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Silvia BJ, Shetty S, Behera R, Khandelwal A, Gore M, Bairy M, Ajjanagadde A, Shaheeda A, Bhat GK, Kabekkodu SP. A comprehensive review on the role of PIWI-interacting RNA (piRNA) in gynecological cancers. Life Sci 2024; 357:123065. [PMID: 39299387 DOI: 10.1016/j.lfs.2024.123065] [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: 01/12/2024] [Revised: 05/15/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Gynecological cancers are currently a major public health concern due to increase in incidence and mortality globally. PIWI-interacting RNA (piRNA) are small non-coding RNA consisting of 24-32 nucleotides that plays regulatory role by interacting with piwi family of protein. Recent studies have revealed that piRNAs are expressed in various kinds of human tissues and influences key signalling pathways at transcriptional and post transcriptional levels. Studies have also that suggested piRNA and PIWI proteins display frequently altered expression in several cancers. Recent research has indicated that abnormal expression of piRNA may play a significant role in development and progression of gynecological cancers. Clinical studies suggested that, abnormally expressed piRNAs may serve as diagnostic and prognostic marker, and as potential therapeutic targets in these cancers. In the present review article, we discussed the emerging role of piRNA and their utility as diagnostic and prognostic marker in gynecological cancers.
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Affiliation(s)
- Bobby J Silvia
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Sachin Shetty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Roopal Behera
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Ayush Khandelwal
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Mrudula Gore
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Medha Bairy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Anagha Ajjanagadde
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Aishath Shaheeda
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Gahan Krishna Bhat
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India.
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2
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Shaker FH, Sanad EF, Elghazaly H, Hsia SM, Hamdy NM. piR-823 tale as emerging cancer-hallmark molecular marker in different cancer types: a step-toward ncRNA-precision. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03308-z. [PMID: 39102033 DOI: 10.1007/s00210-024-03308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
PIWI-interacting RNAs (piRNAs) have received a lot of attention for their functions in cancer research. This class of short non-coding RNAs (ncRNA) has roles in genomic stability, chromatin remodeling, messenger RNA (mRNA) integrity, and genome structure. We summarized the mechanisms underlying the biogenesis and regulatory molecular functions of piRNAs. Among all piRNAs studied in cancer, this review offers a comprehensive analysis of the emerging roles of piR-823 in various types of cancer, including colorectal, gastric, liver, breast, and renal cancers, as well as multiple myeloma. piR-823 has emerged as a crucial modulator of various cancer hallmarks through regulating multiple pathways. In the current review, we analyzed several databases and conducted an extensive literature search to explore the influence of piR-823 in carcinogenesis in addition to describing the potential application of piR-823 as prognostic and diagnostic markers as well as the therapeutic potential toward ncRNA precision.
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Affiliation(s)
- Fatma H Shaker
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Eman F Sanad
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Hesham Elghazaly
- Department of Clinical Oncology, Faculty of Medicine, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Shih-Min Hsia
- School of Food and Safety, Nutrition Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 110301, Taiwan
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei, 110301, Taiwan
| | - Nadia M Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt.
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3
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Li Y, Wang K, Liu W, Zhang Y. The potential emerging role of piRNA/PIWI complex in virus infection. Virus Genes 2024; 60:333-346. [PMID: 38833149 DOI: 10.1007/s11262-024-02078-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/18/2024] [Indexed: 06/06/2024]
Abstract
P-element-induced wimpy testis-interacting RNAs (piRNAs), a class of small noncoding RNAs with about 24-32 nucleotides, often interact with PIWI proteins to form a piRNA/PIWI complex that could influence spermiogenesis, transposon silencing, epigenetic regulation, etc. PIWI proteins have a highly conserved function in a variety of species and are usually expressed in germ cells. However, increasing evidence has revealed the important role of the piRNA/PIWI complex in the occurrence and prognosis of various human diseases and suggests its potential application in the diagnosis and treatment of related diseases, becoming a prominent marker for these human diseases. Recent studies have confirmed that piRNA/PIWI complexes or piRNAs are abnormally expressed in some viral infections, effecting disease progression and viral replication. In this study, we reviewed the association between the piRNA/PIWI complex and several human disease-associated viruses, including human papillomavirus, human immunodeficiency virus, human rhinovirus, severe acute respiratory syndrome coronavirus 2, respiratory syncytial virus, and herpes simplex virus type 1.
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Affiliation(s)
- Yanyan Li
- Department of Clinical Laboratory, Zibo Central Hospital, 54 Gongqingtuan Road, Zibo, 255036, China
| | - Kai Wang
- Department of Clinical Laboratory, Zibo Central Hospital, 54 Gongqingtuan Road, Zibo, 255036, China
| | - Wen Liu
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
| | - Yan Zhang
- Department of Clinical Laboratory, Zibo Central Hospital, 54 Gongqingtuan Road, Zibo, 255036, China.
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
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4
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Jiang M, Hong X, Gao Y, Kho AT, Tantisira KG, Li J. piRNA associates with immune diseases. Cell Commun Signal 2024; 22:347. [PMID: 38943141 PMCID: PMC11214247 DOI: 10.1186/s12964-024-01724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024] Open
Abstract
PIWI-interacting RNA (piRNA) is the most abundant small non-coding RNA in animal cells, typically 26-31 nucleotides in length and it binds with PIWI proteins, a subfamily of Argonaute proteins. Initially discovered in germ cells, piRNA is well known for its role in silencing transposons and maintaining genome integrity. However, piRNA is also present in somatic cells as well as in extracellular vesicles and exosomes. While piRNA has been extensively studied in various diseases, particular cancer, its function in immune diseases remains unclear. In this review, we summarize current research on piRNA in immune diseases. We first introduce the basic characteristics, biogenesis and functions of piRNA. Then, we review the association of piRNA with different types of immune diseases, including autoimmune diseases, immunodeficiency diseases, infectious diseases, and other immune-related diseases. piRNA is considered a promising biomarker for diseases, highlighting the need for further research into its potential mechanisms in disease pathogenesis.
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Affiliation(s)
- Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yunfei Gao
- Department of Otolaryngology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, China.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Guangdong, Shenzhen, China.
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5
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Ma Y, Hou B, Zong J, Liu S. Potential molecular mechanisms and clinical implications of piRNAs in preeclampsia: a review. Reprod Biol Endocrinol 2024; 22:73. [PMID: 38915084 PMCID: PMC11194991 DOI: 10.1186/s12958-024-01247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
Preeclampsia is a multisystem progressive condition and is one of the most serious complications of pregnancy. Owing to its unclear pathogenesis, there are no precise and effective therapeutic targets for preeclampsia, and the only available treatment strategy is to terminate the pregnancy and eliminate the clinical symptoms. In recent years, non-coding RNAs have become a hotspot in preeclampsia research and have shown promise as effective biomarkers for the early diagnosis of preeclampsia over conventional biochemical markers. PIWI-interacting RNAs, novel small non-coding RNA that interact with PIWI proteins, are involved in the pathogenesis of various diseases at the transcriptional or post-transcriptional level. However, the mechanisms underlying the role of PIWI-interacting RNAs in the pathogenesis of preeclampsia remain unclear. In this review, we discuss the findings of existing studies on PIWI-interacting RNA biogenesis, functions, and their possible roles in preeclampsia, providing novel insights into the potential application of PIWI-interacting RNAs in the early diagnosis and clinical treatment of preeclampsia.
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Affiliation(s)
- Yuanxuan Ma
- Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, Shandong, China
- Department of Medical Genetics, the Affiliated Hospital of Qingdao University, Qingdao , Shandong, 266003, China
| | - Bo Hou
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao , Shandong, 266003, China
| | - Jinbao Zong
- Department of Laboratory, Qingdao Hiser Hospital Affliated of Qingdao University (Oingdao Traditional Chinese Medicine Hospital), 4 Renmin Road, Qingdao, 266033, China.
| | - Shiguo Liu
- Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, Shandong, China.
- Department of Medical Genetics, the Affiliated Hospital of Qingdao University, Qingdao , Shandong, 266003, China.
- Medical Genetic Department, the Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China.
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Liu Z, Zhao X. piRNAs as emerging biomarkers and physiological regulatory molecules in cardiovascular disease. Biochem Biophys Res Commun 2024; 711:149906. [PMID: 38640879 DOI: 10.1016/j.bbrc.2024.149906] [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: 02/03/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 04/21/2024]
Abstract
Cardiovascular diseases (CVD) represent one of the most considerable global health threats, owing to their high incidence and mortality rates. Despite the ongoing advancements in detection, prevention, treatment, and prognosis of CVD, which have resulted in a decline in both incidence and mortality rates, CVD remains a major public health concern. Therefore, novel diagnostic biomarkers and therapeutic interventions are imperative to minimise the risk of CVD. Non-coding RNAs (ncRNAs) have recently gained increasing attention, with PIWI-interacting RNAs (piRNAs) emerging as a class of small ncRNAs traditionally recognised for their role in silencing transposons within cells. Although the functional roles of PIWI proteins and piRNAs in human cells remain unclear, growing evidence suggests that these molecules are gradually becoming valuable biomarkers for the diagnosis and treatment of CVD. This review provides a comprehensive summary of the latest studies on piRNAs in CVD. This review discusses the roles of piRNAs in various cardiovascular subtypes, including myocardial hypertrophy, heart failure, myocardial infarction, and cardiac regeneration. The perceived insights may contribute novel perspectives for the diagnosis and treatment of CVD.
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Affiliation(s)
- Zhihua Liu
- School of Basic Medical Sciences, Center for Precision Medicine, Kunming YanAn Hospital & Kunming University of Science and Technology, Kunming, China; Department of Biostatistics and Computational Biology, Bayer HealthCare, Harvard University, Boston, MA, USA.
| | - Xi Zhao
- School of Basic Medical Sciences, Center for Precision Medicine, Kunming YanAn Hospital & Kunming University of Science and Technology, Kunming, China
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Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
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Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
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8
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Münch L, Helmprobst F, Volff JN, Chalopin D, Schartl M, Kneitz S. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus. Genes (Basel) 2024; 15:620. [PMID: 38790249 PMCID: PMC11121471 DOI: 10.3390/genes15050620] [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: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different.
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Affiliation(s)
- Luca Münch
- Neurology Asklepios Klinik Barmbek, Rübenkamp 220, 22307 Hamburg, Germany;
| | - Frederik Helmprobst
- Institute of Neuropathology, Philipps-University Marburg, 35037 Marburg, Germany;
| | | | | | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 786666, USA
- Developmental Biochemistry, University of Würzburg, 97974 Würzburg, Germany
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
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Zhang H, Li Y. Potential roles of PIWI-interacting RNAs in breast cancer, a new therapeutic strategy. Pathol Res Pract 2024; 257:155318. [PMID: 38688203 DOI: 10.1016/j.prp.2024.155318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Breast cancer (BC) has been the focus of numerous studies aimed at identifying novel biological markers for its early detection. PIWI-interacting RNAs (piRNAs), a subset of small non-coding RNAs, have emerged as potential markers due to their aberrant expression in various cancers. PiRNAs have recently gained attention due to their aberrant expression in various cancers, including BC. PiRNAs, exhibit diverse biological activities, such as epigenetic regulation of gene and protein expression and their association with cell proliferation and metastasis has been well-established. As the field of non-coding RNAs rapidly evolves, there is great anticipation that therapies targeting piRNAs will advance swiftly. This review will delve into the various biological functions of piRNAs, such as gene suppression, transposon silencing, and epigenetic regulation of genes. The review will also highlight the role of piRNAs as either progenitors or suppressors in cancers, with a particular focus on BC. Lastly, it will touch upon the potential of piRNAs as biomarkers and therapeutic targets for BC.
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Affiliation(s)
- Hongpeng Zhang
- The Second Clinical College, China Medical University, Shenyang 110122, China
| | - Yanshu Li
- School of Life Sciences, China Medical University, Shenyang 110122, China.
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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Jia D, Wang K, Huang L, Zhou Z, Zhang Y, Chen N, Yang Q, Wen Z, Jiang H, Yao C, Wu R. Revealing PPP1R12B and COL1A1 as piRNA pathway genes contributing to abdominal aortic aneurysm through integrated analysis and experimental validation. Gene 2024; 897:148068. [PMID: 38070790 DOI: 10.1016/j.gene.2023.148068] [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: 10/11/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a permanent dilation of the abdominal aorta, with a high mortality rate when rupturing. Although lots of piRNA pathway genes (piRPGs) have recently been linked to both neoplastic and non-neoplastic illnesses, their role in AAA is still unknown. Utilizing integrative bioinformatics methods, this research discovered piRPGs as biomarkers for AAA and explore possible molecular mechanisms. METHODS The datasets were obtained from the Gene Expression Omnibus and piRPGs were identified from the Genecards database. The "limma" and "clusterProfiler" R-packages were used to discover differentially expressed genes and perform enrichment analysis, respectively. Hub piRPGs were further filtered using least absolute shrinkage and selection operator regression, random forests, as well as receiver operating characteristic curve. Additionally, multi-factor logistic regression (MLR), extreme gradient boosting (XGboost), and artificial neural network (ANN) were employed to construct prediction models. The relationship between hub piRPGs and immune infiltrating cells and sgGSEA were further studied. The expression of hub piRPGs was verified by qRT-PCR, immunohistochemistry, and western blotting in AAA and normal vascular tissues and analyzed by scRNA-seq in mouse AAA model. SRAMP and cMAP database were utilized for the prediction of N6-methyladenosine (m6A) targets therapeutic drug. RESULTS 34 differentially expressed piRPGs were identified in AAA and enriched in pathways of immune regulation and gene silence. Three piRPGs (PPP1R12B, LRP10, and COL1A1) were further screened as diagnostic genes and used to construct prediction model. Compared with MLR and ANN, Xgboost showed better predictive ability, and PPP1R12B might have the ability to distinguish small and large AAA. Furthermore, the expression levels of PPP1R12B and COL1A1 were consistent with the results of bioinformatics analysis, and PPP1R12B showed a downward trend that may be related to m6A. CONCLUSION The results suggest that piRPGs might serve a significant role in AAA. PPP1R12B, COL1A1, and LRP10 had potential as diagnostic-specific biomarkers for AAA and performed better in XGboost model. The expression and localization of PPP1R12B and COL1A1 were experimentally verified. Besides, downregulation of PPP1R12B caused by m6A might contribute to the formation of AAA.
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Affiliation(s)
- Dongdong Jia
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Kangjie Wang
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Lin Huang
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Zhihao Zhou
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Yinfeng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, PR China
| | - Nuo Chen
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Qingqi Yang
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Zengjin Wen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, PR China
| | - Hui Jiang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, PR China
| | - Chen Yao
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China
| | - Ridong Wu
- Department of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, PR China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, PR China.
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12
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Zhang Y, Jiao X, Wang T, Yue X, Wang Y, Cai B, Wang C, Lu S. piRNA mmu_piR_037459 suppression alleviated the degeneration of chondrocyte and cartilage. Int Immunopharmacol 2024; 128:111473. [PMID: 38266448 DOI: 10.1016/j.intimp.2023.111473] [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: 10/08/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE Osteoarthritis (OA) is a prevalent chronic degenerative joint ailment. Its primary pathological characteristics encompass degeneration of articular cartilage, inflammation of the synovium, and alterations in the subchondral bone proximate to the cartilage. Chondrocytes, as the sole cell type within articular cartilage, assume a crucial role in upholding the dynamic equilibrium between anabolic and catabolic processes within the extracellular matrix of articular cartilage. IL-1β stands as a pivotal inflammatory factor that instigates cartilage degeneration. piRNA, categorized as a subset of brief non-coding RNAs spanning nucleotide lengths of 26-31nt, assumes a significant regulatory role in cellular function. METHODS Small RNA sequencing and quantitative PCR (qPCR) were employed to investigate the impact of the inflammatory factor IL-1β on piRNA expression within chondrocytes. The regulation of mmu_piR_037459 expression in chondrocytes was achieved using piRNA mimics and inhibitors. Additionally, collagen II expression was assessed through both qPCR and Western blot analysis. Chondrocyte apoptosis was evaluated via flow cytometry and clonogenesis assays. To assess the influence of mmu_piR_037459 on osteoarthritis, a mouse model of anterior cruciate ligament transection (ACLT) was established. Furthermore, the regulatory effect of mmu_piR_037459 on USP7 was investigated using bioinformatics and a luciferase reporter gene assay. RESULTS mmu_piR_037459 inhibited the expression of collagen II in chondrocytes, inhibited the proliferation of chondrocytes, and promoted the apoptosis of chondrocytes. mmu_piR_037459 affected the function of chondrocytes by regulating the expression of USP7. Inhibition of mmu_piR_037459 expression could promote chondrocyte proliferation, inhibit chondrocyte apoptosis, and alleviate the degeneration of OA cartilage. CONCLUSIONS This study suggests that mmu_piR_037459 maybe a new therapeutic targets and strategies for the treatment of OA.
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Affiliation(s)
- Yuxin Zhang
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Rehabilitation Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China; Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xin Jiao
- Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Tianchang Wang
- Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xiaokun Yue
- Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yijia Wang
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Bin Cai
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Rehabilitation Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Shenji Lu
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Rehabilitation Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
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Garcia-Borja E, Siegl F, Mateu R, Slaby O, Sedo A, Busek P, Sana J. Critical appraisal of the piRNA-PIWI axis in cancer and cancer stem cells. Biomark Res 2024; 12:15. [PMID: 38303021 PMCID: PMC10836005 DOI: 10.1186/s40364-024-00563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Small noncoding RNAs play an important role in various disease states, including cancer. PIWI proteins, a subfamily of Argonaute proteins, and PIWI-interacting RNAs (piRNAs) were originally described as germline-specific molecules that inhibit the deleterious activity of transposable elements. However, several studies have suggested a role for the piRNA-PIWI axis in somatic cells, including somatic stem cells. Dysregulated expression of piRNAs and PIWI proteins in human tumors implies that, analogously to their roles in undifferentiated cells under physiological conditions, these molecules may be important for cancer stem cells and thus contribute to cancer progression. We provide an overview of piRNA biogenesis and critically review the evidence for the role of piRNA-PIWI axis in cancer stem cells. In addition, we examine the potential of piRNAs and PIWI proteins to become biomarkers in cancer.
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Affiliation(s)
- Elena Garcia-Borja
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Frantisek Siegl
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Rosana Mateu
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Aleksi Sedo
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Petr Busek
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic.
| | - Jiri Sana
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic.
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- Department of Pathology, University Hospital Brno, Brno, Czech Republic.
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14
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Kaldis P, Zhao LN. Molecular basis of the reaction mechanism of the methyltransferase HENMT1. PLoS One 2024; 19:e0293243. [PMID: 38198468 PMCID: PMC10781085 DOI: 10.1371/journal.pone.0293243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/09/2023] [Indexed: 01/12/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs) are important for ensuring the integrity of the germline. 3'-terminal 2'-O-methylation is essential for piRNA maturation and to protect them from degradation. HENMT1 (HEN Methyltransferase 1) carries out the 2'-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of mammalian HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+ is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3'-O and 2'-O on the 3'-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on substrate and cofactor binding but is essential for catalysis. The reaction consists of deprotonation of the 2'-OH to 2'-O and a methyl transfer from SAM to the 2'-O. The methyl transfer is spontaneous and fast. Our in-depth analysis suggests that the 2'-OH may be deprotonated before entering the active site or it may be partially deprotonated at the active site by His800 and Asp859, which are in a special alignment that facilitates the proton transfer out of the active site. Furthermore, we have developed a detailed potential reaction scenario indicating that HENMT1 is Mg2+ utilizing but is not a Mg2+ dependent enzyme.
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Affiliation(s)
- Philipp Kaldis
- Department of Clinical Sciences, Lund University, Malmö, Skåne, Sweden
- Lund University Diabetes Centre, Lund University, Malmö, Skåne, Sweden
| | - Li Na Zhao
- Department of Clinical Sciences, Lund University, Malmö, Skåne, Sweden
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15
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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16
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Zhang X, Xu X, Song J, Xu Y, Qian H, Jin J, Liang ZF. Non-coding RNAs' function in cancer development, diagnosis and therapy. Biomed Pharmacother 2023; 167:115527. [PMID: 37751642 DOI: 10.1016/j.biopha.2023.115527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
While previous research on cancer biology has focused on genes that code for proteins, in recent years it has been discovered that non-coding RNAs (ncRNAs)play key regulatory roles in cell biological functions. NcRNAs account for more than 95% of human transcripts and are an important entry point for the study of the mechanism of cancer development. An increasing number of studies have demonstrated that ncRNAs can act as tumor suppressor genes or oncogenes to regulate tumor development at the epigenetic level, transcriptional level, as well as post-transcriptional level. Because of the importance of ncRNAs in cancer, most clinical trials have focused on ncRNAs to explore whether ncRNAs can be used as new biomarkers or therapies. In this review, we focus on recent studies of ncRNAs including microRNAs (miRNAs), long ncRNAs (lncRNAs), circle RNAs (circRNAs), PIWI interacting RNAs (piRNAs), and tRNA in different types of cancer and explore the application of these ncRNAs in the development of cancer and the identification of relevant therapeutic targets and tumor biomarkers. Graphical abstract drawn by Fidraw.
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Affiliation(s)
- XinYi Zhang
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Xiaoqing Xu
- Nanjing Renpin ENT Hospital, Nanjing 210000, Jiangsu, China
| | - Jiajia Song
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Yumeng Xu
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Hui Qian
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Jianhua Jin
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China.
| | - Zhao Feng Liang
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China.
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17
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Hashemi Karoii D, Azizi H. Functions and mechanism of noncoding RNA in regulation and differentiation of male mammalian reproduction. Cell Biochem Funct 2023; 41:767-778. [PMID: 37583312 DOI: 10.1002/cbf.3838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023]
Abstract
Noncoding RNAs (ncRNAs) are active regulators of a wide range of biological and physiological processes, including the majority of mammalian reproductive events. Knowledge of the biological activities of ncRNAs in the context of mammalian reproduction will allow for a more comprehensive and comparative understanding of male sterility and fertility. In this review, we describe recent advances in ncRNA-mediated control of mammalian reproduction and emphasize the importance of ncRNAs in several aspects of mammalian reproduction, such as germ cell biogenesis and reproductive organ activity. Furthermore, we focus on gene expression regulatory feedback loops including hormones and ncRNA expression to better understand germ cell commitment and reproductive organ function. Finally, this study shows the role of ncRNAs in male reproductive failure and provides suggestions for further research.
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Affiliation(s)
- Danial Hashemi Karoii
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
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18
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Liu Y, Ding W, Wang J, Ao X, Xue J. Non-coding RNAs in lung cancer: molecular mechanisms and clinical applications. Front Oncol 2023; 13:1256537. [PMID: 37746261 PMCID: PMC10514911 DOI: 10.3389/fonc.2023.1256537] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
Lung cancer (LC) is a heterogeneous disease with high malignant degree, rapid growth, and early metastasis. The clinical outcomes of LC patients are generally poor due to the insufficient elucidation of pathological mechanisms, low efficiency of detection and assessment methods, and lack of individualized therapeutic strategies. Non-coding RNAs (ncRNAs), including microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA), are endogenous regulators that are widely involved in the modulation of almost all aspects of life activities, from organogenesis and aging to immunity and cancer. They commonly play vital roles in various biological processes by regulating gene expression via their interactions with DNA, RNA, or protein. An increasing amount of studies have demonstrated that ncRNAs are closely correlated with the initiation and development of LC. Their dysregulation promotes the progression of LC via distinct mechanisms, such as influencing protein activity, activating oncogenic signaling pathways, or altering specific gene expression. Furthermore, some ncRNAs present certain clinical values as biomarker candidates and therapeutic targets for LC patients. A complete understanding of their mechanisms in LC progression may be highly beneficial to developing ncRNA-based therapeutics for LC patients. This review mainly focuses on the intricate mechanisms of miRNA, lncRNA, and circRNA involved in LC progression and discuss their underlying applications in LC treatment.
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Affiliation(s)
- Ying Liu
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, Shandong, China
| | - Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jianxun Wang
- School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Xiang Ao
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Junqiang Xue
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Rehabilitation Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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19
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Taverna S, Masucci A, Cammarata G. PIWI-RNAs Small Noncoding RNAs with Smart Functions: Potential Theranostic Applications in Cancer. Cancers (Basel) 2023; 15:3912. [PMID: 37568728 PMCID: PMC10417041 DOI: 10.3390/cancers15153912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a new class of small noncoding RNAs (ncRNAs) that bind components of the PIWI protein family. piRNAs are specifically expressed in different human tissues and regulate important signaling pathways. Aberrant expressions of piRNAs and PIWI proteins have been associated with tumorigenesis and cancer progression. Recent studies reported that piRNAs are contained in extracellular vesicles (EVs), nanosized lipid particles, with key roles in cell-cell communication. EVs contain several bioactive molecules, such as proteins, lipids, and nucleic acids, including emerging ncRNAs. EVs are one of the components of liquid biopsy (LB) a non-invasive method for detecting specific molecular biomarkers in liquid samples. LB could become a crucial tool for cancer diagnosis with piRNAs as biomarkers in a precision oncology approach. This review summarizes the current findings on the roles of piRNAs in different cancer types, focusing on potential theranostic applications of piRNAs contained in EVs (EV-piRNAs). Their roles as non-invasive diagnostic and prognostic biomarkers and as new therapeutic options have been also discussed.
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Affiliation(s)
- Simona Taverna
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 90146 Palermo, Italy
| | - Anna Masucci
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine, Laboratory Medicine, University of Palermo, 90127 Palermo, Italy;
| | - Giuseppe Cammarata
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 90146 Palermo, Italy
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Zhang K, Li Y, Huang Y, Sun K. PiRNA in Cardiovascular Disease: Focus on Cardiac Remodeling and Cardiac Protection. J Cardiovasc Transl Res 2023; 16:768-777. [PMID: 37407865 DOI: 10.1007/s12265-023-10353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/08/2023] [Indexed: 07/07/2023]
Abstract
Cardiovascular diseases (CVDs) are common causes of death, which take about 18.6 million lives worldwide every year. Currently, exploring strategies that delay ventricular remodeling, reduce cardiomyocyte death, and promote cardiomyocyte regeneration has been the hotspot and difficulty of the ischemic heart disease (IHD) research field. Previous studies indicate that piwi-interacting RNA (piRNA) plays a vital role in the occurrence and development of cardiac remodeling and may offer novel therapeutic strategies for cardiac repair. The best-known biological function of piRNA is to silence transposons in cells. In the cardiovascular system, piRNA is known to participate in cardiac progenitor cell proliferation, AKT pathway regulation, and cardiac remodeling and decompensation. In this review, we systematically discuss the research progress on piRNA in CVDs, especially the mechanism of cardiac remodeling and the potential functions in cardiac protection, which provides new insights for the progress and treatment of cardiovascular diseases. Piwi-interacting RNA (piRNA) is one of the noncoding RNAs, with the best -known biological function to silence transposons in cells. Now piRNA is found to participate in cardiac progenitor cell proliferation, AKT pathway regulation, cardiac remodeling and decompensation, which implies the potential of piRNA in the diagnosis and treatment of cardiovascular diseases. Over expression of piRNA could promote cardiac apoptosis and cardiac hypertrophy, thus targeted therapy which inhibits expression of associated piRNA may reduce cardiac remodeling and reduce inflammation caused by necrotic cardiomyocytes. PiRNA is also speculated to participate in the proliferation of cardiac progenitor cells, implying the potential to induce cardiac regeneration th erapy, which provides new insights for treatment of cardiovascular diseases. At present, the treatment strategy of cardiac remodeling emphasizes the control of risk factors, prevention of disease progression and individualized treatment. With further studies in mechanism of piRNA, potential therapies above may come true and more therapies in cardiovascular diseases may be found.
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Affiliation(s)
- Kaiyu Zhang
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Yafei Li
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Ying Huang
- Central Laboratory, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Kangyun Sun
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China.
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21
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Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. MICROMACHINES 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
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Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
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22
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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23
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Ao X, Ding W, Li X, Xu Q, Chen X, Zhou X, Wang J, Liu Y. Non-coding RNAs regulating mitochondrial function in cardiovascular diseases. J Mol Med (Berl) 2023; 101:501-526. [PMID: 37014377 DOI: 10.1007/s00109-023-02305-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of disease-related death worldwide and a significant obstacle to improving patients' health and lives. Mitochondria are core organelles for the maintenance of myocardial tissue homeostasis, and their impairment and dysfunction are considered major contributors to the pathogenesis of various CVDs, such as hypertension, myocardial infarction, and heart failure. However, the exact roles of mitochondrial dysfunction involved in CVD pathogenesis remain not fully understood. Non-coding RNAs (ncRNAs), particularly microRNAs, long non-coding RNAs, and circular RNAs, have been shown to be crucial regulators in the initiation and development of CVDs. They can participate in CVD progression by impacting mitochondria and regulating mitochondrial function-related genes and signaling pathways. Some ncRNAs also exhibit great potential as diagnostic and/or prognostic biomarkers as well as therapeutic targets for CVD patients. In this review, we mainly focus on the underlying mechanisms of ncRNAs involved in the regulation of mitochondrial functions and their role in CVD progression. We also highlight their clinical implications as biomarkers for diagnosis and prognosis in CVD treatment. The information reviewed herein could be extremely beneficial to the development of ncRNA-based therapeutic strategies for CVD patients.
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Affiliation(s)
- Xiang Ao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266021, China
| | - Xiaoge Li
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Qingling Xu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Xinhui Chen
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Xuehao Zhou
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China.
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24
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The epigenetic regulatory mechanism of PIWI/piRNAs in human cancers. Mol Cancer 2023; 22:45. [PMID: 36882835 PMCID: PMC9990219 DOI: 10.1186/s12943-023-01749-3] [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: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
PIWI proteins have a strong correlation with PIWI-interacting RNAs (piRNAs), which are significant in development and reproduction of organisms. Recently, emerging evidences have indicated that apart from the reproductive function, PIWI/piRNAs with abnormal expression, also involve greatly in varieties of human cancers. Moreover, human PIWI proteins are usually expressed only in germ cells and hardly in somatic cells, so the abnormal expression of PIWI proteins in different types of cancer offer a promising opportunity for precision medicine. In this review, we discussed current researches about the biogenesis of piRNA, its epigenetic regulatory mechanisms in human cancers, such as N6-methyladenosine (m6A) methylation, histone modifications, DNA methylation and RNA interference, providing novel insights into the markers for clinical diagnosis, treatment and prognosis in human cancers.
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25
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Wang N, Ma T, Yu B. Targeting epigenetic regulators to overcome drug resistance in cancers. Signal Transduct Target Ther 2023; 8:69. [PMID: 36797239 PMCID: PMC9935618 DOI: 10.1038/s41392-023-01341-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/18/2023] Open
Abstract
Drug resistance is mainly responsible for cancer recurrence and poor prognosis. Epigenetic regulation is a heritable change in gene expressions independent of nucleotide sequence changes. As the common epigenetic regulation mechanisms, DNA methylation, histone modification, and non-coding RNA regulation have been well studied. Increasing evidence has shown that aberrant epigenetic regulations contribute to tumor resistance. Therefore, targeting epigenetic regulators represents an effective strategy to reverse drug resistance. In this review, we mainly summarize the roles of epigenetic regulation in tumor resistance. In addition, as the essential factors for epigenetic modifications, histone demethylases mediate the histone or genomic DNA modifications. Herein, we comprehensively describe the functions of the histone demethylase family including the lysine-specific demethylase family, the Jumonji C-domain-containing demethylase family, and the histone arginine demethylase family, and fully discuss their regulatory mechanisms related to cancer drug resistance. In addition, therapeutic strategies, including small-molecule inhibitors and small interfering RNA targeting histone demethylases to overcome drug resistance, are also described.
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Affiliation(s)
- Nan Wang
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Ting Ma
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Bin Yu
- Institute of Drug Discovery & Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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26
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Noyes C, Kitajima S, Li F, Suita Y, Miriyala S, Isaac S, Ahsan N, Knelson E, Vajdi A, Tani T, Thai TC, Xu D, Murai J, Tapinos N, Takahashi C, Barbie DA, Yajima M. The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells. Commun Biol 2023; 6:65. [PMID: 36653474 PMCID: PMC9849207 DOI: 10.1038/s42003-023-04444-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Human cancers often re-express germline factors, yet their mechanistic role in oncogenesis and cancer progression remains unknown. Here we demonstrate that DEAD-box helicase 4 (DDX4), a germline factor and RNA helicase conserved in all multicellular organisms, contributes to increased cell motility and cisplatin-mediated drug resistance in small cell lung cancer (SCLC) cells. Proteomic analysis suggests that DDX4 expression upregulates proteins related to DNA repair and immune/inflammatory response. Consistent with these trends in cell lines, DDX4 depletion compromised in vivo tumor development while its overexpression enhanced tumor growth even after cisplatin treatment in nude mice. Further, the relatively higher DDX4 expression in SCLC patients correlates with decreased survival and shows increased expression of immune/inflammatory response markers. Taken together, we propose that DDX4 increases SCLC cell survival, by increasing the DNA damage and immune response pathways, especially under challenging conditions such as cisplatin treatment.
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Affiliation(s)
- Christopher Noyes
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Fengkai Li
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - Yusuke Suita
- Laboratory of Cancer Epigenetics and Plasticity, Department of Neurosurgery, Brown University, Providence, RI, 02903, USA
| | - Saradha Miriyala
- Laboratory of Cancer Epigenetics and Plasticity, Department of Neurosurgery, Brown University, Providence, RI, 02903, USA
| | - Shakson Isaac
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Nagib Ahsan
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, OK, 73019, USA
- Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK, 73019, USA
| | - Erik Knelson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Amir Vajdi
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tetsuo Tani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Derek Xu
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Nikos Tapinos
- Laboratory of Cancer Epigenetics and Plasticity, Department of Neurosurgery, Brown University, Providence, RI, 02903, USA
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Mamiko Yajima
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA.
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27
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Crosstalk between Methylation and ncRNAs in Breast Cancer: Therapeutic and Diagnostic Implications. Int J Mol Sci 2022; 23:ijms232415759. [PMID: 36555400 PMCID: PMC9779155 DOI: 10.3390/ijms232415759] [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: 11/06/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Breast cancer, as a highly heterogeneous malignant tumor, is one of the primary causes of death among females worldwide. The etiology of breast cancer involves aberrant epigenetic mechanisms and abnormal expression of certain non-coding RNA (ncRNAs). DNA methylation, N6-methyladenosine(m6A), and histone methylation are widely explored epigenetic regulation types in breast cancer. ncRNAs are a group of unique RNA transcripts, mainly including microRNA (miRNAs), long non-coding RNA (lncRNAs), circular RNA (circRNAs), small interfering RNA (siRNAs), piwi-interacting RNA (piRNAs), etc. Different types of methylation and ncRNAs mutually regulate and interact to form intricate networks to mediate precisely breast cancer genesis. In this review, we elaborate on the crosstalk between major methylation modifications and ncRNAs and discuss the role of their interaction in promoting breast cancer oncogenesis. This review can provide novel insights into establishing a new diagnostic marker system on methylation patterns of ncRNAs and therapeutic perspectives of combining ncRNA oligonucleotides and phytochemical drugs for breast cancer therapy.
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28
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Liu Y, Li X, Zhou X, Wang J, Ao X. FADD as a key molecular player in cancer progression. Mol Med 2022; 28:132. [DOI: 10.1186/s10020-022-00560-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractCancer is a leading disease-related cause of death worldwide. Despite advances in therapeutic interventions, cancer remains a major global public health problem. Cancer pathogenesis is extremely intricate and largely unknown. Fas-associated protein with death domain (FADD) was initially identified as an adaptor protein for death receptor-mediated extrinsic apoptosis. Recent evidence suggests that FADD plays a vital role in non-apoptotic cellular processes, such as proliferation, autophagy, and necroptosis. FADD expression and activity of are modulated by a complicated network of processes, such as DNA methylation, non-coding RNA, and post-translational modification. FADD dysregulation has been shown to be closely associated with the pathogenesis of numerous types of cancer. However, the detailed mechanisms of FADD dysregulation involved in cancer progression are still not fully understood. This review mainly summarizes recent findings on the structure, functions, and regulatory mechanisms of FADD and focuses on its role in cancer progression. The clinical implications of FADD as a biomarker and therapeutic target for cancer patients are also discussed. The information reviewed herein may expand researchers’ understanding of FADD and contribute to the development of FADD-based therapeutic strategies for cancer patients.
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29
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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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30
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Xiong Q, Zhang Y, Li J, Zhu Q. Small Non-Coding RNAs in Human Cancer. Genes (Basel) 2022; 13:genes13112072. [PMID: 36360311 PMCID: PMC9690286 DOI: 10.3390/genes13112072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Small non-coding RNAs are widespread in the biological world and have been extensively explored over the past decades. Their fundamental roles in human health and disease are increasingly appreciated. Furthermore, a growing number of studies have investigated the functions of small non-coding RNAs in cancer initiation and progression. In this review, we provide an overview of the biogenesis of small non-coding RNAs with a focus on microRNAs, PIWI-interacting RNAs, and a new class of tRNA-derived small RNAs. We discuss their biological functions in human cancer and highlight their clinical application as molecular biomarkers or therapeutic targets.
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Affiliation(s)
- Qunli Xiong
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junjun Li
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Qing Zhu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence:
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31
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Underlying mechanisms of epithelial splicing regulatory proteins in cancer progression. J Mol Med (Berl) 2022; 100:1539-1556. [PMID: 36163376 DOI: 10.1007/s00109-022-02257-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/31/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022]
Abstract
Cancer is the second-leading disease-related cause of global mortality after cardiovascular disease. Despite significant advances in cancer therapeutic strategies, cancer remains one of the major obstacles to human life extension. Cancer pathogenesis is extremely complicated and not fully understood. Epithelial splicing regulatory proteins (ESRPs), including ESRP1 and ESRP2, belong to the heterogeneous nuclear ribonucleoprotein family of RNA-binding proteins and are crucial regulators of the alternative splicing of messenger RNAs (mRNAs). The expression and activity of ESRPs are modulated by various mechanisms, including post-translational modifications and non-coding RNAs. Although a growing body of evidence suggests that ESRP dysregulation is closely associated with cancer progression, the detailed mechanisms remain inconclusive. In this review, we summarize recent findings on the structures, functions, and regulatory mechanisms of ESRPs and focus on their underlying mechanisms in cancer progression. We also highlight the clinical implications of ESRPs as prognostic biomarkers and therapeutic targets in cancer treatment. The information reviewed herein could be extremely beneficial to the development of individualized therapeutic strategies for cancer patients.
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32
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Zhou X, Ao X, Jia Z, Li Y, Kuang S, Du C, Zhang J, Wang J, Liu Y. Non-coding RNA in cancer drug resistance: Underlying mechanisms and clinical applications. Front Oncol 2022; 12:951864. [PMID: 36059609 PMCID: PMC9428469 DOI: 10.3389/fonc.2022.951864] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/02/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is one of the most frequently diagnosed malignant diseases worldwide, posing a serious, long-term threat to patients’ health and life. Systemic chemotherapy remains the first-line therapeutic approach for recurrent or metastatic cancer patients after surgery, with the potential to effectively extend patient survival. However, the development of drug resistance seriously limits the clinical efficiency of chemotherapy and ultimately results in treatment failure and patient death. A large number of studies have shown that non-coding RNAs (ncRNAs), particularly microRNAs, long non-coding RNAs, and circular RNAs, are widely involved in the regulation of cancer drug resistance. Their dysregulation contributes to the development of cancer drug resistance by modulating the expression of specific target genes involved in cellular apoptosis, autophagy, drug efflux, epithelial-to-mesenchymal transition (EMT), and cancer stem cells (CSCs). Moreover, some ncRNAs also possess great potential as efficient, specific biomarkers in diagnosis and prognosis as well as therapeutic targets in cancer patients. In this review, we summarize the recent findings on the emerging role and underlying mechanisms of ncRNAs involved in cancer drug resistance and focus on their clinical applications as biomarkers and therapeutic targets in cancer treatment. This information will be of great benefit to early diagnosis and prognostic assessments of cancer as well as the development of ncRNA-based therapeutic strategies for cancer patients.
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Affiliation(s)
- Xuehao Zhou
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiang Ao
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Zhaojun Jia
- College of New Materials and Chemical Engineering, Beijing Key Laboratory of Enze Biomass Fine Chemicals, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Yiwen Li
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Shouxiang Kuang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chengcheng Du
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jinyu Zhang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Ying Liu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China.,Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
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