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Hauptman N, Pižem J, Jevšinek Skok D. AmiCa: Atlas of miRNA-gene correlations in cancer. Comput Struct Biotechnol J 2024; 23:2277-2288. [PMID: 38840833 PMCID: PMC11152612 DOI: 10.1016/j.csbj.2024.05.030] [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: 03/12/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024] Open
Abstract
The increasing availability of RNA sequencing data has opened up numerous opportunities to analyze various RNA interactions, including microRNA-target interactions (MTIs). In response to the necessity for a specialized tool to study MTIs in cancer and normal tissues, we developed AmiCa (https://amica.omics.si/), a web server designed for comprehensive analysis of mature microRNA (miRNA) and gene expression in 32 cancer types. Data from 9498 tumor samples and 626 normal samples from The Cancer Genome Atlas were obtained through the Genomic Data Commons and used to calculate differential expression and miRNA-target gene (MTI) correlations. AmiCa provides data on differential expression of miRNAs/genes for cancers for which normal tissue samples were available. In addition, the server calculates and presents correlations separately for tumor and normal samples for cancers for which normal samples are available. Furthermore, it enables the exploration of miRNA/gene expression in all cancer types with different miRNA/gene expression. In addition, AmiCa includes a ranking system for genes and miRNAs that can be used to identify those that are particularly highly expressed in certain cancers compared to other cancers, facilitating targeted and cancer-specific research. Finally, the functionality of AmiCa is illustrated by two case studies.
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Affiliation(s)
- Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Jože Pižem
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Slovenia
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2
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Mao J, Li HM, Huang Z. Comprehensive analysis of the expression and prognosis for cyclin-dependent protein kinase family in osteosarcoma. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-24. [PMID: 39357043 DOI: 10.1080/15257770.2024.2410957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 09/21/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND AND OBJECTIVE Cyclin-dependent protein kinases (CDKs) have been suggested as prospective therapeutic targets because they control processes vital to the survival and growth of cancer cells. However, research on the varied CDK expression profiles and prognostic factors in osteosarcoma is still lacking. METHODS The osteosarcoma microRNA (GSE65071) and gene expression profiles were retrieved from the Gene Expression Omnibus (GEO) database (GSE42352). A substantial variation in prognosis was discovered in CDKs using the TARGET database. Cytoscape was used to construct the miRNAs-CDKs network, and functional and pathway enrichment analyses were completed. It was looked at how immune checkpoint genes, m6A-related genes, and CDKs interact. RESULTS In patients with osteosarcoma compared to normal samples, CDK1-5, CDK18, CDK16, and CDK17 gene expression levels were considerably greater, whereas CDK7-9, CDK11B, CDK16, and CDK20 gene expression levels were significantly lower. Patients with osteosarcoma who had low CDK3 and 18 gene levels or high CDK6, 9 gene levels were predicted to have a favorable prognosis and a long-life expectancy. Immune checkpoint genes, m6A-related gene expression, and CDKs expression all showed some connection. Finally, a network of crucial CDKs and miRNAs was constructed. CONCLUSION According to our research, CDK3, 6, 9, and 18 have been identified as possible therapeutic targets for osteosarcoma, and CDKs may have a role in controlling m6A mutations in tumor cells as well as immune checkpoint regulation.
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Affiliation(s)
- Jianshui Mao
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, P R China
| | - Hui-Min Li
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, P R China
| | - Zhidan Huang
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, P R China
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Bhardwaj S, Grewal AK, Singh S, Dhankar V, Jindal A. An insight into the concept of neuroinflammation and neurodegeneration in Alzheimer's disease: targeting molecular approach Nrf2, NF-κB, and CREB. Inflammopharmacology 2024; 32:2943-2960. [PMID: 38951436 DOI: 10.1007/s10787-024-01502-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Alzheimer's disease (AD) is a most prevalent neurologic disorder characterized by cognitive dysfunction, amyloid-β (Aβ) protein accumulation, and excessive neuroinflammation. It affects various life tasks and reduces thinking, memory, capability, reasoning and orientation ability, decision, and language. The major parts responsible for these abnormalities are the cerebral cortex, amygdala, and hippocampus. Excessive inflammatory markers release, and microglial activation affect post-synaptic neurotransmission. Various mechanisms of AD pathogenesis have been explored, but still, there is a need to debate the role of NF-κB, Nrf2, inflammatory markers, CREB signaling, etc. In this review, we have briefly discussed the signaling mechanisms and function of the NF-ĸB signaling pathway, inflammatory mediators, microglia activation, and alteration of autophagy. NF-κB inhibition is a current strategy to counter neuroinflammation and neurodegeneration in the brain of individuals with AD. In clinical trials, numbers of NF-κB modulators are being examined. Recent reports revealed that molecular and cellular pathways initiate complex pathological competencies that cause AD. Moreover, this review will provide extensive knowledge of the cAMP response element binding protein (CREB) and how these nuclear proteins affect neuronal plasticity.
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Affiliation(s)
- Shaveta Bhardwaj
- G.H.G. Khalsa College of Pharmacy, Gurusar Sudhar, Ludhiana, India
| | - Amarjot Kaur Grewal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India.
| | - Shamsher Singh
- Neuropharmacology Division, Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, 142001, India.
| | - Vaibhav Dhankar
- Neuropharmacology Division, Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Anu Jindal
- G.H.G. Khalsa College of Pharmacy, Gurusar Sudhar, Ludhiana, India
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Zhang G, Chen Z, Wang Y, Huang A, Nie F, Gao L, Wang Y, Ren F. Up-regulated DSG2 promotes tumor growth and reduces immune infiltration in cervical cancer. Pathol Res Pract 2024; 262:155554. [PMID: 39226803 DOI: 10.1016/j.prp.2024.155554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/12/2024] [Accepted: 08/19/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND Desmoglein-2 (DSG2) has been reported to play pivotal roles in various diseases. However, its roles in cervical cancer (CC) remain insufficiently elucidated. Here, we aimed to comprehensively explore the functional mechanisms of DSG2 in CC using bioinformatics and experimental methods. METHODS Several online databases, including Gene Expression Profiling Interactive Analysis (GEPIA), ONCOMINE, LinkedOmics, MetaScape, Human protein atlas (HPA), OMICS and single-cell RNA sequencing (scRNA-seq) data were used to explore the expression, prognosis, gene mutations, and potential signaling pathway of DSG2 in CC. Quantitative real-time PCR (qRT-PCR) and western blotting were used to measure DSG2 expression in collected samples. Experimental assays were conducted to verify the effects of dysregulated DSG2 on cervical cell lines in vitro. RESULTS Bioinformatic analyses revealed that DSG2 was significantly up-regulated in CC compared to normal cervical tissues at both mRNA and protein levels. Elevated DSG2 levels were also associated with poor prognosis and clinical parameters (e.g., cancer stages, tumor grade, nodal metastasis status, etc.). DSG2 expression was predominantly observed in epithelial cells, increasing with disease progression on a single-cell resolution. Additionally, up-regulation of DSG2 significantly enhanced tumor purity by reducing the infiltration of immune cells (e.g., B cells, T cells, NK cells, etc.). Over-expression of DSG2 was further validated in collected CC samples at both mRNA and protein levels. Knockdown of DSG2 markedly reduced the proliferation and invasion of CC cell lines in vitro. CONCLUSIONS In summary, elevated levels of DSG2 were significantly associated with poor prognosis and diminished immune infiltration in CC. Thus, DSG2 may serve as a potential therapeutic and diagnostic biomarker for CC.
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Affiliation(s)
- Gong Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhimin Chen
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanpei Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Anni Huang
- Medical Department,Guangxi Hospital, The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Fangfang Nie
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Limin Gao
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Shihezi University, Shihezi, Xinjiang 832000, China.
| | - Yuyouye Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Fang Ren
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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Huang X, Feng Z, Liu D, Gou Y, Chen M, Tang D, Han C, Peng J, Peng D, Xue Y. PTMD 2.0: an updated database of disease-associated post-translational modifications. Nucleic Acids Res 2024:gkae850. [PMID: 39329270 DOI: 10.1093/nar/gkae850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/10/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024] Open
Abstract
Various post-translational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently associated with human diseases. Here, we present a comprehensive database of PTMs associated with diseases (PTMD 2.0), including 342 624 PTM-disease associations (PDAs) in 15 105 proteins for 93 types of PTMs and 2083 diseases. Based on the distinct PTM states in diseases, we classified all PDAs into six categories: upregulation (U) or downregulation (D) of PTM levels, absence (A) or presence (P) of PTMs, and creation (C) or disruption (N) of PTM sites. We provided detailed annotations for each PDA and carefully annotated disease-associated proteins by integrating the knowledge from 101 additional resources that covered 13 aspects, including disease-associated information, variation and mutation, protein-protein interaction, protein functional annotation, DNA and RNA element, protein structure, chemical-target relationship, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway annotation, functional domain annotation and physicochemical property. With a data volume of ∼8 GB, we anticipate that PTMD 2.0 will serve as a fundamental resource for further analysing the relationships between PTMs and diseases. The online service of PTMD 2.0 is freely available at https://ptmd.biocuckoo.cn/.
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Affiliation(s)
- Xinhe Huang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Zihao Feng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Dan Liu
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Yujie Gou
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Miaomiao Chen
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Dachao Tang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Cheng Han
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Jianzhen Peng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Di Peng
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Xianlin Avenue 163, Nanjing 210031, China
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Xu G, Song X, Wang X, Xue R, Yan X, Qin L, Chang X, Gao J, Chen Z, Song G. Combined miR-181a-5p and Ag Nanoparticles are Effective Against Oral Cancer in a Mouse Model. Int J Nanomedicine 2024; 19:9227-9253. [PMID: 39267724 PMCID: PMC11390847 DOI: 10.2147/ijn.s458484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 06/20/2024] [Indexed: 09/15/2024] Open
Abstract
Purpose Oral squamous cell carcinoma is the most common type of malignant tumor in the head and neck region. Despite advancements, metastasis and recurrence rates remain high, and patient survival has not significantly improved. Although miRNA therapies are promising for cancer gene therapy, their applications in treating oral cancer are limited. Targeted medication delivery systems based on nanotechnology offer an efficient way to enhance oral cancer treatment efficacy. Methods We synthesized nanosilver (AgNPs) and loaded them with the tumor suppressor miR-181a-5p. In vitro experiments were conducted to investigate the inhibitory effects of AgNPs and their composites on the malignant behavior of oral cancer cell lines. The xenograft experiment was utilized to examine their effects on tumorigenesis and the potential molecular mechanisms involved. Results The nanosilver exhibited a spherical morphology with a size distribution ranging from 50 to 100 nm. They exhibited a distinct absorption peak at 330 nm and could be excited to emit green fluorescence. The biocompatible AgNPs effectively shielded miRNA from degradation by RNase and serum. The nanocomposites significantly inhibited the proliferation, invasion, migration, and colony formation of oral cancer cell lines. Notably, treatment with the nanocomposites resulted in substantial tumor growth suppression in the xenograft model. Mechanistically, these composites directly targeted BCL2 and exerted their antitumor effects by suppressing the β-catenin signaling pathway and other downstream genes without inducing acute toxicity. Conclusion Collectively, the findings demonstrate that the miR-181a-5p/AgNPs combination significantly impedes the growth and progression of oral cancer both in vitro and in vivo, highlighting a pivotal role for the β-catenin signaling pathway. This multifaceted approach holds promise as a prospective therapeutic strategy for oral cancer management in the future.
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Affiliation(s)
- Guoqiang Xu
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xiaona Song
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xiaotang Wang
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Rui Xue
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xiaoru Yan
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Litao Qin
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xiaoqi Chang
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
- School of Basic Medical Science, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Jiping Gao
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Zhaoyang Chen
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
| | - Guohua Song
- Laboratory Animal Center Shanxi Key Laboratory of Experimental Animal Science and Human Disease Animal Model, Shanxi Medical University, Taiyuan, People's Republic of China
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Roointan A, Ghaeidamini M, Yavari P, Naimi A, Gheisari Y, Gholaminejad A. Transcriptome meta-analysis and validation to discovery of hub genes and pathways in focal and segmental glomerulosclerosis. BMC Nephrol 2024; 25:293. [PMID: 39232654 PMCID: PMC11375834 DOI: 10.1186/s12882-024-03734-4] [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: 10/30/2023] [Accepted: 08/26/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Focal segmental glomerulosclerosis (FSGS), a histologic pattern of injury in the glomerulus, is one of the leading glomerular causes of end-stage renal disease (ESRD) worldwide. Despite extensive research, the underlying biological alterations causing FSGS remain poorly understood. Studying variations in gene expression profiles offers a promising approach to gaining a comprehensive understanding of FSGS molecular pathogenicity and identifying key elements as potential therapeutic targets. This work is a meta-analysis of gene expression profiles from glomerular samples of FSGS patients. The main aims of this study are to establish a consensus list of differentially expressed genes in FSGS, validate these findings, understand the disease's pathogenicity, and identify novel therapeutic targets. METHODS After a thorough search in the GEO database and subsequent quality control assessments, seven gene expression datasets were selected for the meta-analysis: GSE47183 (GPL14663), GSE47183 (GPL11670), GSE99340, GSE108109, GSE121233, GSE129973, and GSE104948. The random effect size method was applied to identify differentially expressed genes (meta-DEGs), which were then used to construct a regulatory network (STRING, MiRTarBase, and TRRUST) and perform various pathway enrichment analyses. The expression levels of several meta-DEGs, specifically ADAMTS1, PF4, EGR1, and EGF, known as angiogenesis regulators, were analyzed using quantitative reverse transcription polymerase chain reaction (RT-qPCR). RESULTS The identified 2,898 meta-DEGs, including 665 downregulated and 669 upregulated genes, were subjected to various analyses. A co-regulatory network comprising 2,859 DEGs, 2,688 microRNAs (miRNAs), and 374 transcription factors (TFs) was constructed, and the top molecules in the network were identified based on degree centrality. Part of the pathway enrichment analysis revealed significant disruption in the angiogenesis regulatory pathways in the FSGS kidney. The RT-qPCR results confirmed an imbalance in angiogenesis pathways by demonstrating the differential expression levels of ADAMTS1 and EGR1, two key angiogenesis regulators, in the FSGS condition. CONCLUSION In addition to presenting a consensus list of differentially expressed genes in FSGS, this meta-analysis identified significant distortions in angiogenesis-related pathways and factors in the FSGS kidney. Targeting these factors may offer a viable strategy to impede the progression of FSGS.
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Affiliation(s)
- Amir Roointan
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan, 81746-73461, Iran
- NanoBiotechnology Laboratory, Australian Centre for Blood Diseases, School of Translational Medicine, Monash University, Melbourne, VIC, Australia
| | - Maryam Ghaeidamini
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan, 81746-73461, Iran
| | - Parvin Yavari
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan, 81746-73461, Iran
| | - Azar Naimi
- Department of Pathology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yousof Gheisari
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan, 81746-73461, Iran
| | - Alieh Gholaminejad
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan, 81746-73461, Iran.
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Ostrycharz-Jasek E, Fitzner A, Siennicka A, Budkowska M, Hukowska-Szematowicz B. MicroRNAs Regulate the Expression of Genes Related to the Innate Immune and Inflammatory Response in Rabbits Infected with Lagovirus europaeus GI.1 and GI.2 Genotypes. Int J Mol Sci 2024; 25:9531. [PMID: 39273479 PMCID: PMC11394960 DOI: 10.3390/ijms25179531] [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: 07/25/2024] [Revised: 08/23/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
MicroRNAs (miR) are a group of small, non-coding RNAs of 17-25 nucleotides that regulate gene expression at the post-transcriptional level. Dysregulation of miRNA expression or function may contribute to abnormal gene expression and signaling pathways, leading to disease pathology. Lagovirus europaeus (L. europaeus) causes severe disease in rabbits called rabbit hemorrhagic disease (RHD). The symptoms of liver, lung, kidney, and spleen degeneration observed during RHD are similar to those of acute liver failure (ALF) and multi-organ failure (MOF) in humans. In this study, we assessed the expression of miRs and their target genes involved in the innate immune and inflammatory response. Also, we assessed their potential impact on pathways in L. europaeus infection-two genotypes (GI.1 and GI.2)-in the liver, lungs, kidneys, and spleen. The expression of miRs and target genes was determined using quantitative real-time PCR (qPCR). We assessed the expression of miR-155 (MyD88, TAB2, p65, NLRP3), miR-146a (IRAK1, TRAF6), miR-223 (TLR4, IKKα, NLRP3), and miR-125b (MyD88). We also examined biomarkers of inflammation: IL-1β, IL-6, TNF-α, and IL-18 in four tissues at the mRNA level. Our study shows that the main regulators of the innate immune and inflammatory response in L. europaeus/GI.1 and GI.2 infection, as well as RHD, are miR-155, miR-223, and miR-146a. During infection with L. europaeus/RHD, miR-155 has both pro- and anti-inflammatory effects in the liver and anti-inflammatory effects in the kidneys and spleen; miR-146a has anti-inflammatory effects in the liver, lungs and kidneys; miR-223 has anti-inflammatory effects in all tissues; however, miR-125b has anti-inflammatory effects only in the liver. In each case, such an effect may be a determinant of the pathogenesis of RHD. Our research shows that miRs may regulate three innate immune and inflammatory response pathways in L. europaeus infection. However, the result of this regulation may be influenced by the tissue microenvironment. Our research shows that infection of rabbits with L. europaeus/GI.1 and GI.2 genotypes causes an overexpression of two critical acute phase cytokines: IL-6 in all examined tissues and TNF-α (in the liver, lungs, and spleen). IL-1β was highly expressed only in the lungs after L. europaeus infection. These facts indicate a strong and rapid involvement of the local innate immune and inflammatory response in L. europaeus infection-two genotypes (GI.1 and GI.2)-and in the pathogenesis of RHD. Profile of biomarkers of inflammation in rabbits infected with L. europaeus/GI.1 and GI.2 genotypes are similar regarding the nature of changes but are different for individual tissues. Therefore, we propose three inflammation profiles for L. europaeus infection for both GI.1 and GI.2 genotypes (pulmonary, renal, liver, and spleen).
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Affiliation(s)
- Ewa Ostrycharz-Jasek
- Institute of Biology, University of Szczecin, St. Z. Felczaka 3c, 71-412 Szczecin, Poland
- Doctoral School, University of Szczecin, St. A. Mickiewicz 16, 71-412 Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, St. Wąska 13, 71-412 Szczecin, Poland
| | - Andrzej Fitzner
- Department of Foot and Mouth Disease, National Veterinary Research Institute-State Research Institute, St. Wodna 7, 98-220 Zduńska Wola, Poland
- National Reference Laboratory for Rabbit Hemorrhagic Disease (RHD), St. Wodna 7, 98-220 Zduńska Wola, Poland
| | - Aldona Siennicka
- Department of Laboratory Diagnostics, Pomeraniam Medical University, St. Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
| | - Marta Budkowska
- Department of Laboratory Diagnostics, Pomeraniam Medical University, St. Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
| | - Beata Hukowska-Szematowicz
- Institute of Biology, University of Szczecin, St. Z. Felczaka 3c, 71-412 Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, St. Wąska 13, 71-412 Szczecin, Poland
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Xu F, Ren Y, Teng Y, Mu J, Tang J, Sundaram K, Zhang L, Park JW, Hwang JY, Yan J, Dryden G, Zhang H. Tryptophan As a New Member of RNA-Induced Silencing Complexes Prevents Colon Cancer Liver Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307937. [PMID: 39031551 PMCID: PMC11336974 DOI: 10.1002/advs.202307937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/15/2024] [Indexed: 07/22/2024]
Abstract
Essential amino acids (EAA) and microRNAs (miRs) control biological activity of a cell. Whether EAA regulates the activity of miR has never been demonstrated. Here, as proof-of-concept, a tryptophan (Trp, an EAA) complex containing Argonaute 2 (Ago2) and miRs including miR-193a (Trp/Ago2/miR-193a) is identified. Trp binds miR-193a-3p and interacts with Ago2. Trp/Ago2/miR-193a increases miR-193a-3p activity via enhancing Argonaute 2 (Ago2) RNase activity. Other miRs including miR-103 and miR-107 in the Trp complex enhance miR-193a activity by targeting the same genes. Mechanistically, the Trp/Ago2/miR-193a complex interacts with Trp-binding pockets of the PIWI domain of Ago2 to enhance Ago2 mediated miR activity. This newly formed Ago2/Trp/miR-193a-3p complex is more efficient than miR-193a-3p alone in inhibiting the expression of targeted genes and inhibiting colon cancer liver metastasis. The findings show that Trp regulates miR activity through communication with the RNA-induced silencing complexes (RISC), which provides the basis for tryptophan based miR therapy.
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Affiliation(s)
- Fangyi Xu
- Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA
- Department of Central LaboratoryCancer CenterThe affiliated Huaian No. 1 People's Hospital of Nanjing Medical UniversityHuai'an223300China
| | - Yi Ren
- Department of Breast and Thyroid SurgeryThe affiliated Huaian first People's Hospital of Nanjing Medical UniversityHuaianJiangsu223300China
| | - Yun Teng
- Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA
| | - Jingyao Mu
- Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA
| | - Jie Tang
- Department of Breast and Thyroid SurgeryThe affiliated Huaian first People's Hospital of Nanjing Medical UniversityHuaianJiangsu223300China
| | | | - Lifeng Zhang
- Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA
| | - Juw Won Park
- Department of Computer Science and EngineeringUniversity of LouisvilleLouisvilleKY40202USA
| | - Jae Yeon Hwang
- Department of Computer Science and EngineeringUniversity of LouisvilleLouisvilleKY40202USA
| | - Jun Yan
- Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA
| | - Gerald Dryden
- Robley Rex Veterans Affairs Medical CenterLouisvilleKY40206USA
| | - Huang‐Ge Zhang
- Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA
- Robley Rex Veterans Affairs Medical CenterLouisvilleKY40206USA
- Department of Microbiology & ImmunologyUniversity of LouisvilleLouisvilleKY40202USA
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10
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Thomas BL, Montero-Melendez T, Oggero S, Kaneva MK, Chambers D, Pinto AL, Nerviani A, Lucchesi D, Austin-Williams S, Hussain MT, Pitzalis C, Allen B, Malcangio M, Dell'Accio F, Norling LV, Perretti M. Molecular Determinants of Neutrophil Extracellular Vesicles That Drive Cartilage Regeneration in Inflammatory Arthritis. Arthritis Rheumatol 2024. [PMID: 39041647 DOI: 10.1002/art.42958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/02/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
OBJECTIVE This study was undertaken to establish the potential therapeutic profile of neutrophil-derived extracellular vesicles (EVs) in experimental inflammatory arthritis and associate pharmacological activity with specific EV components, focusing on microRNAs. METHODS Neutrophil EVs were administered intra-articularly through a prophylactic or therapeutic protocol to male C57BL/6 mice undergoing serum-transfer-induced inflammatory arthritis. Transcriptomic analysis of knees was performed on joints following EV administration, naive and arthritic mice (untreated; n = 4/group) and EV-treated diseased mice (intra-articular administration) with contralateral (vehicle-treated; n = 8/group). Comparison of healthy donor and patients with rheumatoid arthritis (RA) neutrophil EVs was performed. RESULTS EVs afforded cartilage protection with an increase in collagen-II and reduced collagen-X expression within the joint. To gain mechanistic insights, RNA sequencing of the arthritic joints was conducted. A total of 5,231 genes were differentially expressed (P < 0.05), with 257 unique to EV treatment. EVs affected key regenerative pathways involved in joint development, including Wnt and Notch signaling. This wealth of genomic alteration prompted to identify microRNAs in EVs, 10 of which are associated with RA. As a proof of concept, we focused on miR-455-3p, which was detected in both healthy donor and RA EVs. EV addition to chondrocyte cultures elevated miR-455-3p and exerted anticatabolic effects upon interleukin-1β stimulation; these effects were blocked by actinomycin or miR-455-3p antagomir. CONCLUSION Neutrophils from patients with RA yielded EVs with composition, efficacy, and miR-455-3p content similar to those of healthy volunteers, suggesting that neutrophil EVs could be developed as an autologous treatment to protect and repair joint tissue of patients affected by inflammatory arthritides.
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Affiliation(s)
| | | | - Silvia Oggero
- Queen Mary University of London and Kings College London, Guys' Campus, London, United Kingdom
| | | | - David Chambers
- Kings College London, Guys' Campus, London, United Kingdom
| | - Andreia L Pinto
- Royal Brompton & Harefield NHS Foundation Trust, London, United Kingdom
| | - Alessandra Nerviani
- Queen Mary University of London, Barts Health NHS Trust, and National Institute for Health and Care Research Barts Biomedical Research Centre, London, United Kingdom
| | | | | | | | - Costantino Pitzalis
- Queen Mary University of London, Barts Health NHS Trust, and National Institute for Health and Care Research Barts Biomedical Research Centre, London, United Kingdom
| | - Benjamin Allen
- Kings College London, Guys' Campus, London, United Kingdom
| | | | - Francesco Dell'Accio
- Queen Mary University of London, Barts Health NHS Trust, and National Institute for Health and Care Research Barts Biomedical Research Centre, London, United Kingdom
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11
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Krause C, Britsemmer JH, Bernecker M, Molenaar A, Taege N, Lopez-Alcantara N, Geißler C, Kaehler M, Iben K, Judycka A, Wagner J, Wolter S, Mann O, Pfluger P, Cascorbi I, Lehnert H, Stemmer K, Schriever SC, Kirchner H. Liver microRNA transcriptome reveals miR-182 as link between type 2 diabetes and fatty liver disease in obesity. eLife 2024; 12:RP92075. [PMID: 39037913 PMCID: PMC11262792 DOI: 10.7554/elife.92075] [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] [Indexed: 07/24/2024] Open
Abstract
Background The development of obesity-associated comorbidities such as type 2 diabetes (T2D) and hepatic steatosis has been linked to selected microRNAs in individual studies; however, an unbiased genome-wide approach to map T2D induced changes in the miRNAs landscape in human liver samples, and a subsequent robust identification and validation of target genes are still missing. Methods Liver biopsies from age- and gender-matched obese individuals with (n=20) or without (n=20) T2D were used for microRNA microarray analysis. The candidate microRNA and target genes were validated in 85 human liver samples, and subsequently mechanistically characterized in hepatic cells as well as by dietary interventions and hepatic overexpression in mice. Results Here, we present the human hepatic microRNA transcriptome of type 2 diabetes in liver biopsies and use a novel seed prediction tool to robustly identify microRNA target genes, which were then validated in a unique cohort of 85 human livers. Subsequent mouse studies identified a distinct signature of T2D-associated miRNAs, partly conserved in both species. Of those, human-murine miR-182-5 p was the most associated with whole-body glucose homeostasis and hepatic lipid metabolism. Its target gene LRP6 was consistently lower expressed in livers of obese T2D humans and mice as well as under conditions of miR-182-5 p overexpression. Weight loss in obese mice decreased hepatic miR-182-5 p and restored Lrp6 expression and other miR-182-5 p target genes. Hepatic overexpression of miR-182-5 p in mice rapidly decreased LRP6 protein levels and increased liver triglycerides and fasting insulin under obesogenic conditions after only seven days. Conclusions By mapping the hepatic miRNA-transcriptome of type 2 diabetic obese subjects, validating conserved miRNAs in diet-induced mice, and establishing a novel miRNA prediction tool, we provide a robust and unique resource that will pave the way for future studies in the field. As proof of concept, we revealed that the repression of LRP6 by miR-182-5 p, which promotes lipogenesis and impairs glucose homeostasis, provides a novel mechanistic link between T2D and non-alcoholic fatty liver disease, and demonstrate in vivo that miR-182-5 p can serve as a future drug target for the treatment of obesity-driven hepatic steatosis. Funding This work was supported by research funding from the Deutsche Forschungsgemeinschaft (KI 1887/2-1, KI 1887/2-2, KI 1887/3-1 and CRC-TR296), the European Research Council (ERC, CoG Yoyo LepReSens no. 101002247; PTP), the Helmholtz Association (Initiative and Networking Fund International Helmholtz Research School for Diabetes; MB) and the German Center for Diabetes Research (DZD Next Grant 82DZD09D1G).
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Affiliation(s)
- Christin Krause
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
- German Center for Diabetes Research (DZD)MunichGermany
| | - Jan H Britsemmer
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
- German Center for Diabetes Research (DZD)MunichGermany
| | - Miriam Bernecker
- German Center for Diabetes Research (DZD)MunichGermany
- Research Unit NeuroBiology of Diabetes, Institute for Diabetes and Obesity, Helmholtz CentreMunichGermany
| | - Anna Molenaar
- German Center for Diabetes Research (DZD)MunichGermany
- Research Unit NeuroBiology of Diabetes, Institute for Diabetes and Obesity, Helmholtz CentreMunichGermany
| | - Natalie Taege
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
- German Center for Diabetes Research (DZD)MunichGermany
| | - Nuria Lopez-Alcantara
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
- Institute for Experimental Endocrinology, University of LübeckLübeckGermany
| | - Cathleen Geißler
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
| | - Meike Kaehler
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus KielKielGermany
| | - Katharina Iben
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
| | - Anna Judycka
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
| | - Jonas Wagner
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Stefan Wolter
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Oliver Mann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Paul Pfluger
- German Center for Diabetes Research (DZD)MunichGermany
- Research Unit NeuroBiology of Diabetes, Institute for Diabetes and Obesity, Helmholtz CentreMunichGermany
- Chair of Neurobiology of Diabetes, TUM School of Medicine, Technical University of MunichMunichGermany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus KielKielGermany
| | - Hendrik Lehnert
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
- German Center for Diabetes Research (DZD)MunichGermany
- University Hospital of Coventry and WarwickshireCoventryUnited Kingdom
| | - Kerstin Stemmer
- German Center for Diabetes Research (DZD)MunichGermany
- Molecular Cell Biology, Institute of Theoretical Medicine, Faculty of Medicine, University of AugsburgAugsburgGermany
| | - Sonja C Schriever
- German Center for Diabetes Research (DZD)MunichGermany
- Research Unit NeuroBiology of Diabetes, Institute for Diabetes and Obesity, Helmholtz CentreMunichGermany
| | - Henriette Kirchner
- Institute for Human Genetics, Division Epigenetics & Metabolism, University of LübeckLübeckGermany
- Center of Brain, Behaviour and Metabolism (CBBM), University of LübeckLübeckGermany
- German Center for Diabetes Research (DZD)MunichGermany
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12
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Li S, Zhang Y, Liu G, Song N, Ruan Z, Guo R, Tang Y, Cao X, Huang X, Gao T, Hao S, Wang Q, Chang T. Exploring the Roles of m6A-Modified circRNAs in Myasthenia Gravis Based on Multi-Omics Analysis. Mol Neurobiol 2024:10.1007/s12035-024-04352-9. [PMID: 39017976 DOI: 10.1007/s12035-024-04352-9] [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: 04/21/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Myasthenia gravis (MG) is an autoimmune disease mediated by autoantibodies. The important roles of circRNAs modified by m6A methylation have been reported in the pathogenesis of other autoimmune diseases, but remain unclear in MG. To address this point, we collected peripheral blood mononuclear cells from six MG patients and six healthy controls and performed m6A‑circRNA epitranscriptomic microarray and RNA sequencing. Differentially m6A-modified circRNAs and differentially expressed genes (DEGs) were analyzed. A network was constructed containing 17 circRNAs, 30 miRNAs, and 34 DEGs. The GSE85452 dataset was downloaded. DEGs that were differentially expressed in the GSE85452 dataset were selected as seed genes. Finally, four candidate m6A-modified circRNAs (hsa_circ_0084735, hsa_circ_0018652, hsa_circ_0025731, and hsa_circ_0030997) were identified through a random walk with restart. We found that they had different degree correlations with different immune cells. The results of MeRIP-qPCR showed that the m6A methylated levels of hsa_circ_0084735 and hsa_circ_0025731 were downregulated in MG patients, while the other two circRNAs were not significantly different between MG and control group. For the first time, we explored the pathogenesis of MG at the epigenetic transcriptome level. Our results will open new perspectives for MG research and identify potential biomarkers and therapeutic targets for MG.
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Affiliation(s)
- Shuang Li
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yu Zhang
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Geyu Liu
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
- The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Na Song
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Zhe Ruan
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Rongjing Guo
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yonglan Tang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiangqi Cao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiaoxi Huang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Gao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Sijia Hao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Qingqing Wang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.
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13
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Ren S, Lee W, Park B, Han K. Constructing lncRNA-miRNA-mRNA networks specific to individual cancer patients and finding prognostic biomarkers. BMC Genom Data 2024; 25:67. [PMID: 38978021 PMCID: PMC11232193 DOI: 10.1186/s12863-024-01251-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The competitive endogenous RNA (ceRNA) hypothesis suggests that microRNAs (miRNAs) mediate a regulatory relation between long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) which share similar miRNA response elements (MREs) to bind to the same miRNA. Since the ceRNA hypothesis was proposed, several studies have been conducted to construct a network of lncRNAs, miRNAs and mRNAs in cancer. However, most cancer-related ceRNA networks are intended for representing a general relation of RNAs in cancer rather than for a patient-specific relation. Due to the heterogeneous nature of cancer, lncRNA-miRNA-mRNA interactions can vary in different patients. RESULTS We have developed a new method for constructing a ceRNA network of lncRNAs, miRNAs and mRNAs, which is specific to an individual cancer patient and for finding prognostic biomarkers consisting of lncRNA-miRNA-mRNA triplets. We tested our method on extensive data sets of three types of cancer (breast cancer, liver cancer, and lung cancer) and obtained potential prognostic lncRNA-miRNA-mRNA triplets for each type of cancer. CONCLUSIONS Analysis of expression patterns of the RNAs involved in the triplets and survival rates of cancer patients revealed several interesting findings. First, even for the same cancer type, prognostic lncRNA-miRNA-mRNA triplets can be different depending on whether lncRNA and mRNA show opposite or similar expression patterns. Second, prognostic lncRNA-miRNA-mRNA triplets are often more predictive of survival rates than RNA pairs or individual RNAs. Our approach will be useful for constructing patient-specific lncRNA-miRNA-mRNA networks and for finding prognostic biomarkers from the networks.
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Affiliation(s)
- Shulei Ren
- Department of Computer Engineering, Inha University, 22212, Incheon, South Korea
| | - Wook Lee
- Department of Computer Engineering, Inha University, 22212, Incheon, South Korea
| | - Byungkyu Park
- Department of Computer Engineering, Inha University, 22212, Incheon, South Korea
| | - Kyungsook Han
- Department of Computer Engineering, Inha University, 22212, Incheon, South Korea.
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14
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Hazari V, Samali SA, Izadpanahi P, Mollaei H, Sadri F, Rezaei Z. MicroRNA-98: the multifaceted regulator in human cancer progression and therapy. Cancer Cell Int 2024; 24:209. [PMID: 38872210 DOI: 10.1186/s12935-024-03386-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/25/2024] [Indexed: 06/15/2024] Open
Abstract
MicroRNA-98 (miR-98) stands as an important molecule in the intricate landscape of oncology. As a subset of microRNAs, these small non-coding RNAs have accompanied a new era in cancer research, underpinning their significant roles in tumorigenesis, metastasis, and therapeutic interventions. This review provides a comprehensive insight into the biogenesis, molecular properties, and physiological undertakings of miR-98, highlighting its double-edged role in cancer progression-acting both as a tumor promoter and suppressor. Intriguingly, miR-98 has profound implications for various aspects of cancer progression, modulating key cellular functions, including proliferation, apoptosis, and the cell cycle. Given its expression patterns, the potential of miR-98 as a diagnostic and prognostic biomarker, especially in liquid biopsies and tumor tissues, is explored, emphasizing the hurdles in translating these findings clinically. The review concludes by evaluating therapeutic avenues to modulate miR-98 expression, addressing the challenges in therapy resistance, and assessing the efficacy of miR-98 interventions. In conclusion, while miR-98's involvement in cancer showcases promising diagnostic and therapeutic avenues, future research should pivot towards understanding its role in tumor-stroma interactions, immune modulation, and metabolic regulation, thereby unlocking novel strategies for cancer management.
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Affiliation(s)
- Vajihe Hazari
- Department of Obstetrics and Gynecology, School of Medicine, Rooyesh Infertility Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Sahar Ahmad Samali
- Department of Microbiology, Yasooj Branch, Islamic Azad University, Yasooj, Iran
| | | | - Homa Mollaei
- Department of Biology, Faculty of Sciences, University of Birjand, Birjand, Iran
| | - Farzad Sadri
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran.
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
| | - Zohreh Rezaei
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran.
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
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15
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Xu D, Gareev I, Beylerli O, Pavlov V, Le H, Shi H. Integrative bioinformatics analysis of miRNA and mRNA expression profiles and identification of associated miRNA-mRNA network in intracranial aneurysms. Noncoding RNA Res 2024; 9:471-485. [PMID: 38511055 PMCID: PMC10950608 DOI: 10.1016/j.ncrna.2024.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 03/22/2024] Open
Abstract
Background Intracranial aneurysms (IAs) represent protrusions in the vascular wall, with their growth and wall thinning influenced by various factors. These processes can culminate in the rupture of the aneurysm, leading to subarachnoid hemorrhage (SAH). Unfortunately, over half of the patients prove unable to withstand SAH, succumbing to adverse outcomes despite intensive therapeutic interventions, even in premier medical facilities. This study seeks to discern the pivotal microRNAs (miRNAs) and genes associated with the formation and progression of IAs. Methods The investigation gathered expression data of miRNAs (from GSE66240) and mRNAs (from GSE158558) within human aneurysm tissue and superficial temporal artery (STA) samples, categorizing them into IA and normal groups. This classification was based on the Gene Expression Omnibus (GEO) database. Results A total of 70 differentially expressed microRNAs (DEMs) and 815 differentially expressed mRNAs (DEGs) were pinpointed concerning IA. Subsequently, a miRNA-mRNA network was constructed, incorporating 9 significantly upregulated DEMs and 211 significantly downregulated DEGs. Simultaneously, functional enrichment and pathway analyses were conducted on both DEMs and DEGs. Through protein-protein interaction (PPI) network analysis and functional enrichment, 9 significantly upregulated DEMs (hsa-miR-188-5p, hsa-miR-590-5p, hsa-miR-320b, hsa-miR-423-5p, hsa-miR-140-5p, hsa-miR-486-5p, hsa-miR-320a, hsa-miR-342-3p, and hsa-miR-532-5p) and 50 key genes (such as ATP6V1G1, KBTBD6, VIM, PA2G4, DYNLL1, METTL21A, MDH2, etc.) were identified, suggesting their potential significant role in IA. Among these genes, ten were notably negatively regulated by at least two key miRNAs. Conclusions The findings of this study provide valuable insights into the potential pathogenic mechanisms underlying IA by elucidating a miRNA-mRNA network. This comprehensive approach sheds light on the intricate interplay between miRNAs and genes, offering a deeper understanding of the molecular dynamics involved in IA development and progression.
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Affiliation(s)
- Dongxiao Xu
- Department of Neurosurgery, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Ilgiz Gareev
- Central Research Laboratory, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 3 Lenin street, 450008, Russia
| | - Ozal Beylerli
- Central Research Laboratory, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 3 Lenin street, 450008, Russia
| | - Valentin Pavlov
- Department of Urology, Bashkir State Medical University, 3 Lenin Street, 450008, Ufa, Russia
| | - Huang Le
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Huaizhang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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16
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Szabados T, Molnár A, Kenyeres É, Gömöri K, Pipis J, Pósa B, Makkos A, Ágg B, Giricz Z, Ferdinandy P, Görbe A, Bencsik P. Identification of New, Translatable ProtectomiRs against Myocardial Ischemia/Reperfusion Injury and Oxidative Stress: The Role of MMP/Biglycan Signaling Pathways. Antioxidants (Basel) 2024; 13:674. [PMID: 38929113 PMCID: PMC11201193 DOI: 10.3390/antiox13060674] [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: 04/09/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION Ischemic conditionings (ICon) were intensively investigated and several protective signaling pathways were identified. Previously, we have shown the role of matrix metalloproteinases (MMP) in myocardial ischemia/reperfusion injury (MIRI) and the cardioprotective role of biglycan (BGN), a small leucine-rich proteoglycan in vitro. Here, we hypothesized that cardiac MMP and BGN signaling are involved in the protective effects of ICon. METHODS A reverse target-microRNA prediction was performed by using the miRNAtarget™ 2.0 software to identify human microRNAs with a possible regulatory effect on MMP and BGN, such as on related genes. To validate the identified 1289 miRNAs in the predicted network, we compared them to two cardioprotective miRNA omics datasets derived from pig and rat models of MIRI in the presence of ICons. RESULTS Among the experimentally measured miRNAs, we found 100% sequence identity to human predicted regulatory miRNAs in the case of 37 porcine and 24 rat miRNAs. Upon further analysis, 42 miRNAs were identified as MIRI-associated miRNAs, from which 24 miRNAs were counter-regulated due to ICons. CONCLUSIONS Our findings highlight 24 miRNAs that potentially regulate cardioprotective therapeutic targets associated with MMPs and BGN in a highly translatable porcine model of acute myocardial infarction.
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Affiliation(s)
- Tamara Szabados
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
| | - Arnold Molnár
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
| | - Éva Kenyeres
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
| | - Kamilla Gömöri
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
| | - Judit Pipis
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
| | - Bence Pósa
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
| | - András Makkos
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, Semmelweis University, Nagyvárad tér 4, H-1089 Budapest, Hungary;
| | - Bence Ágg
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, Semmelweis University, Nagyvárad tér 4, H-1089 Budapest, Hungary;
| | - Zoltán Giricz
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, Semmelweis University, Nagyvárad tér 4, H-1089 Budapest, Hungary;
| | - Péter Ferdinandy
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, Semmelweis University, Nagyvárad tér 4, H-1089 Budapest, Hungary;
| | - Anikó Görbe
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, Semmelweis University, Nagyvárad tér 4, H-1089 Budapest, Hungary;
| | - Péter Bencsik
- Cardiovascular Research Group, Department of Pharmacology and Pharmacotherapy, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 12, H-6720 Szeged, Hungary; (T.S.); (A.M.); (É.K.); (K.G.); (J.P.); (B.P.); (A.G.)
- Pharmahungary Group, Hajnóczy u. 6, H-6722 Szeged, Hungary; (B.Á.); (Z.G.); (P.F.)
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17
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Zhang J, You Q, Wang Y, Ji J. LncRNA GAS5 Modulates the Progression of Glioma Through Repressing miR-135b-5p and Upregulating APC. Biologics 2024; 18:129-142. [PMID: 38817552 PMCID: PMC11137960 DOI: 10.2147/btt.s454058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Purpose The main purpose of this paper is to explore the interaction between GAS5 and miR-135b-5p to understand their function in the metastasis, invasion, and proliferation of glioma. This may provide new ideas for the pathogenesis and treatment of glioma. Patients and Methods Western blotting assays and RT‑qPCR were employed to investigate the expression of related genes in glioma tissues or cell lines. CCK-8 was used to examine the impact of GAS5 on cell viability. Motile activities were adopted by the transwell and wound healing experiments. A double luciferase experiment was performed to elucidate transcriptional regulation. Results GAS5 showed low expression in glioma cells and tissues, and up-regulation of GAS5 could depress the invasion, proliferation, and metastasis of glioma. GAS5 negatively regulates miR-135b-5p, which can counteract the cellular effects caused by GAS5. APC was the target of miR-135b-5p, and GAS5 can regulate the expression of APC by sponging miR-135b-5p. APC overexpression reversed the effects of miR-135b-5p promotion on glioma cells, while miR-135b-5p has the opposite function. As a downstream target gene of GAS5, miR-135b-5p was negatively regulated by GAS5. The restoration of miR-135b-5p can remarkably reverse the impact of GAS5 on glioma cells. In addition, GAS5 increased the expression of APC in glioma cells by inhibiting miR-135b-5p. Conclusion GAS5 increased APC expression by restraining miR-135b-5p and partially blocked the progression of glioma, suggesting that it could be an advantageous therapeutic target for glioma intervention.
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Affiliation(s)
- Jidong Zhang
- Center for Neurological Diseases, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, People’s Republic of China
| | - Qiuxiang You
- Center for Neurological Diseases, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, People’s Republic of China
| | - Yutao Wang
- Center for Neurological Diseases, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, People’s Republic of China
| | - Jianwen Ji
- Center for Neurological Diseases, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, People’s Republic of China
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18
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Biegała Ł, Kołat D, Gajek A, Płuciennik E, Marczak A, Śliwińska A, Mikula M, Rogalska A. Uncovering miRNA-mRNA Regulatory Networks Related to Olaparib Resistance and Resensitization of BRCA2MUT Ovarian Cancer PEO1-OR Cells with the ATR/CHK1 Pathway Inhibitors. Cells 2024; 13:867. [PMID: 38786089 PMCID: PMC11119970 DOI: 10.3390/cells13100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Resistance to olaparib is the major obstacle in targeted therapy for ovarian cancer (OC) with poly(ADP-ribose) polymerase inhibitors (PARPis), prompting studies on novel combination therapies to enhance olaparib efficacy. Despite identifying various mechanisms, understanding how OC cells acquire PARPi resistance remains incomplete. This study investigated microRNA (miRNA) expression in olaparib-sensitive (PEO1, PEO4) and previously established olaparib-resistant OC cell lines (PEO1-OR) using high-throughput RT-qPCR and bioinformatic analyses. The role of miRNAs was explored regarding acquired resistance and resensitization with the ATR/CHK1 pathway inhibitors. Differentially expressed miRNAs were used to construct miRNA-mRNA regulatory networks and perform functional enrichment analyses for target genes with miRNet 2.0. TCGA-OV dataset was analyzed to explore the prognostic value of selected miRNAs and target genes in clinical samples. We identified potential processes associated with olaparib resistance, including cell proliferation, migration, cell cycle, and growth factor signaling. Resensitized PEO1-OR cells were enriched in growth factor signaling via PDGF, EGFR, FGFR1, VEGFR2, and TGFβR, regulation of the cell cycle via the G2/M checkpoint, and caspase-mediated apoptosis. Antibody microarray analysis confirmed dysregulated growth factor expression. The addition of the ATR/CHK1 pathway inhibitors to olaparib downregulated FGF4, FGF6, NT-4, PLGF, and TGFβ1 exclusively in PEO1-OR cells. Survival and differential expression analyses for serous OC patients revealed prognostic miRNAs likely associated with olaparib resistance (miR-99b-5p, miR-424-3p, and miR-505-5p) and resensitization to olaparib (miR-324-5p and miR-424-3p). Essential miRNA-mRNA interactions were reconstructed based on prognostic miRNAs and target genes. In conclusion, our data highlight distinct miRNA profiles in olaparib-sensitive and olaparib-resistant cells, offering molecular insights into overcoming resistance with the ATR/CHK1 inhibitors in OC. Moreover, some miRNAs might serve as potential predictive signature molecules of resistance and therapeutic response.
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Affiliation(s)
- Łukasz Biegała
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (Ł.B.); (A.G.); (A.M.)
- Doctoral School of Exact and Natural Sciences, University of Lodz, Jana Matejki 21/23, 90-237 Lodz, Poland
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Żeligowskiego 7/9, 90-752 Lodz, Poland; (D.K.); (E.P.)
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland
| | - Arkadiusz Gajek
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (Ł.B.); (A.G.); (A.M.)
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Żeligowskiego 7/9, 90-752 Lodz, Poland; (D.K.); (E.P.)
| | - Agnieszka Marczak
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (Ł.B.); (A.G.); (A.M.)
| | - Agnieszka Śliwińska
- Department of Nucleic Acid Biochemistry, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland;
| | - Aneta Rogalska
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (Ł.B.); (A.G.); (A.M.)
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19
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Bi Y, Li T, Zhang S, Yang Y, Dong M. Bioinformatics-based analysis of the dialog between COVID-19 and RSA. Heliyon 2024; 10:e30371. [PMID: 38737245 PMCID: PMC11088317 DOI: 10.1016/j.heliyon.2024.e30371] [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: 08/10/2023] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
Pregnant women infected with SARS-CoV-2 in early pregnancy may face an increased risk of miscarriage due to immune imbalance at the maternal-fetal interface. However, the molecular mechanisms underlying the crosstalk between COVID-19 infection and recurrent spontaneous abortion (RSA) remain poorly understood. This study aimed to elucidate the transcriptomic molecular dialog between COVID-19 and RSA. Based on bioinformatics analysis, 307 common differentially expressed genes were found between COVID-19 (GSE171110) and RSA (GSE165004). Common DEGs were mainly enriched in ribosome-related and cell cycle-related signaling pathways. Using degree algorithm, the top 10 hub genes (RPS27A, RPL5, RPS8, RPL4, RPS2, RPL30, RPL23A, RPL31, RPL26, RPL37A) were selected from the common DEGs based on their scores. The results of the qPCR were in general agreement with the results of the raw letter analysis. The top 10 candidate drugs were also selected based on P-values. In this study, we provide molecular markers, signaling pathways, and small molecule compounds that may associate COVID-19. These findings may increase the accurate diagnosis and treatment of COVID-19 patients.
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Affiliation(s)
- Yin Bi
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, 530000, China
| | - Ting Li
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, 530000, China
| | - Shun Zhang
- Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Yihua Yang
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Guangxi Medical University, Ministry of Education, Nanning, 530000, China
| | - Mingyou Dong
- Guangxi Reproductive Medical Center, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, China
- The Key Laboratory of Molecular Pathology (For Hepatobiliary Diseases) of Guangxi, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, China
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20
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Ullah S, Rahman W, Ullah F, Ullah A, Ahmad G, Ijaz M, Ullah H, Sharafmal DM. The HABD: Home of All Biological Databases Empowering Biological Research With Cutting-Edge Database Systems. Curr Protoc 2024; 4:e1063. [PMID: 38808697 DOI: 10.1002/cpz1.1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The emergence of computer technologies and computing power has led to the development of several database systems that provide standardized access to vast quantities of data, making it possible to collect, search, index, evaluate, and extract useful knowledge across various fields. The Home of All Biological Databases (HABD) has been established as a continually expanding platform that aims to store, organize, and distribute biological data in a searchable manner, removing all dead and non-accessible data. The platform meticulously categorizes data into various categories, such as COVID-19 Pandemic Database (CO-19PDB), Database relevant to Human Research (DBHR), Cancer Research Database (CRDB), Latest Database of Protein Research (LDBPR), Fungi Databases Collection (FDBC), and many other databases that are categorized based on biological phenomena. It currently provides a total of 22 databases, including 6 published, 5 submitted, and the remaining in various stages of development. These databases encompass a range of areas, including phytochemical-specific and plastic biodegradation databases. HABD is equipped with search engine optimization (SEO) analyzer and Neil Patel tools, which ensure excellent SEO and high-speed value. With timely updates, HABD aims to facilitate the processing and visualization of data for scientists, providing a one-stop-shop for all biological databases. Computer platforms, such as PhP, html, CSS, Java script and Biopython, are used to build all the databases. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Shahid Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Farhan Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Anees Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Gulzar Ahmad
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Hameed Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
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21
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Qiu M, Chen Y, Zeng C. Biological functions of circRNA in regulating the hallmarks of gastrointestinal cancer (Review). Int J Oncol 2024; 64:49. [PMID: 38488023 PMCID: PMC10997371 DOI: 10.3892/ijo.2024.5637] [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: 11/04/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Circular RNA (circRNA) was first observed in the cytoplasm of eukaryotic cells in 1979, but it was not characterized in detail until 2012, when high‑throughput sequencing technology was more advanced and available. Consequently, the mechanism of circRNA formation and its biological function have been progressively elucidated by researchers. circRNA is abundant in eukaryotic cells and exhibits a certain degree of organization, timing and disease‑specificity. Additionally, it is poorly degradable, meeting the characteristics of an ideal clinical biomarker. In the present review, the recent research progress of circRNAs in digestive tract malignant tumors was primarily discussed. This included the roles, biological functions and clinical significance of circRNA, providing references for its research value and clinical potential in gastrointestinal cancer.
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Affiliation(s)
- Mengjun Qiu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chunyan Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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22
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Zhang R, Li Y, Li X, Ni A, Gao Y, Zong Y, Sun Y, Yuan J, Chen J, Ma H. Pigeon novel-miR-741 targets OTUD1 to inhibit proliferation and promote apoptosis of crop fibroblasts. Poult Sci 2024; 103:103587. [PMID: 38479099 PMCID: PMC11067753 DOI: 10.1016/j.psj.2024.103587] [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: 12/12/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 05/01/2024] Open
Abstract
Trichomonas gallinae (T. gallinae) is a globally distributed protozoan parasite and could cause serious damage to the pigeon industry. MiRNAs have important roles in regulating parasite infection, but its impacts on T. gallinae resistance have rarely been reported. In the present study, we identified a new miRNA (novel-miR-741) and its predicted target OTU deubiquitinase 1 (OTUD1) that might be associated with immunity to T. gallinae in pigeon. Novel-miR-741 and OTUD1 over-expression vectors and interference vectors were constructed. Results from dual luciferase activity assay demonstrated that OTUD1 was a downstream target of novel-miR-741. The Cell Counting Kit-8 and apoptosis assays showed that novel-miR-741 inhibited the proliferation and promoted apoptosis of pigeon crop fibroblasts. Meanwhile, mRNA levels of OTUD1 were significantly reduced in novel-miR-741 mimic-transfected fibroblasts, while mRNA levels of OTUD1 were significantly increased in the novel-miR-741 inhibitor-transfected fibroblasts. The regulatory roles of si-OTUD1 on fibroblasts proliferation, apoptosis, and migration were similar to novel-miR-741 mimic. Our findings demonstrated that novel-miR-741 inhibited the proliferation, and migration of crop fibroblasts, while OTUD1 promoted the proliferation and migration of crop fibroblasts. Therefore, the regulation of OTUD1 by novel-miR-741 was proposed as a potential therapeutic strategy for T. gallinae.
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Affiliation(s)
- Ran Zhang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunlei Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinyi Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Aixin Ni
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuxin Gao
- College of Animal Science, Shanxi Agricultural University, Taigu 030800, China
| | - Yunhe Zong
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanyan Sun
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingwei Yuan
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jilan Chen
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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23
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Du A, Xu R, Yang Q, Lu Y, Luo X. Exploration of shared gene signatures and molecular mechanisms between type 2 diabetes and osteoporosis. J Cell Mol Med 2024; 28:e18141. [PMID: 38742851 PMCID: PMC11092535 DOI: 10.1111/jcmm.18141] [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: 07/07/2023] [Revised: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 05/16/2024] Open
Abstract
Type 2 diabetes mellitus (T2D) and osteoporosis (OP) are systemic metabolic diseases and often coexist. The mechanism underlying this interrelationship remains unclear. We downloaded microarray data for T2D and OP from the Gene Expression Omnibus (GEO) database. Using weighted gene co-expression network analysis (WGCNA), we identified co-expression modules linked to both T2D and OP. To further investigate the functional implications of these associated genes, we evaluated enrichment using ClueGO software. Additionally, we performed a biological process analysis of the genes unique in T2D and OP. We constructed a comprehensive miRNA-mRNA network by incorporating target genes and overlapping genes from the shared pool. Through the implementation of WGCNA, we successfully identified four modules that propose a plausible model that elucidates the disease pathway based on the associated and distinct gene profiles of T2D and OP. The miRNA-mRNA network analysis revealed co-expression of PDIA6 and SLC16A1; their expression was upregulated in patients with T2D and islet β-cell lines. Remarkably, PDIA6 and SLC16A1 were observed to inhibit the proliferation of pancreatic β cells and promote apoptosis in vitro, while downregulation of PDIA6 and SLC16A1 expression led to enhanced insulin secretion. This is the first study to reveal the significant roles of PDIA6 and SLC16A1 in the pathogenesis of T2D and OP, thereby identifying additional genes that hold potential as indicators or targets for therapy.
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Affiliation(s)
- Ashuai Du
- Department of Infectious DiseasesGuizhou Provincial People's HospitalGuiyangChina
| | - Rong Xu
- Department of PathologyThe First People's Hospital of Changde CityChangdeChina
| | - Qinglong Yang
- Department of General SurgeryGuizhou Provincial People's HospitalGuiyangChina
| | - Yingxue Lu
- Department of Infectious DiseasesGuizhou Provincial People's HospitalGuiyangChina
| | - Xinhua Luo
- Department of Infectious DiseasesGuizhou Provincial People's HospitalGuiyangChina
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24
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Aguiar TFM, Rivas MP, de Andrade Silva EM, Pires SF, Dangoni GD, Macedo TC, Defelicibus A, Barros BDDF, Novak E, Cristofani LM, Odone V, Cypriano M, de Toledo SRC, da Cunha IW, da Costa CML, Carraro DM, Tojal I, de Oliveira Mendes TA, Krepischi ACV. First Transcriptome Analysis of Hepatoblastoma in Brazil: Unraveling the Pivotal Role of Noncoding RNAs and Metabolic Pathways. Biochem Genet 2024:10.1007/s10528-024-10764-y. [PMID: 38649558 DOI: 10.1007/s10528-024-10764-y] [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: 10/27/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues. The analysis unveiled 1,492 differentially expressed genes (1,031 upregulated and 461 downregulated), including 920 protein-coding genes (62%). Upregulated biological processes were linked to cell differentiation, signaling, morphogenesis, and development, involving known hepatoblastoma-associated genes (DLK1, MEG3, HDAC2, TET1, HMGA2, DKK1, DKK4), alongside with novel findings (GYNG4, CDH3, and TNFRSF19). Downregulated processes predominantly centered around oxidation and metabolism, affecting amines, nicotinamides, and lipids, featuring novel discoveries like the repression of SYT7, TTC36, THRSP, CCND1, GCK and CAMK2B. Two genes, which displayed a concordant pattern of DNA methylation alteration in their promoter regions and dysregulation in the transcriptome, were further validated by RT-qPCR: the upregulated TNFRSF19, a key gene in the embryonic development, and the repressed THRSP, connected to lipid metabolism. Furthermore, based on protein-protein interaction analysis, we identified genes holding central positions in the network, such as HDAC2, CCND1, GCK, and CAMK2B, among others, that emerged as prime candidates warranting functional validation in future studies. Notably, a significant dysregulation of non-coding RNAs (ncRNAs), predominantly upregulated transcripts, was observed, with 42% of the top 50 highly expressed genes being ncRNAs. An integrative miRNA-mRNA analysis revealed crucial biological processes associated with metabolism, oxidation reactions of lipids and carbohydrates, and methylation-dependent chromatin silencing. In particular, four upregulated miRNAs (miR-186, miR-214, miR-377, and miR-494) played a pivotal role in the network, potentially targeting multiple protein-coding transcripts, including CCND1 and CAMK2B. In summary, our transcriptome analysis highlighted disrupted embryonic development as well as metabolic pathways, particularly those involving lipids, emphasizing the emerging role of ncRNAs as epigenetic regulators in hepatoblastomas. These findings provide insights into the complexity of the hepatoblastoma transcriptome and identify potential targets for future therapeutic interventions.
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Affiliation(s)
- Talita Ferreira Marques Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, USA
| | - Maria Prates Rivas
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Edson Mario de Andrade Silva
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Minas Gerais, Brazil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
| | - Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Gustavo Dib Dangoni
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Taiany Curdulino Macedo
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Dirce Maria Carraro
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil.
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Mandić K, Milutin Gašperov N, Božinović K, Dediol E, Krasić J, Sinčić N, Grce M, Sabol I, Barešić A. Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers. Sci Rep 2024; 14:9062. [PMID: 38643268 PMCID: PMC11032388 DOI: 10.1038/s41598-024-59312-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024] Open
Abstract
Head and neck cancer is the sixth most common malignancy worldwide, with the relatively low 5-year survival rate, mainly because it is diagnosed at a late stage. Infection with HPV is a well known aetiology, which affects the nature of these cancers and patients' survival. Besides, it is considered that the main driving force for this type of cancer could be epigenetics. In this study we aimed to find potential epigenetic biomarkers, by integrating miRNome, methylome, and transcriptome analyses. From the fresh head and neck cancer tissue samples, we chose a group for miRNome, methylome and transcriptome profiling, in comparison to adequate control samples. Bioinformatics analyses are performed in R v4.2.2. Count normalisation and group differential expression for mRNA and the previously obtained miRNA count data was performed with DESeq2 v1.36. Gene set enrichment analysis was performed and visualised using gProfiler2 v0.2.1 Identification of miRNA targets was performed by querying in miRTarBase using multiMiR v1.18.0. Annotation of CpG sites merging into islands was obtained from RnBeads.hg19 v1.28.0. package. For the integrative analysis we performed kmeans clustering using stats v4.2.2 package, using 8-12 clusters and nstart 100. We found that transcriptome analysis divides samples into cancers and controls clusters, with no relation to HPV status or cancer anatomical location. Differentially expressed genes (n = 2781) were predominantly associated with signalling pathways of tumour progression. We identified a cluster of genes under the control of the transcription factor E2F that are significantly underexpressed in cancer tissue, as well as T cell immunity genes and genes related to regulation of transcription. Among overexpressed genes in tumours we found those that belong to cell cycle regulation and vasculature. A small number of genes were found significantly differentially expressed in HPV-positive versus HPV-negative tumours (for example NEFH, ZFR2, TAF7L, ZNF541, and TYMS). In this comprehensive study on an overlapping set of samples where the integration of miRNome, methylome and transcriptome analysis were performed for head and neck cancer, we demonstrated that the majority of genes were associated exclusively with miRNome or methylome and, to a lesser extent, under the control of both epigenetic mechanisms.
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Affiliation(s)
- Katarina Mandić
- Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Ksenija Božinović
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Emil Dediol
- Department of Maxillofacial Surgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | - Jure Krasić
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Nino Sinčić
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
- Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
- Biomedical Research Centre Šalata, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Magdalena Grce
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivan Sabol
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Anja Barešić
- Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia
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26
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Wang Y, Li K, Mo S, Yao P, Zeng J, Lu S, Qin S. Identification of common genes and pathways between type 2 diabetes and COVID-19. Front Genet 2024; 15:1249501. [PMID: 38699234 PMCID: PMC11063347 DOI: 10.3389/fgene.2024.1249501] [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: 06/28/2023] [Accepted: 03/21/2024] [Indexed: 05/05/2024] Open
Abstract
Background Numerous studies have reported a high incidence and risk of severe illness due to coronavirus disease 2019 (COVID-19) in patients with type 2 diabetes (T2DM). COVID-19 patients may experience elevated or decreased blood sugar levels and may even develop diabetes. However, the molecular mechanisms linking these two diseases remain unclear. This study aimed to identify the common genes and pathways between T2DM and COVID-19. Methods Two public datasets from the Gene Expression Omnibus (GEO) database (GSE95849 and GSE164805) were analyzed to identify differentially expressed genes (DEGs) in blood between people with and without T2DM and COVID-19. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the common DEGs. A protein-protein interaction (PPI) network was constructed to identify common genes, and their diagnostic performance was evaluated by receiver operating characteristic (ROC) curve analysis. Validation was performed on the GSE213313 and GSE15932 datasets. A gene co-expression network was constructed using the GeneMANIA database to explore interactions among core DEGs and their co-expressed genes. Finally, a microRNA (miRNA)-transcription factor (TF)-messenger RNA (mRNA) regulatory network was constructed based on the common feature genes. Results In the GSE95849 and GSE164805 datasets, 81 upregulated genes and 140 downregulated genes were identified. GO and KEGG enrichment analyses revealed that these DEGs were closely related to the negative regulation of phosphate metabolic processes, the positive regulation of mitotic nuclear division, T-cell co-stimulation, and lymphocyte co-stimulation. Four upregulated common genes (DHX15, USP14, COPS3, TYK2) and one downregulated common feature gene (RIOK2) were identified and showed good diagnostic accuracy for T2DM and COVID-19. The AUC values of DHX15, USP14, COPS3, TYK2, and RIOK2 in T2DM diagnosis were 0.931, 0.917, 0.986, 0.903, and 0.917, respectively. In COVID-19 diagnosis, the AUC values were 0.960, 0.860, 1.0, 0.9, and 0.90, respectively. Validation in the GSE213313 and GSE15932 datasets confirmed these results. The miRNA-TF-mRNA regulatory network showed that TYH2 was targeted by PITX1, PITX2, CRX, NFYA, SREBF1, RELB, NR1L2, and CEBP, whereas miR-124-3p regulates THK2, RIOK2, and USP14. Conclusion We identified five common feature genes (DHX15, USP14, COPS3, TYK2, and RIOK2) and their co-regulatory pathways between T2DM and COVID-19, which may provide new insights for further molecular mechanism studies.
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Affiliation(s)
- Ya Wang
- Gastroenterology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Endocrinology Department, Liuzhou Peoples’ Hospital Affiliated to Guangxi Medical University, Liuzhou, China
| | - Kai Li
- Orthopedics Department, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Shuangyang Mo
- Gastroenterology Department, Liuzhou Peoples’ Hospital Affiliated to Guangxi Medical University, Liuzhou, China
| | - Peishan Yao
- Gastroenterology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiaxing Zeng
- Department of Traumatic Surgery, Microsurgery, and Hand Surgery, Guangxi Zhuang Autonomous Region People’s Hospital, Nanning, Guangxi, China
| | - Shunyu Lu
- Department of Pharmacy, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shanyu Qin
- Gastroenterology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Corell-Sierra J, Marquez-Molins J, Marqués MC, Hernandez-Azurdia AG, Montagud-Martínez R, Cebriá-Mendoza M, Cuevas JM, Albert E, Navarro D, Rodrigo G, Gómez G. SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity. NPJ Syst Biol Appl 2024; 10:41. [PMID: 38632240 PMCID: PMC11024147 DOI: 10.1038/s41540-024-00367-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.
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Affiliation(s)
- Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - María-Carmen Marqués
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | | | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - José M Cuevas
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010, Valencia, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Gustavo Gómez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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Swindell WR. Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords. Front Genet 2024; 15:1385114. [PMID: 38689650 PMCID: PMC11059082 DOI: 10.3389/fgene.2024.1385114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction ALS is a fatal neurodegenerative disease for which underlying mechanisms are incompletely understood. The motor neuron is a central player in ALS pathogenesis but different transcriptome signatures have been derived from bulk analysis of post-mortem tissue and iPSC-derived motor neurons (iPSC-MNs). Methods This study performed a meta-analysis of six gene expression studies (microarray and RNA-seq) in which laser capture microdissection (LCM) was used to isolate lower motor neurons from post-mortem spinal cords of ALS and control (CTL) subjects. Differentially expressed genes (DEGs) with consistent ALS versus CTL expression differences across studies were identified. Results The analysis identified 222 ALS-increased DEGs (FDR <0.10, SMD >0.80) and 278 ALS-decreased DEGs (FDR <0.10, SMD < -0.80). ALS-increased DEGs were linked to PI3K-AKT signaling, innate immunity, inflammation, motor neuron differentiation and extracellular matrix. ALS-decreased DEGs were associated with the ubiquitin-proteosome system, microtubules, axon growth, RNA-binding proteins and synaptic membrane. ALS-decreased DEG mRNAs frequently interacted with RNA-binding proteins (e.g., FUS, HuR). The complete set of DEGs (increased and decreased) overlapped significantly with genes near ALS-associated SNP loci (p < 0.01). Transcription factor target motifs with increased proximity to ALS-increased DEGs were identified, most notably DNA elements predicted to interact with forkhead transcription factors (e.g., FOXP1) and motor neuron and pancreas homeobox 1 (MNX1). Some of these DNA elements overlie ALS-associated SNPs within known enhancers and are predicted to have genotype-dependent MNX1 interactions. DEGs were compared to those identified from SOD1-G93A mice and bulk spinal cord segments or iPSC-MNs from ALS patients. There was good correspondence with transcriptome changes from SOD1-G93A mice (r ≤ 0.408) but most DEGs were not differentially expressed in bulk spinal cords or iPSC-MNs and transcriptome-wide effect size correlations were weak (bulk tissue: r ≤ 0.207, iPSC-MN: r ≤ 0.037). Conclusion This study defines a robust transcriptome signature from LCM-based motor neuron studies of post-mortem tissue from ALS and CTL subjects. This signature differs from those obtained from analysis of bulk spinal cord segments and iPSC-MNs. Results provide insight into mechanisms underlying gene dysregulation in ALS and highlight connections between these mechanisms, ALS genetics, and motor neuron biology.
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Affiliation(s)
- William R. Swindell
- Department of Internal Medicine, Division of Hospital Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
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Zhang C, Zheng J, Han X, Zhao J, Cheng S, Li A. Bovine Colostrum miR-30a-5p Targets the NF-κB Signaling Pathway to Alleviate Inflammation in Intestinal Epithelial Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38606544 DOI: 10.1021/acs.jafc.3c09856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Inflammatory bowel disease (IBD) is a common disease of the digestive system, and an excessive immune response mediated by the nuclear factor κ-B (NF-κB) signaling pathway is an essential etiology. Recent studies have found that bovine milk exosomes can improve intestinal mucosal health by delivering microRNA (miRNA), but the mechanism of action is so far unknown. In the present study, we analyzed the differential expression profiles of miRNA in colostrum and mature milk exosomes using high-throughput sequencing, based on the demonstration that colostrum exosomes inhibit the lipopolysaccharide (LPS)-induced intestinal epithelial NF-κB inflammatory pathway better than mature milk exosomes. The bta-miR-30a-5p, which is specifically highly expressed in colostrum, was screened, and its predicted target gene TRAM was found to be closely related to the NF-κB signaling pathway by functional enrichment analysis. Further, we used gene overexpression and silencing techniques and found that the bta-miR-30a-5p transfection treatment was confirmed to inhibit LPS-induced NF-κB signaling pathway activation and downstream pro-inflammatory factor expression, while the expression of its potential target gene, TRAM, was also suppressed. It is hypothesized that the high expression of bta-miR-30a-5p in colostrum, which targets TRAM to inhibit the downstream NF-κB inflammatory pathway, may be one of the molecular mechanisms responsible for its superior effect on resisting inflammatory attack compared to mature milk.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Company Limited, Shanghai 200436, China
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jie Zheng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xueting Han
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jingwen Zhao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Shihui Cheng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Aili Li
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Company Limited, Shanghai 200436, China
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
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30
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Wang T, Fang X, Sheng X, Li M, Mei Y, Mei Q, Pan A. Identification of immune characteristic biomarkers and therapeutic targets in cuproptosis for sepsis by integrated bioinformatics analysis and single-cell RNA sequencing analysis. Heliyon 2024; 10:e27379. [PMID: 38495196 PMCID: PMC10943398 DOI: 10.1016/j.heliyon.2024.e27379] [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: 08/12/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Background Cuproptosis is a copper-dependent cell death that is connected to the development and immune response of multiple diseases. However, the function of cuproptosis in the immune characteristics of sepsis remains unclear. Method We obtained two sepsis datasets (GSE9960 and GSE134347) from the GEO database and classified the raw data with R packages. Cuproptosis-related genes were manually curated, and differentially expressed cuproptosis-related genes (DECuGs) were identified. Afterwards, we applied enrichment analysis and identified key DECuGs by performing machine learning techniques. Then, the immune cell infiltrations and correlation between DECuGs and immunocyte features were created by the CIBERSORT algorithm. Subsequently, unsupervised hierarchical clustering analysis was performed based on key DECuGs. We then constructed a ceRNA network based on key DECuGs by using multi-step computational strategies and predicted potential drugs in the DrugBank database. Finally, the role of these key genes in immune cells was validated at the single-cell RNA level between septic patients and healthy controls. Results Overall, 16 DECuGs were obtained, and most of them had lower expression levels in sepsis samples. Afterwards, we obtained six key DECuGs by performing machine learning. Then, the LIPT1-T-cell CD4 memory resting was the most positively correlated DECuG-immunocyte pair. Subsequently, two different subclusters were identified by six DECuGs. Bioinformatics analysis revealed that there were different immune characteristics between the two subclusters. Moreover, we identified the key lncRNA OIP5-AS1 within the ceRNA network and obtained 4 drugs that may represent novel drugs for sepsis. Finally, these key DECuGs were statistically significantly dysregulated in another validation set and showed a major distribution in monocytes, T cells, B cells, NK cells and platelets at the single-cell RNA level. Conclusion These findings suggest that cuproptosis might promote the progression of sepsis by affecting the immune system and metabolic dysfunction, which provides a new direction for understanding potential pathogenic processes and therapeutic targets in sepsis.
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Affiliation(s)
- Tianfeng Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, China
| | - Xiaowei Fang
- Department of Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, China
| | - Ximei Sheng
- WanNan Medical College, Wuhu, Anhui, 241002, China
| | - Meng Li
- Department of Intensive Care Unit, The Affiliated Provincial Hospital of Anhui Medical University, Anhui, 230001, China
| | - Yulin Mei
- WanNan Medical College, Wuhu, Anhui, 241002, China
| | - Qing Mei
- Department of Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, China
| | - Aijun Pan
- Department of Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui Province, 230001, China
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Zou HT, Ji BY, Xie XL. A multi-source molecular network representation model for protein-protein interactions prediction. Sci Rep 2024; 14:6184. [PMID: 38485942 PMCID: PMC10940665 DOI: 10.1038/s41598-024-56286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
The prediction of potential protein-protein interactions (PPIs) is a critical step in decoding diseases and understanding cellular mechanisms. Traditional biological experiments have identified plenty of potential PPIs in recent years, but this problem is still far from being solved. Hence, there is urgent to develop computational models with good performance and high efficiency to predict potential PPIs. In this study, we propose a multi-source molecular network representation learning model (called MultiPPIs) to predict potential protein-protein interactions. Specifically, we first extract the protein sequence features according to the physicochemical properties of amino acids by utilizing the auto covariance method. Second, a multi-source association network is constructed by integrating the known associations among miRNAs, proteins, lncRNAs, drugs, and diseases. The graph representation learning method, DeepWalk, is adopted to extract the multisource association information of proteins with other biomolecules. In this way, the known protein-protein interaction pairs can be represented as a concatenation of the protein sequence and the multi-source association features of proteins. Finally, the Random Forest classifier and corresponding optimal parameters are used for training and prediction. In the results, MultiPPIs obtains an average 86.03% prediction accuracy with 82.69% sensitivity at the AUC of 93.03% under five-fold cross-validation. The experimental results indicate that MultiPPIs has a good prediction performance and provides valuable insights into the field of potential protein-protein interactions prediction. MultiPPIs is free available at https://github.com/jiboyalab/multiPPIs .
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Affiliation(s)
- Hai-Tao Zou
- College of Information Science and Engineering, Guilin University of Technology, Guilin, 541000, China
| | - Bo-Ya Ji
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410000, China.
| | - Xiao-Lan Xie
- College of Information Science and Engineering, Guilin University of Technology, Guilin, 541000, China.
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Ostrycharz E, Fitzner A, Kęsy A, Siennicka A, Hukowska-Szematowicz B. MicroRNAs participate in the regulation of apoptosis and oxidative stress-related gene expression in rabbits infected with Lagovirus europaeus GI.1 and GI.2 genotypes. Front Microbiol 2024; 15:1349535. [PMID: 38516020 PMCID: PMC10955125 DOI: 10.3389/fmicb.2024.1349535] [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: 12/04/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
MicroRNAs (miRs) are a group of small, 17-25 nucleotide, non-coding RNA that regulate gene expression at the post-transcriptional level. To date, little is known about the molecular signatures of regulatory interactions between miRs and apoptosis and oxidative stress in viral diseases. Lagovirus europaeus is a virus that causes severe disease in rabbits (Oryctolagus cuniculus) called Rabbit Hemorrhagic Disease (RHD) and belongs to the Caliciviridae family, Lagovirus genus. Within Lagovirus europaeus associated with RHD, two genotypes (GI.1 and GI.2) have been distinguished, and the GI.1 genotype includes four variants (GI.1a, GI.1b, GI.1c, and GI.1d). The study aimed to assess the expression of miRs and their target genes involved in apoptosis and oxidative stress, as well as their potential impact on the pathways during Lagovirus europaeus-two genotypes (GI.1 and GI.2) infection of different virulences in four tissues (liver, lung, kidneys, and spleen). The expression of miRs and target genes related to apoptosis and oxidative stress was determined using quantitative real-time PCR (qPCR). In this study, we evaluated the expression of miR-21 (PTEN, PDCD4), miR-16b (Bcl-2, CXCL10), miR-34a (p53, SIRT1), and miRs-related to oxidative stress-miR-122 (Bach1) and miR-132 (Nfr-2). We also examined the biomarkers of both processes (Bax, Bax/Bcl-2 ratio, Caspase-3, PARP) and HO-I as biomarkers of oxidative stress. Our report is the first to present the regulatory effects of miRs on apoptosis and oxidative stress genes in rabbit infection with Lagovirus europaeus-two genotypes (GI.1 and GI.2) in four tissues (liver, lungs, kidneys, and spleen). The regulatory effect of miRs indicates that, on the one hand, miRs can intensify apoptosis (miR-16b, miR-34a) in the examined organs in response to a viral stimulus and, on the other hand, inhibit (miR-21), which in both cases may be a determinant of the pathogenesis of RHD and tissue damage. Biomarkers of the Bax and Bax/Bcl-2 ratio promote more intense apoptosis after infection with the Lagovirus europaeus GI.2 genotype. Our findings demonstrate that miR-122 and miR-132 regulate oxidative stress in the pathogenesis of RHD, which is associated with tissue damage. The HO-1 biomarker in the course of rabbit hemorrhagic disease indicates oxidative tissue damage. Our findings show that miR-21, miR-16b, and miR-34a regulate three apoptosis pathways. Meanwhile, miR-122 and miR-132 are involved in two oxidative stress pathways.
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Affiliation(s)
- Ewa Ostrycharz
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Doctoral School, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
| | - Andrzej Fitzner
- Department of Foot and Mouth Disease, National Veterinary Research Institute-State Research Institute, Zduńska Wola, Poland
- National Reference Laboratory for Rabbit Hemorrhagic Disease (RHD), Zduńska Wola, Poland
| | - Andrzej Kęsy
- Department of Foot and Mouth Disease, National Veterinary Research Institute-State Research Institute, Zduńska Wola, Poland
- National Reference Laboratory for Rabbit Hemorrhagic Disease (RHD), Zduńska Wola, Poland
| | - Aldona Siennicka
- Department of Laboratory Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Beata Hukowska-Szematowicz
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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Zhu H, Jia Y, Leung SW. Citations of microRNA Biomarker Articles That Were Retracted: A Systematic Review. JAMA Netw Open 2024; 7:e243173. [PMID: 38512253 PMCID: PMC10958238 DOI: 10.1001/jamanetworkopen.2024.3173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/26/2024] [Indexed: 03/22/2024] Open
Abstract
Importance Retraction is a tool that journals can use to deter research misconduct and alert their audience to erroneous content published in the journals. However, retracted articles may continue to damage science if they are still cited as legitimate articles. Objective To characterize patterns of postretraction citations, particularly in microRNA biomarker research, a field with one of the highest rates of retraction. Evidence Review Retracted scientific articles on microRNAs were retrieved from PubMed, Web of Science, and Retraction Watch between database inception and July 17, 2021, according to preestablished search strategies. Control articles with characteristics in common with retracted articles (ie, published in the same journals in the same years and months and with the same number of authors) were matched and retrieved from PubMed. Citation metrics of retractions and control articles were collected from Web of Science. PubPeer was referenced to examine the public response or comments on included retractions. Data were analyzed from September 2021 through March 2023. Findings A total of 10 461 articles were analyzed, with 887 retractions and 9574 articles as controls. Among retracted articles, which were published from 1999 to 2021, there were 756 articles (85.23%) written by researchers affiliated with Chinese institutions. Retracted articles were cited 6327 times after retraction. Of 792 retracted articles that were cited, 621 articles (78.41%) were cited at least once after retraction and 238 articles (30.05%) were cited more often after retraction than before retraction. Overall citations (comprising citations before and after retraction) and postretraction citations accumulated over time (eg, the median [IQR] number of postretraction citations was 1 [1-2] and 23 [9-44] citations at the first 6 and 66 months, respectively, between retraction and citation retrieval). A random sample of 87 retracted articles (9.81%) recorded 478 citations after retraction, with 208 citations (43.51%) in articles published 12 months or longer after retraction. Of these citing articles, 19 articles (3.97%) mentioned the retractions. Compared with the control group of 1620 nonretracted articles, no significant differences were found in overall number of citations or citations after retraction. Among 478 articles citing retracted articles, 414 articles were found on PubMed and had matched control articles; these articles had higher odds of being subsequently retracted than 7954 matched control articles (odds ratio, 6.57; 95% CI, 3.39-12.72). Conclusions and Relevance In this study, retraction was not associated with a reduction in citations of retracted articles, but articles that cited retracted publications had higher odds of later retraction. These findings suggest that journals may need to implement mechanisms for detection of postretraction citations.
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Affiliation(s)
- Hongmei Zhu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, Third People’s Hospital of Chengdu, Chengdu, Sichuan, China
- Medical Research Center, Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Yongliang Jia
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Siu-wai Leung
- Edinburgh Bayes Centre for AI Research in Shenzhen, College of Science and Engineering, University of Edinburgh, Scotland, United Kingdom
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Diener C, Keller A, Meese E. The miRNA-target interactions: An underestimated intricacy. Nucleic Acids Res 2024; 52:1544-1557. [PMID: 38033323 PMCID: PMC10899768 DOI: 10.1093/nar/gkad1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.
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Affiliation(s)
- Caroline Diener
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
| | - Andreas Keller
- Saarland University (USAAR), Chair for Clinical Bioinformatics, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
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Han J, Duan S, Li Y, Xin C. Time-series analysis of hematopoietic stem cells. Medicine (Baltimore) 2024; 103:e36509. [PMID: 38394540 PMCID: PMC11309688 DOI: 10.1097/md.0000000000036509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/16/2023] [Indexed: 02/25/2024] Open
Abstract
This study aimed to investigate the molecular mechanisms underlying the aging of hematopoietic stem cells (HSCs). Gene expression profile GSE32719 was downloaded from the Gene Expression Omnibus database, including 14 young, 5 middle, and 8 old HSCs. Differential expression analysis, short time-series expression miner analysis, and weighted co-expression network analysis were conducted to screen for hub genes whose expression changed over time during HSC aging. Subsequently, functional enrichment and multiple regulatory network analyses of the hub genes were performed. A total of 124 intersecting time-dependent differentially expressed and module genes were obtained, which were considered hub genes whose expression changed over time during HSC aging. Hub genes were significantly enriched in pathways such as the Hippo and AMP-activated protein kinase (AMPK) signaling pathways. Moreover, AP-1 Transcription Factor Subunit (FOS) and sirtuin 1 (SIRT1) had higher degrees in the protein-protein interaction network, were regulated by more transcription factors (TFs), such as Sp1 transcription factor (SP1) and BRCA1 DNA repair-associated (BRCA1), in the TF-mRNA-miRNA network, were associated with more diseases in the disease-gene network, and could be targeted by more drugs in the drug-gene network. Furthermore, SIRT1 was targeted by miR-9-5p in the TF-mRNA-miRNA network. Hub genes such as FOS and SIRT1 and key pathways such as the Hippo and AMPK signaling pathways may play crucial roles in HSC aging. Moreover, FOS and SIRT1 were regulated by SP1 and BRCA1, respectively, during HSC aging. Furthermore, miR-9-5p may modulate HSC aging by targeting SIRT1. Thus, FOS and SIRT1 may be potential therapeutic targets for age-related hematopoietic dysfunction.
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Affiliation(s)
- Jingjing Han
- Clinical Medical College of Jining Medical University, Jining Medical University, Jining, China
- Jining NO.1 People’s Hospital, Jining, China
| | - Shuangshuang Duan
- Clinical Medical College of Jining Medical University, Jining Medical University, Jining, China
- Jining NO.1 People’s Hospital, Jining, China
| | - Ya Li
- Jining NO.1 People’s Hospital, Jining, China
| | - Chunlei Xin
- Jining NO.1 People’s Hospital, Jining, China
- Yingjisha County People’s Hospital, Xinjiang, China
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Hsu WY, Chiou SS, Lin PC, Liao YM, Yeh CY, Tseng YH. Prediction of miRNA‑mRNA network regulating the migration ability of cytarabine‑resistant HL60 cells. Biomed Rep 2024; 20:20. [PMID: 38170076 PMCID: PMC10758919 DOI: 10.3892/br.2023.1708] [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: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Cytarabine is an important medicine for acute myeloid leukemia (AML) treatment, however, drug resistance hinders the treatment of AML. Although microRNA (miRNA or miR) alteration is one of the well-recognized mechanisms underlying drug resistance in AML, few studies have investigated the role and function of miRNAs in the development of cytarabine resistance. In the present study, total RNA was isolated from parental HL60 and cytarabine-resistant HL60 (R-HL60) cells. Subsequently, miRNAs and mRNAs were detected using small RNA sequencing and gene expression array, respectively. Differentially expressed mRNAs (DEMs) and differentially expressed genes (DEGs) with more than two-fold changes between HL60 and R-HL60 cells were screened out. Negatively associated miRNA-mRNA pairs were selected as candidate miRNA-mRNA target pairs according to the miRDB, Targetscan or miRTar databases. Functional enrichment analysis of DEGs included in the candidate miRNA-mRNA pairs was performed. The results indicated that 10 DEGs (CCL2, SOX9, SLC8A1, ICAM1, CXCL10, SIPR2, FGFR1, OVOL2, MITF and CARD10) were simultaneously involved in seven Gene Ontology pathways related to the regulation of migration ability, namely the 'regulation of cell migration', 'regulation of locomotion', 'regulation of cellular component movement', 'cell migration', 'locomotion', 'cell motility', and 'localization of cell'. DEMs predicted to negatively regulate the aforementioned 10 DEGs were paired with DEGs into 16 candidate miRNA-mRNA pairs related to the regulation of migration ability. In addition, migration assays revealed that the migration ability of R-HL60 cells was greater than that of HL60 cells. These findings provide a new perspective for the treatment of cytarabine-resistant AML and advance our understanding of altered migration ability underlying cytarabine resistance development, specifically related to miRNAs.
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Affiliation(s)
- Wan-Yi Hsu
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Special Hematologic Disease Service Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
| | - Shyh-Shin Chiou
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Special Hematologic Disease Service Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Pei-Chin Lin
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Special Hematologic Disease Service Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Yu-Mei Liao
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Division of Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
- Special Hematologic Disease Service Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
| | - Chung-Yu Yeh
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
| | - Yu-Hsin Tseng
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan, R.O.C
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Yadollahi Farsani M, Amini Farsani Z, Teimuri S, Kolahdouzan M, Eshraghi Samani R, Teimori H. Deregulation of miR-1245b-5p and miR-92a-3p and their potential target gene, GATA3, in epithelial-mesenchymal transition pathway in breast cancer. Cancer Rep (Hoboken) 2024; 7:e1955. [PMID: 38173189 PMCID: PMC10849934 DOI: 10.1002/cnr2.1955] [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: 08/01/2022] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small molecules that have prominent roles in tumor development and metastasis and can be used for diagnostic and therapeutic purposes. This study evaluated the expression of miR-92a-3p and miR-1245b-5p and their potential target gene, GATA3 in patients with breast cancer (BC). MATERIALS AND METHODS In the search for BC-related microRNAs, miR-124b-5p and miR-92a-3p were selected using Medline through PubMed, miR2disease, miRcancer and miRTarBase. Moreover, target gene GATA3 and their possible interaction in the regulating epithelial-mesenchymal transition (EMT) and invasion was evaluated using in silico tools including miRTarBase, TargetScan, STRING-db, and Cytoscape. The expression level of miR-92a-3p, miR1245b-5p, and GATA3 were assessed on extracted RNAs of tumor and nontumor tissues from 36 patients with BC using qPCR. Additionally, clinical-pathologic characteristics, such as tumor grade, tumor stage, lymph node were taken into consideration and the diagnostic power of these miRNAs and GATA3 was evaluated using the ROC curve analysis. RESULTS In silico evaluation of miR-92a-3p and miR-1245b-5p supports their potential association with EMT and invasion signaling pathways in BC pathogenesis. Comparing tumor tissues to nontumor tissues, we found a significant downregulation of miR-1245b-5p and miR-92a-3p and upregulation of GATA3. Patients with BC who had decreased miR-92a-3p expression also had higher rates of advanced stage/grade and ER expression, whereas decreased miR-1245b-5p expression was only linked to ER expression and was not associated with lymph node metastasis. The AUC of miR-1245b-5p, miR-92a-3p, and GATA3 using ROC curve was determined 0.6449 (p = .0239), 0.5980 (p = .1526), and 0.7415 (p < .0001), respectively, which showed a significant diagnostic accuracy of miR-1245b-5p and GATA3 between the BC patients and healthy individuals. CONCLUSION MiR-1245b-5p, miR-92a-3p, and GATA3 gene contribute to BC pathogenesis and they may be having potential regulatory roles in signaling pathways involved in invasion and EMT pathways in BC pathogenesis, as a result of these findings. More research is needed to determine the regulatory mechanisms that they control.
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Affiliation(s)
- Mahtab Yadollahi Farsani
- Department of Medical Biotechnology, School of Advanced TechnologiesShahrekord University of Medical SciencesShahrekordIran
| | - Zeinab Amini Farsani
- Cellular and Molecular Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
| | | | - Mohsen Kolahdouzan
- Department of Surgery, School of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Reza Eshraghi Samani
- Department of Surgery, School of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Hossein Teimori
- Cellular and Molecular Research Center, Basic Health Sciences InstituteShahrekord University of Medical SciencesShahrekordIran
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Wang H. The RNA m6A writer RBM15 contributes to the progression of esophageal squamous cell carcinoma by regulating miR-3605-5p/KRT4 pathway. Heliyon 2024; 10:e24459. [PMID: 38312624 PMCID: PMC10835169 DOI: 10.1016/j.heliyon.2024.e24459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 02/06/2024] Open
Abstract
Cancer progression can be modulated by N6-methyladenosine (m6A) modification. RNA binding motif protein 15 (RBM15) is an essential RNA m6A writer that influences carcinogenesis, however its significance in esophageal squamous cell carcinoma (ESCC) is uncertain. This research is intended to examine how RBM15 regulates the development of ESCC. We performed qRT-PCR analysis to evaluate the expression of RBM15, microRNA (miR-3605-5p) as well as keratin 4 (KRT4) in ESCC. Target relationship between miR-3605-5p and KRT4 was validated by dual luciferase reporter assay. Western blotting analyzed the protein levels of KRT4, p53, and p21. To demonstrate that RBM15 is responsible for the m6A alteration of miR-3605-5p, RIP and Me-RIP experiments were carried out concurrently. m6A content was measured by m6A quantification assay. Cell growth and migration were assessed using the CCK-8 and transwell assays. In addition, the role of RBM15 in vivo was examined using a mouse tumor xenograft model. RBM15 and miR-3605-5p were both substantially expressed in ESCC, however KRT4 was not expressed highly. Overexpressed RBM15 triggered cell proliferation and migration in ESCC. Besides, RBM15/m6A could mediate pri-3605-5p to form the mature miR-3605-5p, and miR-3605-5p further targeted KRT4. Further investigations showed that upregulation of KRT4 overturned the promoting impact of RBM15 overexpression on cell proliferation as well as on cell migration in ESCC by activating p53 signaling pathway. This work implied the carcinogenic activity of RBM15/m6A in ESCC via miR-3605-5p/KRT4 pathway, providing a novel m6A modification pattern in the tumorigenesis of ESCC.
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Affiliation(s)
- Huan Wang
- General practice section, Wuhan University of Science and Technology Hospital, Wuhan, 430070, Hubei, China
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Lozano-Velasco E, Inácio JM, Sousa I, Guimarães AR, Franco D, Moura G, Belo JA. miRNAs in Heart Development and Disease. Int J Mol Sci 2024; 25:1673. [PMID: 38338950 PMCID: PMC10855082 DOI: 10.3390/ijms25031673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Cardiovascular diseases (CVD) are a group of disorders that affect the heart and blood vessels. They include conditions such as myocardial infarction, coronary artery disease, heart failure, arrhythmia, and congenital heart defects. CVDs are the leading cause of death worldwide. Therefore, new medical interventions that aim to prevent, treat, or manage CVDs are of prime importance. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the posttranscriptional level and play important roles in various biological processes, including cardiac development, function, and disease. Moreover, miRNAs can also act as biomarkers and therapeutic targets. In order to identify and characterize miRNAs and their target genes, scientists take advantage of computational tools such as bioinformatic algorithms, which can also assist in analyzing miRNA expression profiles, functions, and interactions in different cardiac conditions. Indeed, the combination of miRNA research and bioinformatic algorithms has opened new avenues for understanding and treating CVDs. In this review, we summarize the current knowledge on the roles of miRNAs in cardiac development and CVDs, discuss the challenges and opportunities, and provide some examples of recent bioinformatics for miRNA research in cardiovascular biology and medicine.
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Affiliation(s)
- Estefania Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (D.F.)
| | - José Manuel Inácio
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
| | - Inês Sousa
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - Ana Rita Guimarães
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (D.F.)
| | - Gabriela Moura
- Genome Medicine Lab, Department of Medical Sciences, Institute for Biomedicine–iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (I.S.); (A.R.G.); (G.M.)
| | - José António Belo
- Stem Cells and Development Laboratory, iNOVA4Health, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
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Sun Z, Zhang L, Wang R, Wang Z, Liang X, Gao J. Identification of shared pathogenetic mechanisms between COVID-19 and IC through bioinformatics and system biology. Sci Rep 2024; 14:2114. [PMID: 38267482 PMCID: PMC10808107 DOI: 10.1038/s41598-024-52625-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
COVID-19 increased global mortality in 2019. Cystitis became a contributing factor in SARS-CoV-2 and COVID-19 complications. The complex molecular links between cystitis and COVID-19 are unclear. This study investigates COVID-19-associated cystitis (CAC) molecular mechanisms and drug candidates using bioinformatics and systems biology. Obtain the gene expression profiles of IC (GSE11783) and COVID-19 (GSE147507) from the Gene Expression Omnibus (GEO) database. Identified the common differentially expressed genes (DEGs) in both IC and COVID-19, and extracted a number of key genes from this group. Subsequently, conduct Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the DEGs. Additionally, design a protein-protein interaction (PPI) network, a transcription factor gene regulatory network, a TF miRNA regulatory network, and a gene disease association network using the DEGs. Identify and extract hub genes from the PPI network. Then construct Nomogram diagnostic prediction models based on the hub genes. The DSigDB database was used to forecast many potential molecular medicines that are associated with common DEGs. Assess the precision of hub genes and Nomogram models in diagnosing IC and COVID-19 by employing Receiver Operating Characteristic (ROC) curves. The IC dataset (GSE57560) and the COVID-19 dataset (GSE171110) were selected to validate the models' diagnostic accuracy. A grand total of 198 DEGs that overlapped were found and chosen for further research. FCER1G, ITGAM, LCP2, LILRB2, MNDA, SPI1, and TYROBP were screened as the hub genes. The Nomogram model, built using the seven hub genes, demonstrates significant utility as a diagnostic prediction model for both IC and COVID-19. Multiple potential molecular medicines associated with common DEGs have been discovered. These pathways, hub genes, and models may provide new perspectives for future research into mechanisms and guide personalised and effective therapeutics for IC patients infected with COVID-19.
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Affiliation(s)
- Zhenpeng Sun
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Li Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Ruihong Wang
- Department of Outpatient, Qingdao Central Hospital, Qingdao University, Qingdao, China
| | - Zheng Wang
- Zhucheng People's Hospital, Zhucheng, China
| | - Xin Liang
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China
| | - Jiangang Gao
- Department of Urology, Qingdao Municipal Hospital, No.5, Donghai Middle Road, Shinan District, Qingdao, 266001, Shandong, China.
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Hu C, Mi W, Li F, Zhu L, Ou Q, Li M, Li T, Ma Y, Zhang Y, Xu Y. Optimizing drug combination and mechanism analysis based on risk pathway crosstalk in pan cancer. Sci Data 2024; 11:74. [PMID: 38228620 PMCID: PMC10791624 DOI: 10.1038/s41597-024-02915-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: 03/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
Combination therapy can greatly improve the efficacy of cancer treatment, so identifying the most effective drug combination and interaction can accelerate the development of combination therapy. Here we developed a computational network biological approach to identify the effective drug which inhibition risk pathway crosstalk of cancer, and then filtrated and optimized the drug combination for cancer treatment. We integrated high-throughput data concerning pan-cancer and drugs to construct miRNA-mediated crosstalk networks among cancer pathways and further construct networks for therapeutic drug. Screening by drug combination method, we obtained 687 optimized drug combinations of 83 first-line anticancer drugs in pan-cancer. Next, we analyzed drug combination mechanism, and confirmed that the targets of cancer-specific crosstalk network in drug combination were closely related to cancer prognosis by survival analysis. Finally, we save all the results to a webpage for query ( http://bio-bigdata.hrbmu.edu.cn/oDrugCP/ ). In conclusion, our study provided an effective method for screening precise drug combinations for various cancer treatments, which may have important scientific significance and clinical application value for tumor treatment.
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Affiliation(s)
- Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Wanqi Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qi Ou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Maohao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Tengyue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yuheng Ma
- Department of Pharmacy, Inner Mongolia Medical University, Jinshan Development Zone, Hohhot, 010100, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
- Department of Pharmacy, Inner Mongolia Medical University, Jinshan Development Zone, Hohhot, 010100, China.
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Engin AB, Engin A. Next-Cell Hypothesis: Mechanism of Obesity-Associated Carcinogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1460:727-766. [PMID: 39287871 DOI: 10.1007/978-3-031-63657-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Higher body fat content is related to a higher risk of mortality, and obesity-related cancer represents approximately 40% of all cancer patients diagnosed each year. Furthermore, epigenetic mechanisms are involved in cellular metabolic memory and can determine one's predisposition to being overweight. Low-grade chronic inflammation, a well-established characteristic of obesity, is a central component of tumor development and progression. Cancer-associated adipocytes (CAA), which enhance inflammation- and metastasis-related gene sets within the cancer microenvironment, have pro-tumoral effects. Adipose tissue is a major source of the exosomal micro ribonucleic acids (miRNAs), which modulate pathways involved in the development of obesity and obesity-related comorbidities. Owing to their composition of cargo, exosomes can activate receptors at the target cell or transfer molecules to the target cells and thereby change the phenotype of these cells. Exosomes that are released into the extracellular environment are internalized with their cargo by neighboring cells. The tumor-secreted exosomes promote organ-specific metastasis of tumor cells that normally lack the capacity to metastasize to a specific organ. Therefore, the communication between neighboring cells via exosomes is defined as the "next-cell hypothesis." The reciprocal interaction between the adipocyte and tumor cell is realized through the adipocyte-derived exosomal miRNAs and tumor cell-derived oncogenic miRNAs. The cargo molecules of adipocyte-derived exosomes are important messengers for intercellular communication involved in metabolic responses and have very specific signatures that direct the metabolic activity of target cells. RNA-induced silencing regulates gene expression through various mechanisms. Destabilization of DICER enzyme, which catalyzes the conversion of primary miRNA (pri-miRNA) to precursor miRNA (pre-miRNA), is an important checkpoint in cancer development and progression. Interestingly, adipose tissue in obesity and tumors share similar pathogenic features, and the local hypoxia progress in both. While hypoxia in obesity leads to the adipocyte dysfunction and metabolic abnormalities, in obesity-related cancer cases, it is associated with worsened prognosis, increased metastatic potential, and resistance to chemotherapy. Notch-interleukin-1 (IL-1)-Leptin crosstalk outcome is referred to as "NILCO effect." In this chapter, obesity-related cancer development is discussed in the context of "next-cell hypothesis," miRNA biogenesis, and "NILCO effect."
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Affiliation(s)
- Ayse Basak Engin
- Faculty of Pharmacy, Department of Toxicology, Gazi University, Hipodrom, Ankara, Turkey.
| | - Atilla Engin
- Faculty of Medicine, Department of General Surgery, Gazi University, Besevler, Ankara, Turkey
- Mustafa Kemal Mah. 2137. Sok. 8/14, 06520, Cankaya, Ankara, Turkey
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Choubey J, Wolkenhauer O, Chatterjee T. Systems Biology Approach to Analyze Microarray Datasets for Identification of Disease-Causing Genes: Case Study of Oral Squamous Cell Carcinoma. Methods Mol Biol 2024; 2719:13-31. [PMID: 37803110 DOI: 10.1007/978-1-0716-3461-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
The discovery of potential disease-causing genes can aid medical progress. The post-genomic era has made this a more difficult task. Modern high-throughput methods have not solved the problem of identifying disease genes. Conventional methods cannot be used to investigate many rare or lethal diseases. Monitoring gene expression values in different samples using microarray technology is one of the best and most accurate ways to identify disease-causing genes. One of the most recent advances in experimental molecular biology is microarrays, which allow researchers to simultaneously monitor the expression levels of thousands of genes. Statistical analysis of microarray data might aid gene discovery by revealing pathways related to the target gene and facilitating identification of candidate genes. Systems biology, an interdisciplinary approach, has emerged as a crucial analytic tool with the potential to reveal previously unidentified causes and consequences of human illness. Genetic, environmental, immunological, or neurological factors have been implicated in the developing complex disorders like cancer. Because of this, it is important to approach the study of such disease from a novel perspective. The system biology approach allows us to rapidly identify disease-causing genes and assess their viability as therapeutic targets. This chapter demonstrates systems biology approaches to identify candidate genes using public database. Oral squamous cell carcinoma (OSCC) is used as a model disease to show how systems biology can be used successfully to identify and prioritize disease genes.
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Affiliation(s)
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
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Alsharoh H, Chiroi P, Nutu A, Raduly L, Zanoaga O, Berindan-Neagoe I. Vinorelbine Alters lncRNA Expression in Association with EGFR Mutational Status and Potentiates Tumor Progression Depending on NSCLC Cell Lines' Genetic Profile. Biomedicines 2023; 11:3298. [PMID: 38137519 PMCID: PMC10741193 DOI: 10.3390/biomedicines11123298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Lung cancer remains the leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) as the most common type. In addition, NSCLC has a high mortality rate and an overall adverse patient outcome. Although significant improvements have been made in therapeutic options, effectiveness is still limited in late stages, so the need for a better understanding of the genomics events underlying the current therapies is crucial to aid future drug development. Vinorelbine (VRB) is an anti-mitotic chemotherapy drug (third-generation vinca alkaloid) used to treat several malignancies, including NSCLC. However, despite its widespread clinical use, very little is known about VRB-associated genomic alterations in different subtypes of NSCLC. This article is an in vitro investigation of the cytotoxic effects of VRB on three different types of NSCLC cell lines, A549, Calu-6, and H1792, with a closer focus on post-treatment genetic alterations. Based on the obtained results, VRB cytotoxicity produces modifications on a cellular level, altering biological processes such as apoptosis, autophagy, cellular motility, cellular adhesion, and cell cycle, but also at a genomic level, dysregulating the expression of some coding genes, such as EGFR, and long non-coding RNAs (lncRNAs), including CCAT1, CCAT2, GAS5, MALAT1, NEAT1, NORAD, XIST, and HOTAIR, that are implicated in the mitogen-activated protein kinase (MAPK) signaling pathway. Therefore, although extensive validation is required, these results pave the way towards a better understanding of the cellular and genomic alterations underlying the cytotoxicity of VRB.
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Affiliation(s)
| | | | | | | | | | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania; (H.A.); (L.R.); (O.Z.)
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Gao L, Kyubwa EM, Starbird MA, Diaz de Leon J, Nguyen M, Rogers CJ, Menon N. Circulating miRNA profiles in COVID-19 patients and meta-analysis: implications for disease progression and prognosis. Sci Rep 2023; 13:21656. [PMID: 38065980 PMCID: PMC10709343 DOI: 10.1038/s41598-023-48227-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
We compared circulating miRNA profiles of hospitalized COVID-positive patients (n = 104), 27 with acute respiratory distress syndrome (ARDS) and age- and sex-matched healthy controls (n = 18) to identify miRNA signatures associated with COVID and COVID-induced ARDS. Meta-analysis incorporating data from published studies and our data was performed to identify a set of differentially expressed miRNAs in (1) COVID-positive patients versus healthy controls as well as (2) severe (ARDS+) COVID vs moderate COVID. Gene ontology enrichment analysis of the genes these miRNAs interact with identified terms associated with immune response, such as interferon and interleukin signaling, as well as viral genome activities associated with COVID disease and severity. Additionally, we observed downregulation of a cluster of miRNAs located on chromosome 14 (14q32) among all COVID patients. To predict COVID disease and severity, we developed machine learning models that achieved AUC scores between 0.81-0.93 for predicting disease, and between 0.71-0.81 for predicting severity, even across diverse studies with different sample types (plasma versus serum), collection methods, and library preparations. Our findings provide network and top miRNA feature insights into COVID disease progression and contribute to the development of tools for disease prognosis and management.
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Zhuang Q, Liu C, Hu Y, Liu Y, Lyu Y, Liao Y, Chen L, Yang H, Mao Y. Identification of RP11-770J1.4 as immune-related lncRNA regulating the CTXN1-cGAS-STING axis in histologically lower-grade glioma. MedComm (Beijing) 2023; 4:e458. [PMID: 38116063 PMCID: PMC10728758 DOI: 10.1002/mco2.458] [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: 05/24/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Human gliomas are lethal brain cancers. Emerging evidence revealed the regulatory role of long noncoding RNAs (lncRNAs) in tumors. Here, we performed a comprehensive analysis of the expression profiles of RNAs in histologically lower-grade glioma (LGG). Enrichment analysis revealed that glioma is influenced by immune-related signatures. Survival analysis further established the close correlation between network features and glioma prognosis. Subsequent experiments showed lncRNA RP11-770J1.4 regulates CTXN1 expression through hsa-miR-124-3p. Correlation analysis identified lncRNA RP11-770J1.4 was immune related, specifically involved in the cytosolic DNA sensing pathway. Downregulated lncRNA RP11-770J1.4 resulted in increased spontaneous gene expression of the cGAS-STING pathway. Single-cell RNA sequencing analysis, along with investigations in a glioblastoma stem cell model and patient sample analysis, demonstrated the predominant localization of CTXN1 within tumor cores rather than peripheral regions. Immunohistochemistry staining established a negative correlation between CTXN1 expression and infiltration of CD8+ T cells. In vivo, Ctxn1 knockdown in GL261 cells led to decreased tumor burden and improved survival while increasing infiltration of CD8+ T cells. These findings unveil novel insights into the lncRNA RP11-770J1.4-CTXN1 as a potential immune regulatory axis, highlighting its therapeutic implications for histologically LGGs.
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Affiliation(s)
- Qiyuan Zhuang
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Chaxian Liu
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Yihan Hu
- School of Life Sciences, Fudan UniversityShanghaiChina
| | - Ying Liu
- Department of PathologySchool of Basic Medical Sciences, Fudan UniversityShanghaiChina
| | - Yingying Lyu
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
| | - Yuheng Liao
- Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology LabInstitute of Biomedical Sciences, Shanghai Medical College, Fudan UniversityShanghaiChina
| | - Liang Chen
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
- National Center for Neurological DisordersHuashan Hospital, Fudan UniversityShanghaiChina
| | - Hui Yang
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
- National Center for Neurological DisordersHuashan Hospital, Fudan UniversityShanghaiChina
- Institute for Translational Brain ResearchShanghai Medical College, Fudan UniversityShanghaiChina
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Ying Mao
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityShanghaiChina
- School of Life Sciences, Fudan UniversityShanghaiChina
- National Center for Neurological DisordersHuashan Hospital, Fudan UniversityShanghaiChina
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
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Fu X, Baranova A, Cao H, Liu Y, Sun J, Zhang F. miR-9-5p deficiency contributes to schizophrenia. Schizophr Res 2023; 262:168-174. [PMID: 37992560 DOI: 10.1016/j.schres.2023.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
MicroRNA-9-5p (miR-9-5p) is highly expressed in the brain and has been implicated in the risk of schizophrenia. We compared the expression levels of miR-9-5p in schizophrenia cases and healthy controls and evaluated whether regulatory targets of miR-9-5p are enriched in schizophrenia genome-wide risk genes. Literature-based analysis was conducted to construct molecular pathways connecting miR-9-5p and schizophrenia. We found that the expression levels of miR-9-5p were down-regulated in the peripheral blood of schizophrenia patients compared with those in healthy controls. miR-9-5p can regulate 24 out of the 1136 genome-wide risk genes of schizophrenia, which was higher than by chance (hypergeometric test P = 4.09E-06). The literature-based analysis showed that quantitative genetic changes driven by miR-9 exert more inhibitory (the IL1B, ABCB1, FGFR1 genes) than promoting (the INS gene) effects on schizophrenia, suggesting that miR-9 may protect against schizophrenia. Our results suggest that miR-9-5p deficiency may contribute to the development of schizophrenia.
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Affiliation(s)
- Xiaoqian Fu
- Medical College of Soochow University, Suzhou 215137, China; Suzhou Guangji Hospital, The Affiliated Guangji Hospital of Soochow University, Suzhou 215137, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Manassas 20110, USA; Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Manassas 20110, USA
| | - Yansong Liu
- Suzhou Guangji Hospital, The Affiliated Guangji Hospital of Soochow University, Suzhou 215137, China
| | - Jing Sun
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Fuquan Zhang
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China; Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China.
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Abdolahi F, Shahraki A, Sheervalilou R, Mortazavi SS. Identification of differentially expressed genes associated with the pathogenesis of gastric cancer by bioinformatics analysis. BMC Med Genomics 2023; 16:311. [PMID: 38041130 PMCID: PMC10690994 DOI: 10.1186/s12920-023-01720-7] [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: 05/28/2023] [Accepted: 10/29/2023] [Indexed: 12/03/2023] Open
Abstract
AIM Gastric cancer (GC) is one of the most diagnosed cancers worldwide. GC is a heterogeneous disease whose pathogenesis has not been entirely understood. Besides, the GC prognosis for patients remains poor. Hence, finding reliable biomarkers and therapeutic targets for GC patients is urgently needed. METHODS GSE54129 and GSE26942 datasets were downloaded from Gene Expression Omnibus (GEO) database to detect differentially expressed genes (DEGs). Then, gene set enrichment analyses and protein-protein interactions were investigated. Afterward, ten hub genes were identified from the constructed network of DEGs. Then, the expression of hub genes in GC was validated. Performing survival analysis, the prognostic value of each hub gene in GC samples was investigated. Finally, the databases were used to predict microRNAs that could regulate the hub genes. Eventually, top miRNAs with more interactions with the list of hub genes were introduced. RESULTS In total, 203 overlapping DEGs were identified between both datasets. The main enriched KEGG pathway was "Protein digestion and absorption." The most significant identified GO terms included "primary alcohol metabolic process," "basal part of cell," and "extracellular matrix structural constituent conferring tensile strength." Identified hub modules were COL1A1, COL1A2, TIMP1, SPP1, COL5A2, THBS2, COL4A1, MUC6, CXCL8, and BGN. The overexpression of seven hub genes was associated with overall survival. Moreover, among the list of selected miRNAs, hsa-miR-27a-3, hsa-miR-941, hsa-miR-129-2-3p, and hsa-miR-1-3p, were introduced as top miRNAs targeting more than five hub genes. CONCLUSIONS The present study identified ten genes associated with GC, which may help discover novel prognostic and diagnostic biomarkers as well as therapeutic targets for GC. Our results may advance the understanding of GC occurrence and progression.
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Affiliation(s)
- Fatemeh Abdolahi
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Shahraki
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Roghayeh Sheervalilou
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.
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Zupanc C, Franko A, Strbac D, Kovac V, Dolzan V, Goricar K. The association of genetic factors with serum calretinin levels in asbestos-related diseases. Radiol Oncol 2023; 57:473-486. [PMID: 38038422 PMCID: PMC10690752 DOI: 10.2478/raon-2023-0061] [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: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Asbestos exposure is associated with different asbestos-related diseases, including malignant mesothelioma (MM). MM diagnosis is confirmed with immunohistochemical analysis of several markers, including calretinin. Increased circulating calretinin was also observed in MM. The aim of the study was to determine if CALB2 polymorphisms or polymorphisms in genes that can regulate calretinin expression are associated with serum calretinin levels or MM susceptibility. SUBJECTS AND METHODS The study included 288 MM patients and 616 occupationally asbestos-exposed subjects without MM (153 with asbestosis, 380 with pleural plaques and 83 without asbestos-related disease). Subjects were genotyped for seven polymorphisms in CALB2, E2F2, MIR335, NRF1 and SEPTIN7 genes using competitive allele-specific polymerase chain reaction (PCR). Serum calretinin was determined with ELISA in 545 subjects. Nonparametric tests, logistic regression and receiver operating characteristic (ROC) curve analysis were used for statistical analysis. RESULTS Carriers of at least one polymorphic CALB2 rs889704 allele had lower calretinin levels (P = 0.036). Carriers of two polymorphic MIR335 rs3807348 alleles had higher calretinin (P = 0.027), while carriers of at least one polymorphic NRF1 rs13241028 allele had lower calretinin levels (P = 0.034) in subjects without MM. Carriers of two polymorphic E2F2 rs2075995 alleles were less likely to develop MM (odds ratio [OR] = 0.64, 95% confidence interval [CI] = 0.43-0.96, P = 0.032), but the association was no longer significant after adjustment for age (P = 0.093). Optimal serum calretinin cut-off values differentiating MM patients from other subjects differed according to CALB2, NRF1, E2F2, and MIR335 genotypes. CONCLUSIONS The results of presented study suggest that genetic variability could influence serum calretinin levels. These findings could contribute to a better understanding of calretinin regulation and potentially to earlier MM diagnosis.
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Affiliation(s)
- Cita Zupanc
- Military Medical Unit-Slovenian Army, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | - Alenka Franko
- University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
- University Medical Centre Ljubljana, Clinical Institute of Occupational Medicine, Ljubljana, Slovenia
| | - Danijela Strbac
- University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
- Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Viljem Kovac
- University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
- Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Vita Dolzan
- University of Ljubljana, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Pharmacogenetics Laboratory, Ljubljana, Slovenia
| | - Katja Goricar
- University of Ljubljana, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Pharmacogenetics Laboratory, Ljubljana, Slovenia
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Lin Y, Shi H, Wu L, Ge L, Ma Z. Research progress of N6-methyladenosine in colorectal cancer: A review. Medicine (Baltimore) 2023; 102:e36394. [PMID: 38013272 PMCID: PMC10681580 DOI: 10.1097/md.0000000000036394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Colorectal cancer is the third most common malignant tumor worldwide, causing serious harm to human health. Epigenetic modification, especially RNA methylation modification, plays a critical role in the occurrence and development of colorectal cancer via post-transcriptional regulation of mRNA and non-coding RNA expression. Among these, N6-methyladenosine (m6A) is the most common chemical modification in mammals, which plays an important role in the progress of cancer, including colorectal cancer. m6A is a dynamic and reversible process and is mainly regulated by m6A methyltransferase ("writers"), m6A demethylases ("erasers"), and m6A binding proteins ("readers"). Herein, we reviewed recent advances in the role of m6A modification in colorectal cancer and focused on the factors affecting m6A modification. Furthermore, we discussed the clinical application of m6A modifications for colorectal cancer diagnosis, prognosis, and treatment and provided guides in clinical practice. m6A modification and m6A regulators play significant roles in the occurrence and development of colorectal cancer by regulating the stability and translation of mRNAs, the maturation of miRNAs, and the function of lncRNAs. m6A regulators can play biological roles in colorectal cancer through m6A-dependent manner or m6A-independent manner. Multiplies of internal factors, including miRNAs and lncRNAs, and external factors can also regulate the m6A modification by completing with m6A regulators in a base complement manner, regulating the expression of m6A and mutating the m6A site. m6A regulators and m6A modificantion are diagnostic and prognostic markers for CRC. Therefore, m6A regulators and m6A modificantion may be potential therapeutic target for CRC in the future.
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Affiliation(s)
- Yu Lin
- Department of Respiratory, Nanjing Gaochun People’s Hospital, Nanjing, China
| | - Hongjun Shi
- Department of Pharmacy, Nanjing Gaochun People’s Hospital, Nanjing, China
| | - Lianping Wu
- Department of Pharmacy, Nanjing Gaochun People’s Hospital, Nanjing, China
| | - Linyang Ge
- Department of Respiratory, Nanjing Gaochun People’s Hospital, Nanjing, China
| | - Zengqing Ma
- Department of Pharmacy, Nanjing Gaochun People’s Hospital, Nanjing, China
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