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Ahmadi Asouri S, Aghadavood E, Mirzaei H, Abaspour A, Esmaeil Shahaboddin M. PIWI-interacting RNAs (PiRNAs) as emerging biomarkers and therapeutic targets in biliary tract cancers: A comprehensive review. Heliyon 2024; 10:e33767. [PMID: 39040379 PMCID: PMC11261894 DOI: 10.1016/j.heliyon.2024.e33767] [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: 10/20/2023] [Revised: 06/09/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Cancers affecting the biliary tract, such as gallbladder cancer and cholangiocarcinoma, make up a small percentage of adult gastrointestinal malignancies, but their incidence is on the rise. Due to the lack of dependable molecular biomarkers for diagnosis and prognosis, these cancers are often not detected until later stages and have limited treatment options. Piwi-interacting RNAs (piRNAs) are a type of small noncoding RNA that interacts with Piwi proteins and has been linked to various diseases, especially cancer. Manipulation of piRNA expression has the potential to serve as an important biomarker and target for therapy. This review uncovers the relationship between PIWI-interacting RNA (piRNA) and a variety of gastrointestinal cancers, including biliary tract cancer (BTC). It is evident that piRNAs have the ability to impact gene expression and regulate key genes and pathways related to the advancement of digestive cancers. Abnormal expression of piRNAs plays a significant role in the development and progression of digestive-related malignancies. The potential of piRNAs as potential biomarkers for diagnosis and prognosis, as well as therapeutic targets in BTC, is noteworthy. Nevertheless, there are obstacles and limitations that require further exploration to fully comprehend piRNAs' role in BTC and to devise effective diagnostic and therapeutic approaches using piRNAs. In summary, this review underscores the value of piRNAs as valuable biomarkers and promising targets for treating BTC, as we delve into the association between piRNAs and various gastrointestinal cancers, including BTC, and how piRNAs can impact gene expression and control essential pathways for digestive cancer advancement. The present research consists of a thorough evaluation presented in a storytelling style. The databases utilized to locate original sources were PubMed, MEDLINE, and Google Scholar, and the search was conducted using the designated keywords.
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Affiliation(s)
- Sahar Ahmadi Asouri
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Esmat Aghadavood
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Alireza Abaspour
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Esmaeil Shahaboddin
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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Motamedi H, Ari MM, Alvandi A, Abiri R. Principle, application and challenges of development siRNA-based therapeutics against bacterial and viral infections: a comprehensive review. Front Microbiol 2024; 15:1393646. [PMID: 38939184 PMCID: PMC11208694 DOI: 10.3389/fmicb.2024.1393646] [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: 02/29/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
While significant progress has been made in understanding and applying gene silencing mechanisms and the treatment of human diseases, there have been still several obstacles in therapeutic use. For the first time, ONPATTRO, as the first small interfering RNA (siRNA) based drug was invented in 2018 for treatment of hTTR with polyneuropathy. Additionally, four other siRNA based drugs naming Givosiran, Inclisiran, Lumasiran, and Vutrisiran have been approved by the US Food and Drug Administration and the European Medicines Agency for clinical use by hitherto. In this review, we have discussed the key and promising advances in the development of siRNA-based drugs in preclinical and clinical stages, the impact of these molecules in bacterial and viral infection diseases, delivery system issues, the impact of administration methods, limitations of siRNA application and how to overcome them and a glimpse into future developments.
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Affiliation(s)
- Hamid Motamedi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Amirhoushang Alvandi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Hammad G, Mamdouh S, Seoudi DM, Seleem MI, Safwat G, Mohamed RH. Elevated expression patterns of P-element Induced Wimpy Testis (PIWI) transcripts are potential candidate markers for Hepatocellular Carcinoma. Cancer Biomark 2024; 39:95-111. [PMID: 38043006 PMCID: PMC11002723 DOI: 10.3233/cbm-230134] [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: 05/02/2023] [Accepted: 09/25/2023] [Indexed: 12/04/2023]
Abstract
BACKGROUND P-Element-induced wimpy testis (PIWI) proteins, when in combination with PIWI-interacting RNA (piRNA), are engaged in the epigenetic regulation of gene expression in germline cells. Different types of tumour cells have been found to exhibit abnormal expression of piRNA, PIWIL-mRNAs, and proteins. We aimed to determine the mRNA expression profiles of PIWIL1, PIWIL2, PIWIL3, & PIWIL4, in hepatocellular carcinoma patients, and to associate their expression patterns with clinicopathological features. METHODS The expression patterns of PIWIL1, PIWIL2, PIWIL3, PIWIL4 mRNA, was assessed via real-time quantitative polymerase chain reaction (RT-QPCR), on tissue and serum samples from HCC patients, their impact for diagnosis was evaluated by ROC curves, prognostic utility was determined, and In Silico analysis was conducted for predicted variant detection, association with HCC microRNAs and Network Analysis. RESULTS Expression levels were significantly higher in both HCC tissue and serum samples than in their respective controls (p< 0.001). Additionally, the diagnostic performance was assessed, Risk determination was found to be statistically significant. CONCLUSION PIWIL mRNAs are overexpressed in HCC tissue and serum samples, the expression patterns could be valuable molecular markers for HCC, due to their association with age, tumour grade and pattern. To the best of our knowledge, our study is the first to report the expression levels of all PIWIL mRNA and to suggest their remarkable values as diagnostic and prognostic biomarkers, in addition to their correlation to HCC development. Additionally, a therapeutic opportunity might be also suggested through in silico miRNA prediction for HCC and PIWIL genes through DDX4 and miR-124-3p.
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Affiliation(s)
- Gehan Hammad
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Samah Mamdouh
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Cairo, Egypt
| | - Dina Mohamed Seoudi
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed Ismail Seleem
- Department of Surgery, National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt
| | - Gehan Safwat
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt
| | - Rania Hassan Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
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Chen MJ, Hsu A, Lin PY, Chen YL, Wu KW, Chen KC, Wang T, Yi YC, Kung HF, Chang JC, Yang WJ, Lu F, Guu HF, Chen YF, Chuan ST, Chen LY, Chen CH, Yang PE, Huang JYJ. Development of a Predictive Model for Optimization of Embryo Transfer Timing Using Blood-Based microRNA Expression Profile. Int J Mol Sci 2023; 25:76. [PMID: 38203247 PMCID: PMC10779357 DOI: 10.3390/ijms25010076] [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] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
MicroRNAs (miRNAs) can regulate the expression of genes involved in the establishment of the window of implantation (WOI) in the endometrium. Recent studies indicated that cell-free miRNAs in uterine fluid and blood samples could act as alternative and non-invasive sample types for endometrial receptivity analysis. In this study, we attempt to systematically evaluate whether the expression levels of cell-free microRNAs in blood samples could be used as non-invasive biomarkers for assessing endometrial receptivity status. We profiled the miRNA expression levels of 111 blood samples using next-generation sequencing to establish a predictive model for the assessment of endometrial receptivity status. This model was validated with an independent dataset (n = 73). The overall accuracy is 95.9%. Specifically, we achieved accuracies of 95.9%, 95.9%, and 100.0% for the pre-receptive group, the receptive group, and the post-respective group, respectively. Additionally, we identified a set of differentially expressed miRNAs between different endometrial receptivity statuses using the following criteria: p-value < 0.05 and fold change greater than 1.5 or less than -1.5. In conclusion, the expression levels of cell-free miRNAs in blood samples can be utilized in a non-invasive manner to distinguish different endometrial receptivity statuses.
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Affiliation(s)
- Ming-Jer Chen
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - An Hsu
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Pei-Yi Lin
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Yu-Ling Chen
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Ko-Wen Wu
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Kuan-Chun Chen
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Tiffany Wang
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Yu-Chiao Yi
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Hsiao-Fan Kung
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Jui-Chun Chang
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Wen-Jui Yang
- Taiwan IVF Group Center for Reproductive Medicine and Infertility, Hsinchu 30274, Taiwan; (W.-J.Y.); (F.L.); (C.-H.C.)
| | - Farn Lu
- Taiwan IVF Group Center for Reproductive Medicine and Infertility, Hsinchu 30274, Taiwan; (W.-J.Y.); (F.L.); (C.-H.C.)
| | - Hwa-Fen Guu
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Ya-Fang Chen
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Shih-Ting Chuan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Li-Yu Chen
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics Gynecology & Women’s Health, Taichung Veterans General Hospital, Taichung 40764, Taiwan; (M.-J.C.); (Y.-C.Y.); (H.-F.K.); (J.-C.C.); (H.-F.G.); (Y.-F.C.); (S.-T.C.); (L.-Y.C.)
| | - Ching-Hung Chen
- Taiwan IVF Group Center for Reproductive Medicine and Infertility, Hsinchu 30274, Taiwan; (W.-J.Y.); (F.L.); (C.-H.C.)
| | - Pok Eric Yang
- Inti Labs, Hsinchu 30261, Taiwan; (A.H.); (P.-Y.L.); (Y.-L.C.); (K.-W.W.); (K.-C.C.); (T.W.)
| | - Jack Yu-Jen Huang
- Taiwan IVF Group Center for Reproductive Medicine and Infertility, Hsinchu 30274, Taiwan; (W.-J.Y.); (F.L.); (C.-H.C.)
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA 94305, USA
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Szymanowska A, Rodriguez-Aguayo C, Lopez-Berestein G, Amero P. Non-Coding RNAs: Foes or Friends for Targeting Tumor Microenvironment. Noncoding RNA 2023; 9:52. [PMID: 37736898 PMCID: PMC10514839 DOI: 10.3390/ncrna9050052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a group of molecules critical for cell development and growth regulation. They are key regulators of important cellular pathways in the tumor microenvironment. To analyze ncRNAs in the tumor microenvironment, the use of RNA sequencing technology has revolutionized the field. The advancement of this technique has broadened our understanding of the molecular biology of cancer, presenting abundant possibilities for the exploration of novel biomarkers for cancer treatment. In this review, we will summarize recent achievements in understanding the complex role of ncRNA in the tumor microenvironment, we will report the latest studies on the tumor microenvironment using RNA sequencing, and we will discuss the potential use of ncRNAs as therapeutics for the treatment of cancer.
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Affiliation(s)
- Anna Szymanowska
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers. Int J Mol Sci 2023; 24:12407. [PMID: 37569782 PMCID: PMC10419249 DOI: 10.3390/ijms241512407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to refine diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing specific CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and verification of new markers are described, and the existing problems and potential solutions for them are highlighted.
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Affiliation(s)
- Anastasia A. Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Elena Yu. Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Anastasia I. Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050 Tomsk, Russia
| | - Anna S. Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Dmitry N. Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Alexey Yu. Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Sergey A. Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Nadezhda V. Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050 Tomsk, Russia
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Anashkina AA, Orlova NG, Ignatov AN, Chen M, Orlov YL. Editorial: Bioinformatics of genome regulation and systems biology, Volume III. Front Genet 2023; 14:1215987. [PMID: 37274783 PMCID: PMC10233740 DOI: 10.3389/fgene.2023.1215987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Affiliation(s)
- Anastasia A. Anashkina
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nina G. Orlova
- Department of Mathematics, Financial University Under the Government of the Russian Federation, Moscow, Russia
| | - Alexander N. Ignatov
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuriy L. Orlov
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Life Sciences and Biomedicine, Far East Federal University, Vladivostok, Russia
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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Akimniyazova AN, Niyazova TK, Yurikova OY, Pyrkova AY, Zhanuzakov MA, Ivashchenko AT. piRNAs may regulate expression of candidate genes of esophageal adenocarcinoma. Front Genet 2022; 13:1069637. [PMID: 36531220 PMCID: PMC9747755 DOI: 10.3389/fgene.2022.1069637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 07/29/2023] Open
Abstract
Elucidation of ways to regulate the expression of candidate cancer genes will contribute to the development of methods for cancer diagnosis and therapy. The aim of the present study was to show the role of piRNAs as efficient regulators of mRNA translation of esophageal adenocarcinoma (EAC) candidate genes. We used bioinformatic methods to study the interaction characteristics of up to 200 thousand piRNAs with mRNAs of 38 candidate EAC genes. The piRNAs capable of binding to mRNA of AR, BTG3, CD55, ERBB3, FKBP5, FOXP1, LEP, SEPP1, SMAD4, and TP53 genes with high free energy by the formation of hydrogen bonds between canonical (G-C, A-U) and noncanonical (G-U, A-C) piRNA and mRNA nucleotide pairs were revealed. The organization of piRNA binding sites (BSs) in the mRNA of candidate genes was found to overlap nucleotide sequences to form clusters. Clusters of piRNA BSs were detected in the 5'-untranslated region, coding domain sequence, and 3'-untranslated region of mRNA. Due to the formation of piRNA binding site clusters, compaction of BSs occurs and competition between piRNAs for binding to mRNA of candidate EAC genes occurs. Associations of piRNA and candidate genes were selected for use as markers for the diagnosis of EAC.
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Affiliation(s)
- A. N. Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - T. K. Niyazova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - O. Yu. Yurikova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - A. Yu. Pyrkova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty, Kazakhstan
| | - M. A. Zhanuzakov
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Zhang Q, Li H, Liu Y, Li J, Wu C, Tang H. Exosomal Non-Coding RNAs: New Insights into the Biology of Hepatocellular Carcinoma. CURRENT ONCOLOGY (TORONTO, ONT.) 2022; 29:5383-5406. [PMID: 36005165 PMCID: PMC9406833 DOI: 10.3390/curroncol29080427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/07/2023]
Abstract
Exosomes, extracellular vesicles with a diameter of 40 to 160 nm, are among the smallest extracellular vesicles released by cells. They deliver different cargoes, including proteins, DNAs, and RNAs, and facilitate communication between cells to coordinate a variety of physiological and pathological functions. Hepatocellular carcinoma (HCC) is the sixth common malignant tumor and the fourth leading cause of cancer-related death worldwide. Its molecular mechanism remains largely unknown, and there is a lack of reliable and noninvasive biomarkers for early diagnosis and prognosis prediction. Mounting evidence has shown that exosomes carry a variety of ncRNAs, such as long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), which play critical roles in the occurrence and progression of HCC. In this review, we summarize the recent findings of exosomal miRNAs, lncRNAs, and circRNAs in HCC from their impact on the development of HCC to their potential applications in the diagnosis and treatment of HCC.
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Affiliation(s)
- Qian Zhang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (Q.Z.); (H.L.); (Y.L.)
| | - Hanlin Li
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (Q.Z.); (H.L.); (Y.L.)
| | - Yang Liu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (Q.Z.); (H.L.); (Y.L.)
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu 610106, China;
| | - Chunling Wu
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (Q.Z.); (H.L.); (Y.L.)
- Correspondence: (C.W.); (H.T.)
| | - Hua Tang
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; (Q.Z.); (H.L.); (Y.L.)
- Central Nervous System Drug Key Laboratory of Sichuan Province, Luzhou 646000, China
- Engineering, Informatics Fusion and Transformation Key Laboratory, Luzhou 646000, China
- Correspondence: (C.W.); (H.T.)
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