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Bader S, Tuller T. Advanced computational predictive models of miRNA-mRNA interaction efficiency. Comput Struct Biotechnol J 2024; 23:1740-1754. [PMID: 38689718 PMCID: PMC11058727 DOI: 10.1016/j.csbj.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 05/02/2024] Open
Abstract
The modeling of miRNA-mRNA interactions holds significant implications for synthetic biology and human health. However, this research area presents specific challenges due to the multifaceted nature of mRNA downregulation by miRNAs, influenced by numerous factors including competition or synergism among miRNAs and mRNAs. In this study, we present an improved computational model for predicting miRNA-mRNA interactions, addressing aspects not previously modeled. Firstly, we integrated a novel set of features that significantly enhanced the predictor's performance. Secondly, we demonstrated the cell-specific nature of certain aspects of miRNA-mRNA interactions, highlighting the importance of designing models tailored to specific cell types for improved accuracy. Moreover, we introduce a miRNA binding site interaction model (miBSIM) that, for the first time, accounts for both the distribution of miRNA binding sites along the mRNA and their respective strengths in regulating mRNA stability. Our analysis suggests that distant miRNA sites often compete with each other, revealing the intricate interplay of binding site interactions. Overall, our new predictive model shows a significant improvement of up to 6.43% over previous models in the field. The code of our model is available at https://www.cs.tau.ac.il/~tamirtul/miBSIM.
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Affiliation(s)
- Sharon Bader
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
- The Segol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
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2
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Zhang W, Li P. The suppression of nuclear factor kappa B/microRNA 222 axis alleviates lipopolysaccharide-induced acute lung injury through increasing the alkylglyceronephosphate synthase expression. J Infect Chemother 2024:S1341-321X(24)00232-0. [PMID: 39209261 DOI: 10.1016/j.jiac.2024.08.015] [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: 06/02/2024] [Revised: 08/01/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Acute lung injury (ALI) is a serious and rapidly progressing pulmonary disorder with a high mortality rate. In this study, we aimed to investigate the relationship between miR-222 and NF-κB (p65) activation in ALI. METHODS ALI was induced in mice using lipopolysaccharide (LPS). Lung tissues and bronchoalveolar lavage fluid were collected for analysis. MH-S cell lines were used as an ALI model. Various techniques including histopathology, molecular analysis, and cell culture assays were employed. RESULTS Increased miR-222 levels were observed in the LPS-induced ALI mouse model. ALI mice exhibited severe lung pathology, inflammatory cell infiltration, edema, elevated W/D ratio, MPO activity, and increased TNFα, IL1, and IL6 levels, which were reversed by miR-222 antagomir, confirming miR-222's exacerbation of LPS-induced ALI. miR-222 directly targeted the 3'-UTR of alkylglyceronephosphate synthase (AGPS) mRNA, reducing its expression. AGPS is crucial for plasmalogen synthesis, which protects against oxidative stress. NF-κB (p-p65) levels were increased in ALI models, and LPS promoted the enrichment of the miR-222 promoter region, suggesting NF-κB (p65) involvement in miR-222 transcriptional regulation. The NF-κB/miR-222/AGPS axis played a significant role in ALI progression. CONCLUSIONS The present study indicates that NF-κB (p65) activates miR-222 transcription by enriching its promoter region, leading to increased miR-222 expression. Elevated miR-222 levels downregulate AGPS, thereby accelerating the progression of ALI. Targeting the NF-κB/miR-222/AGPS axis may hold promise as a therapeutic approach for ALI, although further research is needed to fully understand its significance.
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Affiliation(s)
- Wei Zhang
- Intensive care unit, Shandong Provincial Third Hospital, Shandong University, Jinan, 250031, China.
| | - Pibao Li
- Intensive care unit, Shandong Provincial Third Hospital, Shandong University, Jinan, 250031, China.
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3
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Scalavino V, Piccinno E, Labarile N, Armentano R, Giannelli G, Serino G. Anti-Inflammatory Effects of miR-369-3p via PDE4B in Intestinal Inflammatory Response. Int J Mol Sci 2024; 25:8463. [PMID: 39126032 PMCID: PMC11312748 DOI: 10.3390/ijms25158463] [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: 07/02/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Cyclic nucleotide phosphodiesterases (PDEs) consist of a family of enzymes expressed in several types of cells, including inflammatory cells, that play a pivotal role in inflammation. Several studies have demonstrated that the inhibition of PDE4 results in a reduced inflammatory response via PKA and CREB signaling. Hence, PDE4 suppression improves the inflammatory feedback typical of several diseases, such as inflammatory bowel disease (IBD). In our previous studies, we have demonstrated that miR-369-3p regulates inflammatory responses, modulating different aspects of the inflammatory process. The aim of this study was to demonstrate an additional anti-inflammatory effect of miR-369-3p targeting PDE4B, one of the widely expressed isoforms in immune cells. We found that miR-369-3p was able to reduce the expression of PDE4B, elevating the intracellular levels of cAMP. This accumulation increased the expression of PKA and pCREB, mitigating the release of pro-inflammatory cytokines and promoting the release of anti-inflammatory cytokines. To prove that PDE4B is a good therapeutic target in IBD, we also demonstrate that the expression of PDE4B was increased in UC patients compared to healthy controls, affecting the immune infiltrate. PDE4B is considered an important player in inflammatory progression; hence, our results show the ability of miR-369-3p to ameliorate inflammation by targeting PDE4B, supporting its future application as a new therapeutic approach in IBD.
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Affiliation(s)
| | | | | | | | | | - Grazia Serino
- National Institute of Gastroenterology S. De Bellis, IRCCS Research Hospital, Via Turi 27, 70013 Castellana Grotte, Italy; (V.S.); (E.P.); (N.L.); (R.A.)
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4
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Menadi S, Kucuk B, Cacan E. Promoter Hypomethylation Upregulates ANXA2 Expression in Pancreatic Cancer and is Associated with Poor Prognosis. Biochem Genet 2024; 62:2721-2742. [PMID: 38001391 DOI: 10.1007/s10528-023-10577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/26/2023] [Indexed: 11/26/2023]
Abstract
Pancreatic cancer (PC) is one of the world's most aggressive and deadly cancers, owing to non-specific early clinical symptoms, late-stage diagnosis, and poor survival. Therefore, it is critical to identify specific biomarkers for its early diagnosis. Annexin A2 (ANXA2) is a calcium-dependent phospholipid-binding protein that has been reported to be upregulated in several cancer types, making it an emerging biomarker and potential cancer therapeutic target. However, the mechanism underlying the regulation of ANXA2 overexpression is still unclear. It is well established that genetic and epigenetic alterations may lead to widespread dysregulation of gene expression. Hence, in this study, we focused on exploring the regulatory mechanism of ANXA2 by investigating the transcriptional profile, methylation pattern, somatic mutation, and prognostic value of ANXA2 in PC using several bioinformatics databases. Our results revealed that the expression levels of ANXA2 were remarkably increased in PC tissues comparing to normal tissues. Furthermore, the high expression of ANXA2 was significantly related to the poor prognosis of PC patients. More importantly, we demonstrated for the first time that the ANXA2 promoter is hypomethylated in PC tissues compared to normal tissues which may result in ANXA2 overexpression in PC. However, more experimental research is required to corroborate our findings.
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Affiliation(s)
- Soumaya Menadi
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, 60250, Tokat, Turkey
| | - Burak Kucuk
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, 60250, Tokat, Turkey
| | - Ercan Cacan
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, 60250, Tokat, Turkey.
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5
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Sharma V, Vinchure OS, Yadav G, Sarkar C, Kulshreshtha R. A novel interplay between PRC2 and miR-3189 regulates epithelial-mesenchymal transition (EMT) via modulating COL6A2 in glioblastoma. J Cell Physiol 2024; 239:e31326. [PMID: 38860406 DOI: 10.1002/jcp.31326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/12/2024]
Abstract
Recent studies have shed light on disrupted collagen signaling in Gliomas, yet the regulatory landscape remains largely unexplored. This study enquired into the role of polycomb repressive complex-2 (PRC2)-mediated H3K27me3 modification, a key epigenetic factor in glioma. Using in-house data, we identified miRNAs downregulated in glioblastoma (GBM) with the potential to regulate Collagen VI family genes. Notably, miR-3189 emerged as a prime PRC2 target. Its expression was significantly downregulated in Indian GBM patients as well as other glioma cohorts. Mechanistic insights, involving Luciferase assays, mutagenesis, and Western blot analysis, confirmed direct targeting of Collagen VI member COL6A2 by miR-3189-3p. Functional assays demonstrated that miR-3189-3p restrained GBM malignancy by inhibiting proliferation, migration, and epithelial-mesenchymal transition (EMT). Conversely, COL6A2 overexpressed in GBM patients, countered miR-3189, and promoted the malignant phenotype. Gene set enrichment analysis highlighted EMT enrichment in GBM patients with elevated COL6A2 expression, carrying prognostic implications. This study uncovers intricate interactions between two epigenetic regulators-H3K27me3 and miR-3189-working synergistically to modulate Collagen VI gene; thus, influencing the malignancy of GBM. Targeting this H3K27me3|miR-3189-3p|COL6A2 axis presents a potential therapeutic avenue against GBM.
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Affiliation(s)
- Vikas Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- Centralized Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Omkar Suhas Vinchure
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Garima Yadav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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6
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Xu C, Wang Z, Liu Y, Duan K, Guan J. Delivery of miR-15b-5p via magnetic nanoparticle-enhanced bone marrow mesenchymal stem cell-derived extracellular vesicles mitigates diabetic osteoporosis by targeting GFAP. Cell Biol Toxicol 2024; 40:52. [PMID: 38967699 PMCID: PMC11226493 DOI: 10.1007/s10565-024-09877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/15/2024] [Indexed: 07/06/2024]
Abstract
Diabetic osteoporosis (DO) presents significant clinical challenges. This study aimed to investigate the potential of magnetic nanoparticle-enhanced extracellular vesicles (GMNPE-EVs) derived from bone marrow mesenchymal stem cells (BMSCs) to deliver miR-15b-5p, thereby targeting and downregulating glial fibrillary acidic protein (GFAP) expression in rat DO models. Data was sourced from DO-related RNA-seq datasets combined with GEO and GeneCards databases. Rat primary BMSCs, bone marrow-derived macrophages (BMMs), and osteoclasts were isolated and cultured. EVs were separated, and GMNPE targeting EVs were synthesized. Bioinformatic analysis revealed a high GFAP expression in DO-related RNA-seq and GSE26168 datasets for disease models. Experimental results confirmed elevated GFAP in rat DO bone tissues, promoting osteoclast differentiation. miR-15b-5p was identified as a GFAP inhibitor, but was significantly downregulated in DO and enriched in BMSC-derived EVs. In vitro experiments showed that GMNPE-EVs could transfer miR-15b-5p to osteoclasts, downregulating GFAP and inhibiting osteoclast differentiation. In vivo tests confirmed the therapeutic potential of this approach in alleviating rat DO. Collectively, GMNPE-EVs can effectively deliver miR-15b-5p to osteoclasts, downregulating GFAP expression, and hence, offering a therapeutic strategy for rat DO.
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Affiliation(s)
- Chen Xu
- Department of Orthopedics, Bengbu Medical University Affiliated to First Hospital, Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, No. 287, Changhuai Road, Longzihu District, Bengbu, 233000, Anhui Province, China
- Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, Bengbu, 233030, China
| | - Zhaodong Wang
- Department of Orthopedics, Bengbu Medical University Affiliated to First Hospital, Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, No. 287, Changhuai Road, Longzihu District, Bengbu, 233000, Anhui Province, China
- Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, Bengbu, 233030, China
| | - Yajun Liu
- Department of Orthopedics, Bengbu Medical University Affiliated to First Hospital, Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, No. 287, Changhuai Road, Longzihu District, Bengbu, 233000, Anhui Province, China
- Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, Bengbu, 233030, China
| | - Keyou Duan
- Department of Orthopedics, Bengbu Medical University Affiliated to First Hospital, Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, No. 287, Changhuai Road, Longzihu District, Bengbu, 233000, Anhui Province, China
- Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, Bengbu, 233030, China
| | - Jianzhong Guan
- Department of Orthopedics, Bengbu Medical University Affiliated to First Hospital, Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, No. 287, Changhuai Road, Longzihu District, Bengbu, 233000, Anhui Province, China.
- Anhui Province Key Laboratory of Tissue Transplantation (Bengbu Medical College), 2600 Donghai Avenue, Bengbu, 233030, China.
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7
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Poggio P, Rocca S, Fusella F, Ferretti R, Ala U, D'Anna F, Giugliano E, Panuzzo C, Fontana D, Palumbo V, Carrà G, Taverna D, Gambacorti-Passerini C, Saglio G, Fava C, Piazza R, Morotti A, Orso F, Brancaccio M. miR-15a targets the HSP90 co-chaperone Morgana in chronic myeloid leukemia. Sci Rep 2024; 14:15089. [PMID: 38956394 PMCID: PMC11220062 DOI: 10.1038/s41598-024-65404-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
Morgana is a ubiquitous HSP90 co-chaperone protein coded by the CHORDC1 gene. Morgana heterozygous mice develop with age a myeloid malignancy resembling human atypical myeloid leukemia (aCML), now renamed MDS/MPN with neutrophilia. Patients affected by this pathology exhibit low Morgana levels in the bone marrow (BM), suggesting that Morgana downregulation plays a causative role in the human malignancy. A decrease in Morgana expression levels is also evident in the BM of a subgroup of Philadelphia-positive (Ph+) chronic myeloid leukemia (CML) patients showing resistance or an incomplete response to imatinib. Despite the relevance of these data, the mechanism through which Morgana expression is downregulated in patients' bone marrow remains unclear. In this study, we investigated the possibility that Morgana expression is regulated by miRNAs and we demonstrated that Morgana is under the control of four miRNAs (miR-15a/b and miR-26a/b) and that miR-15a may account for Morgana downregulation in CML patients.
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MESH Headings
- Animals
- Humans
- Mice
- Bone Marrow/metabolism
- Bone Marrow/pathology
- Down-Regulation
- Gene Expression Regulation, Leukemic
- HSP90 Heat-Shock Proteins/metabolism
- HSP90 Heat-Shock Proteins/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Chaperones/metabolism
- Molecular Chaperones/genetics
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Affiliation(s)
- Pietro Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Stefania Rocca
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federica Fusella
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Roberta Ferretti
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ugo Ala
- Department of Veterinary Sciences, University of Turin, Grugliasco, TO, Italy
| | - Flora D'Anna
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Emilia Giugliano
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Cristina Panuzzo
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Valeria Palumbo
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Giovanna Carrà
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Daniela Taverna
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Carmen Fava
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- Hematology Division and Bone Marrow Unit, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Science, University of Turin, Orbassano, Italy
| | - Francesca Orso
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Translational Medicine (DIMET), University of Piemonte Orientale, Novara, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
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Zhang J, Zhu J, Zou X, Liu Y, Zhao B, Chen L, Li B, Chen B. Identifying autophagy-related mRNAs and potential ceRNA networks in meniscus degeneration based on RNA sequencing and experimental validation. Heliyon 2024; 10:e32782. [PMID: 38975204 PMCID: PMC11226846 DOI: 10.1016/j.heliyon.2024.e32782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/25/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose The intimate connection between long noncoding RNA (lncRNA) and autophagy has been established in cartilage degeneration. However, their roles in meniscal degeneration remain ambiguous. This study aimed to identify the key autophagy-related lncRNA and its associated regulatory network in meniscal degeneration in the context of osteoarthritis (OA). Methods RNA sequencing was performed to identify differentially expressed lncRNAs (DELs) and mRNAs (DEMs), which were then conducted to enrichment analyses using the DAVID database and Metascape. Autophagy-related DEMs were identified by combining DEMs with data from the Human Autophagy Database. Three databases were used to predict miRNA, and the DIANA LncBase Predicted database was utilized to predict miRNA-lncRNA interactions. Based on these predictions, comprehensive competitive endogenous RNA (ceRNA) network were constructed. The expression levels of the classical autophagy markers and autophagy-related ceRNA network were validated. Additionally, Gene Set Enrichment Analysis (GSEA) was performed using autophagy-related DEMs. Results 310 DELs and 320 DEMs were identified, with five upregulated and one downregulated autophagy-related DEMs. Through reverse prediction of miRNA, paired miRNA-lncRNA interactions, and verification using RT-qPCR, two lncRNAs (PCAT19, CLIP1-AS1), two miRNA (has-miR-3680-3p and has-miR-4795-3p) and two mRNAs (BAG3 and HSP90AB1) were included in the constructed ceRNA regulatory networks. GSEA indicated that the increased expression of autophagy-related mRNAs inhibited glycosaminoglycan biosynthesis in the degenerative meniscus. Conclusion This study presented the first construction of regulatory ceRNA network involving autophagy-related lncRNA-miRNA-mRNA interactions in OA meniscus. These findings offered valuable insights into the mechanisms underlying meniscal degeneration and provided potential targets for therapeutic intervention.
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Affiliation(s)
- Jun Zhang
- Department of Orthopedics, The First Hospital of Nanchang, The Third Affiliated Hospital of Nanchang University, Nanchang, 330008, Jiangxi, China
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Jiayong Zhu
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Xinyu Zou
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Yiming Liu
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Boming Zhao
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Liaobin Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Bin Li
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
| | - Biao Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430000, Hubei, China
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Bludau A, Schwartz U, Zeitler DM, Royer M, Meister G, Neumann ID, Menon R. Functional involvement of septal miR-132 in extinction and oxytocin-mediated reversal of social fear. Mol Psychiatry 2024; 29:1754-1766. [PMID: 37938765 PMCID: PMC11371636 DOI: 10.1038/s41380-023-02309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Social interactions are critical for mammalian survival and evolution. Dysregulation of social behavior often leads to psychopathologies such as social anxiety disorder, denoted by intense fear and avoidance of social situations. Using the social fear conditioning (SFC) paradigm, we analyzed expression levels of miR-132-3p and miR-124-3p within the septum, a brain region essential for social preference and avoidance behavior, after acquisition and extinction of social fear. Here, we found that SFC dynamically altered both microRNAs. Functional in vivo approaches using pharmacological strategies, inhibition of miR-132-3p, viral overexpression of miR-132-3p, and shRNA-mediated knockdown of miR-132-3p specifically within oxytocin receptor-positive neurons confirmed septal miR-132-3p to be critically involved not only in social fear extinction, but also in oxytocin-induced reversal of social fear. Moreover, Argonaute-RNA-co-immunoprecipitation-microarray analysis and further in vitro and in vivo quantification of target mRNA and protein, revealed growth differentiation factor-5 (Gdf-5) as a target of miR-132-3p. Septal application of GDF-5 impaired social fear extinction suggesting its functional involvement in the reversal of social fear. In summary, we show that septal miR-132-3p and its downstream target Gdf-5 regulate social fear expression and potentially mediate oxytocin-induced reversal of social fear.
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Affiliation(s)
- Anna Bludau
- Department of Behavioral and Molecular Neurobiology, University of Regensburg, Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Center, Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Daniela M Zeitler
- Regensburg Center for Biochemistry, Laboratory of RNA Biology, University of Regensburg, Regensburg, Germany
| | - Melanie Royer
- Department of Behavioral and Molecular Neurobiology, University of Regensburg, Regensburg, Germany
- Regensburg Center for Biochemistry, Laboratory of RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry, Laboratory of RNA Biology, University of Regensburg, Regensburg, Germany
| | - Inga D Neumann
- Department of Behavioral and Molecular Neurobiology, University of Regensburg, Regensburg, Germany.
| | - Rohit Menon
- Department of Behavioral and Molecular Neurobiology, University of Regensburg, Regensburg, Germany
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10
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Yang Y, Wang X, Li M, Wang S, Wang H, Chen Q, Lu S. Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy. PeerJ 2024; 12:e17486. [PMID: 38832038 PMCID: PMC11146330 DOI: 10.7717/peerj.17486] [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: 12/08/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs. The ASF-related mRNA expression dataset GSE136754 was retrieved from the Gene Expression Omnibus (GEO) database and systematically analyzed using a comprehensive bioinformatics method. A total of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in the p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network, consisting of 540 nodes and 1,065 edges, was constructed, and the top ten genes with the highest degree scores-ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1 and UQCRFS1-were identified as hub genes in the whole PPI network. Especially HDAC1, MDM2, MRPS10 and RPL7L1 were identified as potential robust obese-specific biomarkers due to their significant differences in single gene expression levels and high ROC area; this was further verified by quantitative real-time PCR (qRT-PCR) on abdominal subcutaneous fat samples from obese-type (Saba) and lean-type (Large White) pigs. Additionally, a mRNA-miRNA-lncRNA ceRNA network consisting of four potential biomarkers, 15 miRNAs and 51 lncRNAs was established, and two targeted lncRNAs with more connections, XIST and NEAT1, were identified as potentially important regulatory factors. The findings of this study may provide novel insights into the molecular mechanism involved in ASFD.
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Affiliation(s)
- Yongli Yang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Shuyan Wang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
- Faculty of Animal Science, Xichang University, Xichang, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
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11
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Orang A, Marri S, McKinnon RA, Petersen J, Michael MZ. Restricting Colorectal Cancer Cell Metabolism with Metformin: An Integrated Transcriptomics Study. Cancers (Basel) 2024; 16:2055. [PMID: 38893174 PMCID: PMC11171104 DOI: 10.3390/cancers16112055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Metformin is a first-line therapy for type 2 diabetes as it disrupts cellular metabolism. Despite the association between metformin and lower cancer incidence, the anti-tumour activity of the drug in colorectal cancer (CRC) is incompletely understood. This study identifies underlying molecular mechanisms by which metformin slows colorectal cancer cell proliferation by investigating metformin-associated microRNA (miRNA) and target gene pairs implicated in signalling pathways. METHODS The present study analysed changes in miRNAs and the coding transcriptome in CRC cells treated with a sublethal dose of metformin, followed by the contextual validation of potential miRNA-target gene pairs. RESULTS Analyses of small RNA and transcriptome sequencing data revealed 104 miRNAs and 1221 mRNAs to be differentially expressed in CRC cells treated with metformin for 72 h. Interaction networks between differentially expressed miRNAs and putative target mRNAs were identified. Differentially expressed genes were mainly implicated in metabolism and signalling processes, such as the PI3K-Akt and MAPK/ERK pathways. Further validation of potential miRNA-target mRNA pairs revealed that metformin induced miR-2110 and miR-132-3p to target PIK3R3 and, consequently, regulate CRC cell proliferation, cell cycle progression and the PI3K-Akt signalling pathway. Metformin also induced miR-222-3p and miR-589-3p, which directly target STMN1 to inhibit CRC cell proliferation and cell cycle progression. CONCLUSIONS This study identified novel changes in the coding transcriptome and small non-coding RNAs associated with metformin treatment of CRC cells. Integration of these datasets highlighted underlying mechanisms by which metformin impedes cell proliferation in CRC. Importantly, it identified the post-transcriptional regulation of specific genes that impact both metabolism and cell proliferation.
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Affiliation(s)
- Ayla Orang
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (A.O.); (S.M.); (R.A.M.); (J.P.)
| | - Shashikanth Marri
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (A.O.); (S.M.); (R.A.M.); (J.P.)
| | - Ross A. McKinnon
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (A.O.); (S.M.); (R.A.M.); (J.P.)
| | - Janni Petersen
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (A.O.); (S.M.); (R.A.M.); (J.P.)
- Nutrition and Metabolism, South Australia Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Michael Z. Michael
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (A.O.); (S.M.); (R.A.M.); (J.P.)
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Bedford Park, SA 5042, Australia
- Flinders Centre for Innovation in Cancer, Flinders Medical Centre, Bedford Park, SA 5042, Australia
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12
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Liu X, Nishikubo K, Ohgaki R, Okanishi H, Okuda S, Xu M, Kanai Y. Identification of tumor-suppressive miRNAs that target amino acid transporter LAT1 and exhibit anti-proliferative effects on cholangiocarcinoma cells. J Pharmacol Sci 2024; 154:301-311. [PMID: 38485348 DOI: 10.1016/j.jphs.2024.02.012] [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: 12/04/2023] [Revised: 01/24/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Amino acid transporter LAT1 is highly upregulated in various cancer types, including cholangiocarcinoma (CHOL), and contributes to the rapid proliferation of cancer cells and disease progression. However, the molecular mechanisms underlying the pathological upregulation of LAT1 remain largely unknown. This study pursued the possibility of miRNA-mediated regulation of the LAT1 expression in CHOL cells. Using online target prediction methods, we extracted five candidate miRNAs commonly predicted to regulate the LAT1 expression. Three of them, miR-194-5p, miR-122-5p, and miR-126-3p, were significantly downregulated in CHOL cancer compared to normal tissues. Correlation analysis revealed weak-to-moderate negative correlations between the expression of these miRNAs and LAT1 mRNA in CHOL cancer tissues. We selected miR-194-5p and miR-122-5p for further analyses and found that both miRNAs functionally target 3'UTR of LAT1 mRNA by a luciferase-based reporter assay. Transfection of the miRNA mimics significantly suppressed the LAT1 expression at mRNA and protein levels and inhibited the proliferation of CHOL cells, with a trend of affecting intracellular amino acids and amino acid-related signaling pathways. This study indicates that the decreased expression of these LAT1-targeting tumor-suppressive miRNAs contributes to the upregulation of LAT1 and the proliferation of CHOL cells, highlighting their potential for developing novel cancer therapeutics and diagnostics.
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Affiliation(s)
- Xingming Liu
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kou Nishikubo
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichi Ohgaki
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hiroki Okanishi
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Suguru Okuda
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Minhui Xu
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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13
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Abdoli Shadbad M, Baghbanzadeh A, Baradaran B. hsa-miR-34a-5p enhances temozolomide anti-tumoral effects on glioblastoma: in-silico and in-vitro study. EXCLI JOURNAL 2024; 23:384-400. [PMID: 38655096 PMCID: PMC11036064 DOI: 10.17179/excli2023-6404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024]
Abstract
Glioblastoma multiform (GBM) is a commonly diagnosed brain neoplasm with a poor prognosis. Accumulating evidence has highlighted the significance of microRNA (miR) dysregulation in tumor development and progression. This study investigated the effect of hsa-miR-34a-5p and its combination with temozolomide on GBM, the related molecular mechanisms, and the signaling pathway using in-silico and in-vitro approaches. The in-silico tumor bulk and single-cell RNA sequencing analyses were done on TCGA-GTEx, CGGA, GSE13276, GSE90603, and GSE182109 datasets. After selecting the A172 cell line, hsa-miR-34a-5p mimics were transfected, and the cell viability, migration, cell cycle, clonogenicity, and apoptosis of studied groups were studied using MTT, scratch, flow cytometry, colony formation, and Annexin V/PI assays. The mRNA expression of CASP9, CASP3, CASP8, MMP2, CD44, CDK6, CDK4, CCND1, RAF1, MAP2K1, MET, SRC, and CD274 was studied using qRT-PCR method. hsa-miR-34a-5p downregulated RAF1 expression, as the signaling factor of the MAPK pathway. The combined treatment significantly downregulated the expression of MET, SRC, and MAP2K1, leading to the inhibition of the MET/MAPK pathway compared to temozolomide. Besides exerting anti-tumoral effects on the cell viability, migration, cell cycle, apoptosis, and clonogenicity of A172 cells, its combination with temozolomide enhanced temozolomide anti-tumoral effect. Compared to temozolomide, the combined treatment significantly decreased CDK4, CDK6, CCND1, and MMP2 expression. hsa-miR-34a-5p targets RAF1, as the signaling factor of the MAPK pathway, and potentiates the temozolomide anti-tumoral effect on A172 cells.
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Affiliation(s)
- Mahdi Abdoli Shadbad
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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14
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Yu L, Ye J, Chen Q, Hong Q. lncRNA TTTY14 participates in the progression of repeated implantation failure by regulating the miR-6088/SEMA5A axis. J Assist Reprod Genet 2024; 41:727-737. [PMID: 38294620 PMCID: PMC10957803 DOI: 10.1007/s10815-024-03032-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
PURPOSE To identify potential biomarkers and the molecular mechanisms associated with repeated implantation failure (RIF), three microarray datasets, GSE71331 (lncRNA + mRNA), GSE111974 (lncRNA + mRNA), and GSE71332 (miRNA), were retrieved from the Gene Expression Omnibus (GEO) database. METHODS The differentially expressed mRNAs (DEMs), lncRNAs (DElncRNAs), and miRNAs (DEmiRNAs) between normal control samples (C group) and RIF samples (RIF group) were identified, and then a module partition analysis was performed based on weighted correlation network analysis (WGCNA). Following enrichment analysis of the genes, the lncRNA-miRNA-mRNA interactions (ceRNA) were examined. The mRNAs in the ceRNA network were evaluated using the GSE58144 dataset. Finally, the key RNAs were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). RESULTS Fifty-three DEmiRNAs, 327 DEMs, and 13 DElncRNAs were identified between the C and RIF groups. According to WGCNA, the magenta module was positively correlated with RIF disease status. The lncRNA-mRNA interaction analysis based on genes in the magenta module revealed the intersecting lncRNAs, including peptidylprolyl isomerase E-like pseudogene (PPIEL) and the testis-specific transcript, y-Linked 14 (TTTY14); these lncRNAs are mainly involved in functions, such as plasma membrane organization. The ceRNA network analysis revealed several interactions, such as TTTY14-miR-6088-semaphorin 5 A (SEMA5A). Finally, SEMA5A and the zinc finger protein 555 (ZNF555) were identified to be significantly upregulated in the RIF group compared with those in the C group in the GSE58144 dataset. The RT-qPCR results aligned with the above results. CONCLUSIONS Overall, TTTY14, ZNF555, SEMA5A, PPIEL, and miR-6088 could serve as novel biomarkers of RIF.
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Affiliation(s)
- Lingzhu Yu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China
| | - Jing Ye
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China
| | - Qiuju Chen
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China
| | - Qingqing Hong
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, No.639 Zhizaoju Road, Huangpu District, Shanghai, 200011, P.R. China.
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15
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Amber S, Zahid S. An in silico approach to identify potential downstream targets of miR-153 involved in Alzheimer's disease. Front Genet 2024; 15:1271404. [PMID: 38299037 PMCID: PMC10824926 DOI: 10.3389/fgene.2024.1271404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Background: In recent years, microRNAs (miRNAs) have emerged as key players in the pathophysiology of multiple diseases including Alzheimer's disease (AD). Messenger RNA (mRNA) targeting for regulation of gene expression by miRNAs has been implicated in the annotation of disease pathophysiology as well as in the explication of their starring role in contemporary therapeutic interventions. One such miRNA is miR-153 which mediates the survival of cortical neurons and inhibits plaque formation. However, the core mRNA targets of miR-153 have not been fully illustrated. Objective: The present study aimed to elucidate the potential involvement of miR-153 in AD pathogenesis and to reveal its downstream targets. Methods: miRanda was used to identify AD-associated targets of miR-153. TargetScan, PicTar, miRmap, and miRDB were further used to validate these targets. STRING 12 was employed to assess the protein-protein interaction network while Gene ontology (GO) analysis was carried out to identify the molecular functions exhibited by these gene targets. Results: In silico analysis using miRanda predicted five important AD-related targets of miR-153, including APP, SORL1, PICALM, USF1, and PSEN1. All five target genes are negatively regulated by miR-153 and are substantially involved in AD pathogenesis. A protein interaction network using STRING 12 uncovered 30 potential interacting partners for SORL1, PICALM, and USF1. GO analysis revealed that miR-153 target genes play a critical role in neuronal survival, differentiation, exon guidance, amyloid precursor protein processing, and synapse formation. Conclusion: These findings unravel the potential role of miR-153 in the pathogenesis of AD and provide the basis for forthcoming experimental studies.
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Affiliation(s)
| | - Saadia Zahid
- Department of Healthcare Biotechnology, Neurobiology Research Laboratory, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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16
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Perdaens O, van Pesch V. MicroRNAs are dysregulated in peripheral blood mononuclear cells in multiple sclerosis and correlate with T cell mediators. J Neuroimmunol 2024; 386:578196. [PMID: 38101084 DOI: 10.1016/j.jneuroim.2023.578196] [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: 03/07/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 12/17/2023]
Abstract
T cell mediators and microRNAs are involved in the pathogenesis of multiple sclerosis (MS), but their interaction largely remains undetermined. We investigated by RT-qPCR the dysregulation of microRNAs in peripheral blood mononuclear cells of MS patients versus healthy controls, according to radiological disease activity or treatment. Several microRNAs correlated positively/negatively with IL21/FOXP3 mRNA expression, but not with serum neurofilament light chain levels. Cytokine expression is conceivably balanced by several regulators, whereas microRNAs possibly target upstream transcription factors rather than directly cytokine mRNAs. Functional studies are needed to investigate their interaction, notably for the predicted targeting of FOXP3 by miR-34c-5p.
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Affiliation(s)
- Océane Perdaens
- Neurochemistry Group, Institute of NeuroScience (IoNS), Université catholique de Louvain (UCLouvain), avenue Emmanuel Mounier 53/B1.53.03, 1200 Brussels, Belgium.
| | - Vincent van Pesch
- Neurochemistry Group, Institute of NeuroScience (IoNS), Université catholique de Louvain (UCLouvain), avenue Emmanuel Mounier 53/B1.53.03, 1200 Brussels, Belgium; Department of Neurology, Cliniques universitaires Saint-Luc, Université catholique de Louvain (UCLouvain), avenue Hippocrate 10, 1200 Brussels, Belgium.
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17
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Ahirwar SS, Rizwan R, Sethi S, Shahid Z, Malviya S, Khandia R, Agarwal A, Kotnis A. Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species. Microrna 2024; 13:2-13. [PMID: 37929739 DOI: 10.2174/0122115366261005231018070640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Micro-RNAs are endogenous non-coding RNA moieties of 22-27 nucleotides that play a crucial role in the regulation of various biological processes and make them useful prognostic and diagnostic biomarkers. Discovery and experimental validation of miRNA is a laborious and time-consuming process. For early prediction, multiple bioinformatics databases are available for miRNA target prediction; however, their utility can confuse amateur researchers in selecting the most appropriate tools for their study. OBJECTIVE This descriptive review aimed to analyse the usability of the existing database based on the following criteria: accessibility, efficiency, interpretability, updatability, and flexibility for miRNA target prediction of 3'UTR of mRNA in diverse species so that the researchers can utilize the database most appropriate to their research. METHODS A systematic literature search was performed in PubMed, Google Scholar and Scopus databases up to November 2022. ≥10,000 articles found online, including ⁓130 miRNA tools, which contain various information on miRNA. Out of them, 31 databases that provide information on validated 3'UTR miRNAs target databases were included and analysed in this review. RESULTS These miRNA database tools are being used in varied areas of biological research to select the most suitable miRNA for their experimental validation. These databases, updated until the year 2021, consist of miRNA-related data from humans, animals, mice, plants, viruses etc. They contain 525-29806351 data entries, and information from most databases is freely available on the online platform. CONCLUSION Reviewed databases provide significant information, but not all information is accurate or up-to-date. Therefore, Diana-TarBase and miRWalk are the most comprehensive and up-to-date databases.
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Affiliation(s)
- Sonu Singh Ahirwar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Rehma Rizwan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Samdish Sethi
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Zainab Shahid
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Shivani Malviya
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Amit Agarwal
- Department of Neurosurgery, All India Institute of Medical Sciences Bhopal, Bhopal MP, 462020, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
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18
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Ortiz HG, Domingues WB, Kremer FS, Campos VF. An exploratory data analysis on genetic architecture in Bos taurus through miRNAs within QTLs and their target genes. Anim Biotechnol 2023; 34:4394-4402. [PMID: 36519853 DOI: 10.1080/10495398.2022.2154223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the genetic architecture is important because it allows us to understand the relationship between molecular markers, like miRNAs, QTLs and SNPs, and traits of interest such as milk yield, lipidic content in milk, heat tolerance etc. In the present study we performed an exploratory analysis that found an association of 480 miRNAs within QTLs related to 155 traits. We also discovered that those 480 miRNAs might modulate the expression of 12.374 genes. The most predominant traits available in the data were milk related, such as milk yield and fatty acids content in milk. Besides, the functional enrichment analysis revealed that some of those genes were linked to sensory perception, olfactory perception, perception of stimulus and chemical stimulus, localization, establishment of localization, transport etc. Furthermore, the discovery of miRNAs within QTLs and their target analysis suggests that they might be associated with characteristics of interest. By analyzing these relationships, we strongly encourage that future QTL studies should include miRNAs analysis. Altogether, our analysis enabled us to explore the association between multiple complex traits, miRNAs within QTLs and their target genes in Bos taurus that might have implications in breeding programs.
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Affiliation(s)
- Hadassa G Ortiz
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Frederico S Kremer
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius F Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
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19
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Kumar R, Madhavan T, Ponnusamy K, Sohn H, Haider S. Computational study of the motor neuron protein KIF5A to identify nsSNPs, bioactive compounds, and its key regulators. Front Genet 2023; 14:1282234. [PMID: 38028604 PMCID: PMC10667939 DOI: 10.3389/fgene.2023.1282234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Kinesin family member 5A (KIF5A) is a motor neuron protein expressed in neurons and involved in anterograde transportation of organelles, proteins, and RNA. Variations in the KIF5A gene that interfere with axonal transport have emerged as a distinguishing feature in several neurodegenerative disorders, including hereditary spastic paraplegia (HSP10), Charcot-Marie-Tooth disease type 2 (CMT2), and Amyotrophic Lateral Sclerosis (ALS). Methods: In this study, we implemented a computational structural and systems biology approach to uncover the role of KIF5A in ALS. Using the computational structural biology method, we explored the role of non-synonymous Single Nucleotide Polymorphism (nsSNPs) in KIF5A. Further, to identify the potential inhibitory molecule against the highly destabilizing structure variant, we docked 24 plant-derived phytochemicals involved in ALS. Results: We found KIF5AS291F variant showed the most structure destabilizing behavior and the phytocompound "epigallocatechin gallate" showed the highest binding affinity (-9.0 Kcal/mol) as compared to wild KIF5A (-8.4 Kcal/mol). Further, with the systems biology approach, we constructed the KIF5A protein-protein interaction (PPI) network to identify the associated Kinesin Families (KIFs) proteins, modules, and their function. We also constructed a transcriptional and post-transcriptional regulatory network of KIF5A. With the network topological parameters of PPIN (Degree, Bottleneck, Closeness, and MNC) using CytoHubba and computational knock-out experiment using Network Analyzer, we found KIF1A, 5B, and 5C were the significant proteins. The functional modules were highly enriched with microtubule motor activity, chemical synaptic transmission in neurons, GTP binding, and GABA receptor activity. In regulatory network analysis, we found KIF5A post-transcriptionally down-regulated by miR-107 which is further transcriptionally up-regulated by four TFs (HIF1A, PPARA, SREBF1, and TP53) and down-regulated by three TFs (ZEB1, ZEB2, and LIN28A). Discussion: We concluded our study by finding a crucial variant of KIF5A and its potential therapeutic target (epigallocatechin gallate) and KIF5A associated significant genes with important regulators which could decrypt the novel therapeutics in ALS and other neurodegenerative diseases.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Thirumurthy Madhavan
- Department of Genetic Engineering, Computational Biology Lab, SRM Institute of Science and Technology, Chennai, India
| | | | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, Republic of Korea
| | - Shazia Haider
- Department of Biosciences, Jamia Millia University, New Delhi, India
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20
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Xu LB, Qin YF, Su L, Huang C, Xu Q, Zhang R, Shi XD, Sun R, Chen J, Song Z, Jiang X, Shang L, Xiao G, Kong X, Liu C, Wong PP. Cathepsin-facilitated invasion of BMI1-high hepatocellular carcinoma cells drives bile duct tumor thrombi formation. Nat Commun 2023; 14:7033. [PMID: 37923799 PMCID: PMC10624910 DOI: 10.1038/s41467-023-42930-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
Bile duct tumor thrombosis (BDTT) is a complication mostly observed in patients with advanced hepatocellular carcinoma (HCC), causing jaundice and associated with poor clinical outcome. However, its underlying molecular mechanism is unclear. Here, we develop spontaneous preclinical HCC animal models with BDTT to identify the role of BMI1 expressing tumor initiating cells (BMI1high TICs) in inducing BDTT. BMI1 overexpression transforms liver progenitor cells into BMI1high TICs, which possess strong tumorigenicity and increased trans-intrahepatic biliary epithelial migration ability by secreting lysosomal cathepsin B (CTSB). Orthotopic liver implantation of BMI1high TICs into mice generates tumors and triggers CTSB mediated bile duct invasion to form tumor thrombus, while CTSB inhibitor treatment prohibits BDTT and extends mouse survival. Clinically, the elevated serum CTSB level determines BDTT incidence in HCC patients. Mechanistically, BMI1 epigenetically up-regulates CTSB secretion in TICs by repressing miR-218-1-3p expression. These findings identify a potential diagnostic and therapeutic target for HCC patients with BDTT.
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Affiliation(s)
- Lei-Bo Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Yu-Fei Qin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Liangping Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Cheng Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Qiuping Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Rui Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xiang-De Shi
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Ruipu Sun
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Jiali Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Zhixiao Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xue Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Lihuan Shang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Gang Xiao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xiangzhan Kong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Chao Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China.
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
- Guangzhou Key Laboratory of Precise Diagnosis and Treatment of Biliary Tract Cancer, Department of Biliary-Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Ping-Pui Wong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510120, China.
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
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21
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Chen Y, Xu H, Tang H, Li H, Zhang C, Jin S, Bai D. miR-9-5p expression is associated with vascular invasion and prognosis in hepatocellular carcinoma, and in vitro verification. J Cancer Res Clin Oncol 2023; 149:14657-14671. [PMID: 37584711 DOI: 10.1007/s00432-023-05257-1] [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: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is a common liver malignancy. Early vascular invasion (VI) has been associated with poor prognosis in HCC patients. MicroRNAs (miRNAs) play a significant role in the emergence and development of many tumor types. METHODS Differential expression analysis of miRNAs related to VI was performed based on data from the TCGA database, and survival-associated miRNAs identified. We identified miR-9-5p as a survival-related miRNA and verified its expression in 61 clinical samples using quantitative real-time PCR. We further performed functional enrichment analysis, protein-protein interaction analysis, univariate and multivariate analysis of the survival-related miRNAs, and cell function assays. RESULTS In this study, we identified miR-9-5p that could predict VI and prognosis in HCC patients. Cellular experiments demonstrated that downregulation of miR‑9‑5p inhibits migration, invasion, and angiogenesis of HCC cells. Further, we explored and verified the possible mechanism through which miR-9-5p is involved in HCC progression. Univariate and multivariate analysis revealed that miR-9-5p was an independent risk factor for HCC. Finally, the nomogram based on miR-9-5p showed a good predictive value of HCC survival. CONCLUSIONS MiR-9-5p is associated with VI in HCC, and higher expression of miR-9-5p indicates poor prognosis in HCC.
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Affiliation(s)
- Yuan Chen
- Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Hao Xu
- Yangzhou University Medical College, Yangzhou, Jiangsu, China
- General Surgery Department of Siyang Hospital, Suqian, Jiangsu, China
| | - Hao Tang
- Yangzhou University Medical College, Yangzhou, Jiangsu, China
| | - Hongyuan Li
- Dalian Medical University, Dalian, Liaoning, China
| | - Chi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shengjie Jin
- Department of Hepatobiliary and Pancreatic Surgery, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dousheng Bai
- Department of Hepatobiliary and Pancreatic Surgery, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu, China.
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22
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Nath A, Bora U. RNAinsecta: A tool for prediction of precursor microRNA in insects and search for their target in the model organism Drosophila melanogaster. PLoS One 2023; 18:e0287323. [PMID: 37812647 PMCID: PMC10561860 DOI: 10.1371/journal.pone.0287323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/03/2023] [Indexed: 10/11/2023] Open
Abstract
INTRODUCTION AND BACKGROUND Pre-MicroRNAs are the hairpin loops from which microRNAs are produced that have been found to negatively regulate gene expression in several organisms. In insects, microRNAs participate in several biological processes including metamorphosis, reproduction, immune response, etc. Numerous tools have been designed in recent years to predict novel pre-microRNA using binary machine learning classifiers where prediction models are trained with true and pseudo pre-microRNA hairpin loops. Currently, there are no existing tool that is exclusively designed for insect pre-microRNA detection. AIM Application of machine learning algorithms to develop an open source tool for prediction of novel precursor microRNA in insects and search for their miRNA targets in the model insect organism, Drosophila melanogaster. METHODS Machine learning algorithms such as Random Forest, Support Vector Machine, Logistic Regression and K-Nearest Neighbours were used to train insect true and false pre-microRNA features with 10-fold Cross Validation on SMOTE and Near-Miss datasets. miRNA targets IDs were collected from miRTarbase and their corresponding transcripts were collected from FlyBase. We used miRanda algorithm for the target searching. RESULTS In our experiment, SMOTE performed significantly better than Near-Miss for which it was used for modelling. We kept the best performing parameters after obtaining initial mean accuracy scores >90% of Cross Validation. The trained models on Support Vector Machine achieved accuracy of 92.19% while the Random Forest attained an accuracy of 80.28% on our validation dataset. These models are hosted online as web application called RNAinsecta. Further, searching target for the predicted pre-microRNA in Drosophila melanogaster has been provided in RNAinsecta.
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Affiliation(s)
- Adhiraj Nath
- Department of BSBE, IIT Guwahati, North Guwahati, Assam, India
| | - Utpal Bora
- Department of BSBE, IIT Guwahati, North Guwahati, Assam, India
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23
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Winters AN, Berry AK, Dewenter TA, Chowdhury NU, Wright KL, Cameron JE. MicroRNA expression associated with low-grade cervical intraepithelial neoplasia outcomes. J Cancer Res Clin Oncol 2023; 149:11969-11978. [PMID: 37421453 PMCID: PMC10465678 DOI: 10.1007/s00432-023-05023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/24/2023] [Indexed: 07/10/2023]
Abstract
PURPOSE Only a fraction of low-grade cervical intraepithelial neoplasia (CIN) progresses to high-grade CIN; however, the biological processes that differentiate progressive CIN from CIN that resolves naturally are poorly understood. MicroRNAs (miRNAs) are important epigenetic regulators of gene expression and thus, miRNA expression profiling can reveal the dysregulated biology underlying disease processes. The purpose of this case-control study was to reveal miRNA expression patterns and predict the underlying biological pathways that are associated with clinical outcomes of low-grade CIN. METHODS Women with low-grade CIN diagnosis and definitive clinical outcomes (n = 51) were identified retrospectively using electronic clinical records. Comprehensive miRNA expression profiling was performed on the low-grade CIN diagnostic cervical biopsies retrieved from pathology archives. Differential miRNA expression was analyzed by comparing women with CIN that progressed to women with CIN that resolved naturally. RESULTS Differential expression of 29 miRNAs was observed in low-grade CIN that progressed to high-grade compared to low-grade CIN that resolved. Of these, 24 were significantly downregulated in progressive CIN, including miR-638, miR-3196, miR-4488, and miR-4508, while 5 miRNAs, including miR-1206a, were significantly upregulated. Computational gene ontology analysis based on the discovered miRNAs and their putative mRNA targets revealed biological processes associated with oncogenic phenotypes. CONCLUSION Distinct miRNA expression profiles are associated with clinical outcomes of low-grade CIN. The functional effects of the differentially expressed miRNAs may be biological determinants of CIN progression or resolution.
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Affiliation(s)
- Ashley N Winters
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA
| | - Alex K Berry
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Ave. 8638, New Orleans, LA, 70112, USA
| | - Tracy A Dewenter
- Department of Pathology, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA
| | - Nowrin U Chowdhury
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, 1161 21St Ave S Medical Center North T-2219, Nashville, TN, 37232, USA
| | - Kelly L Wright
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA
- Medical Science Liaison, Gynecologic Oncology, AstraZeneca. 1 Medimmune Way, Gaithersburg, MD, 20878, USA
| | - Jennifer E Cameron
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA.
- The Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, 1901 Perdido St., New Orleans, LA, 70112, USA.
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24
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Mansoori B, Kiani S, Mezajin AA, Zandi P, Banaie H, Rostamzadeh D, Cho WC, Duijf PHG, Mansoori B, Baradaran B. MicroRNA-143-5p Suppresses ER-Positive Breast Cancer Development by Targeting Oncogenic HMGA2. Clin Breast Cancer 2023; 23:e480-e490.e3. [PMID: 37596147 DOI: 10.1016/j.clbc.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND About 70%-80% of breast cancers (BCs) express estrogen receptors (ER-positive). MicroRNAs (miRNAs) are a group of small endogenous noncoding RNAs that play a critical regulatory role in cancer development and progression, including in BC. MiRNA deficiency promotes the development of BCs. MiR-143-5p is one of the most commonly dysregulated miRNAs in BC but its role as a tumor suppressor remains unclear. MATERIALS AND METHODS MiR-143-3p and -5p expression in breast tissue was analyzed using TCGA and StarBase databases. Expression in BC subclasses and survival analyses were conducted. Clinical samples were collected, cell cultures created, and gene expression assays performed following previous studies. Protein expression, luciferase reporter, wound healing, DAPI staining, cell cycle, colony formation, spheroid, CD44 FACS, and proliferation assays were conducted following various protocols. RESULTS Here, we find that both miR-143-3p and miR-143-5p levels are considerably lower in BC tissue compared to normal breast tissue and low miR-143 expression predicts poor prognosis in ER+ BC patients. In-depth analyses identified 3 miR-143-5p binding sites in the 3' untranslated region (UTR) of the DNA binding protein High Mobility Group AT-Hook 2 (HMGA2). Luciferase reporter assays using wild-type and mutant HMGA2 3'UTR sequences and Western blot analyses demonstrated that HMGA2 is a direct and bona fide miR-143-5p target in BC cells. In addition, we show that restoration of miR-143-5p expression suppresses metastasis-related features of ER+ BC cells, including reduced tumor cell migration, increased E-cadherin expression, and decreased vimentin and N-cadherin expression. Furthermore, miR-143-5p reduces cell proliferation, cell cycle entry, and stemness, while promoting apoptosis moderately. Finally, patient sample pathway analyses demonstrated that these mechanisms are also active in BC. CONCLUSIONS Altogether, our findings shed new light on miR-143-5p's anticancer biological functions in BC progression by directly targeting HMGA2. This suggests that restoration of miR-143-5p could be a promising new therapeutic approach for the treatment of ER+ BC.
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Affiliation(s)
- Behnaz Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, East Azerbaijan, Iran; Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shiva Kiani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | - Homadokht Banaie
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Khuzestan, Iran
| | - Davoud Rostamzadeh
- Department of Clinical Biochemistry, Yasuj University of Medical Sciences, Yasuj, Iran; Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Pascal H G Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane QLD, Australia; Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane QLD, Australia; Centre for Data Science, Queensland University of Technology, Brisbane QLD, Australia; Cancer and Aging Research Program, Queensland University of Technology, Brisbane QLD, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Behzad Mansoori
- The Wistar Institute, Molecular and Cellular Oncogenesis Program, Philadelphia, PA.
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, East Azerbaijan, Iran.
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25
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Hackl LM, Fenn A, Louadi Z, Baumbach J, Kacprowski T, List M, Tsoy O. Alternative splicing impacts microRNA regulation within coding regions. NAR Genom Bioinform 2023; 5:lqad081. [PMID: 37705830 PMCID: PMC10495541 DOI: 10.1093/nargab/lqad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. Through alternative splicing, transcripts might lose the exon with the miRNA target site and become unresponsive to miRNA regulation. To check this hypothesis, we studied the role of miRNA target sites in both coding and non-coding regions using six cancer data sets from The Cancer Genome Atlas (TCGA) and Parkinson's disease data from PPMI. First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. To check whether alternative splicing interferes with this regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites in the coding regions to that of transcripts without target sites. Models containing transcripts with target sites perform significantly better. We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.
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Affiliation(s)
- Lena Maria Hackl
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
| | - Amit Fenn
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Zakaria Louadi
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Campusvej 50, 5230 Odense, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Rebenring 56, 38106 Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Olga Tsoy
- Institute for Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607 Hamburg, Germany
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26
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Yang Y, Wang X, Wang S, Chen Q, Li M, Lu S. Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning. Genes (Basel) 2023; 14:1695. [PMID: 37761835 PMCID: PMC10531182 DOI: 10.3390/genes14091695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Intramuscular fat (IMF) content is a key determinant of pork quality. Controlling the genetic and physiological factors of IMF and the expression patterns of various genes is important for regulating the IMF content and improving meat quality in pig breeding. Growing evidence has suggested the role of genetic factors and breeds in IMF deposition; however, research on the sex factors of IMF deposition is still lacking. The present study aimed to identify potential sex-specific biomarkers strongly associated with IMF deposition in low- and high-IMF pig populations. The GSE144780 expression dataset of IMF deposition-related genes were obtained from the Gene Expression Omnibus. Initially, differentially expressed genes (DEGs) were detected in male and female low-IMF (162 DEGs, including 64 up- and 98 down-regulated genes) and high-IMF pigs (202 DEGs, including 147 up- and 55 down-regulated genes). Moreover, hub genes were screened via PPI network construction. Furthermore, hub genes were screened for potential sex-specific biomarkers using the least absolute shrinkage and selection operator machine learning algorithm, and sex-specific biomarkers in low-IMF (troponin I (TNNI1), myosin light chain 9(MYL9), and serpin family C member 1(SERPINC1)) and high-IMF pigs (CD4 molecule (CD4), CD2 molecule (CD2), and amine oxidase copper-containing 2(AOC2)) were identified, and then verified by quantitative real-time PCR (qRT-PCR) in semimembranosus muscles. Additionally, the gene set enrichment analysis and single-sample gene set enrichment analysis of hallmark gene sets were collectively performed on the identified biomarkers. Finally, the transcription factor-biomarker and lncRNA-miRNA-mRNA (biomarker) networks were predicted. The identified potential sex-specific biomarkers may provide new insights into the molecular mechanisms of IMF deposition and the beneficial foundation for improving meat quality in pig breeding.
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Affiliation(s)
| | | | | | | | | | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.Y.); (X.W.); (S.W.); (Q.C.); (M.L.)
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27
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Hejenkowska ED, Mitash N, Donovan JE, Chandra A, Bertrand C, De Santi C, Greene CM, Mu F, Swiatecka-Urban A. TGF-β1 Inhibition of ACE2 Mediated by miRNA Uncovers Novel Mechanism of SARS-CoV-2 Pathogenesis. J Innate Immun 2023; 15:629-646. [PMID: 37579743 PMCID: PMC10601633 DOI: 10.1159/000533606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for COVID-19, utilizes receptor binding domain (RBD) of spike glycoprotein to interact with angiotensin (Ang)-converting enzyme 2 (ACE2). Altering ACE2 levels may affect entry of SARS-CoV-2 and recovery from COVID-19. Decreased cell surface density of ACE2 leads to increased local levels of Ang II and may contribute to mortality resulting from acute lung injury and fibrosis during COVID-19. Studies published early during the COVID-19 pandemic reported that people with cystic fibrosis (PwCF) had milder symptoms, compared to people without CF. This finding was attributed to elevated ACE2 levels and/or treatment with the high efficiency CFTR modulators. Subsequent studies did not confirm these findings reporting variable effects of CFTR gene mutations on ACE2 levels. Transforming growth factor (TGF)-β signaling is essential during SARS-CoV-2 infection and dominates the chronic immune response in severe COVID-19, leading to pulmonary fibrosis. TGF-β1 is a gene modifier associated with more severe lung disease in PwCF but its effects on the COVID-19 course in PwCF is unknown. To understand whether TGF-β1 affects ACE2 levels in the airway, we examined miRNAs and their gene targets affecting SARS-CoV-2 pathogenesis in response to TGF-β1. Small RNAseq and micro(mi)RNA profiling identified pathways uniquely affected by TGF-β1, including those associated with SARS-CoV-2 invasion, replication, and the host immune responses. TGF-β1 inhibited ACE2 expression by miR-136-3p and miR-369-5p mediated mechanism in CF and non-CF bronchial epithelial cells. ACE2 levels were higher in two bronchial epithelial cell models expressing the most common CF-causing mutation in CFTR gene F508del, compared to controls without the mutation. After TGF-β1 treatment, ACE2 protein levels were still higher in CF, compared to non-CF cells. TGF-β1 prevented the modulator-mediated rescue of F508del-CFTR function while the modulators did not prevent the TGF-β1 inhibition of ACE2 levels. Finally, TGF-β1 reduced the interaction between ACE2 and the recombinant spike RBD by lowering ACE2 levels and its binding to RBD. Our data demonstrate novel mechanism whereby TGF-β1 inhibition of ACE2 in CF and non-CF bronchial epithelial cells may modulate SARS-CoV-2 pathogenicity and COVID-19 severity. By reducing ACE2 levels, TGF-β1 may decrease entry of SARS-CoV-2 into the host cells while hindering the recovery from COVID-19 due to loss of the anti-inflammatory and regenerative effects of ACE2. The above outcomes may be modulated by other, miRNA-mediated effects exerted by TGF-β1 on the host immune responses, leading to a complex and yet incompletely understood circuitry.
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Affiliation(s)
| | - Nilay Mitash
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joshua E. Donovan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Anvita Chandra
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Carol Bertrand
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Catherine M. Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Fangping Mu
- Center for Research Computing, University of Pittsburgh, Pittsburgh, PA, USA
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28
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Hu Y, Zhang G, Yang Q, Pu N, Li K, Li B, Cooper DN, Tong Z, Li W, Chen JM. The East Asian-specific LPL p.Ala288Thr (c.862G > A) missense variant exerts a mild effect on protein function. Lipids Health Dis 2023; 22:119. [PMID: 37550668 PMCID: PMC10405562 DOI: 10.1186/s12944-023-01875-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Lipoprotein lipase (LPL) is the key enzyme responsible for the hydrolysis of triglycerides. Loss-of-function variants in the LPL gene are associated with hypertriglyceridemia (HTG) and HTG-related diseases. Unlike nonsense, frameshift and canonical GT-AG splice site variants, a pathogenic role for clinically identified LPL missense variants should generally be confirmed by functional analysis. Herein, we describe the clinical and functional analysis of a rare LPL missense variant. METHODS Chinese patients with HTG-associated acute pancreatitis (HTG-AP) were screened for rare nonsense, frameshift, missense or canonical GT-AG splice site variants in LPL and four other lipid metabolism-related genes (APOC2, APOA5, GPIHBP1 and LMF1) by Sanger sequencing. The functional consequences of the LPL missense variant of interest were characterized by in vitro expression in HEK-293T and COS-7 cells followed by Western blot and LPL activity assays. RESULTS Five unrelated HTG-AP patients were found to be heterozygous for a rare East Asian-specific LPL missense variant, c.862G > A (p.Ala288Thr). All five patients were adult males, and all were overweight and had a long history of alcohol consumption. Transfection of LPL wild-type and c.862G > A expression vectors into two cell lines followed by Western blot analysis served to exclude the possibility that the p.Ala288Thr missense variant either impaired protein synthesis or increased protein degradation. Contrary to a previous functional study that claimed that p.Ala288Thr had a severe impact on LPL function (reportedly having 36% normal activity), our experiments consistently demonstrated that the variant had a comparatively mild effect on LPL functional activity, which was mediated through its impact upon LPL protein secretion (~ 20% reduced secretion compared to wild-type). CONCLUSIONS In this study, we identified the East Asian-specific LPL c.862G > A (p.Ala288Thr) missense variant in five unrelated HTG-AP patients. We demonstrated that this variant exerted only a relatively mild effect on LPL function in two cell lines. Heterozygosity for this LPL variant may have combined with alcohol consumption to trigger HTG-AP in these patients.
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Affiliation(s)
- Yuepeng Hu
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - Guofu Zhang
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - Qi Yang
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - Na Pu
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - Kaiwei Li
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - Baiqiang Li
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Zhihui Tong
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China
| | - Weiqin Li
- Department of Critical Care Medicine, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, No.305 East Zhongshan Road, Xuanwu District, Nanjing, 210002, Jiangsu, China.
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, F-29200, France
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Fatima SA, Nasim MT, Malik A, Rehman SU, Waris S, Rauf M, Ali SS, Haq F, Awan HM. In silico analysis and experimental validation shows negative correlation between miR-1183 and cell cycle progression gene 1 expression in colorectal cancer. PLoS One 2023; 18:e0289082. [PMID: 37540697 PMCID: PMC10403070 DOI: 10.1371/journal.pone.0289082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression by binding to the 3' untranslated regions (UTR) of target genes. Aberrant expression of miRNAs can lead to disease, including cancer. Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Among several factors, differential expression of miRNA can have serious consequences on disease progression. This study was designed to computationally identify and experimentally verify strong miRNA candidates that could influence CRC progression. In silico analysis of publicly available gene expression microarray datasets revealed significant upregulation of miR-1183 in CRC. Comparison of mRNA microarray expression data with predicted miR-1183 targets led to the identification of cell cycle progression gene 1 (CCPG1) as strong, negatively correlated miR-1183 target. Expression analysis by means of quantitative PCR validated the inverse correlation between miR-1183 and CCPG1 in colorectal cancer tissues. CCPG1 indirectly modulates the cell cycle by interacting with the PH/DH domain of Dbs (Rho-specific guanine nucleotide exchange factor). Interestingly, the computational analysis also showed that miR-1183 is upregulated in liver and gastric cancer. This finding is notable as the liver and stomach are the primary metastatic sites for colorectal cancer and hepatocellular carcinoma respectively. This novel finding highlights the broader implications of miR-1183 dysregulation beyond primary CRC, potentially serving as a valuable prognostic marker and a therapeutic target for both primary and metastatic CRC.
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Affiliation(s)
- Syeda Alina Fatima
- Department of Biosciences, Cancer Genetics and Epigenetics Lab, COMSATS University Islamabad, Islamabad, Pakistan
| | - Mubeen Tabish Nasim
- Department of Biosciences, Cancer Genetics and Epigenetics Lab, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ambrin Malik
- Department of Biosciences, Cancer Genetics and Epigenetics Lab, COMSATS University Islamabad, Islamabad, Pakistan
| | - Saif Ur Rehman
- Department of Biosciences, Cancer Genetics and Epigenetics Lab, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Manal Rauf
- Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Syed Salman Ali
- Combined Military Hospital, Kharian, Pakistan
- Department of Cellular Pathology, Royal London Hospital, Barts Health, NHS Trust, London, United Kingdom
| | - Farhan Haq
- Department of Biosciences, Cancer Genetics and Epigenetics Lab, COMSATS University Islamabad, Islamabad, Pakistan
- Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Hassaan Mehboob Awan
- Department of Biosciences, Cancer Genetics and Epigenetics Lab, COMSATS University Islamabad, Islamabad, Pakistan
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Takahashi S, Takagane K, Itoh G, Kuriyama S, Umakoshi M, Goto A, Yanagihara K, Yashiro M, Iijima K, Tanaka M. CCDC85A is regulated by miR-224-3p and augments cancer cell resistance to endoplasmic reticulum stress. Front Oncol 2023; 13:1196546. [PMID: 37534255 PMCID: PMC10391547 DOI: 10.3389/fonc.2023.1196546] [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: 03/30/2023] [Accepted: 06/29/2023] [Indexed: 08/04/2023] Open
Abstract
MicroRNAs (miRNAs) play pivotal roles in the tumor microenvironment. Here, we analyzed miRNAs in tumor stromal fibroblasts. Expression of miR-224-3p in cancer-associated fibroblasts (CAF) from scirrhous gastric cancer patients was lower than in normal fibroblasts (NF). Introduction of a miR-224-3p mimic attenuated migration and invasion of CAF. Coiled-coil domain containing 85A (CCDC85A), whose function in tumors is not understood, was the target gene of miR-224-3p. Immunohistological analysis revealed that CCDC85A is expressed to varying degrees by cancer cells and CAFs in gastric and pancreatic carcinomas. Downregulation of CCDC85A in cancer cells revealed that these cells are vulnerable to endoplasmic reticulum (ER) stress induced by thapsigargin or tunicamycin, which were ameliorated after addback of CCDC85A. Injection of NF-derived exosomes containing miR-224-3p into the xenograft tumor increased tumor shrinkage by cisplatin treatment. Mechanistically, CCDC85A associated with the molecular chaperone GRP78 and GRP94, thereby inhibiting association of these negative regulators of the unfolded protein response (UPR), leading to sustained activation of PERK and downstream eIF2〈 and ATF4 upon ER stress. These data suggest a novel miR-224-3p-mediated function for CCDC85A: protection from ER stress and cisplatin resistance.
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Affiliation(s)
- So Takahashi
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
- Department of Gastroenterology, Akita University Graduate School of Medicine, Akita, Japan
| | - Kurara Takagane
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Go Itoh
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Sei Kuriyama
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Michinobu Umakoshi
- Department of Cellular and Organ Pathology, Akita University Graduate School of Medicine, Akita, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Akita University Graduate School of Medicine, Akita, Japan
| | - Kazuyoshi Yanagihara
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Masakazu Yashiro
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Katsunori Iijima
- Department of Gastroenterology, Akita University Graduate School of Medicine, Akita, Japan
| | - Masamitsu Tanaka
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
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Liu Z, Zhou X, Chen B, Wu Z, Zhang C, Gu C, Li J, Yang X. Noncoding RNAs-based high KIF26B expression correlates with poor prognosis and tumor immune infiltration in colon cancer. Cell Cycle 2023; 22:1726-1742. [PMID: 37436127 PMCID: PMC10446804 DOI: 10.1080/15384101.2023.2222520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND The protein kinesin family member 26B (KIF26B) is aberrantly expressed in various cancers. However, its particular role and association with tumor immune infiltration in colon adenocarcinoma (COAD) remain unclear. METHODS All original data were downloaded directly from The Cancer Genome Atlas (TCGA), UCSC Xena, and Gene Expression Omnibus (GEO) databases and processed with R 3.6.3. KIF26B expression was analyzed using Oncomine, TIMER, TCGA, GEO databases, and our clinical specimens. KIF26B expression at the protein level was explored with Human Protein Atlas (HPA) database. The upstream miRNAs and lncRNAs were predicted by StarBase and validated using RT-qPCR. Correlation of KIF26B expression with the expression of immune-related or immune checkpoint genes and GSEA analysis of KIF26B-related genes were investigated via R software. Relationship of KIF26B expression with immune biomarkers or tumor immune infiltration levels was studied through GEPIA2 and TIMER databases. RESULTS KIF26B was upregulated, and its overexpression was closely related to overall survival (OS), disease-specific survival (DSS), progression-free interval (PFI), T stage, N stage, and CEA levels in COAD. MIR4435-2HG/hsa-miR-500a-3p/KIF26B axis was identified as the promising regulatory pathway of KIF26B. KIF26B expression was positively correlated with immune-related genes, tumor immune infiltration, and biomarker genes of immune cells in COAD, and KIF26B-related genes were significantly enriched in macrophage activation-related pathways. Expression of immune checkpoint genes, including PDCD1, CD274, and CTLA4, was also closely related to KIF26B expression. CONCLUSIONS Our results clarified that ncRNA-based increased KIF26B expression was associated with a worse prognosis and high tumor immune infiltration in COAD.
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Affiliation(s)
- Zhihong Liu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xin Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Chen
- Nursing Department, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ziyu Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Cuifeng Zhang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Changji Gu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Juan Li
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Liu Y, Ding M, Pan S, Zhou R, Yao J, Fu R, Yu H, Lu Z. MicroRNA-23a-3p is upregulated in plasma exosomes of bulbar-onset ALS patients and targets ERBB4. Neuroscience 2023:S0306-4522(23)00250-6. [PMID: 37290686 DOI: 10.1016/j.neuroscience.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease related to the progressive death of motor neurons. Understanding the pathogenesis of ALS continues to provide considerable challenges. Bulbar-onset ALS involves faster functional loss and shorter survival time than spinal cord-onset ALS. However, debate is ongoing regarding typical plasma miRNA changes in ALS patients with bulbar onset. Exosomal miRNAs have not yet been described as a tool for bulbar-onset ALS diagnosis or prognosis prediction. In this study, candidate exosomal miRNAs were identified by small RNA sequencing using samples from patients with bulbar-onset ALS and healthy controls. Potential pathogenic mechanisms were identified through enrichment analysis of target genes for differential miRNAs. Expression of miR-16-5p, miR-23a-3p, miR-22-3p, and miR-93-5p was significantly up-regulated in plasma exosomes from bulbar-onset ALS patients compared with healthy control subjects. Among them, miR-16-5p and miR-23a-3p were significantly lower in spinal-onset ALS patients than those with bulbar-onset. Furthermore, up-regulation of miR-23a-3p in motor neuron-like NSC-34 cells promoted apoptosis and inhibited cell viability. This miRNA was found to directly target ERBB4 and regulate the AKT/GSK3β pathway. Collectively, the above miRNAs and their targets are related to the development of bulbar-onset ALS. Our research indicates that miR-23a-3p might have an effect on motor neuron loss observed in bulbar-onset ALS and may be a novel target for the therapy of ALS in the future.
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Affiliation(s)
- Yue Liu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Man Ding
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sijia Pan
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rumeng Zhou
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiajia Yao
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rong Fu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hang Yu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zuneng Lu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China.
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Ortega-Ribera M, Gibert-Ramos A, Abad-Jordà L, Magaz M, Téllez L, Paule L, Castillo E, Pastó R, de Souza Basso B, Olivas P, Orts L, Lozano JJ, Villa R, Bosch J, Albillos A, García-Pagán JC, Gracia-Sancho J. Increased sinusoidal pressure impairs liver endothelial mechanosensing, uncovering novel biomarkers of portal hypertension. JHEP Rep 2023; 5:100722. [PMID: 37151732 PMCID: PMC10154975 DOI: 10.1016/j.jhepr.2023.100722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background & Aims Portal hypertension (PH) is a frequent and severe clinical syndrome associated with chronic liver disease. Considering the mechanobiological effects of hydrostatic pressure and shear stress on endothelial cells, we hypothesised that PH might influence the phenotype of liver sinusoidal endothelial cells (LSECs) during disease progression. The aim of this study was to investigate the effects of increased hydrodynamic pressure on LSECs and to identify endothelial-derived biomarkers of PH. Methods Primary LSECs were cultured under normal or increased hydrodynamic pressure within a pathophysiological range (1 vs. 12 mmHg) using a microfluidic liver-on-a-chip device. RNA sequencing was used to identify pressure-sensitive genes, which were validated in liver biopsies from two independent cohorts of patients with chronic liver disease with PH (n = 73) and participants without PH (n = 23). Biomarker discovery was performed in two additional independent cohorts of 104 patients with PH and 18 patients without PH. Results Transcriptomic analysis revealed marked deleterious effect of pathological pressure in LSECs and identified chromobox 7 (CBX7) as a key transcription factor diminished by pressure. Hepatic CBX7 downregulation was validated in patients with PH and significantly correlated with hepatic venous pressure gradient. MicroRNA 181a-5p was identified as pressure-induced upstream regulator of CBX7. Two downstream targets inhibited by CBX7, namely, E-cadherin (ECAD) and serine protease inhibitor Kazal-type 1 (SPINK1), were found increased in the bloodstream of patients with PH and were highly predictive of PH and clinically significant PH. Conclusions We characterise the detrimental effects of increased hydrodynamic pressure on the sinusoidal endothelium, identify CBX7 as a pressure-sensitive transcription factor, and propose the combination of two of its reported products as biomarkers of PH. Impact and Implications Increased pressure in the portal venous system that typically occurs during chronic liver disease (called portal hypertension) is one of the main drivers of related clinical complications, which are linked to a higher risk of death. In this study, we found that pathological pressure has a harmful effect on liver sinusoidal endothelial cells and identified CBX7 as a key protein involved in this process. CBX7 regulates the expression of E-cadherin and SPINK1, and consequently, measuring these proteins in the blood of patients with chronic liver disease allows the prediction of portal hypertension and clinically significant portal hypertension.
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Affiliation(s)
- Martí Ortega-Ribera
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
| | - Albert Gibert-Ramos
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
| | - Laia Abad-Jordà
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Marta Magaz
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Luis Téllez
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Biosanitaria (IRYCIS), Universidad de Alcalá, Madrid, Spain
| | - Lorena Paule
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Biosanitaria (IRYCIS), Universidad de Alcalá, Madrid, Spain
| | - Elisa Castillo
- Gastroenterology and Hepatology Department, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Biosanitaria (IRYCIS), Universidad de Alcalá, Madrid, Spain
| | - Raül Pastó
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
| | - Bruno de Souza Basso
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- PUCRS, Escola de Ciências, Laboratório de Pesquisa em Biofísica Celular e Inflamação, Porto Alegre, Brazil
| | - Pol Olivas
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
| | - Lara Orts
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Juan José Lozano
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Rosa Villa
- Grupo de Aplicaciones Biomédicas, Institut de Microelectrònica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Bellaterra, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBERBBN), Madrid, Spain
| | - Jaime Bosch
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Agustín Albillos
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Gastroenterology and Hepatology Department, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Biosanitaria (IRYCIS), Universidad de Alcalá, Madrid, Spain
| | - Joan Carles García-Pagán
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Jordi Gracia-Sancho
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Laboratory, IDIBAPS Biomedical Research Institute, Barcelona, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBEREHD), Madrid, Spain
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Corresponding author. Address: IDIBAPS Biomedical Research Institute, Rosselló 149, 08036, Barcelona, Spain. Tel.: +34 932275400 #4306
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Pimenta R, Mioshi CM, Gonçalves GL, Candido P, Camargo JA, Guimarães VR, Chiovatto C, Ghazarian V, Romão P, da Silva KS, Dos Santos GA, Silva IA, Srougi M, Nahas WC, Leite KR, Viana NI, Reis ST. Intratumoral Restoration of miR-137 Plus Cholesterol Favors Homeostasis of the miR-137/Coactivator p160/AR Axis and Negatively Modulates Tumor Progression in Advanced Prostate Cancer. Int J Mol Sci 2023; 24:ijms24119633. [PMID: 37298588 DOI: 10.3390/ijms24119633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/18/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
MicroRNAs (miRNAs) have gained a prominent role as biomarkers in prostate cancer (PCa). Our study aimed to evaluate the potential suppressive effect of miR-137 in a model of advanced PCa with and without diet-induced hypercholesterolemia. In vitro, PC-3 cells were treated with 50 pmol of mimic miR-137 for 24 h, and gene and protein expression levels of SRC-1, SRC-2, SRC-3, and AR were evaluated by qPCR and immunofluorescence. We also assessed migration rate, invasion, colony-forming ability, and flow cytometry assays (apoptosis and cell cycle) after 24 h of miRNA treatment. For in vivo experiments, 16 male NOD/SCID mice were used to evaluate the effect of restoring miR-137 expression together with cholesterol. The animals were fed a standard (SD) or hypercholesterolemic (HCOL) diet for 21 days. After this, we xenografted PC-3 LUC-MC6 cells into their subcutaneous tissue. Tumor volume and bioluminescence intensity were measured weekly. After the tumors reached 50 mm3, we started intratumor treatments with a miR-137 mimic, at a dose of 6 μg weekly for four weeks. Ultimately, the animals were killed, and the xenografts were resected and analyzed for gene and protein expression. The animals' serum was collected to evaluate the lipid profile. The in vitro results showed that miR-137 could inhibit the transcription and translation of the p160 family, SRC-1, SRC-2, and SRC-3, and indirectly reduce the expression of AR. After these analyses, it was determined that increased miR-137 inhibits cell migration and invasion and impacts reduced proliferation and increased apoptosis rates. The in vivo results demonstrated that tumor growth was arrested after the intratumoral restoration of miR-137, and proliferation levels were reduced in the SD and HCOL groups. Interestingly, the tumor growth retention response was more significant in the HCOL group. We conclude that miR-137 is a potential therapeutic miRNA that, in association with androgen precursors, can restore and reinstate the AR-mediated axis of transcription and transactivation of androgenic pathway homeostasis. Further studies involving the miR-137/coregulator/AR/cholesterol axis should be conducted to evaluate this miR in a clinical context.
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Affiliation(s)
- Ruan Pimenta
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
- D'Or Institute for Research and Education (ID'Or), São Paulo 04501000, SP, Brazil
| | - Carolina Mie Mioshi
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
- Campus Santo André, Universidade Federal do ABC, Santo André 09210580, SP, Brazil
| | - Guilherme L Gonçalves
- Laboratory of Renal Physiology, Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508000, SP, Brazil
| | - Patrícia Candido
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Juliana A Camargo
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Vanessa R Guimarães
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Caroline Chiovatto
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
- Campus Ipiranga, Centro Universitário São Camilo, São Paulo 04263200, SP, Brazil
| | - Vitória Ghazarian
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Poliana Romão
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Karina Serafim da Silva
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
- Campus Ipiranga, Centro Universitário São Camilo, São Paulo 04263200, SP, Brazil
| | - Gabriel A Dos Santos
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Iran A Silva
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Miguel Srougi
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
- D'Or Institute for Research and Education (ID'Or), São Paulo 04501000, SP, Brazil
| | - William C Nahas
- Uro-Oncology Group, Urology Department, Institute of Cancer Estate of São Paulo (ICESP), São Paulo 01246000, SP, Brazil
| | - Kátia R Leite
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
| | - Nayara I Viana
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
- Campus Passos, Universidade do Estado de Minas Gerais-UEMG, Passos 37900106, MG, Brazil
| | - Sabrina T Reis
- Laboratório de Investigação Médica 55 (LIM55), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246903, SP, Brazil
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Qiao XR, Zheng T, Xie Y, Yao X, Yuan Z, Wu Y, Zhou D, Chen T. MiR-146a rs2910164 (G/C) polymorphism is associated with the development and prognosis of acute coronary syndromes: an observational study including case control and validation cohort. J Transl Med 2023; 21:325. [PMID: 37189131 DOI: 10.1186/s12967-023-04140-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Polymorphisms in microRNAs (miRNAs) play an important role in acute coronary syndromes (ACS). The purpose of this study was to assess the association of miR-146a rs2910164 and miR-34b rs4938723 polymorphisms with the development and prognosis of ACS and to explore the underlying mechanisms. METHODS A case-control study of 1171 subjects was included to determine the association of miR-146a rs2910164 and miR-34b rs4938723 polymorphisms with ACS risk. An additional 612 patients with different miR-146a rs2910164 genotypes, who underwent percutaneous coronary intervention (PCI) were included in the validation cohort and followed for 14 to 60 months. The endpoint was major adverse cardiovascular events (MACE). A luciferase reporter gene assay was used to validate the interaction of oxi-miR-146a(G) with the IKBA 3'UTR. Potential mechanisms were validated using immunoblotting and immunostaining. RESULTS The miR-146a rs2910164 polymorphism was significantly associated with the risk of ACS (Dominant model: CG + GG vs. CC, OR = 1.270, 95% CI (1.000-1.613), P = 0.049; Recessive model: GG vs. CC + CG, OR = 1.402, 95% CI (1.017-1.934), P = 0.039). Serum inflammatory factor levels were higher in patients with the miR-146a rs2910164 G allele than in those with the C allele. MiR-146a rs2910164 polymorphism in dominant model was associated with the incidence of MACE in post-PCI patients (CG + GG vs. CC, HR = 1.405, 95% CI (1.018-1.939), P = 0.038). However, the miR-34b rs4938723 polymorphism was not associated with the prevalence and prognosis of ACS. The G allele of miR-146a rs2910164 tends to be oxidized in ACS patients. The miRNA fractions purified from monocytes isolated from ACS patients were recognized by the 8OHG antibody. Mispairing of Oxi-miR-146a(G) with the 3'UTR of IKBA results in decreased IκBα protein expression and activation of the NF-κB inflammatory pathway. P65 expression was higher in atherosclerotic plaques from patients carrying the miR-146a rs2910164 G allele. CONCLUSION The variant of miR-146a rs2910164 is closely associated with the risk of ACS in Chinese Han population. Patients carrying miR-146a rs2910164 G allele may have worse pathological change and poorer post-PCI prognosis, partly due to the oxidatively modified miR-146a mispairing with 3'UTR of IKBA and activating NF-κB inflammatory pathways.
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Affiliation(s)
- Xiang-Rui Qiao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Tao Zheng
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Yifei Xie
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Xinyi Yao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Zuyi Yuan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Yue Wu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China
| | - Dong Zhou
- Department of Cardiovascular Medicine, Yongchuan Hospital of Chongqing Medical University, 439 XuanHua Road, Chongqing, 402160, China.
| | - Tao Chen
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Molecular Cardiology, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, 710061, China.
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Kalantzakos T, Hooper K, Das S, Sullivan T, Canes D, Moinzadeh A, Rieger-Christ K. MicroRNA-155-5p Targets JADE-1, Promoting Proliferation, Migration, and Invasion in Clear Cell Renal Cell Carcinoma Cells. Int J Mol Sci 2023; 24:ijms24097825. [PMID: 37175531 PMCID: PMC10178234 DOI: 10.3390/ijms24097825] [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: 03/03/2023] [Revised: 03/30/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) incidence has been rising in recent years, with strong association between differential microRNA (miRNA) expression and neoplastic progression. Specifically, overexpression of miR-155-5p has been associated with promoting aggressive cancer in ccRCC and other cancers. In this study, we further investigate the role of this miRNA and one of its protein targets, Jade-1, to better understand the mechanism behind aggressive forms of ccRCC. Jade-1, a tumor suppressor, is stabilized by Von-Hippel Lindau (VHL), which is frequently mutated in ccRCC. Experiments featuring downregulation of miR-155-5p in two ccRCC cell lines (786-O and Caki-1) attenuated their oncogenic potential and led to increased levels of Jade-1. Conversely, knockdown experiments with an anti-Jade-1 shRNA in 786-O and Caki-1 cells showed increased metastatic potential through elevated proliferation, migration, and invasion rates. In a mouse xenograft model, downregulation of miR-155 decreased the rate of tumor implantation and proliferation. Direct interaction between miR-155-5p and Jade-1 was confirmed through a 3'UTR luciferase reporter assay. These findings further elucidate the mechanism of action of miR-155-5p in driving an aggressive phenotype in ccRCC through its role in regulating Jade-1.
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Affiliation(s)
- Thomas Kalantzakos
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
| | - Kailey Hooper
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
| | - Sanjna Das
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
| | - Travis Sullivan
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
| | - David Canes
- Department of Urology, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
| | - Alireza Moinzadeh
- Department of Urology, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
| | - Kimberly Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
- Department of Urology, Lahey Hospital and Medical Center, Burlington, MA 01805, USA
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Balaskas P, Goljanek-Whysall K, Clegg PD, Fang Y, Cremers A, Smagul A, Welting TJM, Peffers MJ. MicroRNA Signatures in Cartilage Ageing and Osteoarthritis. Biomedicines 2023; 11:biomedicines11041189. [PMID: 37189806 DOI: 10.3390/biomedicines11041189] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Osteoarthritis is the most common degenerative joint disorder. MicroRNAs are gene expression regulators that act post-transcriptionally to control tissue homeostasis. Microarray analysis was undertaken in osteoarthritic intact, lesioned and young intact cartilage. Principal component analysis showed that young intact cartilage samples were clustered together; osteoarthritic samples had a wider distribution; and osteoarthritic intact samples were separated into two subgroups, osteoarthritic-Intact-1 and osteoarthritic-Intact-2. We identified 318 differentially expressed microRNAs between young intact and osteoarthritic lesioned cartilage, 477 between young intact and osteoarthritic-Intact-1 cartilage and 332 between young intact and osteoarthritic-Intact-2 cartilage samples. For a selected list of differentially expressed microRNAs, results were verified in additional cartilage samples using qPCR. Of the validated DE microRNAs, four-miR-107, miR-143-3p, miR-361-5p and miR-379-5p-were selected for further experiments in human primary chondrocytes treated with IL-1β. Expression of these microRNAs decreased in human primary chondrocytes treated with IL-1β. For miR-107 and miR-143-3p, gain- and loss-of-function approaches were undertaken and associated target genes and molecular pathways were investigated using qPCR and mass spectrometry proteomics. Analyses showed that WNT4 and IHH, predicted targets of miR-107, had increased expression in osteoarthritic cartilage compared to young intact cartilage and in primary chondrocytes treated with miR-107 inhibitor, and decreased expression in primary chondrocytes treated with miR-107 mimic, suggesting a role of miR-107 in chondrocyte survival and proliferation. In addition, we identified an association between miR-143-3p and EIF2 signalling and cell survival. Our work supports the role of miR-107 and miR-143-3p in important chondrocyte mechanisms regulating proliferation, hypertrophy and protein translation.
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Affiliation(s)
- Panagiotis Balaskas
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Katarzyna Goljanek-Whysall
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
- Department of Physiology, College of Medicine, Nursing and Health Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Peter D Clegg
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Andy Cremers
- Department of Orthopaedic Surgery, Medical Centre, Maastricht University, 6202 AZ Maastricht, The Netherlands
| | - Aibek Smagul
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Tim J M Welting
- Department of Orthopaedic Surgery, Medical Centre, Maastricht University, 6202 AZ Maastricht, The Netherlands
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
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Jaśkiewicz M, Moszyńska A, Gebert M, Collawn JF, Bartoszewski R. EPAS1 resistance to miRNA-based regulation contributes to prolonged expression of HIF-2 during hypoxia in human endothelial cells. Gene 2023; 868:147376. [PMID: 36934786 DOI: 10.1016/j.gene.2023.147376] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
The cellular adaptation to hypoxia is regulated by hypoxia inducible factors: HIF-1 and HIF-2. HIF-1 mediates response to acute hypoxia, whereas HIF-2 allows adaptation to chronic oxygen deprivation. The hypoxic transition from HIF-1 to HIF-2 is possible due to the low stability of HIF-1α subunit transcript (HIF1A) and the stable mRNA of HIF-2α (EPAS1). Notably, although many micro-RNAs (miRNAs) that regulate endothelial HIF-1 levels during hypoxia have been identified, in case of HIF-2, no analogous ones have been found so far. In this work, using different methods, we tested 23 microRNA that were predicted to interact with the EPAS1 transcript (18 of which were induced during prolonged hypoxia), and we demonstrated that none of them were functional in vitro. This suggests that HIF-2α transcript is much less prone to miRNA-related destabilization during hypoxia.
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Affiliation(s)
- Maciej Jaśkiewicz
- International Research Agenda 3P- Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.
| | | | - Magdalena Gebert
- Department of Medical Laboratory Diagnostics - Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, Gdansk, Poland.
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Rafał Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.
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Tripodi L, Sasso E, Feola S, Coluccino L, Vitale M, Leoni G, Szomolay B, Pastore L, Cerullo V. Systems Biology Approaches for the Improvement of Oncolytic Virus-Based Immunotherapies. Cancers (Basel) 2023; 15:1297. [PMID: 36831638 PMCID: PMC9954314 DOI: 10.3390/cancers15041297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Oncolytic virus (OV)-based immunotherapy is mainly dependent on establishing an efficient cell-mediated antitumor immunity. OV-mediated antitumor immunity elicits a renewed antitumor reactivity, stimulating a T-cell response against tumor-associated antigens (TAAs) and recruiting natural killer cells within the tumor microenvironment (TME). Despite the fact that OVs are unspecific cancer vaccine platforms, to further enhance antitumor immunity, it is crucial to identify the potentially immunogenic T-cell restricted TAAs, the main key orchestrators in evoking a specific and durable cytotoxic T-cell response. Today, innovative approaches derived from systems biology are exploited to improve target discovery in several types of cancer and to identify the MHC-I and II restricted peptide repertoire recognized by T-cells. Using specific computation pipelines, it is possible to select the best tumor peptide candidates that can be efficiently vectorized and delivered by numerous OV-based platforms, in order to reinforce anticancer immune responses. Beyond the identification of TAAs, system biology can also support the engineering of OVs with improved oncotropism to reduce toxicity and maintain a sufficient portion of the wild-type virus virulence. Finally, these technologies can also pave the way towards a more rational design of armed OVs where a transgene of interest can be delivered to TME to develop an intratumoral gene therapy to enhance specific immune stimuli.
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Affiliation(s)
- Lorella Tripodi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Emanuele Sasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Sara Feola
- Laboratory of Immunovirotherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00100 Helsinki, Finland
- Translational Immunology Research Program (TRIMM), University of Helsinki, 00100 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00100 Helsinki, Finland
| | - Ludovica Coluccino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Maria Vitale
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Guido Leoni
- Nouscom Srl, via Castel Romano 100, 00128 Rome, Italy
| | - Barbara Szomolay
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4YS, UK
| | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Vincenzo Cerullo
- Laboratory of Immunovirotherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00100 Helsinki, Finland
- Translational Immunology Research Program (TRIMM), University of Helsinki, 00100 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00100 Helsinki, Finland
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Genetic Variation in ATXN3 (Ataxin-3) 3'UTR: Insights into the Downstream Regulatory Elements of the Causative Gene of Machado-Joseph Disease/Spinocerebellar Ataxia Type 3. CEREBELLUM (LONDON, ENGLAND) 2023; 22:37-45. [PMID: 35034258 DOI: 10.1007/s12311-021-01358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 02/01/2023]
Abstract
Untranslated regions are involved in the regulation of transcriptional and post-transcriptional processes. Characterization of these regions remains poorly explored for ATXN3, the causative gene of Machado-Joseph disease (MJD). Although a few genetic modifiers have been identified for MJD age at onset (AO), they only explain a small fraction of the AO variance. Our aim was to analyse variation at the 3'UTR of ATXN3 in MJD patients, analyse its impact on AO and attempt to build haplotypes that might discriminate between normal and expanded alleles.After assessing ATXN3 3'UTR variants in molecularly confirmed MJD patients, an in silico analysis was conducted to predict their functional impact (e.g. their effect on miRNA-binding sites). Alleles in cis with the expanded (CAG)n were inferred from family data, and haplotypes were built. The effect of the alternative alleles on the AO and on SARA and NESSCA ataxia scales was tested.Nine variants, all previously described, were found. For eight variants, in silico analyses predicted (a) deleterious effects (rs10151135; rs55966267); (b) changes on miRNA-binding sites (rs11628764; rs55966267; rs709930) and (c) alterations of RNA-binding protein (RBP)-binding sites (rs1055996; rs910369; rs709930; rs10151135; rs3092822; rs7158733). Patients harbouring the alternative allele at rs10151135 had significantly higher SARA Axial subscores (p = 0.023), comparatively with those homozygous for the reference allele. Ten different haplotypes were obtained, one of which was exclusively found in cis with the expanded and four with the normal allele. These findings, which are relevant for the design of allele-specific therapies, warrant further investigation in independent MJD cohorts.
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Ju Y, Shen T, Guo Z, Kong Y, Huang Y, Hu J. Identification of methylation-driven genes, circulating miRNAs and their potential regulatory mechanisms in gestational diabetes mellitus. Am J Transl Res 2023; 15:336-349. [PMID: 36777869 PMCID: PMC9908470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/06/2022] [Indexed: 02/14/2023]
Abstract
OBJECTIVE Gestational diabetes mellitus (GDM) is a major pregnancy complication. The purpose of this study is to investigate the molecular regulatory mechanisms of GDM. METHODS RNA-seq and methylation data of GDM were retrieved from the Gene Expression Omnibus database. Following principal component analysis (PCA), differentially expressed mRNAs and microRNAs (miRNAs) in the blood were highlighted between GDM and the control. Then, an abnormally expressed miRNA-mRNA network was constructed, based on which a protein-protein interaction (PPI) network was established to identify hub genes. Differentially expressed and methylated genes were identified for GDM, followed by functional enrichment analysis. RESULTS According to PCA results, no outlier samples were found. A total of 35 differentially expressed circulating miRNAs were identified for GDM. The miRNA-mRNA regulatory network consisted of 94 miRNA-mRNA pairs. The PPI network contained 10 hub genes, including HIF1A, TLR2, FOS, IL6R, MYLIP, ABCA1, SELL, BCL3, AP1G1 and NECAP1. Furthermore, 22 down-regulated and hypermethylated genes and 8 up-regulated and hypomethylated genes were identified for GDM, which are related to helper T cell (Th) differentiation. CONCLUSION We identified methylation-driven genes and circulating miRNAs for GDM, which have the potential to serve as novel diagnostic biomarkers.
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Affiliation(s)
- Yuejun Ju
- Department of Endocrinology, The Second Affiliated Hospital of Soochow UniversitySuzhou 215000, Jiangsu, P. R. China,Department of Endocrinology, Changshu No. 2 People’s HospitalChangshu 215500, Jiangsu, P. R. China
| | - Ting Shen
- Department of Endocrinology, Changshu No. 2 People’s HospitalChangshu 215500, Jiangsu, P. R. China
| | - Zhanhong Guo
- Department of Endocrinology, Changshu No. 2 People’s HospitalChangshu 215500, Jiangsu, P. R. China
| | - Yinghong Kong
- Department of Endocrinology, Changshu No. 2 People’s HospitalChangshu 215500, Jiangsu, P. R. China
| | - Yun Huang
- Department of Endocrinology, The Second Affiliated Hospital of Soochow UniversitySuzhou 215000, Jiangsu, P. R. China
| | - Ji Hu
- Department of Endocrinology, The Second Affiliated Hospital of Soochow UniversitySuzhou 215000, Jiangsu, P. R. China
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Using Single-Cell RNA Sequencing and MicroRNA Targeting Data to Improve Colorectal Cancer Survival Prediction. Cells 2023; 12:cells12020228. [PMID: 36672162 PMCID: PMC9856396 DOI: 10.3390/cells12020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Colorectal cancer has proven to be difficult to treat as it is the second leading cause of cancer death for both men and women worldwide. Recent work has shown the importance of microRNA (miRNA) in the progression and metastasis of colorectal cancer. Here, we develop a metric based on miRNA-gene target interactions, previously validated to be associated with colorectal cancer. We use this metric with a regularized Cox model to produce a small set of top-performing genes related to colon cancer. We show that using the miRNA metric and a Cox model led to a meaningful improvement in colon cancer survival prediction and correct patient risk stratification. We show that our approach outperforms existing methods and that the top genes identified by our process are implicated in NOTCH3 signaling and general metabolism pathways, which are essential to colon cancer progression.
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Xuan DTM, Wu CC, Wang WJ, Hsu HP, Ta HDK, Anuraga G, Chiao CC, Wang CY. Glutamine synthetase regulates the immune microenvironment and cancer development through the inflammatory pathway. Int J Med Sci 2023; 20:35-49. [PMID: 36619229 PMCID: PMC9812810 DOI: 10.7150/ijms.75625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022] Open
Abstract
Although adjuvant tamoxifen therapy is beneficial to estrogen receptor-positive (ER+) breast cancer patients, a significant number of patients still develop metastasis or undergo recurrence. Therefore, identifying novel diagnostic and prognostic biomarkers for these patients is urgently needed. Predictive markers and therapeutic strategies for tamoxifen-resistant ER+ breast cancer are not clear, and micro (mi)RNAs have recently become a focal research point in cancer studies owing to their regulation of gene expressions, metabolism, and many other physiological processes. Therefore, systematic investigation is required to understand the modulation of gene expression in tamoxifen-resistant patients. High-throughput technology uses a holistic approach to observe differences among expression profiles of thousands of genes, which provides a comprehensive level to extensively investigate functional genomics and biological processes. Through a bioinformatics analysis, we revealed that glutamine synthetase/glutamate-ammonia ligase (GLUL) might play essential roles in the recurrence of tamoxifen-resistant ER+ patients. GLUL increases intracellular glutamine usage via glutaminolysis, and further active metabolism-related downstream molecules in cancer cell. However, how GLUL regulates the tumor microenvironment for tamoxifen-resistant ER+ breast cancer remains unexplored. Analysis of MetaCore pathway database demonstrated that GLUL is involved in the cell cycle, immune response, interleukin (IL)-4-induced regulators of cell growth, differentiation, and metabolism-related pathways. Experimental data also confirmed that the knockdown of GLUL in breast cancer cell lines decreased cell proliferation and influenced expressions of specific downstream molecules. Through a Connectivity Map (CMap) analysis, we revealed that certain drugs/molecules, including omeprazole, methacholine chloride, ioversol, fulvestrant, difenidol, cycloserine, and MK-801, may serve as potential treatments for tamoxifen-resistant breast cancer patients. These drugs may be tested in combination with current therapies in tamoxifen-resistant breast cancer patients. Collectively, our study demonstrated the crucial roles of GLUL, which provide new targets for the treatment of tamoxifen-resistant breast cancer patients.
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Affiliation(s)
- Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Chung-Che Wu
- Department of Neurosurgery, Taipei Medical University Hospital, Taipei 11031, Taiwan.,Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Jan Wang
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan.,Department of Statistics, Faculty of Science and Technology, PGRI Adi Buana University, East Java, Surabaya 60234, Indonesia
| | - Chung-Chieh Chiao
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science, Taipei Medical University, Taipei 11031, Taiwan.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
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circAR-E2E4-miR-665-STAT3 axis is a potential regulatory network in triple-negative breast cancer. Heliyon 2022; 9:e12654. [PMID: 36691537 PMCID: PMC9860453 DOI: 10.1016/j.heliyon.2022.e12654] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/13/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel type of endogenous non-coding RNAs (ncRNA). Many studies showed that circRNAs played different biological functions in triple-negative breast cancer (TNBC). However, the potential molecular mechanism of circRNAs in TNBC still remains to be investigated. In this study, circAR-E2E4 was defined as a novel circRNA involved in TNBC progression, derived from and regulated by androgen receptor (AR). CCK-8 assay showed circAR-E2E4 regulated TNBC cell proliferation. Potential binding miRNAs of circAR-E2E4 were predicted and miR-665 was identified to have a great prognosis value. Three databases were employed to predict target genes of miR-665, and STAT3 was regarded as the most potential downstream genes analyzed by protein-protein interaction (PPI), hub gene screening, correlation analysis, and survival analysis. Finally, knockdown of circAR-E2E4 led to the decrease of STAT3 expression. Collectively, the regulatory network circAR-E2E4-miR-665-STAT3 axis we constructed was associated with TNBC progression, providing a promising diagnostic, prognostic, and therapeutic target in future treatment for TNBC.
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Yan T, Zhu M, Weng F, Zhu S, Wang C, Guo C. Comprehensive analysis of roles of atrial-fibrillation-related genes in lung adenocarcinoma using bioinformatic methods. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 40:55. [PMID: 36542177 DOI: 10.1007/s12032-022-01912-8] [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: 09/20/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
Atrial fibrillation (AF) is the most common tachyarrhythmia in the world. Lung cancer is the leading cause of cancer deaths in 93 countries. Previous studies demonstrated that the prevalence of AF was higher in patients with lung cancer. However, research on the associations between AF and lung cancer is still rare. In the present study, we first identified AF-related genes using weighted gene correlation network analysis. We then analyzed the expression profiles, prognosis, immune infiltration, and methylation characteristics of these genes in LUAD patients using bioinformatics analysis. We found several AF-related genes, including CBX3, BUB1, DSC2, P4HA1, and CYP4Z1, which differently expressed between tumor and normal tissues. Survival analysis demonstrated that CYP4Z1 was positively correlated with overall survival in LUAD patients, while CBX3, BUB1, DSC2, and P4HA1 were negatively correlated. Moreover, we found that the methylation level of DSC2 in normal lung tissues was significantly higher than that in tumor tissues, and six methylation sites in the DNA sequences of DSC2 were identified negatively correlated with its expression levels. Immune infiltration analysis suggested that levels of immune cell infiltration were related to gene expression levels in varying degrees. We identified AF-related genes and found these genes were correlated with prognosis, immune infiltration, and methylation levels in lung cancer patients. We also constructed a risk signature based on these genes in LUAD patients. We hoped that the current study could provide a novel insight into roles of AF-related genes in lung cancer patients.
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Affiliation(s)
- Tao Yan
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Miao Zhu
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Fan Weng
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Shijie Zhu
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Chunsheng Wang
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Changfa Guo
- Department of Cardiovascular Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
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Zhang X, Tan J, Chen Y, Ma S, Bai W, Peng Y, Shi G. Identification of serum MiRNAs as candidate biomarkers for non-small cell lung cancer diagnosis. BMC Pulm Med 2022; 22:479. [PMID: 36522766 PMCID: PMC9756610 DOI: 10.1186/s12890-022-02267-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lung cancer is one of the most common solid tumors worldwide and the leading cause of cancer-associated death. Non-small cell lung cancer (NSCLC) is accounts for approximately 85% of all the lung cancers and lung squamous carcinoma (SCC) and adenocarcinoma (ADC) are the main subtypes of NSCLC. Early diagnose using serum biomarkers could improve the overall survival of patients. In this study, we aimed to identify miRNAs from serum with clinical utility in the diagnosis of NSCLC. METHODS Ten patients with SCC, ten patients with ADC and five noncancerous individuals were enrolled in the screening cohort. miRNA expression levels in serum were measured by microarray analysis. Candidate miRNAs were validated by real-time quantitative polymerase chain reaction analysis in a validation cohort of 78 NSCLC patients and 44 noncancerous individuals. Receiver operating characteristic curves were used to assess the diagnostic performance of serum miRNAs for NSCLC. Logistic regression was used to evaluate the diagnostic value of the combination of markers. RESULTS Six candidate miRNAs were differentially expressed between NSCLC patients and noncancerous individuals in the screening set (fold change > 2, p < 0.05). Among them, expression levels of miR-3149 and miR-4769.3p were confirmed to be significantly increased in tumor serum in the validation set. The area under the curve values of miR-3149 and miR-4769.3p in distinguishing NSCLC patients from noncancerous controls were 0.830 and 0.735, respectively. When combined with tumor markers CEA and Cyfra21-1, the joint diagnostic model increased the area under the curve to 0.898. CONCLUSION Serum miRNAs miR-3149 and miR-4769.3p were up-regulated in NSCLC and may be potential biomarkers for early diagnosis of lung cancer.
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Affiliation(s)
- Xintong Zhang
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Jinjing Tan
- Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China ,grid.414341.70000 0004 1757 0026Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yan Chen
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Shang Ma
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Wanqiu Bai
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Yanjing Peng
- Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China ,grid.414341.70000 0004 1757 0026Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Guangli Shi
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
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Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. BIOLOGY 2022; 11:biology11121798. [PMID: 36552307 PMCID: PMC9775672 DOI: 10.3390/biology11121798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/27/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. They are suggested to be involved in most biological processes of the cell primarily by targeting messenger RNAs (mRNAs) for cleavage or translational repression. Their binding to their target sites is mediated by the Argonaute (AGO) family of proteins. Thus, miRNA target prediction is pivotal for research and clinical applications. Moreover, transfer-RNA-derived fragments (tRFs) and other types of small RNAs have been found to be potent regulators of Ago-mediated gene expression. Their role in mRNA regulation is still to be fully elucidated, and advancements in the computational prediction of their targets are in their infancy. To shed light on these complex RNA-RNA interactions, the availability of good quality high-throughput data and reliable computational methods is of utmost importance. Even though the arsenal of computational approaches in the field has been enriched in the last decade, there is still a degree of discrepancy between the results they yield. This review offers an overview of the relevant advancements in the field of bioinformatics and machine learning and summarizes the key strategies utilized for small RNA target prediction. Furthermore, we report the recent development of high-throughput sequencing technologies, and explore the role of non-miRNA AGO driver sequences.
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Systems Biology in Chronic Heart Failure-Identification of Potential miRNA Regulators. Int J Mol Sci 2022; 23:ijms232315226. [PMID: 36499552 PMCID: PMC9740605 DOI: 10.3390/ijms232315226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Heart failure (HF) is a complex disease entity with high clinical impact, poorly understood pathophysiology and scantly known miRNA-mediated epigenetic regulation. We have analysed miRNA patterns in patients with chronic HF (cHF) and a sex- and age-matched reference group and pursued an in silico system biology analysis to discern pathways involved in cHF pathophysiology. Twenty-eight miRNAs were identified in cHF that were up-regulated in the reference group, and eight of them were validated by RT-qPCR. In silico analysis of predicted targets by STRING protein-protein interaction networks revealed eight cluster networks (involving seven of the identified miRNAs) enriched in pathways related to cell cycle, Ras, chemokine, PI3K-AKT and TGF-β signaling. By ROC curve analysis, combined probabilities of these seven miRNAs (let-7a-5p, miR-107, miR-125a-5p, miR-139-5p, miR-150-5p, miR-30b-5p and miR-342-3p; clusters 1-4 [C:1-4]), discriminated between HF with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF), and ischaemic and non-ischaemic aetiology. A combination of miR-107, miR-139-5p and miR-150-5p, involved in clusters 5 and 7 (C:5+7), discriminated HFpEF from HFrEF. Pathway enrichment analysis of miRNAs present in C:1-4 (let-7a-5p, miR-125a-5p, miR-30b-5p and miR-342-3p) revealed pathways related to HF pathogenesis. In conclusion, we have identified a differential signature of down-regulated miRNAs in the plasma of HF patients and propose novel cellular mechanisms involved in cHF pathogenesis.
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Zhu R, Gao C, Feng Q, Guan H, Wu J, Samant H, Yang F, Wang X. Ferroptosis-related genes with post-transcriptional regulation mechanisms in hepatocellular carcinoma determined by bioinformatics and experimental validation. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1390. [PMID: 36660631 PMCID: PMC9843431 DOI: 10.21037/atm-22-5750] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/05/2022] [Indexed: 01/01/2023]
Abstract
Background Ferroptosis is a form of iron-dependent cell death with increased free iron and massive lipid peroxidation. The discovery of ferroptosis offers insights into hepatocellular carcinoma (HCC) treatment. However, post-transcriptional regulation mechanisms of ferroptosis in HCC remain to be elucidated. The present study explored ferroptosis-related genes and their post-transcriptional regulation mechanisms in HCC. Methods A ferroptosis score was computed in The Cancer Genome Atlas (TCGA) cohort via gene set variation analysis (GSVA), and ferroptosis-related genes were screened by differential expression and correlation analyses. CircRNA/miRNA-mediated ferroptosis-related genes were predicted, and associations of ferroptosis-related genes with m1A/m5C/m6A regulators were analyzed. Immune cell infiltrations were inferred via CIBERSORT. NUDCD1 expression was examined in L-02, SMMC7721, and HepG2 cells via real time quantitative polymerase chain reaction (RT-qPCR) and western blots. After NUDCD1 was silenced, cell viability, glutathione peroxidase 4 (GPX4) and ferritin heavy chain 1 (FTH1) expression, and oxidized glutathione/glutathione (GSSG/GSH) and glutathione (GSH) levels were detected in SMMC7721 and HepG2 cells. Results The ferroptosis score was linked to poor overall survival (OS) of HCC, which was independent of other clinicopathological parameters. Ten ferroptosis-related genes were determined, namely UGT1A6, ATP6V1C1, MAFG, NUDCD1, PPP1R1A, TSKU, CTSB, AIFM2, CTSA, and CTNND2, which were post-transcriptionally regulated by circRNA/miRNA and m1A/m5C/m6A modifications in HCC. Most were significantly linked with most immune cell compositions within the immune microenvironment, and contributed to undesirable clinical outcomes. NUDCD1 was up-regulated in HCC cells, and its loss facilitated the ferroptosis of HCC cells. Conclusions Overall, our findings determined ferroptosis-related genes post-transcriptionally regulated by circRNA/miRNA and m1A/m5C/m6A RNA modifications, and experiments demonstrated that loss of NUDCD1 may facilitate the ferroptosis of HCC cells, which provides novel insights into the regulatory mechanisms of ferroptosis in HCC.
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Affiliation(s)
- Renfei Zhu
- 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, China;,Department of Hepatobiliary, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Cheng Gao
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical College of Nantong University, Nantong, China
| | - Qiuqi Feng
- Department of Hepatobiliary, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Haitao Guan
- Department of Ultrasound, Suzhou Science & Technology Town Hospital, Suzhou, China
| | - Jianjun Wu
- Department of Hepatobiliary, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Hrishikesh Samant
- Division of Gastroenterology and Hepatology, LSU Health Science Center, Shreveport, LA, USA
| | - Fan Yang
- Department of ICU, Affiliated Nantong Hospital of Shanghai University, Nantong, China;,Department of ICU, The Sixth People’s Hospital of Nantong, Nantong, China
| | - Xuehao 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, China
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50
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Shojaee S, Romano G, Sanchez TM, Yermakhanova G, Saviana M, Le P, Nigita G, Calore F, Guthrie R, Hess K, Kang L, Swift-Scanlan T, Graham JT, Rahman NM, Nana-Sinkam PS, Acunzo M. Extracellular Vesicle MicroRNA in Malignant Pleural Effusion. Genes (Basel) 2022; 13:2159. [PMID: 36421832 PMCID: PMC9691121 DOI: 10.3390/genes13112159] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 10/24/2023] Open
Abstract
Lung and breast cancer are the two most common causes of malignant pleural effusion (MPE). MPE diagnosis plays a crucial role in determining staging and therapeutic interventions in these cancers. However, our understanding of the pathogenesis and progression of MPE at the molecular level is limited. Extracellular Vesicles (EVs) and their contents, including microRNAs (miRNAs), can be isolated from all bodily fluids, including pleural fluid. This study aims to compare EV-miRNA patterns of expression in MPE caused by breast (BA-MPE) and lung (LA-MPE) adenocarcinomas compared to the control group of heart-failure-induced effusions (HF-PE). We conducted an analysis of 24 pleural fluid samples (8 LA-MPE, 8 BA-MPE, and 8 HF-PE). Using NanoString technology, we profiled miRNAs within EVs isolated from 12 cases. Bioinformatic analysis demonstrated differential expression of miR-1246 in the MPE group vs. HF-PE group and miR-150-5p and miR-1246 in the BA-MPE vs. LA-MPE group, respectively. This difference was demonstrated and validated in an independent cohort using real-time PCR (RT-PCR). miRNA-1246 demonstrated 4-fold increased expression (OR: 3.87, 95% CI: 0.43, 35) in the MPE vs. HF-PE group, resulting in an area under the curve of 0.80 (95% CI: 0.60, 0.99). The highest accuracy for differentiating MPE vs. HF-PE was seen with a combination of miRNAs compared to each miRNA alone. Consistent with prior studies, this study demonstrates dysregulation of specific EV-based miRNAs in breast and lung cancer; pleural fluid provides direct access for the analysis of these EV-miRNAs as biomarkers and potential targets and may provide insight into the underlying pathogenesis of tumor progression. These findings should be explored in large prospective studies.
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Affiliation(s)
- Samira Shojaee
- Vanderbilt University Medical Center, Department of Internal Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, 1301 Medical Center Drive, Suite B187, Nashville, TN 37232, USA
| | - Giulia Romano
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Trinidad M. Sanchez
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Gulmira Yermakhanova
- Vanderbilt University Medical Center, Department of Internal Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, 1301 Medical Center Drive, Suite B187, Nashville, TN 37232, USA
| | - Michela Saviana
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
| | - Patricia Le
- Vanderbilt University Medical Center, Department of Internal Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, 1301 Medical Center Drive, Suite B187, Nashville, TN 37232, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Federica Calore
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Rachel Guthrie
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Kathryn Hess
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Le Kang
- Virginia Commonwealth University Health System, Department of Biostatistics, Richmond, VA 23298, USA
| | | | - Jacob T. Graham
- Virginia Commonwealth University School of Nursing, Richmond, VA 23298, USA
| | - Najib M. Rahman
- Oxford Respiratory Trials Unit, University of Oxford, Oxford NIHR Biomedical Research Centre, Oxford and Chinese Academy of Medical Sciences Oxford Institute, Oxford OX3 7LE, UK
| | - Patrick S. Nana-Sinkam
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
| | - Mario Acunzo
- Virginia Commonwealth University Health System, Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Richmond, VA 23298, USA
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