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Al Sharie AH, Al Masoud EB, Jadallah RK, Alzghoul SM, Darweesh RF, Al-Bataineh R, Lataifeh LN, Salameh ST, Daoud MN, Rawashdeh TH, El-Elimat T, Alali FQ. Transcriptome analysis revealed a novel nine-gene prognostic risk score of clear cell renal cell carcinoma. Medicine (Baltimore) 2024; 103:e39678. [PMID: 39331921 PMCID: PMC11441924 DOI: 10.1097/md.0000000000039678] [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] [Indexed: 09/29/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) continues to pose a significant global health concern, with rising incidence and high mortality rate. Accordingly, identifying molecular alternations associated with ccRCC is crucial to boost our understanding of its onset, persistence, and progression as well as developing prognostic biomarkers and novel therapies. Bulk RNA sequencing data and its associated clinicopathological variables of ccRCC were obtained from The Cancer Genome Atlas Program. Atypical differential gene expression analysis of advanced disease states using the extreme categories of staging and grading components was performed. Upregulated differentially expressed genes shared across the aforementioned components were selected. The risk-score construction pipeline started with univariate Cox logistic regression analysis, least absolute shrinkage and selection operator, and multivariate Cox logistic regression analysis in sequence. The generated risk score classified patients into low- vs high-risk groups. The predictive power of the constructed risk score was assessed using Kaplan-Meier curves analysis, multivariate Cox logistic regression analysis, and receiver operator curve of the overall survival. External validation of the risk score was performed using the E-MTAB-1980 cohort. The analysis work scheme established a novel nine-gene prognostic risk score composed of the following genes: ZIC2, TNNT1, SAA1, OTX1, C20orf141, CDHR4, HOXB13, IGFL2, and IGFN1. The high-risk group was associated with shortened overall survival and possessed an independent predictive power (hazard ratio: 1.942, 95% CI: 1.367-2.758, P < .0001, area under the curve = 0.719). In addition, the high-risk score was associated with advance clinicopathological parameters. The same pattern was observed within the external validation dataset (E-MTAB-1980 cohort), in which the high-risk score held a poor prognostic signature as well as independent predictive potential (hazard ratio: 5.121, 95% CI: 1.412-18.568, P = .013, area under the curve = 0.787). In the present work, a novel nine-gene prognostic risk score was constructed and validated. The risk score correlated with tumor immune microenvironment, somatic mutation patterns, and altered molecular pathways involved in tumorigenesis. Further experimental data are warranted to expand the work.
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Affiliation(s)
- Ahmed H Al Sharie
- Department of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Eyad B Al Masoud
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Rand K Jadallah
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Saja M Alzghoul
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Reem F Darweesh
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Rania Al-Bataineh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Leen N Lataifeh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Shatha T Salameh
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Majd N Daoud
- Department of Endocrinology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY
| | | | - Tamam El-Elimat
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Feras Q Alali
- College of Pharmacy, QU Health, Qatar University, Doha, Qatar
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2
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Neha N, Das P. Exploring G-quadruplex structure in PRCC-TFE3 fusion oncogene: Plausible use as anti cancer therapy for translocation Renal cell carcinoma (tRCC). J Biotechnol 2024; 390:39-49. [PMID: 38740306 DOI: 10.1016/j.jbiotec.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
The TFE3 fusion gene, byproduct of Xp11.2 translocation, is the diagnostic marker for translocation renal cell carcinoma (tRCC). Absence of any clinically recognized therapy for tRCC, pressing a need to create novel and efficient therapeutic approaches. Previous studies shown that stabilization of the G-quadruplex structure in oncogenes suppresses their expression machinery. To combat the oncogenesis caused by fusion genes, our objective is to locate and stabilize the G-quadruplex structure within the PRCC-TFE3 fusion gene. Using the Quadruplex-forming G Rich Sequences (QGRS) mapper and the Non-B DNA motif search tool (nBMST) online server, we found putative G-quadruplex forming sequences (PQS) in the PRCC-TFE3 fusion gene. Circular dichroism demonstrating a parallel G-quadruplex in the targeted sequence. Fluorescence and UV-vis spectroscopy results suggest that pyridostatin binds to this newly discovered G-quadruplex. The PCR stop assay, as well as transcriptional or translational inhibition using real time PCR and Dual luciferase assay, revealed that stable G-quadruplex formation affects biological processes. Confocal microscopy of HEK293T cells transfected with the fusion transcript confirmed G-quadruplexes formation in cell. This investigation may shed light on G-quadruplex's functions in fusion genes and may help in the development of therapies specifically targeted against fusion oncogenes, which would enhance the capability of current tRCC therapy approach.
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Affiliation(s)
- Neha Neha
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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3
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Xiang L, Zhang X, Li S, Feng Q, Niu K. Ratio of the Primers Used in Polymerase Chain Reaction-Stop Analysis Impacts the Resultant Banding Pattern. ACS OMEGA 2023; 8:37369-37373. [PMID: 37841166 PMCID: PMC10568717 DOI: 10.1021/acsomega.3c05220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
G-quadruplex (G4), as a dynamic nucleic acid secondary structure, widely exists in organism genomes and plays regulatory roles in a variety of cellular functions. Polymerase chain reaction stop assay (PCR-Stop) is a simple, quick, and low-cost widely used method for detection of the binding between G4 and its binding compounds. Different from the common PCR approach, no double-stranded DNA template is needed in the PCR-Stop assay, in which the forward and reverse primers extend against each other in the presence of DNA polymerase to produce a single DNA product. However, unexpected results, such as two or more PCR products, are often generated, and the mechanism is unclear. We found that the ratio of pair primers significantly impacts the generation and components of PCR-Stop products, which is crucial for the interpretation of the experiment results.
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Affiliation(s)
- Lijun Xiang
- Guangdong
Provincial Key Laboratory of Insect Developmental Biology and Applied
Technology, Guangzhou Key Laboratory of Insect Development Regulation
and Application Research, Institute of Insect Science and Technology,
School of Life Sciences, South China Normal
University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong
Provincial Key Laboratory of Insect Developmental Biology and Applied
Technology, Guangzhou Key Laboratory of Insect Development Regulation
and Application Research, Institute of Insect Science and Technology,
School of Life Sciences, South China Normal
University, Guangzhou 510631, China
| | - Sheng Li
- Guangdong
Provincial Key Laboratory of Insect Developmental Biology and Applied
Technology, Guangzhou Key Laboratory of Insect Development Regulation
and Application Research, Institute of Insect Science and Technology,
School of Life Sciences, South China Normal
University, Guangzhou 510631, China
- Guangmeiyuan
R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental
Biology and Applied Technology, South China
Normal University, Meizhou 514779, China
| | - Qili Feng
- Guangdong
Provincial Key Laboratory of Insect Developmental Biology and Applied
Technology, Guangzhou Key Laboratory of Insect Development Regulation
and Application Research, Institute of Insect Science and Technology,
School of Life Sciences, South China Normal
University, Guangzhou 510631, China
| | - Kangkang Niu
- Guangdong
Provincial Key Laboratory of Insect Developmental Biology and Applied
Technology, Guangzhou Key Laboratory of Insect Development Regulation
and Application Research, Institute of Insect Science and Technology,
School of Life Sciences, South China Normal
University, Guangzhou 510631, China
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4
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Apsley AT, Domico ER, Verbiest MA, Brogan CA, Buck ER, Burich AJ, Cardone KM, Stone WJ, Anisimova M, Vandenbergh DJ. A novel hypervariable variable number tandem repeat in the dopamine transporter gene ( SLC6A3). Life Sci Alliance 2023; 6:e202201677. [PMID: 36754567 PMCID: PMC9909461 DOI: 10.26508/lsa.202201677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
The dopamine transporter gene, SLC6A3, has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats (VNTRs) present in SLC6A3 have been tested in genetic association studies, results have not been consistent. VNTRs in SLC6A3 that have not been examined genetically were characterized. The Tandem Repeat Annotation Library was used to characterize the VNTRs of 64 unrelated long-read haplotype-phased SLC6A3 sequences. Sequence similarity of each repeat unit of the five VNTRs is reported, along with the correlations of SNP-SNP, SNP-VNTR, and VNTR-VNTR alleles across the gene. One of these VNTRs is a novel hyper-VNTR (hyVNTR) in intron 8 of SLC6A3, which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38 bp, with 82% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. In addition, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it might be a recombination hotspot.
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Affiliation(s)
- Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
- The Molecular, Cellular and Integrative Biosciences Program, The Pennsylvania State University, State College, PA, USA
| | - Emma R Domico
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Max A Verbiest
- Institute of Computational Life Science, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Wädenswil, Switzerland
- Department of Molecular Life Sciences, Faculty of Science, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Carly A Brogan
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Evan R Buck
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Andrew J Burich
- Department of Information Science and Technologies - Applied Data Sciences, The Pennsylvania State University, State College, PA, USA
| | - Kathleen M Cardone
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Wesley J Stone
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
| | - Maria Anisimova
- Institute of Computational Life Science, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David J Vandenbergh
- Department of Biobehavioral Health, The Pennsylvania State University, State College, PA, USA
- The Molecular, Cellular and Integrative Biosciences Program, The Pennsylvania State University, State College, PA, USA
- Institute of the Neurosciences, The Pennsylvania State University, State College, PA, USA
- The Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
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5
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Apostolidi M, Stamatopoulou V. Aberrant splicing in human cancer: An RNA structural code point of view. Front Pharmacol 2023; 14:1137154. [PMID: 36909167 PMCID: PMC9995731 DOI: 10.3389/fphar.2023.1137154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Alternative splicing represents an essential process that occurs widely in eukaryotes. In humans, most genes undergo alternative splicing to ensure transcriptome and proteome diversity reflecting their functional complexity. Over the last decade, aberrantly spliced transcripts due to mutations in cis- or trans-acting splicing regulators have been tightly associated with cancer development, largely drawing scientific attention. Although a plethora of single proteins, ribonucleoproteins, complexed RNAs, and short RNA sequences have emerged as nodal contributors to the splicing cascade, the role of RNA secondary structures in warranting splicing fidelity has been underestimated. Recent studies have leveraged the establishment of novel high-throughput methodologies and bioinformatic tools to shed light on an additional layer of splicing regulation in the context of RNA structural elements. This short review focuses on the most recent available data on splicing mechanism regulation on the basis of RNA secondary structure, emphasizing the importance of the complex RNA G-quadruplex structures (rG4s), and other specific RNA motifs identified as splicing silencers or enhancers. Moreover, it intends to provide knowledge on newly established techniques that allow the identification of RNA structural elements and highlight the potential to develop new RNA-oriented therapeutic strategies against cancer.
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Affiliation(s)
- Maria Apostolidi
- Agilent Laboratories, Agilent Technologies, Santa Clara, CA, United States
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6
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Tseng YC, Shu CW, Chang HM, Lin YH, Tseng YH, Hsu HS, Goan YG, Tseng CJ. Next Generation Sequencing for Potential Regulated Genes and Micro-RNAs of Early Growth Response-1 in the Esophageal Squamous Cell Carcinoma. Protein J 2022; 41:563-571. [PMID: 36207572 DOI: 10.1007/s10930-022-10079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2022] [Indexed: 11/25/2022]
Abstract
Esophageal cancer has a poor prognosis due to its aggressiveness and low survival rate. In Ease Asia, esophageal squamous cell carcinoma (ESCC) outnumbers esophageal adenocarcinoma (EAC). The ESCC patients still have high mortality despite modern surgical resection and neoadjuvant treatment. Determining patient and outcome prognostic factors is critical in ESCC treatment. In esophageal cancer, early growth response-1 (Egr-1) is a tumor suppressor gene, but the mechanism and associated genes are unknown. The study utilizes RNA interference method, the platform of Next Generation Sequencing (NGS) and bioinformatics analysis to investigate the influences after the Egr-1 gene slicing on the ESCC cells. The heat maps of differentially expressed mRNA and microRNAs were analyzed using the algorithm, Burrows-Wheller Aligner. The study showed that the expression of 51 mRNA and 26 microRNAs have significant changes in ESCC cells after Egr-1 knockdown. The KEGG enrichment analysis linked Egr-1-regulated genes and microRNAs. Egr-1 interactions with these genes and microRNAs may be important in tumor progression. In conclusions, this study provided the transcriptome patterns and relating pathway analysis for Egr-1 knockdown in ESCC cells. The mRNA and microRNAs altered by Egr-1 gene silencing might provide key information in the treatment of ESCC.
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Affiliation(s)
- Yen-Chiang Tseng
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chih-Wen Shu
- Institute of BioPharmaceutical Sciences, National Sun Yat-Sen University, No. 70, Lianhai Rd., Gushan Dist, Kaohsiung, 80424, Taiwan. .,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Hui-Min Chang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, No. 386, Dazhong 1st Rd., Zuoying Dist, Kaohsiung, 81362, Taiwan
| | - Yi-Hsuan Lin
- Department of Family Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yen-Han Tseng
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Han-Shui Hsu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yih-Gang Goan
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Jiunn Tseng
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Department of Medical Education and Research, Kaohsiung Veterans General Hospital, No. 386, Dazhong 1st Rd., Zuoying Dist, Kaohsiung, 81362, Taiwan.
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7
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Ren J, Yuan Q, Liu J, Zhong L, Li H, Wu G, Chen F, Tang Q. Identifying the role of transient receptor potential channels (TRPs) in kidney renal clear cell carcinoma and their potential therapeutic significances using genomic and transcriptome analyses. BMC Med Genomics 2022; 15:156. [PMID: 35831825 PMCID: PMC9277847 DOI: 10.1186/s12920-022-01312-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is among the major causes of cancer-caused mortality around the world. Transient receptor potential channels (TRPs), due to their role in various human diseases, might become potential drug targets in cancer. The mRNA expression, copy number variation, single-nucleotide variation, prognostic values, drug sensitivity, and pathway regulation of TRPs were studied across cancer types. The ArrayExpress and The Cancer Genome Atlas (TCGA) databases were used to retrieve KIRC samples. Simultaneously, training, internal, and external cohorts were grouped. In KIRC, a prognostic signature with superior survival prediction in contrast with other well-established signatures was created after a stepwise screening of optimized genes linked to TRPs using univariate Cox, weighted gene co-expression network analysis, multivariate Cox, and least absolute shrinkage and selection operator regression analyses. Subsequent to the determination of risk levels, the variations in the expression of immune checkpoint genes, tumor mutation burden, and immune subtypes and response between low-risk and high-risk subgroups were studied using a variety of bioinformatics algorithms, including ESTIMATE, XCELL, EPIC, CIBERSORT-ABS, CIBERSORT, MCPCOUNTER, TIMER, and QUANTISEQ. Gene set enrichment analysis helped in the identification of abnormal pathways across the low- and high-risk subgroups. Besides, high-risk KIRC patients might benefit from ABT888, AZD6244, AZD7762, Bosutinib, Camptothecin, CI1040, JNK inhibitor VIII, KU55933, Lenalidomide, Nilotinib, PLX4720, RO3306, Vinblastine, and ZM.447439; however, low-risk populations might benefit from Bicalutamide, FH535, and OSI906. Finally, calibration curves were used to validate the nomogram with a satisfactory predictive survival probability. In conclusion, this research provides useful insight that can aid and guide clinical practice and scientific research.
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Affiliation(s)
- Jie Ren
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jifeng Liu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Lei Zhong
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hanshuo Li
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Feng Chen
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
| | - Qizhen Tang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
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Katsuda Y, Sato SI, Inoue M, Tsugawa H, Kamura T, Kida T, Matsumoto R, Asamitsu S, Shioda N, Shiroto S, Oosawatsu Y, Yatsuzuka K, Kitamura Y, Hagihara M, Ihara T, Uesugi M. Small molecule-based detection of non-canonical RNA G-quadruplex structures that modulate protein translation. Nucleic Acids Res 2022; 50:8143-8153. [PMID: 35801908 PMCID: PMC9371906 DOI: 10.1093/nar/gkac580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/24/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Tandem repeats of guanine-rich sequences in RNA often form thermodynamically stable four-stranded RNA structures. Such RNA G-quadruplexes have long been considered to be linked to essential biological processes, yet their physiological significance in cells remains unclear. Here, we report a approach that permits the detection of RNA G-quadruplex structures that modulate protein translation in mammalian cells. The approach combines antibody arrays and RGB-1, a small molecule that selectively stabilizes RNA G-quadruplex structures. Analysis of the protein and mRNA products of 84 cancer-related human genes identified Nectin-4 and CapG as G-quadruplex-controlled genes whose mRNAs harbor non-canonical G-quadruplex structures on their 5′UTR region. Further investigations revealed that the RNA G-quadruplex of CapG exhibits a structural polymorphism, suggesting a possible mechanism that ensures the translation repression in a KCl concentration range of 25–100 mM. The approach described in the present study sets the stage for further discoveries of RNA G-quadruplexes.
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Affiliation(s)
- Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Maimi Inoue
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Hisashi Tsugawa
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Takuto Kamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rio Matsumoto
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shuhei Shiroto
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Yoshiki Oosawatsu
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masaki Hagihara
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,School of Pharmacy, Fudan University, Shanghai 201203, China
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9
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Lu CH, Wei ST, Liu JJ, Chang YJ, Lin YF, Yu CS, Chang SLY. Recognition of a Novel Gene Signature for Human Glioblastoma. Int J Mol Sci 2022; 23:ijms23084157. [PMID: 35456975 PMCID: PMC9029857 DOI: 10.3390/ijms23084157] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 12/10/2022] Open
Abstract
Glioblastoma (GBM) is one of the most common malignant and incurable brain tumors. The identification of a gene signature for GBM may be helpful for its diagnosis, treatment, prediction of prognosis and even the development of treatments. In this study, we used the GSE108474 database to perform GSEA and machine learning analysis, and identified a 33-gene signature of GBM by examining astrocytoma or non-GBM glioma differential gene expression. The 33 identified signature genes included the overexpressed genes COL6A2, ABCC3, COL8A1, FAM20A, ADM, CTHRC1, PDPN, IBSP, MIR210HG, GPX8, MYL9 and PDLIM4, as well as the underexpressed genes CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C, SHANK2 and VIPR2. Protein functional analysis by CELLO2GO implied that these signature genes might be involved in regulating various aspects of biological function, including anatomical structure development, cell proliferation and adhesion, signaling transduction and many of the genes were annotated in response to stress. Of these 33 signature genes, 23 have previously been reported to be functionally correlated with GBM; the roles of the remaining 10 genes in glioma development remain unknown. Our results were the first to reveal that GBM exhibited the overexpressed GPX8 gene and underexpressed signature genes including CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C and SHANK2, which might play crucial roles in the tumorigenesis of different gliomas.
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Affiliation(s)
- Chih-Hao Lu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404333, Taiwan; (C.-H.L.); (J.-J.L.); (Y.-J.C.)
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404333, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan
| | - Sung-Tai Wei
- Department of Neurosurgery, China Medical University Hospital, Taichung 404332, Taiwan;
| | - Jia-Jun Liu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404333, Taiwan; (C.-H.L.); (J.-J.L.); (Y.-J.C.)
| | - Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404333, Taiwan; (C.-H.L.); (J.-J.L.); (Y.-J.C.)
| | - Yu-Feng Lin
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 413305, Taiwan;
| | - Chin-Sheng Yu
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung 407102, Taiwan;
| | - Sunny Li-Yun Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan
- Correspondence:
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10
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Teng X, Dai Y, Li J. Methodological advances of bioanalysis and biochemical targeting of intracellular G-quadruplexes. EXPLORATION (BEIJING, CHINA) 2022; 2:20210214. [PMID: 37323879 PMCID: PMC10191030 DOI: 10.1002/exp.20210214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 06/17/2023]
Abstract
G-quadruplexes (G4s) are a kind of non-canonical nucleic acid secondary structures, which involve in various biological processes in living cells. The relationships between G4s and human diseases, such as tumors, neurodegenerative diseases, and viral infections, have attracted great attention in the last decade. G4s are considered as a promising new target for disease treatment. For instance, G4 ligands are reported to be potentially effective in SARS-COV-2 treatment. However, because of the lack of analytical methods with high performance for the identification of intracellular G4s, the detailed mechanisms of the biofunctions of G4s remain elusive. Meanwhile, through demonstrating the principles of how the G4s systematically modulate the cellular processes with advanced detection methods, biochemical targeting of G4s in living cells can be realized by chemical and biological tools and becomes useful in biomedicine. This review highlights recent methodological advances about intracellular G4s and provides an outlook on the improvement of the bioanalysis and biochemical targeting tools of G4s.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Yicong Dai
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical BiologyTsinghua UniversityBeijingChina
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11
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Hoque ME, Mahendran T, Basu S. Reversal of G-Quadruplexes' Role in Translation Control When Present in the Context of an IRES. Biomolecules 2022; 12:314. [PMID: 35204814 PMCID: PMC8869680 DOI: 10.3390/biom12020314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5' UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5' UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5' cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5' UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5' cap. In this review, we will focus only on the role of RNA GQs present in the 5' UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA; (M.E.H.); (T.M.)
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12
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Dai Y, Teng X, Li J. Single‐Cell Visualization of Monogenic RNA G‐quadruplex and Occupied G‐quadruplex Ratio through a Module‐Assembled Multifunctional Probes Assay (MAMPA). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yicong Dai
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Xucong Teng
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Jinghong Li
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
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13
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Dai Y, Teng X, Li J. Single-cell Visualization of Monogenic RNA G-quadruplex and Occupied G-quadruplex Ratio through Module Assembled Multifunctional Probes Assay (MAMPA). Angew Chem Int Ed Engl 2021; 61:e202111132. [PMID: 34773681 DOI: 10.1002/anie.202111132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/24/2021] [Indexed: 11/12/2022]
Abstract
G-quadruplexes (G4s), non-canonical nucleic acid secondary structure, regulate many biological functions and are considered as potential molecular targets for therapeutics of cancers. However, due to the lack of analytical methods, the regulating mechanism of monogenic G4s is still unclear. Here, we developed a Module Assembled Multifunctional Probes Assay (MAMPA) for visualizing endogenous G4s in individual genes in single cells. Two modular probes separately recognize G4 structures and the adjacent RNA sequences, and the module assembly enables imaging of G4s in an individual RNA with high specificity. Through imaging G4s in several individual genes, we found that G4s were steadily occupied by G4 Binding Proteins (G4BPs) in various mRNAs in every cell line and defined "Occupied G4 Ratio". In all, we demonstrated MAMPA was suitable for most experiment situations and found that Occupied G4 Ratios had the potential to become a new parameter for the study of G4s in living cells.
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Affiliation(s)
- Yicong Dai
- Tsinghua University, Department of Chemistry, 100084, CHINA
| | - Xucong Teng
- Tsinghua University, Department of Chemistry, CHINA
| | - Jinghong Li
- Tsinghua University, Department of Chemistry, Haidian Street, Beijing, CHINA
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14
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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15
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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16
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Prados-Carvajal R, Rodriguez-Real G, Gutierrez-Pozo G, Huertas P. CtIP -mediated alternative mRNA splicing finetunes the DNA damage response. RNA (NEW YORK, N.Y.) 2020; 27:rna.078519.120. [PMID: 33298529 PMCID: PMC7901839 DOI: 10.1261/rna.078519.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
In order to survive to the exposure of DNA damaging agents, cells activate a complex response that coordinates the cellular metabolism, cell cycle progression and DNA repair. Among many other events, recent evidence has described global changes in mRNA splicing in cells treated with genotoxic agents. Here, we explore further this DNA damage-dependent alternative splicing. Indeed, we show that both the splicing factor SF3B2 and the repair protein CtIP contribute to the global pattern of splicing both in cells treated or not to DNA damaging agents. Additionally, we focus on a specific DNA damage- and CtIP-dependent alternative splicing event of the helicase PIF1 and explore its relevance for the survival of cells upon exposure to ionizing radiation. Indeed, we described how the nuclear, active form of PIF1 is substituted by a splicing variant, named vPIF1, in a fashion that requires both the presence of DNA damage and CtIP. Interestingly, timely expression of vPIF1 is required for optimal survival to exposure to DNA damaging agents, but early expression of this isoform delays early events of the DNA damage response. On the contrary, expression of the full length PIF1 facilitates those early events, but increases the sensitivity to DNA damaging agents if the expression is maintained long-term.
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17
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Das P, Verma SP. Dual role of G-quadruplex in translocation renal cell carcinoma: Exploring plausible Cancer therapeutic innovation. Biochim Biophys Acta Gen Subj 2020; 1864:129719. [PMID: 32882363 DOI: 10.1016/j.bbagen.2020.129719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Renal Cell Carcinoma (RCC) is the ninth leading cause of death among kidney cancer. Xp11.2 translocation harboring TFE3 fusion proteins, act as an oncogene in translocation cancers that constitute the hallmark of translocation renal cell carcinoma (tRCC). G-quadruplex (G4), an alternative nucleic acid structure is an emerging and promising factor in cancer. The presence of G4 within the genome plays a pioneering role in cancer as it contributes to genomic aberration as well as inhibition in cell proliferation. SCOPE OF REVIEW Here we discuss the link between G4 and tRCC. We compile the available information of G-quadruplex & propose their dual role in tRCC, suggesting both stabilization and destabilization of G-quadruplex could be considered targets for tRCC. MAJOR CONCLUSIONS Our in Silico analysis of TFE3 and their three fusions partner's PRCC, SFPQ, and ASPSCR1 discloses a few putative G4 forming sequences (PQS) in their corresponding fusion gene or fusion transcript. Stabilization of G4 structure within fusion gene/transcript can be of great use towards potential therapeutics targeting fusion protein derived oncogenesis, as G4 is a serious menace for DNA polymerization, transcription & translation. G-quadruplex at intron-2 of the TFE3 has been reported to mediate its translocation also. Both stabilization and destabilization of the G4 structure would be a promising approach in the suppression of cancerous cell proliferation. GENERAL SIGNIFICANCE Pioneering studies discovered the relevance of G4 in cancer therapy and explore our approaches towards therapeutic innovation against oncogenic fusion protein and tRCC. Selectively targeting G4 in oncogenic fusion transcript will emerge as potential druggable structures.
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Affiliation(s)
- Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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18
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Kharel P, Balaratnam S, Beals N, Basu S. The role of RNA G-quadruplexes in human diseases and therapeutic strategies. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1568. [PMID: 31514263 DOI: 10.1002/wrna.1568] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are four-stranded secondary structures formed by G-rich nucleic acid sequence(s). DNA GQs are present abundantly in the genome and affect a wide range of processes associated with DNA. Recent studies show that RNA GQs are present in different transcripts, including coding and noncoding areas of mRNA, telomeric RNA as well as in other premature and mature noncoding RNAs. When present at specific locations within the RNAs, GQs play important roles in key biological functions, including the regulation of gene expression and telomere homeostasis. RNA GQs regulate pre-mRNA processing, such as splicing and polyadenylation. Evidently, among other processes, RNA GQs also control mRNA translation, miRNA and piRNA biogenesis, and RNA localization. The regulatory mechanisms controlled by RNA GQs mainly involve binding to RNA binding protein that modulate GQ conformation or serve as an entity in recruiting additional protein regulators to act as a block element to the processing machinery. Here we provide an overview of the ever-increasing number of discoveries revealing the role of RNA GQs in biology and their relevance in human diseases and therapeutics. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nathan Beals
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio
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19
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Sengupta A, Ganguly A, Chowdhury S. Promise of G-Quadruplex Structure Binding Ligands as Epigenetic Modifiers with Anti-Cancer Effects. Molecules 2019; 24:E582. [PMID: 30736345 PMCID: PMC6384772 DOI: 10.3390/molecules24030582] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 11/16/2022] Open
Abstract
Evidences from more than three decades of work support the function of non-duplex DNA structures called G-quadruplex (G4) in important processes like transcription and replication. In addition, G4 structures have been studied in connection with DNA base modifications and chromatin/nucleosome arrangements. Recent work, interestingly, shows promise of G4 structures, through interaction with G4 structure-interacting proteins, in epigenetics-in both DNA and histone modification. Epigenetic changes are found to be intricately associated with initiation as well as progression of cancer. Multiple oncogenes have been reported to harbor the G4 structure at regulatory regions. In this context, G4 structure-binding ligands attain significance as molecules with potential to modify the epigenetic state of chromatin. Here, using examples from recent studies we discuss the emerging role of G4 structures in epigenetic modifications and, therefore, the promise of G4 structure-binding ligands in epigenetic therapy.
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Affiliation(s)
- Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi-110001, India.
| | - Akansha Ganguly
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi-110001, India.
- GNR Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi-110025, India.
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