, China; Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jiao Sun
- Postgraduate School, Medical School of Chinese PLA, Beijing, China; Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jian-Pin Guo
- Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hong-Tao Yuan
- Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiang-Min Shi
- Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hong-Yang Guo
- Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Shi-Xing Li
- Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhao-Liang Shan
- Postgraduate School, Medical School of Chinese PLA, Beijing, China; Department of Cardiology, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China.
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Chen X, Zhang Y, Meng H, Chen G, Ma Y, Li J, Liu S, Liang Z, Xie Y, Liu Y, Guo H, Wang Y, Shan Z. Identification of miR-1 and miR-499 in chronic atrial fibrillation by bioinformatics analysis and experimental validation. Front Cardiovasc Med 2024; 11:1400643. [PMID: 39221422 PMCID: PMC11361948 DOI: 10.3389/fcvm.2024.1400643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Background Atrial fibrillation (AF) is one of the most prevalent arrhythmias and is characterized by a high risk of heart failure and embolic stroke, yet its underlying mechanism is unclear. The primary goal of this study was to establish a miRNA-mRNA network and identify the miRNAs associated with chronic AF by bioinformatics and experimental validation. Methods The GSE79768 dataset was collected from the Gene Expression Omnibus(GEO) database to extract data from patients with or without persistent AF. Differentially expressed genes (DEGs) were identified in left atrial appendages (LAAs). The STRING platform was utilized for protein-protein interaction (PPI) network analysis. The target miRNAs for the top 20 hub genes were predicted by using the miRTarBase Web tool. The miRNA-mRNA network was established and visualized using Cytoscape software. The key miRNAs selected for verification in the animal experiment were confirmed by miRwalk Web tool. We used a classic animal model of rapid ventricular pacing for chronic AF. Two groups of animals were included in the experiment, namely, the ventricular pacing group (VP group), where ventricular pacing was maintained at 240-280 bpm for 2 weeks, and the control group was the sham-operated group (SO group). Finally, we performed reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to validate the expression of miR-1 and miR-499 in LAA tissues of the VP group and the SO group. Left atrial fibrosis and apoptosis were evaluated by Masson staining and caspase-3 activity assays, respectively. Results The networks showed 48 miRNAs in LAA tissues. MiR-1 and miR-499 were validated using an animal model of chronic AF. The expression level of miR-1 was increased, and miR-499 was decreased in VP group tissues compared to SO group tissues in LAAs (P < 0.05), which were correlated with left atrial fibrosis and apoptosis in AF. Conclusion This study provides a better understanding of the alterations in miRNA-1 and miR-499 in chronic AF from the perspective of the miRNA-mRNA network and corroborates findings through experimental validation. These findings may offer novel potential therapeutic targets for AF in the future.
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Affiliation(s)
- Xinpei Chen
- Munich Medical Research School, Ludwig-Maximilians University Munich, Munich, Germany
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
- Department of Cardiac Arrhythmia, Fuwai Yunnan Hospital, Chinese Academy of Medical Sciences, Kunming Medical University, Kunming, Yunnan, China
| | - Yu Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Beijing, China
| | - He Meng
- Department of Cardiology, Tianjin Chest Hospital, Tianjin, China
| | - Guiying Chen
- Department of Pneumology, Tianjin Chest Hospital, Tianjin, China
| | - Yongjiang Ma
- Department of Cardiology, The Sixth Medical Center of PLA General Hospital, Beijing, China
| | - Jian Li
- Munich Medical Research School, Ludwig-Maximilians University Munich, Munich, Germany
| | - Saizhe Liu
- Munich Medical Research School, Ludwig-Maximilians University Munich, Munich, Germany
| | - Zhuo Liang
- Department of Cardiology, Beijing Anzhen Hospital, Beijing, China
| | - Yinuo Xie
- Munich Medical Research School, Ludwig-Maximilians University Munich, Munich, Germany
| | - Ying Liu
- Department of Cardiology, Beijing Jing Mei Group General Hospital, Beijing, China
| | - Hongyang Guo
- Munich Medical Research School, Ludwig-Maximilians University Munich, Munich, Germany
| | - Yutang Wang
- Department of Geriatric Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Zhaoliang Shan
- Munich Medical Research School, Ludwig-Maximilians University Munich, Munich, Germany
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Gad A, Menjivar NG, Felton R, Durrant B, Tesfaye D, Ruggeri E. Mapping the follicle-specific regulation of extracellular vesicle-mediated microRNA transport in the southern white rhinoceros (Ceratotherium simum simum)†. Biol Reprod 2024; 111:376-390. [PMID: 38775197 PMCID: PMC11327318 DOI: 10.1093/biolre/ioae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/25/2024] [Accepted: 05/20/2024] [Indexed: 08/17/2024] Open
Abstract
Efforts to implement effective assisted reproductive technologies (ARTs) for the conservation of the northern white rhinoceros (NWR; Ceratotherium simum cottoni) to prevent its forthcoming extinction, could be supported by research conducted on the closely related southern white rhinoceros (SWR; Ceratotherium simum simum). Within the follicle, extracellular vesicles (EVs) play a fundamental role in the bidirectional communication facilitating the crucial transport of regulatory molecules such as microRNAs (miRNAs) that control follicular growth and oocyte development. This study aimed to elucidate the dynamics of EV-miRNAs in stage-dependent follicular fluid (FF) during SWR ovarian antral follicle development. Three distinct follicular stages were identified based on diameter: Growing (G; 11-17 mm), Dominant (D; 18-29 mm), and Pre-ovulatory (P; 30-34 mm). Isolated EVs from the aspirated FF of segmented follicle stages were used to identify EV-miRNAs previously known via subsequent annotation to all equine (Equus caballus; eca), bovine (Bos taurus; bta), and human (Homo sapiens; hsa) miRNAs. A total of 417 miRNAs were detected, with 231 being mutually expressed across all three stages, including eca-miR-148a and bta-miR-451 as the top highly expressed miRNAs. Distinct expression dynamics in miRNA abundance were observed across the three follicular stages, including 31 differentially expressed miRNAs that target various pathways related to follicular growth and development, with 13 miRNAs commonly appearing amidst two different comparisons. In conclusion, this pioneering study provides a comprehensive understanding of the stage-specific expression dynamics of FF EV-miRNAs in the SWR. These findings provide insights that may lead to novel approaches in enhancing ARTs to catalyze rhinoceros conservation efforts.
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Affiliation(s)
- Ahmed Gad
- Animal Reproduction and Biotechnology Laboratory (ARBL), Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Nico G Menjivar
- Animal Reproduction and Biotechnology Laboratory (ARBL), Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Rachel Felton
- Reproductive Sciences, Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Barbara Durrant
- Reproductive Sciences, Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Dawit Tesfaye
- Animal Reproduction and Biotechnology Laboratory (ARBL), Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Elena Ruggeri
- Reproductive Sciences, Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
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Li X, Meng Z, Hua Y, Li Z, Yin B, Qian B, Yu H, Li Z, Zhou Y, Feng Z, Lu S, Ke S, Bai M, Fu Y, Ma Y. Identification and validation of ferroptosis-related hub genes and immune infiltration in liver ischemia-reperfusion injury. Genomics 2024; 116:110918. [PMID: 39147333 DOI: 10.1016/j.ygeno.2024.110918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/15/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Ischemia-reperfusion injury (IRI) is a cumulation of pathophysiological processes that involves cell and organelle damage upon blood flow constraint and subsequent restoration. However, studies on overall immune infiltration and ferroptosis in liver ischemia-reperfusion injury (LIRI) are limited. This study explored immune cell infiltration and ferroptosis in LIRI using bioinformatics and experimental validation. The GSE151648 dataset, including 40 matched pairs of pre- and post- transplant liver samples was downloaded for bioinformatic analysis. Eleven hub genes were identified by overlapping differentially expressed genes (DEGs), iron genes, and genes identified through weighted gene co-expression network analysis (WGCNA). Subsequently, the pathway enrichment, transcription factor-target, microRNA-mRNA and protein-protein interaction networks were investigated. The diagnostic model was established by logistic regression, which was validated in the GSE23649 and GSE100155 datasets and verified using cytological experiments. Moreover, several drugs targeting these genes were found in DrugBank, providing a more effective treatment for LIRI. In addition, the expression of 11 hub genes was validated using quantitative real-time polymerase chain reaction (qRT-PCR) in liver transplantation samples and animal models. The expression of the 11 hub genes increased in LIRI compared with the control. Five genes were significantly enriched in six biological process terms, six genes showed high enrichment for LIRI-related signaling pathways. There were 56 relevant transcriptional factors and two central modules in the protein-protein interaction network. Further immune infiltration analysis indicated that immune cells including neutrophils and natural killer cells were differentially accumulated in the pre- and post-transplant groups, and this was accompanied by changes in immune-related factors. Finally, 10 targeted drugs were screened. Through bioinformatics and further experimental verification, we identified hub genes related to ferroptosis that could be used as potential targets to alleviate LIRI.
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Affiliation(s)
- Xinglong Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhanzhi Meng
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongliang Hua
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zihao Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Yin
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Baolin Qian
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongjun Yu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhongyu Li
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongzhi Zhou
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhigang Feng
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; The First Department of General Surgery, Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Shounan Lu
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shanjia Ke
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Miaoyu Bai
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yao Fu
- Department of Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yong Ma
- Department of Minimally Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
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Chen RX, Liu SC, Kan XC, Wang YR, Wang JF, Wang TL, Li C, Jiang WJ, Chen YAL, Zhou T, Fan SL, Chang J, Xu X, Shi KH, Zhang YD, Wu MY, Yu Y, Li CX, Li XC. CircUGP2 Suppresses Intrahepatic Cholangiocarcinoma Progression via p53 Signaling Through Interacting With PURB to Regulate ADGRB1 Transcription and Sponging miR-3191-5p. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402329. [PMID: 39120980 DOI: 10.1002/advs.202402329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/17/2024] [Indexed: 08/11/2024]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver cancer and its prognosis remains poor. Although growing numbers of studies have verified the involvement of circular RNAs (circRNAs) in various cancer types, their specific functions in ICC remain elusive. Herein, a circRNA, circUGP2 is identified by circRNA sequencing, which is downregulated in ICC tissues and correlated with patients' prognosis. Moreover, circUGP2 overexpression suppresses tumor progression in vitro and in vivo. Mechanistically, circUGP2 functions as a transcriptional co-activator of PURB over the expression of ADGRB1. It can also upregulate ADGRB1 expression by sponging miR-3191-5p. As a result, ADGRB1 prevents MDM2-mediated p53 polyubiquitination and thereby activates p53 signaling to inhibit ICC progression. Based on these findings, circUGP2 plasmid is encapsulated into a lipid nanoparticle (LNP) system, which has successfully targeted tumor site and shows superior anti-tumor effects. In summary, the present study has identified the role of circUGP2 as a tumor suppressor in ICC through regulating ADGRB1/p53 axis, and the application of LNP provides a promising translational strategy for ICC treatment.
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Affiliation(s)
- Rui Xiang Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Shuo Chen Liu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Xue Chun Kan
- School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Yi Rui Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Ji Fei Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Tian Lin Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Chang Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Wang Jie Jiang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Yan An Lan Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Tao Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Shi Long Fan
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Jiang Chang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Xiao Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Kuang Heng Shi
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Yao Dong Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Ming Yu Wu
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Yue Yu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Chang Xian Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
| | - Xiang Cheng Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu, 210029, China
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, Jiangsu, 214023, China
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Zhang J, Liu J, Li Y, Zhang X, Yang C. Regulatory Role and Molecular Mechanism of Mammalian Sterile 20-Like Kinase 1 in 1-Methyl-4-Phenylpyridinium Ion-Induced Parkinson's Disease Cell Model. Rejuvenation Res 2024. [PMID: 39003528 DOI: 10.1089/rej.2024.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024] Open
Abstract
Parkinson's disease (PD) is a multifactorial degenerative disease in the elder. Given the involvement of mammalian sterile 20-like kinase 1 (MST1) in PD, this article was to illustrate the mechanism of MST1 in 1-methyl-4-phenylpyridinium ion (MPP+)-induced PD cell model. Cells were treated with different concentrations of MPP+ to establish a PD cell model. Reverse transcription-quantitative polymerase chain reaction and Western blot revealed that MST1 expression and iron ion concentration increased, but cellular viability decreased with MPP+ concentration. Inhibition of MST1 decreased ferroptosis; increased cellular viability, iron ion content, and levels of glutathione peroxidase 4; and decreased reactive oxygen species and lactate dehydrogenase release. Upregulation of ferroptosis levels using ferroptosis agonist Erastin reduced the protective effect of MST1 inhibition on PD cells. Mechanistically, dual-luciferase analysis identified that miR-23b-3p targeted MST1 and inhibited its expression. Overexpression of miR-23b-3p inhibited MST1 levels, thereby reducing cellular ferroptosis and attenuating MPP+-induced cell injury. Collectively, MST1 expression increased with increasing MPP+ concentration, and miR-23b-3p targeted MST1 to reduce ferroptosis and MPP+-induced cell injury.
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Affiliation(s)
- Jun Zhang
- Department of Neurology, Jingmen People's Hospital, Jingmen, China
| | - Jie Liu
- Department of Neurology, Jingmen People's Hospital, Jingmen, China
| | - Yongle Li
- Department of Neurology, Jingmen People's Hospital, Jingmen, China
| | - Xuexian Zhang
- Department of Neurology, Jingmen People's Hospital, Jingmen, China
| | - Chunxiang Yang
- Department of Neurology, Jingmen People's Hospital, Jingmen, China
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Kong X, Wu T, Cai H, Chen Z, Wang Y, He P, Liu P, Li L, Peng S, Xu F, Wang J, Zhang H, Wang L. Construction of ceRNA network mediated by circRNAs screening from microarray and identification of novel biomarkers for myasthenia gravis. Gene 2024; 918:148463. [PMID: 38631652 DOI: 10.1016/j.gene.2024.148463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Recent studies have revealed that circRNA can serve as ceRNA to participate in multiple autoimmune diseases. Our study aims to explore the key circRNA as ceRNA and biomarker for MG. METHODS We used circRNA microarray to explore differentially expressed circRNAs (DECs) from MG and compare with control. Then, we predicted the target miRNA associated with DECs and screened miRNAs by the algorithm of random walk with restart (RWR). Next, we constructed the circRNA-miRNA-mRNA ceRNA regulated network (CMMC) to identify the hub objects. Following, we detected the expression of hub-circRNAs by RT-PCR. We verify has_circ_0004183 (circFRMD4) sponging miR-145-5p regulate cells proliferation using luciferase assay and CCK-8. RESULTS We found that the expression level of circFRMD4 and has_circ_0035381 (circPIGB) were upregulated and has_circ_0089153(circ NUP214) had the lowest expression level in MG. Finally, we proved circFRMD4 sponging miR-145-5p regulate Jurkat cells proliferation. CircFRMD4 take part in the genesis and development of MG via circFRMD4/miR145-5p axis. CONCLUSIONS We found that circFRMD4, circPIGB and circNUP214 can be considered as valuable potential novel biomarkers for AchR + MG. CircFRMD4 participate in the development of AchR + MG via targeting binding with miR-145-5p.
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Affiliation(s)
- Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Tao Wu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hanlu Cai
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhimin Chen
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China; Department of Neurology, The Second Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Yu Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Ping He
- Department of Neurology, The First Hospital of Harbin, Harbin, Heilongjiang Province, China
| | - Peifang Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lei Li
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Shanshan Peng
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Fanfan Xu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China.
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang Province, China.
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Albaqami WF, Alshamrani AA, Almubarak AA, Alotaibi FE, Alotaibi BJ, Alanazi AM, Alotaibi MR, Alhoshani A, As Sobeai HM. Genetic and Epigenetic Biomarkers Associated with Early Relapse in Pediatric Acute Lymphoblastic Leukemia: A Focused Bioinformatics Study on DNA-Repair Genes. Biomedicines 2024; 12:1766. [PMID: 39200230 PMCID: PMC11351110 DOI: 10.3390/biomedicines12081766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Genomic instability is one of the main drivers of tumorigenesis and the development of hematological malignancies. Cancer cells can remedy chemotherapeutic-induced DNA damage by upregulating DNA-repair genes and ultimately inducing therapy resistance. Nevertheless, the association between the DNA-repair genes, drug resistance, and disease relapse has not been well characterized in acute lymphoblastic leukemia (ALL). This study aimed to explore the role of the DNA-repair machinery and the molecular mechanisms by which it is regulated in early- and late-relapsing pediatric ALL patients. We performed secondary data analysis on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)-ALL expansion phase II trial of 198 relapsed pediatric precursor B-cell ALL. Comprehensive genetic and epigenetic investigations of 147 DNA-repair genes were conducted in the study. Gene expression was assessed using Microarray and RNA-sequencing platforms. Genomic alternations, methylation status, and miRNA transcriptome were investigated for the candidate DNA-repair genes. We identified three DNA-repair genes, ALKBH3, NHEJ1, and PARP1, that were upregulated in early relapsers compared to late relapsers (p < 0.05). Such upregulation at diagnosis was significantly associated with disease-free survival and overall survival in precursor-B-ALL (p < 0.05). Moreover, PARP1 upregulation accompanied a significant downregulation of its targeting miRNA, miR-1301-3p (p = 0.0152), which was strongly linked with poorer disease-free and overall survivals. Upregulation of DNA-repair genes, PARP1 in particular, increases the likelihood of early relapse of precursor-B-ALL in children. The observation that PARP1 was upregulated in early relapsers relative to late relapsers might serve as a valid rationale for proposing alternative treatment approaches, such as using PARP inhibitors with chemotherapy.
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Affiliation(s)
- Walaa F. Albaqami
- Department of Science, Prince Sultan Military College of Health Sciences, Dhahran 31932, Saudi Arabia;
| | - Ali A. Alshamrani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Ali A. Almubarak
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Faris E. Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Basil Jamal Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Abdulrahman M. Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
- Pharmaceutical Care Division, King Faisal Specialist Hospital & Research Centre, Madinah 42523, Saudi Arabia
| | - Moureq R. Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Ali Alhoshani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Homood M. As Sobeai
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
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Babaei A, Yazdi AT, Ranji R, Bahadoran E, Taheri S, Nikkhahi F, Ghorbani S, Abbasi A. Therapeutic Effects of Exosomal miRNA-4731-5p from Adipose Tissue-Derived Stem Cells on Human Glioblastoma Cells. Arch Med Res 2024; 55:103061. [PMID: 39098111 DOI: 10.1016/j.arcmed.2024.103061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
BACKGROUND AND AIM Several microRNAs (miRNAs) are differentially expressed and serve as tumor suppressors in glioblastoma (GBM). The present study aimed to elucidate the function of exosomal microRNA-4731-5p (miR-4731-5p) from adipose tissue-derived mesenchymal stem cells (AD-MSCs) in the activity of human GBM cell lines. METHOD First, GBM-related miRNAs, their expression, and potential target genes and cytokines of miR-4731-5p were identified using bioinformatic datasets. Subsequently, purified AD-MSCs were transfected with a miRNA-4731-5p expression plasmid, and exosomes were isolated and characterized. Next, the transfection process was confirmed and the 50% inhibitory concentration (IC50) of the overexpressed exosomal miRNA-4731-5p was inhibited for cancer cells. The probable anticancer action of exosomal miRNA-4731-5p on U-87 and U-251 GBM cell lines was verified by flow cytometry, DAPI staining, cell cycle, real-time PCR, and wound healing assays. RESULTS A concentration of 50 ng/mL of miRNA-4731-5p-transfected exosomes was the safe dose for anticancer settings. The results showed that the exosomal miR-4731-5p exerted an inhibitory effect on the cell cycle and migration and induced apoptosis in GBM cell lines by regulating the phosphoinositide-3-kinase-AKT (PI3K-AKT) and nuclear factor-kB (NF-kB) signaling pathways. CONCLUSION This study reveals that the expression of exosomal miRNA-4731-5p has favorable antitumor properties for the treatment of GBM cell lines and may be a fundamental therapeutic option for this type of brain tumor.
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Affiliation(s)
- Abouzar Babaei
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran; Department of Microbiology and Immunology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran.
| | - Amin Torabi Yazdi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Reza Ranji
- Department of Genetics, Faculty of Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ensiyeh Bahadoran
- School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Shiva Taheri
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farhad Nikkhahi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Saied Ghorbani
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ardeshir Abbasi
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Chatterjee B, Thakur SS. miRNA-protein-metabolite interaction network reveals the regulatory network and players of pregnancy regulation in dairy cows. Front Cell Dev Biol 2024; 12:1377172. [PMID: 39156977 PMCID: PMC11329941 DOI: 10.3389/fcell.2024.1377172] [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: 01/26/2024] [Accepted: 07/05/2024] [Indexed: 08/20/2024] Open
Abstract
Pregnancy is a complex process involving complex molecular interaction networks, such as between miRNA-protein, protein-protein, metabolite-metabolite, and protein-metabolite interactions. Advances in technology have led to the identification of many pregnancy-associated microRNA (miRNA), protein, and metabolite fingerprints in dairy cows. An array of miRNA, protein, and metabolite fingerprints produced during the early pregnancy of dairy cows were described. We have found the in silico interaction networks between miRNA-protein, protein-protein, metabolite-metabolite, and protein-metabolite. We have manually constructed miRNA-protein-metabolite interaction networks such as bta-miR-423-3p-IGFBP2-PGF2α interactomes. This interactome is obtained by manually combining the interaction network formed between bta-miR-423-3p-IGFBP2 and the interaction network between IGFBP2-PGF2α with IGFBP2 as a common interactor with bta-miR-423-3p and PGF2α with the provided sources of evidence. The interaction between bta-miR-423-3p and IGFBP2 has many sources of evidence including a high miRanda score of 169, minimum free energy (MFE) score of -25.14, binding probability (p) of 1, and energy of -25.5. The interaction between IGFBP2 and PGF2α occurs at high confidence scores (≥0.7 or 70%). Interestingly, PGF2α is also found to interact with different metabolites, such as PGF2α-PGD2, PGF2α-thromboxane B2, PGF2α-PGE2, and PGF2α-6-keto-PGF1α at high confidence scores (≥0.7 or 70%). Furthermore, the interactions between C3-PGE2, C3-PGD2, PGE2-PGD2, PGD2-thromboxane B2, PGE2-thromboxane B2, 6-keto-PGF1α-thromboxane B2, and PGE2-6-keto-PGF1α were also obtained at high confidence scores (≥0.7 or 70%). Therefore, we propose that miRNA-protein-metabolite interactomes involving miRNA, protein, and metabolite fingerprints of early pregnancy of dairy cows such as bta-miR-423-3p, IGFBP2, PGF2α, PGD2, C3, PGE2, 6-keto-PGF1 alpha, and thromboxane B2 may form the key regulatory networks and players of pregnancy regulation in dairy cows. This is the first study involving miRNA-protein-metabolite interactomes obtained in the early pregnancy stage of dairy cows.
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Wu Z, Dong L, Tian Z, Yu C, Shu Q, Chen W, Li H. Integrative Analysis of the Age-Related Dysregulated Genes Reveals an Inflammation and Immunity-Associated Regulatory Network in Alzheimer's Disease. Mol Neurobiol 2024; 61:5353-5368. [PMID: 38190023 DOI: 10.1007/s12035-023-03900-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: 10/05/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease with a long incubation period. While extensive research has led to the construction of long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) regulatory networks, which primarily derived from differential analyses between clinical AD patients and control individuals or mice, there remains a critical knowledge gap pertaining to the dynamic alterations in transcript expression profiles that occur with age, spanning from the pre-symptomatic stage to the onset of AD. In the present study, we examined the transcriptomic changes in AD model mice at three distinct stages: the unaffected (un-) stage, the pre-onset stage, and the late-onset stage, and identified 14, 57, and 99 differentially expressed mRNAs (DEmRs) in AD model mice at 3, 6, and 12 months, respectively. Among these, we pinpointed 16 mRNAs closely associated with inflammation and immunity and excavated their lncRNA-mRNA regulatory network based on a comprehensive analysis. Notably, our preliminary analysis suggested that four lncRNAs (NONMMUT102943, ENSMUST00000160309, NONMMUT083044, and NONMMUT126468), eight miRNAs (miR-34a-5p, miR-22-5p, miR-302a/b-3p, miR-340-5p, miR-376a/b-5p, and miR-487b-5p), and four mRNAs (C1qa, Cd68, Ctss, and Slc11a1) may play pivotal roles in orchestrating immune and inflammatory responses during the early stages of AD. Our study has unveiled age-related AD risk genes, and provided an analytical framework for constructing lncRNA-mRNA networks using time series data and correlation analysis. Most notably, we have successfully constructed a comprehensive regulatory ceRNA network comprising genes intricately linked to inflammatory and immune functions in AD.
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Affiliation(s)
- Zhuoze Wu
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Lei Dong
- School of Medical Imaging, North Sichuan Medical College, Nanchong, 637100, China
| | - Zhixiao Tian
- School of Medical Imaging, North Sichuan Medical College, Nanchong, 637100, China
| | - Chenhui Yu
- School of Medical Imaging, North Sichuan Medical College, Nanchong, 637100, China
| | - Qingrong Shu
- School of Medical Imaging, North Sichuan Medical College, Nanchong, 637100, China
| | - Wei Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Hao Li
- Department of Pathophysiology, School of Basic Medicine and Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Hu Y, Cao H, Sheng J, Sun Y, Zhu Y, Lin Q, Yi N, He S, Peng L, Li L. Functional role of circRNA CHRC through miR-431-5p/KLF15 signaling axis in the progression of heart failure. J Genet Genomics 2024; 51:844-854. [PMID: 38575112 DOI: 10.1016/j.jgg.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Pathological myocardial hypertrophy is a common early clinical manifestation of heart failure, with noncoding RNAs exerting regulatory influence. However, the molecular function of circular RNAs (circRNAs) in the progression from cardiac hypertrophy to heart failure remains unclear. To uncover functional circRNAs and identify the core circRNA signaling pathway in heart failure, we construct a global triple network (microRNA, circRNA, and mRNA) based on the competitive endogenous RNA (ceRNA) theory. We observe that cardiac hypertrophy-related circRNA (circRNA CHRC), within the ceRNA network, is down-regulated in both transverse aortic constriction mice and Ang-II--treated primary mouse cardiomyocytes. Silencing circRNA CHRC increases cross-sectional cell area, atrial natriuretic peptide, and β-myosin heavy chain levels in primary mouse cardiomyocytes. Further screening shows that circRNA CHRC targets the miR-431-5p/KLF15 axis implicated in heart failure progression in vivo and in vitro. Immunoprecipitation with anti-Ago2-RNA confirms the interaction between circRNA CHRC and miR-431-5p, while miR-431-5p mimics reverse Klf15 activation caused by circRNA CHRC overexpression. In summary, circRNA CHRC attenuates cardiac hypertrophy via sponging miR-431-5p to maintain the normal level of Klf15 expression.
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Affiliation(s)
- Yi Hu
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Huaming Cao
- Department of Cardiology, Shanghai Shibei Hospital, Shanghai 200435, China
| | - Jie Sheng
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Yizhuo Sun
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Yuping Zhu
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Qin Lin
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Na Yi
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Siyu He
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China
| | - Luying Peng
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200120, China.
| | - Li Li
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Shanghai Arrhythmias Research Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Laboratory of Molecular Genetics and Stem Cell Differentiation, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200120, China.
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Li S, Wang Y. Regulatory mechanism of DDX5 in ox-LDL-induced endothelial cell injury through the miR-640/SOX6 axis. Clin Hemorheol Microcirc 2024:CH242254. [PMID: 39093065 DOI: 10.3233/ch-242254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
BACKGROUND Endothelial dysfunction is an early and pre-clinical manifestation of coronary heart disease (CHD). OBJECTIVE This study investigates the role of DDX5 in oxidized low-density lipoprotein (ox-LDL)-induced endothelial cell injury to confer novel targets for the treatment of CHD. METHODS Endothelial cells were induced by ox-LDL. DDX5, pri-miR-640, pre-miR-640, miR-640, and SOX6 expressions were analyzed by RT-qPCR and Western blot. DDX5 expression was intervened by shRNA, followed by CCK-8 analysis of proliferation, flow cytometry detection of apoptosis, and tube formation assay analysis of angiogenic potential of cells. The binding between DDX5 and pri-miR-640 was determined by RIP, and the pri-miR-640 RNA stability was measured after actinomycin D treatment. Dual-luciferase assay verified the targeting relationship between miR-640 and SOX6. RESULTS DDX5 and miR-640 were highly expressed while SOX6 was poorly expressed in ox-LDL-induced endothelial cells. Silence of DDX5 augmented cell proliferation, abated apoptosis, and facilitated angiogenesis. Mechanistically, RNA binding protein DDX5 elevated miR-640 expression by weakening the degradation of pri-miR-640, thereby reducing SOX6 expression. Combined experimental results indicated that overexpression of miR-640 or low expression of SOX6 offset the protective effect of DDX5 silencing on cell injury. CONCLUSION DDX5 elevates miR-640 expression by repressing the degradation of pri-miR-640 and then reduces SOX6 expression, thus exacerbating ox-LDL-induced endothelial cell injury.
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Affiliation(s)
- Shuo Li
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of Panvascular Disease, Harbin, Heilongjiang, China
| | - Yu Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Park SW, Han MR. A pan-cancer analysis unveiling the function of NR4A family genes in tumor immune microenvironment, prognosis, and drug response. Genes Genomics 2024; 46:977-990. [PMID: 38976216 DOI: 10.1007/s13258-024-01539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/22/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND NR4A family genes play crucial roles in cancers. However, the role of NR4A family genes in cancers remains paradoxical as they promote or suppress tumorigenesis. OBJECTIVE We aimed to conduct comprehensive analyses of the association between the expression of NR4A family genes and tumor microenvironment (TME) based on bioinformatics methods. METHODS We collected RNA-seq data from 33 cancer types and 20 normal tissue sites from the TCGA and GTEx databases. Expression patterns of NR4A family genes and their associations with DNA methylation, miRNA, overall survival, drug responses, and tumor microenvironment were investigated. RESULTS Significant downregulation of all NR4A family genes was observed in 15 cancer types. DNA promoter methylation and expression of NR4A family genes were negatively correlated in five cancers. The expression of 10 miRNAs targeting NR4A family genes was negatively correlated with the expression of NR4A family genes. High expression of all NR4A family genes was associated with poor prognosis in stomach adenocarcinoma and increased expressions of NR4A2 and NR4A3 were associated with poor prognosis in adrenocortical carcinoma. In addition, we found an elevated expression of NR4A2, which enhances the response to various chemotherapeutic drugs, whereas NR4A3 decreases drug sensitivity. Interestingly, in breast cancer, NR4A3 was significantly associated with C2 (IFN-γ dominant), C3 (inflammatory), and C6 (TGF-β dominant) immune subtypes and infiltrated immune cell types, implying both oncogenic and tumor-suppressive functions of NR4A3 in breast cancer. CONCLUSION The NR4A family genes have the potential to serve as a diagnostic, prognostic, and immunological marker of human cancers.
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Affiliation(s)
- Seong-Woo Park
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Korea
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012, Korea.
- Institute for New Drug Development, College of Life Science and Bioengineering, Incheon National University, Incheon, 22012, Korea.
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45
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Xavier G, Mauer J, Ota VK, Santoro ML, Belangero SI. Influence of antipsychotic drugs on microRNA expression in schizophrenia patients - A systematic review. J Psychiatr Res 2024; 176:163-172. [PMID: 38870782 DOI: 10.1016/j.jpsychires.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/23/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Schizophrenia (SCZ) is a severe psychiatric disorder with unclear pathophysiology. Moreover, there is no specific biological marker to help clinicians to define a diagnosis, and medication is decided according to the psychiatrist's experience. In this scenario, microRNAs (miRNAs), which are small noncoding RNA molecules that regulate several genes, emerge as potential peripheral biomarkers to help not only the evaluation of the disease state but also the treatment response. Here, we systematically reviewed indexed literature and evaluated follow-up studies investigating the changes in miRNA expression due to antipsychotic treatment. We also assessed target genes and performed pathway enrichment analysis of miRNAs listed in this systematic review. A total of 11 studies were selected according to research criteria, and we observed that 28 miRNAs play a relevant role in schizophrenia pathogenesis or response to antipsychotic treatment, seven of those of extreme interest as possible biomarkers either for condition or treatment. Predicted targets of the miRNAs reviewed here were previously associated with schizophrenia in genome-wide studies, and pathway analysis showed enrichment for genes related to neural processes. With this review, we expect to highlight the importance of miRNAs in schizophrenia pathogenesis and its treatment and point out interesting miRNAs to future studies.
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Affiliation(s)
- Gabriela Xavier
- LiNC, Laboratory of Integrative Neuroscience - Department of Psychiatry - Universidade Federal de São Paulo, Brazil; Genetics Division - Department of Morphology and Genetics - Universidade Federal de São Paulo, Brazil
| | - Jessica Mauer
- LiNC, Laboratory of Integrative Neuroscience - Department of Psychiatry - Universidade Federal de São Paulo, Brazil; Genetics Division - Department of Morphology and Genetics - Universidade Federal de São Paulo, Brazil
| | - Vanessa K Ota
- LiNC, Laboratory of Integrative Neuroscience - Department of Psychiatry - Universidade Federal de São Paulo, Brazil; Genetics Division - Department of Morphology and Genetics - Universidade Federal de São Paulo, Brazil
| | - Marcos L Santoro
- LiNC, Laboratory of Integrative Neuroscience - Department of Psychiatry - Universidade Federal de São Paulo, Brazil; Disciplina de Biologia Molecular - Departamento de Bioquímica - Universidade Federal de São Paulo, Brazil
| | - Sintia I Belangero
- LiNC, Laboratory of Integrative Neuroscience - Department of Psychiatry - Universidade Federal de São Paulo, Brazil; Genetics Division - Department of Morphology and Genetics - Universidade Federal de São Paulo, Brazil.
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Zhou X, Lv Y, Xie H, Li Y, Liu C, Zheng M, Wu R, Zhou S, Gu X, Li J, Mi D. RNA sequencing of exosomes secreted by fibroblast and Schwann cells elucidates mechanisms underlying peripheral nerve regeneration. Neural Regen Res 2024; 19:1812-1821. [PMID: 38103248 PMCID: PMC10960293 DOI: 10.4103/1673-5374.387980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202408000-00035/figure1/v/2023-12-16T180322Z/r/image-tiff Exosomes exhibit complex biological functions and mediate a variety of biological processes, such as promoting axonal regeneration and functional recovery after injury. Long non-coding RNAs (lncRNAs) have been reported to play a crucial role in axonal regeneration. However, the role of the lncRNA-microRNA-messenger RNA (mRNA)-competitive endogenous RNA (ceRNA) network in exosome-mediated axonal regeneration remains unclear. In this study, we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts (FC-EXOs) and Schwann cells (SC-EXOs). Differential gene expression analysis, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, and protein-protein interaction network analysis were used to explore the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs. We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs, which suggests that it may promote axonal regeneration. In addition, using the miRWalk and Starbase prediction databases, we constructed a regulatory network of ceRNAs targeting Rps5, including 27 microRNAs and five lncRNAs. The ceRNA regulatory network, which included Ftx and Miat, revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury. Our findings suggest that exosomes derived from fibroblast and Schwann cells could be used to treat injuries of peripheral nervous system.
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Affiliation(s)
- Xinyang Zhou
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Yehua Lv
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, Jiangsu Province, China
| | - Huimin Xie
- Nantong Stomatological Hospital Affiliated to Nantong University, Nantong, Jiangsu Province, China
| | - Yan Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Chang Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Mengru Zheng
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Ronghua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Songlin Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xiaosong Gu
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Jingjing Li
- Department of General Practice, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Daguo Mi
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, Jiangsu Province, China
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Wipplinger M, Mink S, Bublitz M, Gassner C. Regulation of the Lewis Blood Group Antigen Expression: A Literature Review Supplemented with Computational Analysis. Transfus Med Hemother 2024; 51:225-236. [PMID: 39135855 PMCID: PMC11318966 DOI: 10.1159/000538863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 08/15/2024] Open
Abstract
Background The Lewis (Le) blood group system, unlike most other blood groups, is not defined by antigens produced internally to the erythrocytes and their precursors but rather by glycan antigens adsorbed on to the erythrocyte membrane from the plasma. These oligosaccharides are synthesized by the two fucosyltransferases FUT2 and FUT3 mainly in epithelial cells of the digestive tract and transferred to the plasma. At their place of synthesis, some Lewis blood group carbohydrate antigen variants also seem to be involved in various gastrointestinal malignancies. However, relatively little is known about the transcriptional regulation of FUT2 and FUT3. Summary To address this question, we screened existing literature and additionally used in silico prediction tools to identify novel candidate regulators for FUT2 and FUT3 and combine these findings with already known data on their regulation. With this approach, we were able to describe a variety of transcription factors, RNA binding proteins and microRNAs, which increase FUT2 and FUT3 transcription and translation upon interaction. Key Messages Understanding the regulation of FUT2 and FUT3 is crucial to fully understand the blood group system Lewis (ISBT 007 LE) phenotypes, to shed light on the role of the different Lewis antigens in various pathologies, and to identify potential new diagnostic targets for these diseases.
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Affiliation(s)
- Martin Wipplinger
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Sylvia Mink
- Central Medical Laboratories, Feldkirch, Austria
- Medical-Scientific Faculty, Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Maike Bublitz
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
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Hong Y, Yuan Q, Wang L, Yang Z, Xu P, Guan X, Chen C. Integrative bioinformatics analysis to identify ferroptosis-related genes in non-obstructive azoospermia. J Assist Reprod Genet 2024; 41:2145-2161. [PMID: 38902567 PMCID: PMC11339017 DOI: 10.1007/s10815-024-03155-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
PURPOSE The objective of this study was to discern ferroptosis-related genes (FRGs) linked to non-obstructive azoospermia and investigate the associated molecular mechanisms. METHOD A dataset related to azoospermia was retrieved from the Gene Expression Omnibus database, and FRGs were sourced from GeneCards. Ferroptosis-related differentially expressed genes (FRDEGs) were discerned. Subsequently, these genes underwent analyses encompassing Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, as well as protein-protein interaction (PPI) networks and assessments of functional similarity. Following the identification of hub genes, an exploration of immune infiltration, single-cell expression, diagnostic utility, and interactions involving hub genes, RNA-binding proteins (RBPs), transcription factors (TFs), microRNAs (miRNAs), and drugs was conducted. RESULTS A total of 35 differentially expressed FRGs were discerned. These genes demonstrated enrichment in functions and pathways associated with ferroptosis. From the PPI network, eight hub genes were selected. Functional similarity analysis highlighted the potential pivotal roles of HMOX1 and GPX4 in azoospermia. Analysis of immune cell infiltration indicated a significant decrease in activated dendritic cells in the azoospermia group, with notable correlations between hub genes, particularly SAT1 and HMGCR, and immune cell infiltration. Unique expression patterns of hub genes across various cell types in the human testis were observed, with GPX4 prominently enriched in spermatid/sperm. Eight hub genes exhibited robust diagnostic value (AUC > 0.75). Lastly, a comprehensive hub gene-miRNA-TF-RBP-drug network was constructed. CONCLUSION In summary, our investigation unveiled eight FRDEGs associated with azoospermia, which hold potential as biomarkers for the diagnosis and treatment of azoospermia.
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Affiliation(s)
- Yanggang Hong
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China
| | - Qichao Yuan
- Department of Pediatric Urology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China
| | - Lingfei Wang
- Department of Pediatric Urology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China
| | - Zihan Yang
- Department of Pediatric Urology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China
| | - Peiyu Xu
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China
| | - Xiaoju Guan
- Department of Pediatric Urology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China.
| | - Congde Chen
- Department of Pediatric Urology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
- Key Laboratory of Children Genitourinary Diseases of Wenzhou, Wenzhou, 325000, Zhejiang, China.
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Abulimiti M, Jia ZY, Wu Y, Yu J, Gong YH, Guan N, Xiong DQ, Ding N, Uddin N, Wang J. Exploring and clinical validation of prognostic significance and therapeutic implications of copper homeostasis-related gene dysregulation in acute myeloid leukemia. Ann Hematol 2024; 103:2797-2826. [PMID: 38879648 DOI: 10.1007/s00277-024-05841-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/08/2024] [Indexed: 07/28/2024]
Abstract
The patterns and biological functions of copper homeostasis-related genes (CHRGs) in acute myeloid leukemia (AML) remain unclear. We explored the patterns and biological functions of CHRGs in AML. Using independent cohorts, including TCGA-GTEx, GSE114868, GSE37642, and clinical samples, we identified 826 common differentially expressed genes. Specifically, 12 cuproptosis-related genes (e.g., ATP7A, ATP7B) were upregulated, while 17 cuproplasia-associated genes (e.g., ATOX1, ATP7A) were downregulated in AML. We used LASSO-Cox, Kaplan-Meier, and Nomogram analyses to establish prognostic risk models, effectively stratifying patients with AML into high- and low-risk groups. Subgroup analysis revealed that high-risk patients exhibited poorer overall survival and involvement in fatty acid metabolism, apoptosis, and glycolysis. Immune infiltration analysis indicated differences in immune cell composition, with notable increases in B cells, cytotoxic T cells, and memory T cells in the low-risk group, and increased monocytes and neutrophils in the high-risk group. Single-cell sequencing analysis corroborated the expression characteristics of critical CHRGs, such as MAPK1 and ATOX1, associated with the function of T, B, and NK cells. Drug sensitivity analysis suggested potential therapeutic agents targeting copper homeostasis, including Bicalutamide and Sorafenib. PCR validation confirmed the differential expression of 4 cuproptosis-related genes (LIPT1, SLC31A1, GCSH, and PDHA1) and 9 cuproplasia-associated genes (ATOX1, CCS, CP, MAPK1, SOD1, COA6, PDK1, DBH, and PDE3B) in AML cell line. Importantly, these genes serve as potential biomarkers for patient stratification and treatment. In conclusion, we shed light on the expression patterns and biological functions of CHRGs in AML. The developed risk models provided prognostic implications for patient survival, offering valuable information on the regulatory characteristics of CHRGs and potential avenues for personalized treatment in AML.
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Affiliation(s)
| | - Zheng-Yi Jia
- School of Pharmacy, Xinjiang Medical University, Urumqi, 830011, China
| | - Yun Wu
- Department of General Medicine, The First Affiliated Hospital of the Xinjiang Medical University, Urumqi, 830011, China
| | - Jing Yu
- Department of Teaching and Research, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Yue-Hong Gong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Na Guan
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Dai-Qin Xiong
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Nan Ding
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China
| | - Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Jie Wang
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, 830011, China.
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Dekkers MC, Lambooij JM, Pu X, Fagundes RR, Enciso-Martinez A, Kats K, Giepmans BNG, Guigas B, Zaldumbide A. Extracellular vesicles derived from stressed beta cells mediate monocyte activation and contribute to islet inflammation. Front Immunol 2024; 15:1393248. [PMID: 39114661 PMCID: PMC11303142 DOI: 10.3389/fimmu.2024.1393248] [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: 02/28/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Objective Beta cell destruction in type 1 diabetes (T1D) results from the combined effect of inflammation and recurrent autoimmunity. In recent years, the role played by beta cells in the development of T1D has evolved from passive victims of the immune system to active contributors in their own destruction. We and others have demonstrated that perturbations in the islet microenvironment promote endoplasmic reticulum (ER) stress in beta cells, leading to enhanced immunogenicity. Among the underlying mechanisms, secretion of extracellular vesicles (EVs) by beta cells has been suggested to mediate the crosstalk with the immune cell compartment. Methods To study the role of cellular stress in the early events of T1D development, we generated a novel cellular model for constitutive ER stress by modulating the expression of HSPA5, which encodes BiP/GRP78, in EndoC-βH1 cells. To investigate the role of EVs in the interaction between beta cells and the immune system, we characterized the EV miRNA cargo and evaluated their effect on innate immune cells. Results Analysis of the transcriptome showed that HSPA5 knockdown resulted in the upregulation of signaling pathways involved in the unfolded protein response (UPR) and changes the miRNA content of EVs, including reduced levels of miRNAs involved in IL-1β signaling. Treatment of primary human monocytes with EVs from stressed beta cells resulted in increased surface expression of CD11b, HLA-DR, CD40 and CD86 and upregulation of IL-1β and IL-6. Conclusion These findings indicate that the content of EVs derived from stressed beta cells can be a mediator of islet inflammation.
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Affiliation(s)
- Mette C. Dekkers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Joost M. Lambooij
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Xudong Pu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Raphael R. Fagundes
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Agustin Enciso-Martinez
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- Oncode institute, Leiden University Medical Center, Leiden, Netherlands
- Amsterdam Vesicle Center, Biomedical Engineering and Physics and Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Kim Kats
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ben N. G. Giepmans
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bruno Guigas
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
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