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Yang J, Chen T, Xiang Q, Li D, Zhou W, Xu F. Target-responsive triplex aptamer nanoswitch enables label-free and ultrasensitive detection of antibody in human serum via lighting-up RNA aptamer transcriptions. Talanta 2024; 278:126455. [PMID: 38917548 DOI: 10.1016/j.talanta.2024.126455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Accurate and sensitive monitoring of the concentration change of anti-digoxigenin (Anti-Dig) antibody is of great importance for diagnosing infectious and immunological diseases. Combining a novel triplex aptamer nanoswitch and the high signal-to-noise ratio of lighting-up RNA aptamer signal amplification, a label-free and ultrasensitive fluorescent sensing approach for detecting Anti-Dig antibodies is described. The target Anti-Dig antibodies recognize and bind with the nanoswitch to open its triplex helix stem structure to release Taq DNA polymerase and short ssDNA primer simultaneously, which activates the Taq DNA polymerase to initiate downstream strand extension of ssDNA primer to yield specific dsDNA containing RNA promoter sequence. T7 RNA polymerase recognizes and binds to these promoter sequences to initiate RNA transcription reaction to produce many RNA aptamer sequences. These aptamers can recognize and bind with Malachite Green (MG) dye specifically and produce highly amplified fluorescent signal for monitoring Anti-Dig antibodies from 50 pM to 50 nM with a detection limit down to 33 pM. The method also exhibits high selectivity for Anti-Dig antibodies and can be used to discriminate trace Anti-Dig antibodies in diluted serum samples. Our method is superior to many immunization-based Anti-Dig antibody detection methods and thus holds great potential for monitoring disease progression and efficacy.
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Affiliation(s)
- Jirong Yang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Tiantian Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Qian Xiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Daxiu Li
- College Pharmacy and Biological Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Wenjiao Zhou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Fengfeng Xu
- Organization Department of the Communist Party of China, Chongqing University of Technology, Chongqing, 400054, PR China.
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Varathan A, Senthooran S, Jeyananthan P. Role of different omics data in the diagnosis of schizophrenia disorder: A machine learning study. Schizophr Res 2024; 271:38-46. [PMID: 39003990 DOI: 10.1016/j.schres.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 06/19/2024] [Accepted: 07/07/2024] [Indexed: 07/16/2024]
Abstract
Schizophrenia is a serious mental disorder that affects millions of people worldwide. This disorder slowly disintegrates thinking ability and changes behaviours of patients. These patients will show some psychotic symptoms such as hallucinations, delusions, thought disorder and movement disorder. These symptoms are in common with some other psychiatric disorders such as bipolar disorder, major depressive disorder and mood spectrum disorder. As patients would require immediate treatment, an on-time diagnosis is critical. This study explores the use of omics data in diagnosis of schizophrenia. Transcriptome, miRNA and epigenome data are used in diagnosis of patients with schizophrenia with the aid of machine learning algorithms. As the data is in high dimension, mutual information and feature importance are independently used for selecting relevant features for the study. Selected sets of features (biomarkers) are individually used with different machine learning algorithms and their performances are compared to select the best-performing model. This study shows that the top 140 miRNA features selected using mutual information along with support vector machines give the highest accuracy (0.86 ± 0.07) in the diagnosis of schizophrenia. All reported accuracies are validated using 5-fold cross validation. They are further validated using leave one out cross validation and the accuracies are reported in the supplementary material.
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Affiliation(s)
- Aarthy Varathan
- Department of Computer Engineering, Faculty of Engineering, University of Jaffna, Sri Lanka.
| | | | - Pratheeba Jeyananthan
- Department of Computer Engineering, Faculty of Engineering, University of Jaffna, Sri Lanka.
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Yuan L, Jiang N, Li Y, Wang X, Wang W. RGS1 Enhancer RNA Promotes Gene Transcription by Recruiting Transcription Factor FOXJ3 and Facilitates Osteoclastogenesis Through PLC-IP3R-dependent Ca 2+ Response in Rheumatoid Arthritis. Inflammation 2024:10.1007/s10753-024-02067-6. [PMID: 38904871 DOI: 10.1007/s10753-024-02067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024]
Abstract
Recent evidence has highlighted the functions of enhancers in modulating transcriptional machinery and affecting the development of human diseases including rheumatoid arthritis (RA). Enhancer RNAs (eRNAs) are RNA molecules transcribed from active enhancer regions. This study investigates the specific function of eRNA in gene transcription and osteoclastogenesis in RA. Regulator of G protein signaling 1 (RGS1)-associated eRNA was highly activated in osteoclasts according to bioinformatics prediction. RGS1 mRNA was increased in mice with collagen-induced arthritis as well as in M-CSF/soluble RANKL-stimulated macrophages (derived from monocytes). This was ascribed to increased RGS1 eRNA activity. Silencing of 5'-eRNA blocked the binding between forkhead box J3 (FOXJ3) and the RGS1 promoter, thus suppressing RGS1 transcription. RGS1 accelerated osteoclastogenesis through PLC-IP3R-dependent Ca2+ response. Knockdown of either FOXJ3 or RGS1 ameliorated arthritis severity, improved pathological changes, and reduced osteoclastogenesis and bone erosion in vivo and in vitro. However, the effects of FOXJ3 silencing were negated by RGS1 overexpression. In conclusion, this study demonstrates that the RGS1 eRNA-driven transcriptional activation of the FOXJ3/RGS1 axis accelerates osteoclastogenesis through PLC-IP3R dependent Ca2+ response in RA. The finding may offer novel insights into the role of eRNA in gene transcription and osteoclastogenesis in RA.
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Affiliation(s)
- Lin Yuan
- Department of Health Management, The First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, P.R. of China
| | - Nan Jiang
- Department of Price, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning, P.R. China
| | - Yuxuan Li
- Department of Rheumatology and Immunology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, P.R. China
| | - Xin Wang
- Department of Health Management, The First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, P.R. of China
| | - Wei Wang
- Department of Health Management, The First Affiliated Hospital of China Medical University, No. 155, Nanjing North Street, Heping District, Shenyang, 110001, Liaoning, P.R. of China.
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024; 56:1235-1249. [PMID: 38871819 PMCID: PMC11263585 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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To KKW, Huang Z, Zhang H, Ashby CR, Fu L. Utilizing non-coding RNA-mediated regulation of ATP binding cassette (ABC) transporters to overcome multidrug resistance to cancer chemotherapy. Drug Resist Updat 2024; 73:101058. [PMID: 38277757 DOI: 10.1016/j.drup.2024.101058] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Multidrug resistance (MDR) is one of the primary factors that produces treatment failure in patients receiving cancer chemotherapy. MDR is a complex multifactorial phenomenon, characterized by a decrease or abrogation of the efficacy of a wide spectrum of anticancer drugs that are structurally and mechanistically distinct. The overexpression of the ATP-binding cassette (ABC) transporters, notably ABCG2 and ABCB1, are one of the primary mediators of MDR in cancer cells, which promotes the efflux of certain chemotherapeutic drugs from cancer cells, thereby decreasing or abolishing their therapeutic efficacy. A number of studies have suggested that non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a pivotal role in mediating the upregulation of ABC transporters in certain MDR cancer cells. This review will provide updated information about the induction of ABC transporters due to the aberrant regulation of ncRNAs in cancer cells. We will also discuss the measurement and biological profile of circulating ncRNAs in various body fluids as potential biomarkers for predicting the response of cancer patients to chemotherapy. Sequence variations, such as alternative polyadenylation of mRNA and single nucleotide polymorphism (SNPs) at miRNA target sites, which may indicate the interaction of miRNA-mediated gene regulation with genetic variations to modulate the MDR phenotype, will be reviewed. Finally, we will highlight novel strategies that could be used to modulate ncRNAs and circumvent ABC transporter-mediated MDR.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Zoufang Huang
- Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Hang Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, United States
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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