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Deng T, Xiao Y, Dai Y, Xie L, Li X. Roles of Key Epigenetic Regulators in the Gene Transcription and Progression of Prostate Cancer. Front Mol Biosci 2021; 8:743376. [PMID: 34977151 PMCID: PMC8714908 DOI: 10.3389/fmolb.2021.743376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/25/2021] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is a top-incidence malignancy, and the second most common cause of death amongst American men and the fifth leading cause of cancer death in men around the world. Androgen receptor (AR), the key transcription factor, is critical for the progression of PCa by regulating a series of target genes by androgen stimulation. A number of co-regulators of AR, including co-activators or co-repressors, have been implicated in AR-mediated gene transcription and PCa progression. Epigenetic regulators, by modifying chromatin integrity and accessibility for transcription regulation without altering DNA sequences, influence the transcriptional activity of AR and further regulate the gene expression of AR target genes in determining cell fate, PCa progression and therapeutic response. In this review, we summarized the structural interaction of AR and epigenetic regulators including histone or DNA methylation, histone acetylation or non-coding RNA, and functional synergy in PCa progression. Importantly, epigenetic regulators have been validated as diagnostic markers and therapeutic targets. A series of epigenetic target drugs have been developed, and have demonstrated the potential to treat PCa alone or in combination with antiandrogens.
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Affiliation(s)
- Tanggang Deng
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yugang Xiao
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yi Dai
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lin Xie
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiong Li
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
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202
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Rana V, Parama D, Khatoon E, Girisa S, Sethi G, Kunnumakkara AB. Reiterating the Emergence of Noncoding RNAs as Regulators of the Critical Hallmarks of Gall Bladder Cancer. Biomolecules 2021; 11:biom11121847. [PMID: 34944491 PMCID: PMC8699045 DOI: 10.3390/biom11121847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 12/04/2021] [Indexed: 01/17/2023] Open
Abstract
Gall bladder cancer (GBC) is a rare and one of the most aggressive types of malignancies, often associated with a poor prognosis and survival. It is a highly metastatic cancer and is often not diagnosed at the initial stages, which contributes to a poor survival rate of patients. The poor diagnosis and chemoresistance associated with the disease limit the scope of the currently available surgical and nonsurgical treatment modalities. Thus, there is a need to explore novel therapeutic targets and biomarkers that will help relieve the severity of the disease and lead to advanced therapeutic strategies. Accumulating evidence has correlated the atypical expression of various noncoding RNAs (ncRNAs), including circular RNAs (circRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and small nucleolar RNAs (snoRNA) with the increased cell proliferation, epithelial-mesenchymal transition (EMT), invasion, migration, metastasis, chemoresistance, and decreased apoptosis in GBC. Numerous reports have indicated that the dysregulated expression of ncRNAs is associated with poor prognosis and lower disease-free and overall survival in GBC patients. These reports suggest that ncRNAs might be considered novel diagnostic and prognostic markers for the management of GBC. The present review recapitulates the association of various ncRNAs in the initiation and progression of GBC and the development of novel therapeutic strategies by exploring their functional and regulatory role.
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Affiliation(s)
- Varsha Rana
- Cancer Biology Laboratory & DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India; (V.R.); (D.P.); (E.K.); (S.G.)
| | - Dey Parama
- Cancer Biology Laboratory & DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India; (V.R.); (D.P.); (E.K.); (S.G.)
| | - Elina Khatoon
- Cancer Biology Laboratory & DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India; (V.R.); (D.P.); (E.K.); (S.G.)
| | - Sosmitha Girisa
- Cancer Biology Laboratory & DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India; (V.R.); (D.P.); (E.K.); (S.G.)
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- Correspondence: (G.S.); (A.B.K.)
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory & DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India; (V.R.); (D.P.); (E.K.); (S.G.)
- Correspondence: (G.S.); (A.B.K.)
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203
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Sinha N, Lydia Walker G, Sen A. Looking at the Future Through the Mother's Womb: Gestational Diabetes and Offspring Fertility. Endocrinology 2021; 162:6379047. [PMID: 34597389 PMCID: PMC8520322 DOI: 10.1210/endocr/bqab209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 12/12/2022]
Abstract
Altered nutrition or intrauterine exposure to various adverse conditions during fetal development or earlier in a mother's life can lead to epigenetic changes in fetal tissues, predisposing those tissues to diseases that manifest when offspring become adults. An example is a maternal obesity associated with gestational diabetes (GDM), where fetal exposure to a hyperglycemic, hyperinsulinemic, and/or hyperlipidemic gestational environment can provoke epigenetic changes that predispose offspring to various diseased conditions later in life. While it is now well established that offspring exposed to GDM have an increased risk of developing obesity, metabolic disorders, and/or cardiovascular disease in adult life, there are limited studies assessing the reproductive health of these offspring. This mini-review discusses the long-term effect of in utero exposure to GDM-associated adverse prenatal environment on the reproductive health of the offspring. Moreover, using evidence from various animal models and human epidemiological studies, this review offers molecular insight and understanding of how epigenetic reprogramming of genes culminates in reproductive dysfunction and the development of subfertility or infertility later in adult life.
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Affiliation(s)
- Niharika Sinha
- Reproductive and Developmental Sciences Program, East Lansing, Michigan 48824, USA
- Department of Animal Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Gretchen Lydia Walker
- Reproductive and Developmental Sciences Program, East Lansing, Michigan 48824, USA
- Department of Animal Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Aritro Sen
- Reproductive and Developmental Sciences Program, East Lansing, Michigan 48824, USA
- Department of Animal Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Correspondence: Aritro Sen, PhD, Reproductive and Developmental Sciences Program, 3013 Interdisciplinary Science & Technology Building, Michigan State University, 766 Service Rd, East Lansing, MI 48824, USA.
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204
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Mokarram P, Niknam M, Sadeghdoust M, Aligolighasemabadi F, Siri M, Dastghaib S, Brim H, Ashktorab H. PIWI interacting RNAs perspectives: a new avenues in future cancer investigations. Bioengineered 2021; 12:10401-10419. [PMID: 34723746 PMCID: PMC8809986 DOI: 10.1080/21655979.2021.1997078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As a currently identified small non-coding RNAs (ncRNAs) category, the PIWI-interacting RNAs (piRNAs) are crucial mediators of cell biology. The human genome comprises over 30.000 piRNA genes. Although considered a new field in cancer research, the piRNA pathway is shown by the existing evidence as an active pathway in a variety of different types of cancers with critical impacts on main aspects of cancer progression. Among the regulatory molecules that contribute to maintaining the dynamics of cancer cells, the P-element Induced WImpy testis (PIWI) proteins and piRNAs, as new players, have not been broadly studied so far. Therefore, the identification of cancer-related piRNAs and the assessment of target genes of piRNAs may lead to better cancer prevention and therapy strategies. This review articleaimed to highlight the role and function of piRNAs based on existing data. Understanding the role of piRNA in cancer may provide perspectives on their applications as particular biomarker signature in diagnosis in early stage, prognosis and therapeutic strategies.
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Affiliation(s)
- Pooneh Mokarram
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran,CONTACT Pooneh Mokarram Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Niknam
- Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammadamin Sadeghdoust
- Department of Internal Medicine, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Farnaz Aligolighasemabadi
- Department of Internal Medicine, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Dastghaib
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Brim
- Pathology and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, Dc, USA
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205
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Sellem E, Jammes H, Schibler L. Sperm-borne sncRNAs: potential biomarkers for semen fertility? Reprod Fertil Dev 2021; 34:160-173. [PMID: 35231268 DOI: 10.1071/rd21276] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Semen infertility or sub-fertility, whether in humans or livestock species, remains a major concern for clinicians and technicians involved in reproduction. Indeed, they can cause tragedies in human relationships or have a dramatic overall negative impact on the sustainability of livestock breeding. Understanding and predicting semen fertility issues is therefore crucial and quality control procedures as well as biomarkers have been proposed to ensure sperm fertility. However, their predictive values appeared to be too limited and additional relevant biomarkers are still required to diagnose sub-fertility efficiently. During the last decade, the study of molecular mechanisms involved in spermatogenesis and sperm maturation highlighted the regulatory role of a variety of small non-coding RNAs (sncRNAs) and led to the discovery that sperm sncRNAs comprise both remnants from spermatogenesis and post-testicular sncRNAs acquired through interactions with extracellular vesicles along epididymis. This has led to the hypothesis that sncRNAs may be a source of relevant biomarkers, associated either with sperm functionality or embryo development. This review aims at providing a synthetic overview of the current state of knowledge regarding implication of sncRNA in spermatogenesis defects and their putative roles in sperm maturation and embryo development, as well as exploring their use as fertility biomarkers.
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Affiliation(s)
- Eli Sellem
- R&D Department, ALLICE, 149 rue de Bercy, 75012 Paris, France
| | - Hélène Jammes
- Université Paris Saclay, UVSQ, INRAE, BREED, 78350 Jouy en Josas, France; and Ecole Nationale Vétérinaire d'Alfort, BREED, 94700 Maisons-Alfort, France
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206
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Verma S, Singh A, Varshney A, Chandru RA, Acharya M, Rajput J, Sangwan VS, Tiwari AK, Bhowmick T, Tiwari A. Infectious Keratitis: An Update on Role of Epigenetics. Front Immunol 2021; 12:765890. [PMID: 34917084 PMCID: PMC8669721 DOI: 10.3389/fimmu.2021.765890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
Epigenetic mechanisms modulate gene expression and function without altering the base sequence of DNA. These reversible, heritable, and environment-influenced mechanisms generate various cell types during development and orchestrate the cellular responses to external stimuli by regulating the expression of genome. Also, the epigenetic modifications influence common pathological and physiological responses including inflammation, ischemia, neoplasia, aging and neurodegeneration etc. In recent past, the field of epigenetics has gained momentum and become an increasingly important area of biomedical research As far as eye is concerned, epigenetic mechanisms may play an important role in many complex diseases such as corneal dystrophy, cataract, glaucoma, diabetic retinopathy, ocular neoplasia, uveitis, and age-related macular degeneration. Focusing on the epigenetic mechanisms in ocular diseases may provide new understanding and insights into the pathogenesis of complex eye diseases and thus can aid in the development of novel treatments for these diseases. In the present review, we summarize the clinical perspective of infectious keratitis, role of epigenetics in infectious keratitis, therapeutic potential of epigenetic modifiers and the future perspective.
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Affiliation(s)
- Sudhir Verma
- Department of Zoology, Deen Dayal Upadhyaya College (University of Delhi), New Delhi, India
| | - Aastha Singh
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Akhil Varshney
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - R Arun Chandru
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
| | - Manisha Acharya
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Jyoti Rajput
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
| | | | - Amit K Tiwari
- Department of Pharmacology and Experimental Therapeutics, The University of Toledo, Toledo, OH, United States
| | - Tuhin Bhowmick
- Pandorum Technologies Ltd., Bangalore Bioinnovation Centre, Bangalore, India
| | - Anil Tiwari
- Department of Cornea and Uveitis, Dr. Shroff's Charity Eye Hospital, New Delhi, India
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207
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RAP1/TERF2IP-A Multifunctional Player in Cancer Development. Cancers (Basel) 2021; 13:cancers13235970. [PMID: 34885080 PMCID: PMC8657031 DOI: 10.3390/cancers13235970] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary RAP1 (TERF2IP) is a member of the shelterin complex that protects telomeric DNA and plays a critical role in maintaining chromosome stability. However, mammalian RAP1 was recently found to have additional functions apart from telomeres, acting as a regulator of the NF-κB pathway and transcription factor, and has been suggested that they have putative roles in cancer development. Here, we focus on the main roles of RAP1 in different mechanisms of oncogenesis, progression, and chemoresistance, and consider the clinical significance of findings about its regulation and biological functions. Abstract Mammalian RAP1 (TERF2IP), the most conserved shelterin component, plays a pleiotropic role in the regulation of a variety of cellular processes, including cell metabolism, DNA damage response, and NF-κB signaling, beyond its canonical telomeric role. Moreover, it has been demonstrated to be involved in oncogenesis, progression, and chemoresistance in human cancers. Several mutations and different expression patterns of RAP1 in cancers have been reported. However, the functions and mechanisms of RAP1 in various cancers have not been extensively studied, suggesting the necessity of further investigations. In this review, we summarize the main roles of RAP1 in different mechanisms of cancer development and chemoresistance, with special emphasis on the contribution of RAP1 mutations, expression patterns, and regulation by non-coding RNA, and briefly discuss telomeric and non-telomeric functions.
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208
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Liu Y, Gan L, Cui DX, Yu SH, Pan Y, Zheng LW, Wan M. Epigenetic regulation of dental pulp stem cells and its potential in regenerative endodontics. World J Stem Cells 2021; 13:1647-1666. [PMID: 34909116 PMCID: PMC8641018 DOI: 10.4252/wjsc.v13.i11.1647] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/07/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
Regenerative endodontics (RE) therapy means physiologically replacing damaged pulp tissue and regaining functional dentin–pulp complex. Current clinical RE procedures recruit endogenous stem cells from the apical papilla, periodontal tissue, bone marrow and peripheral blood, with or without application of scaffolds and growth factors in the root canal space, resulting in cementum-like and bone-like tissue formation. Without the involvement of dental pulp stem cells (DPSCs), it is unlikely that functional pulp regeneration can be achieved, even though acceptable repair can be acquired. DPSCs, due to their specific odontogenic potential, high proliferation, neurovascular property, and easy accessibility, are considered as the most eligible cell source for dentin–pulp regeneration. The regenerative potential of DPSCs has been demonstrated by recent clinical progress. DPSC transplantation following pulpectomy has successfully reconstructed neurovascularized pulp that simulates the physiological structure of natural pulp. The self-renewal, proliferation, and odontogenic differentiation of DPSCs are under the control of a cascade of transcription factors. Over recent decades, epigenetic modulations implicating histone modifications, DNA methylation, and noncoding (nc)RNAs have manifested as a new layer of gene regulation. These modulations exhibit a profound effect on the cellular activities of DPSCs. In this review, we offer an overview about epigenetic regulation of the fate of DPSCs; in particular, on the proliferation, odontogenic differentiation, angiogenesis, and neurogenesis. We emphasize recent discoveries of epigenetic molecules that can alter DPSC status and promote pulp regeneration through manipulation over epigenetic profiles.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Lu Gan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Di-Xin Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Si-Han Yu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Yue Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Li-Wei Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Mian Wan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
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209
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Panyushev N, Okorokova L, Danilov L, Adonin L. Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus. Biomedicines 2021; 9:1736. [PMID: 34829966 PMCID: PMC8615465 DOI: 10.3390/biomedicines9111736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of biological processes remains unknown. The aim of this study was to identify the RE expression at different stages of embryogenesis. REs occupied 44% of genomic DNA of Strongylocentrotus purpuratus. The most prevalent among these elements were the unknown elements-in total, they contributed 78.5% of REs (35% in total genome occupancy). It was revealed that the transcription pattern of genes and REs changes significantly during gastrulation. Using the de novo transcriptome assembly, we showed that the expression of RE is independent of its copy number in the genome. We also identified copies that are expressed. Only active RE copies were used for mapping and quantification of RE expression in the single-cell RNA sequencing data. REs expression was observed in all cell lineages and they were detected as population markers. Moreover, the primary mesenchyme cell (PMC) line had the greatest diversity of REs among the markers. Our data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level.
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Affiliation(s)
- Nick Panyushev
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (N.P.); (L.O.)
| | - Larisa Okorokova
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (N.P.); (L.O.)
| | - Lavrentii Danilov
- St. Petersburg State University, Department of Genetics and Biotechnology, 199034 St. Petersburg, Russia;
| | - Leonid Adonin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
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210
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DNAJC3-AS1 Is Associated with Proliferation, Metastasis, and Poor Prognosis of Breast Cancer. DISEASE MARKERS 2021. [DOI: 10.1155/2021/3443474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objective. Long noncoding RNA DNAJC3-AS1 (DNAJC3-AS1) was a newly identified tumor-related lncRNA. The aim of the present study was to explore the prognostic value and diagnostic of DNAJC3-AS1 (DNAJC3-AS1) expression in breast cancer (BC) patients. Patients and Methods. The expression of DNAJC3-AS1 was detected in 170 BC tissues and matched normal breast samples by qRT-PCR. The diagnostic value of DNAJC3-AS1 was examined by receiver-operating characteristic (ROC) assays. The correlation of DNAJC3-AS1 with clinicopathological features and prognosis was also statistically analyzed. CCK-8 assays, colony formation assays, and Transwell assays were applied to examine the potential function of DNAJC3-AS1 on tumor progression. Western blot was used to examine the expression of EMT-related proteins. Results. The expression of DNAJC3-AS1 in BC specimens was higher than that in the adjacent nontumor tissues (
). Diagnostic assays revealed that DNAJC3-AS1 has considerable diagnostic accuracy, with an area under the ROC curve (AUC) of 0.7457 (
). High DNAJC3-AS1 expression was positively associated with lymph node metastasis (
) and clinical stage (
). A survival study revealed that patients with high DNAJC3-AS1 expression had shorter overall survival (
) and disease-free survival (
) than those with low DNAJC3-AS1 expression. More importantly, multivariate assays indicated that DNAJC3-AS1 was an independent prognostic factor in BC patients. Functional assays confirmed that silence of DNAJC3-AS1 distinctly suppressed the proliferation, metastasis, and EMT progress of BC cells. Conclusions. DNAJC3-AS1 may be a prognostic and diagnostic biomarker for BC patients.
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211
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Activation of FGD5-AS1 Promotes Progression of Cervical Cancer through Regulating BST2 to Inhibit Macrophage M1 Polarization. J Immunol Res 2021; 2021:5857214. [PMID: 34692852 PMCID: PMC8536446 DOI: 10.1155/2021/5857214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/04/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence has elucidated the biological function of lncRNAs in various tumors. FGD5 antisense RNA 1 (FGD5-AS1) is identified as a significant tumor regulator in malignancies. Up to now, the detailed function of FGD5-AS1 in cervical cancer and its underlying molecular mechanisms remain uninvestigated. Bone marrow stromal cell antigen 2 (BST2) can play critical roles in immune response, and the roles of BST2 in cervical cancer was explored currently. The level of FGD5-AS1 and BST2 was detected by qRT-PCR in cervical cancer cells. FGD5-AS1 and BST2 expression was significantly upregulated in cervical cancer cells. Then, the decrease of FGD5-AS1 greatly repressed cervical cancer cell growth in vitro. In addition, FGD5-AS1 silencing repressed BST2 expression and suppressed M2 macrophage polarization. Mechanistically, we confirmed that FGD5-AS1 sponged miR-129-5p to reduce its inhibition on BST2. Furthermore, lack of BST2 depressed cervical cancer cell growth, while inducing apoptosis. Loss of BST2 induced M1 macrophage polarization while blocking M2 macrophage polarization. For another, we demonstrated that FGD5-AS1-triggered M2 macrophage polarization was remarkably reversed by miR-129-5p via suppressing BST2. In conclusion, FGD5-AS1 induced M2 macrophage polarization via sponging miR-129-5p and modulating BST2, thus contributing to cervical cancer development. Our findings revealed FGD5-AS1/miR-129-5p/BST2 as a new potential target for cervical cancer.
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212
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He F, Ding G, Jiang W, Fan X, Zhu L. Effect of tumor-associated macrophages on lncRNA PURPL/miR-363/PDZD2 axis in osteosarcoma cells. Cell Death Discov 2021; 7:307. [PMID: 34686652 PMCID: PMC8536668 DOI: 10.1038/s41420-021-00700-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/13/2021] [Accepted: 09/27/2021] [Indexed: 01/20/2023] Open
Abstract
Tumor-associated macrophages (TAMs) are known to participate in osteosarcoma (OS) progression. As demonstrated in our previous research, miR-363 played a tumor inhibitory effect in OS cells via lowering the PDZ domain containing 2 (PDZD2) expression. The regulatory roles of TAMs on miR-363/PDZD2 and the internal mechanism relating to long noncoding RNA p53 upregulated regulator of P53 levels (lncRNA PURPL) are examined in this study. TAM-like macrophages were formed by inducing CD14+ peripheral blood mononuclear cells (PBMCs). The TAMs migration was detected after MG-63 cells transfected with miR-363 mimics or inhibitors. We then analyzed the regulatory activity of PURPL on miR-363 expression. We also tested the influences of PURPL overexpression/knockdown on MG-63 cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT), as well as TAMs migration. Silence in PDZD2 expression was used to confirm the effects of PURPL on MG-63 cells. We successfully induced TAM-like macrophages. MG-63 cells transfecting miR-363 mimics suppressed TAMs migration while transfecting a converse effect was seen in miR-363 inhibitor. TAMs raised PURPL expression in MG-63 cells, which was an upstream regulator of miR-363. Along with TAMs migration, PURPL overexpression promoted MG-63 cell proliferation, migration, invasion, and EMT. An opposite influence was seen due to the PURPL knockdown. The silence of PDZD2 weakened the influences of PURPL overexpression on MG-63 cells and TAMs migration. On modulating the PURPL/miR-363/PDZD2 axis, TAMs-promoted OS development might be achieved.
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Affiliation(s)
- Fan He
- Department of Orthopedics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 261 HuanSha Road, ShangCheng, HangZhou, ZheJiang, 310006, China.
| | - Guoming Ding
- Department of Orthopedics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 261 HuanSha Road, ShangCheng, HangZhou, ZheJiang, 310006, China
| | - Wu Jiang
- Department of Orthopedics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 261 HuanSha Road, ShangCheng, HangZhou, ZheJiang, 310006, China
| | - Xiaoliang Fan
- Department of Orthopedics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 261 HuanSha Road, ShangCheng, HangZhou, ZheJiang, 310006, China
| | - Liulong Zhu
- Department of Orthopedics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 261 HuanSha Road, ShangCheng, HangZhou, ZheJiang, 310006, China
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213
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Rincón-Riveros A, Morales D, Rodríguez JA, Villegas VE, López-Kleine L. Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions. Int J Mol Sci 2021; 22:11397. [PMID: 34768830 PMCID: PMC8583695 DOI: 10.3390/ijms222111397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.
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Affiliation(s)
- Andrés Rincón-Riveros
- Bioinformatics and Systems Biology Group, Universidad Nacional de Colombia, Bogotá 111221, Colombia;
| | - Duvan Morales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Josefa Antonia Rodríguez
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá 111221, Colombia;
| | - Victoria E. Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Liliana López-Kleine
- Department of Statistics, Faculty of Science, Universidad Nacional de Colombia, Bogotá 111221, Colombia
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214
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Zhu Q, Li S, Ji K, Zhou H, Luo C, Sui Y. Differentially expressed TUG1 and miR-145-5p indicate different severity of chronic heart failure and predict 2-year survival prognosis. Exp Ther Med 2021; 22:1362. [PMID: 34659508 PMCID: PMC8515550 DOI: 10.3892/etm.2021.10796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) and microRNAs (miRs) have critical roles in the progression of various diseases. The present study aimed to investigate the levels and clinical significance of lncRNA taurine upregulated gene 1 (TUG1) and miR-145-5p in patients with chronic heart failure (CHF) and explore their indicative value regarding disease severity. TUG1 and miR-145-5p levels were detected by reverse-transcription quantitative PCR. Correlations were examined using Pearson's correlation analysis. Receiver operating characteristic analysis was used to evaluate the diagnostic value of TUG1, miR-145-5p and brain natriuretic peptide (BNP). Survival analysis was performed by the Kaplan-Meier method. Cox regression analysis was used to evaluate the prognostic value of TUG1 and miR-145-5p. The levels of interleukin-6 and tumor necrosis factor-α in serum were detected by ELISA. The results indicated that TUG1 was upregulated and miR-145-5p was downregulated in patients with CHF and they were negatively correlated. TUG1 and miR-145-5p were associated with the left ventricle ejection fraction and were able to indicate the severity of CHF. Serum TUG1 and miR-145-5p had a certain diagnostic value and the combination of BNP, TUG1 and miR-145-5p had high diagnostic accuracy. TUG1 and miR-145-5p were closely associated with overall survival and may function as independent prognostic biomarkers for patients with CHF. In addition, TUG1 and miR-145-5p levels were markedly correlated with inflammation in CHF. Upregulated TUG1 and downregulated miR-145-5p may indicate the severity of CHF, may serve as diagnostic and prognostic biomarkers and may be involved in CHF progression by regulating inflammatory responses.
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Affiliation(s)
- Qinwei Zhu
- Department of Emergency, Weifang Hospital of Traditional Chinese Medicine, Weifang, Shandong 261041, P.R. China
| | - Shuanghong Li
- Department of Emergency, Weifang Hospital of Traditional Chinese Medicine, Weifang, Shandong 261041, P.R. China
| | - Kui Ji
- Department of Emergency, Weifang Hospital of Traditional Chinese Medicine, Weifang, Shandong 261041, P.R. China
| | - Hongyuan Zhou
- Department of Emergency, Weifang Hospital of Traditional Chinese Medicine, Weifang, Shandong 261041, P.R. China
| | - Chuanchao Luo
- Department of Emergency, Weifang Hospital of Traditional Chinese Medicine, Weifang, Shandong 261041, P.R. China
| | - Yana Sui
- Department of Emergency, Weifang Hospital of Traditional Chinese Medicine, Weifang, Shandong 261041, P.R. China
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215
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Lee AM, Ferdjallah A, Moore E, Kim DC, Nath A, Greengard E, Huang RS. Long Non-Coding RNA ANRIL as a Potential Biomarker of Chemosensitivity and Clinical Outcomes in Osteosarcoma. Int J Mol Sci 2021; 22:ijms222011168. [PMID: 34681828 PMCID: PMC8538287 DOI: 10.3390/ijms222011168] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/12/2021] [Indexed: 01/06/2023] Open
Abstract
Osteosarcoma has a poor prognosis due to chemo-resistance and/or metastases. Increasing evidence shows that long non-coding RNAs (lncRNAs) can play an important role in drug sensitivity and cancer metastasis. Using osteosarcoma cell lines, we identified a positive correlation between the expression of a lncRNA and ANRIL, and resistance to two of the three standard-of-care agents for treating osteosarcoma-cisplatin and doxorubicin. To confirm the potential role of ANRIL in chemosensitivity, we independently inhibited and over-expressed ANRIL in osteosarcoma cell lines followed by treatment with either cisplatin or doxorubicin. Knocking-down ANRIL in SAOS2 resulted in a significant increase in cellular sensitivity to both cisplatin and doxorubicin, while the over-expression of ANRIL in both HOS and U2OS cells led to an increased resistance to both agents. To investigate the clinical significance of ANRIL in osteosarcoma, we assessed ANRIL expression in relation to clinical phenotypes using the osteosarcoma data from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) dataset. Higher ANRIL expression was significantly associated with increased rates of metastases at diagnosis and death and was a significant predictor of reduced overall survival rate. Collectively, our results suggest that the lncRNA ANRIL can be a chemosensitivity and prognosis biomarker in osteosarcoma. Furthermore, reducing ANRIL expression may be a therapeutic strategy to overcome current standard-of-care treatment resistance.
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Affiliation(s)
- Adam M. Lee
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (A.M.L.); (D.C.K.)
| | - Asmaa Ferdjallah
- Department of Pediatrics, Hematology & Oncology, University of Minnesota, Minneapolis, MN 55455, USA; (A.F.); (E.G.)
| | - Elise Moore
- Department of Natural Sciences, Zanvyl Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Daniel C. Kim
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (A.M.L.); (D.C.K.)
| | - Aritro Nath
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Monrovia, CA 91007, USA;
| | - Emily Greengard
- Department of Pediatrics, Hematology & Oncology, University of Minnesota, Minneapolis, MN 55455, USA; (A.F.); (E.G.)
| | - R. Stephanie Huang
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (A.M.L.); (D.C.K.)
- Correspondence: ; Tel.: +1-612-625-1372
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216
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Chandra K, Banerjee A, Das M. Epigenetic and transcriptional regulation of GnRH gene under altered metabolism and ageing. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00374-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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217
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Correia CCM, Rodrigues LF, de Avila Pelozin BR, Oliveira EM, Fernandes T. Long Non-Coding RNAs in Cardiovascular Diseases: Potential Function as Biomarkers and Therapeutic Targets of Exercise Training. Noncoding RNA 2021; 7:ncrna7040065. [PMID: 34698215 PMCID: PMC8544698 DOI: 10.3390/ncrna7040065] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Despite advances in treatments and therapies, cardiovascular diseases (CVDs) remain one of the leading causes of death worldwide. The discovery that most of the human genome, although transcribed, does not encode proteins was crucial for focusing on the potential of long non-coding RNAs (lncRNAs) as essential regulators of cell function at the epigenetic, transcriptional, and post-transcriptional levels. This class of non-coding RNAs is related to the pathophysiology of the cardiovascular system. The different expression profiles of lncRNAs, in different contexts of CVDs, change a great potential in their use as a biomarker and targets of therapeutic intervention. Furthermore, regular physical exercise plays a protective role against CVDs; on the other hand, little is known about its underlying molecular mechanisms. In this review, we look at the accumulated knowledge on lncRNAs and their functions in the cardiovascular system, focusing on the cardiovascular pathology of arterial hypertension, coronary heart disease, acute myocardial infarction, and heart failure. We discuss the potential of these molecules as biomarkers for clinical use, their limitations, and how the manipulation of the expression profile of these transcripts through physical exercise can begin to be suggested as a strategy for the treatment of CVDs.
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Affiliation(s)
- Camila Caldas Martins Correia
- Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-030, Brazil;
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Luis Felipe Rodrigues
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Bruno Rocha de Avila Pelozin
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Edilamar Menezes Oliveira
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Tiago Fernandes
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
- Correspondence: ; Tel.: + 55-11-2648-1566 (ext. 05508-030)
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218
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Rodriguez FD. Targeting Epigenetic Mechanisms to Treat Alcohol Use Disorders (AUD). Curr Pharm Des 2021; 27:3252-3272. [PMID: 33535943 PMCID: PMC8778698 DOI: 10.2174/1381612827666210203142539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/08/2020] [Indexed: 12/04/2022]
Abstract
BACKGROUND The impact of abusive alcohol consumption on human health is remarkable. According to the World Health Organization (WHO), approximately 3.3 million people die annually because of harmful alcohol consumption (the figure represents around 5.9% of global deaths). Alcohol Use Disorder (AUD) is a chronic disease where individuals exhibit compulsive alcohol drinking and present negative emotional states when they do not drink. In the most severe manifestations of AUD, the individuals lose control over intake despite a decided will to stop drinking. Given the multiple faces and the specific forms of this disease, the term AUD often appears in the plural (AUDs). Since only a few approved pharmacological treatments are available to treat AUD and they do not apply to all individuals or AUD forms, the search for compounds that may help to eliminate the burden of the disease and complement other therapeutical approaches is necessary. METHODS This work reviews recent research focused on the involvement of epigenetic mechanisms in the pathophysiology of AUD. Excessive drinking leads to chronic and compulsive consumption that eventually damages the organism. The central nervous system is a key target and is the focus of this study. The search for the genetic and epigenetic mechanisms behind the intricated dysregulation induced by ethanol will aid researchers in establishing new therapy approaches. CONCLUSION Recent findings in the field of epigenetics are essential and offer new windows for observation and research. The study of small molecules that inhibit key epienzymes involved in nucleosome architecture dynamics is necessary in order to prove their action and specificity in the laboratory and to test their effectivity and safety in clinical trials with selected patients bearing defined alterations caused by ethanol.
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Affiliation(s)
- F. David Rodriguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemistry, University of Salamanca and Group GIR BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
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219
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Grilo LF, Tocantins C, Diniz MS, Gomes RM, Oliveira PJ, Matafome P, Pereira SP. Metabolic Disease Programming: From Mitochondria to Epigenetics, Glucocorticoid Signalling and Beyond. Eur J Clin Invest 2021; 51:e13625. [PMID: 34060076 DOI: 10.1111/eci.13625] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Embryonic and foetal development are critical periods of development in which several environmental cues determine health and disease in adulthood. Maternal conditions and an unfavourable intrauterine environment impact foetal development and may programme the offspring for increased predisposition to metabolic diseases and other chronic pathologic conditions throughout adult life. Previously, non-communicable chronic diseases were only associated with genetics and lifestyle. Now the origins of non-communicable chronic diseases are associated with early-life adaptations that produce long-term dysfunction. Early-life environment sets the long-term health and disease risk and can span through multiple generations. Recent research in developmental programming aims at identifying the molecular mechanisms responsible for developmental programming outcomes that impact cellular physiology and trigger adulthood disease. The identification of new therapeutic targets can improve offspring's health management and prevent or overcome adverse consequences of foetal programming. This review summarizes recent biomedical discoveries in the Developmental Origins of Health and Disease (DOHaD) hypothesis and highlight possible developmental programming mechanisms, including prenatal structural defects, metabolic (mitochondrial dysfunction, oxidative stress, protein modification), epigenetic and glucocorticoid signalling-related mechanisms suggesting molecular clues for the causes and consequences of programming of increased susceptibility of offspring to metabolic disease after birth. Identifying mechanisms involved in DOHaD can contribute to early interventions in pregnancy or early childhood, to re-set the metabolic homeostasis and break the chain of subsequent events that could lead to the development of disease.
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Affiliation(s)
- Luís F Grilo
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,PhD Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Carolina Tocantins
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Mariana S Diniz
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Rodrigo Mello Gomes
- Department of Physiological Sciences, Biological Sciences Institute, Federal University of Goiás, Goiânia, Brazil
| | - Paulo J Oliveira
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Paulo Matafome
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research (iCBR) and Institute of Physiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Department of Complementary Sciences, Instituto Politécnico de Coimbra, Coimbra Health School (ESTeSC), Coimbra, Portugal
| | - Susana P Pereira
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Laboratory of Metabolism and Exercise (LametEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sport, University of Porto, Porto, Portugal
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220
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Duclot F, Kabbaj M. Epigenetics of Aggression. Curr Top Behav Neurosci 2021; 54:283-310. [PMID: 34595741 DOI: 10.1007/7854_2021_252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Aggression is a complex behavioral trait modulated by both genetic and environmental influences on gene expression. By controlling gene expression in a reversible yet potentially lasting manner in response to environmental stimulation, epigenetic mechanisms represent prime candidates in explaining both individual differences in aggression and the development of elevated aggressive behaviors following life adversity. In this manuscript, we review the evidence for an epigenetic basis in the development and expression of aggression in both humans and related preclinical animal models. In particular, we discuss reports linking DNA methylation, histone post-translational modifications, as well as non-coding RNA, to the regulation of a variety of genes implicated in the neurobiology of aggression including neuropeptides, the serotoninergic and dopaminergic systems, and stress response related systems. While clinical reports do reveal interesting patterns of DNA methylation underlying individual differences and experience-induced aggressive behaviors, they do, in general, face the challenge of linking peripheral observations to central nervous system regulations. Preclinical studies, on the other hand, provide detailed mechanistic insights into the epigenetic reprogramming of gene expression following life adversities. Although the functional link to aggression remains unclear in most, these studies together do highlight the involvement of epigenetic events driven by DNA methylation, histone modifications, and non-coding RNA in the neuroadaptations underlying the development and expression of aggression.
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Affiliation(s)
- Florian Duclot
- Department of Biomedical Sciences and Program in Neuroscience, Florida State University, Tallahassee, FL, USA.
| | - Mohamed Kabbaj
- Department of Biomedical Sciences and Program in Neuroscience, Florida State University, Tallahassee, FL, USA.
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221
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Zhao J, Wu F, Yang J. A novel long non-coding RNA TTN-AS1/microRNA-589-5p/FOXP1 positive feedback loop increases the proliferation, migration and invasion of pancreatic cancer cell lines. Oncol Lett 2021; 22:794. [PMID: 34584569 PMCID: PMC8461757 DOI: 10.3892/ol.2021.13055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/12/2021] [Indexed: 12/19/2022] Open
Abstract
Numerous reports have found that long non-coding (lnc) RNAs were associated with pancreatic cancer (PC) initiation and development. The lncRNA titin antisense RNA 1 (TTN-AS1) was identified as a tumor promoter in certain types of cancer; however, its role and mechanism in PC remain unclear. The aim of the present study was to investigate the role of TTN-AS1 in PC and elucidate the underlying mechanism. Reverse transcription-quantitative PCR analysis was performed to examine the mRNA expression level of TTN-AS1, microRNA(miR)-589-5p and forkhead box protein 1 (FOXP1). Knockdown experiments were performed to examine the effect of TTN-AS1 on PC cell proliferation, migration and invasion. Luciferase reporter assays validated the binding of miR-589-5p to TTN-AS1 and FOXP1. Chromatin immunoprecipitation and luciferase reporter assays confirmed the binding ability of FOXP1 to the TTN-AS1 promoter. As a result, TTN-AS1 and FOXP1 were found to be upregulated in PC cell lines and tissues, while miR-589-5p was expressed at low levels. Knockdown experiments indicated the suppressive effect of TTN-AS1 knockdown on cell proliferation, migration and invasion in PC cell lines. Further mechanistic research uncovered that TTN-AS1 functioned as a molecular sponge for miR-589-5p and its mRNA expression level in PC tissues was inversely associated with that of miR-589-5p. Furthermore, miR-589-5p was confirmed to target FOXP1. Of note, it was discovered that FOXP1 transcriptionally activated TTN-AS1 mRNA expression level. Taken together, the findings of the present study demonstrated that the new TTN-AS1/miR-589-5p/FOXP1 feedback loop may play an important role in PC.
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Affiliation(s)
- Jing Zhao
- Department of Gastroenterology, Liyang People's Hospital, Liyang, Jiangsu 213300, P.R. China
| | - Fang Wu
- Department of Gastroenterology, Wuxi People's Hospital, Wuxi, Jiangsu 214023, P.R. China
| | - Jun Yang
- Department of Gastroenterology, Liyang People's Hospital, Liyang, Jiangsu 213300, P.R. China
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Targeting Drug Chemo-Resistance in Cancer Using Natural Products. Biomedicines 2021; 9:biomedicines9101353. [PMID: 34680470 PMCID: PMC8533186 DOI: 10.3390/biomedicines9101353] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer is one of the leading causes of death globally. The development of drug resistance is the main contributor to cancer-related mortality. Cancer cells exploit multiple mechanisms to reduce the therapeutic effects of anticancer drugs, thereby causing chemotherapy failure. Natural products are accessible, inexpensive, and less toxic sources of chemotherapeutic agents. Additionally, they have multiple mechanisms of action to inhibit various targets involved in the development of drug resistance. In this review, we have summarized the basic research and clinical applications of natural products as possible inhibitors for drug resistance in cancer. The molecular targets and the mechanisms of action of each natural product are also explained. Diverse drug resistance biomarkers were sensitive to natural products. P-glycoprotein and breast cancer resistance protein can be targeted by a large number of natural products. On the other hand, protein kinase C and topoisomerases were less sensitive to most of the studied natural products. The studies discussed in this review will provide a solid ground for scientists to explore the possible use of natural products in combination anticancer therapies to overcome drug resistance by targeting multiple drug resistance mechanisms.
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Chen S, Liu D, Zhou Z, Qin S. Role of long non-coding RNA H19 in the development of osteoporosis. Mol Med 2021; 27:122. [PMID: 34583640 PMCID: PMC8480040 DOI: 10.1186/s10020-021-00386-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/22/2021] [Indexed: 12/28/2022] Open
Abstract
Background Osteoporosis is a widespread and serious metabolic bone disease. At present, revealing the molecular mechanisms of osteoporosis and developing effective prevention and treatment methods are of great significance to health worldwide. LncRNA is a non-coding RNA peptide chain with more than 200 nucleotides. Researchers have identified many lncRNAs implicated in the development of diseases and lncRNA H19 is an example. Results A large amount of evidence supports the fact that long non-coding RNA (lncRNA) genes, such as H19, have multiple, far-reaching effects on various biological functions. It has been found that lncRNA H19 has a role in the regulation of different types of cells in the body including the osteoblasts, osteocytes, and osteoclasts found in bones. Therefore, it can be postulated that lncRNA H19 affects the incidence and development of osteoporosis. Conclusion The prospect of targeting lncRNA H19 in the treatment of osteoporosis is promising because of the effects that lncRNA H19 has on the process of osteogenic differentiation. In this review, we summarize the molecular pathways and mechanisms of lncRNA H19 in the pathogenesis of osteoporosis and summarize the research progress of targeting H19 as a treatment option. Research is emerging that explores more effective treatment possibilities for bone metabolism diseases using molecular targets.
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Affiliation(s)
- Senxiang Chen
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Da Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.
| | - Zimo Zhou
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Sen Qin
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
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Romanelli MN, Borgonetti V, Galeotti N. Dual BET/HDAC inhibition to relieve neuropathic pain: Recent advances, perspectives, and future opportunities. Pharmacol Res 2021; 173:105901. [PMID: 34547384 DOI: 10.1016/j.phrs.2021.105901] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Despite the intense research on developing new therapies for neuropathic pain states, available treatments have limited efficacy and unfavorable safety profiles. Epigenetic alterations have a great influence on the development of cancer and neurological diseases, as well as neuropathic pain. Histone acetylation has prevailed as one of the well investigated epigenetic modifications in these diseases. Altered spinal activity of histone deacetylase (HDAC) and Bromo and Extra terminal domain (BET) have been described in neuropathic pain models and restoration of these aberrant epigenetic modifications showed pain-relieving activity. Over the last decades HDACs and BETs have been the focus of drug discovery studies, leading to the development of numerous small-molecule inhibitors. Clinical trials to evaluate their anticancer activity showed good efficacy but raised toxicity concerns that limited translation to the clinic. To maximize activity and minimize toxicity, these compounds can be applied in combination of sub-maximal doses to produce additive or synergistic interactions (combination therapy). Recently, of particular interest, dual BET/HDAC inhibitors (multi-target drugs) have been developed to assure simultaneous modulation of BET and HDAC activity by a single molecule. This review will summarize the most recent advances with these strategies, describing advantages and limitations of single drug treatment vs combination regimens. This review will also provide a focus on dual BET/HDAC drug discovery investigations as future therapeutic opportunity for human therapy of neuropathic pain.
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Affiliation(s)
- Maria Novella Romanelli
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Vittoria Borgonetti
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology and Toxicology, University of Florence, Viale G. Pieraccini 6, 50139 Florence, Italy
| | - Nicoletta Galeotti
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology and Toxicology, University of Florence, Viale G. Pieraccini 6, 50139 Florence, Italy.
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225
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Yang C, Wang K, Liang Q, Tian TT, Zhong Z. Role of NSD1 as potential therapeutic target in tumor. Pharmacol Res 2021; 173:105888. [PMID: 34536546 DOI: 10.1016/j.phrs.2021.105888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/29/2022]
Abstract
Nuclear receptor binding SET Domain Protein 1 (NSD1) is a bifunctional transcriptional regulatory protein that encodes histone methyltransferase. Mono- and di-methylation of H3K36 by NSD1 is mainly primarily involved in the regulation of gene expression, DNA repair, alternative splicing, and other important biological processes. Many types of cancers, including acute myelogenous leukemia (AML), liver cancer, lung cancer, endometrial carcinoma, colorectal cancer, and pancreatic cancer, are associated with NSD1 fusion, missense mutation, nonsense mutation, silent mutation, deletion, and insertion of frameshift, and deletion in a frame. Therefore, targeting NSD1 may be a potential strategy for tumor therapy. An in-depth study of the structure and biological activities of NSD1 sets the groundwork for improving tumor therapy and creating NSD1 inhibitors. This article emphasizes the role of NSD1 in tumorigenesis and the development of NSD1 targeted small-molecule inhibitors.
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Affiliation(s)
- Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, Zhejiang Province 316022, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Qilian Liang
- Oncology Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province 524001, China
| | - Tian-Tian Tian
- Center for Biological Science and Technology, Beijing Normal University, Zhuhai, Guangdong Province 519087, China.
| | - Zhangfeng Zhong
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China.
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226
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A New Specific and Sensitive RT-qPCR Method Based on Splinted 5' Ligation for the Quantitative Detection of RNA Species Shorter than microRNAs. Noncoding RNA 2021; 7:ncrna7030059. [PMID: 34564321 PMCID: PMC8482087 DOI: 10.3390/ncrna7030059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/27/2022] Open
Abstract
Recently, we discovered a new family of unusually short RNAs mapping to 5.8S ribosomal RNA (rRNA) and which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. To confirm these small RNA-sequencing (RNA-Seq) data, validate the existence of the two overly abundant doRNAs-the minimal core 12-nt doRNA sequence and its + 1-nt variant bearing a 5' Cytosine, C-doRNA-and streamline their analysis, we developed a new specific and sensitive splinted 5' ligation reverse transcription (RT)-quantitative polymerase chain reaction (qPCR) method. This method is based on a splint-assisted ligation of an adapter to the 5' end of doRNAs, followed by RT-qPCR amplification and quantitation. Our optimized protocol, which may discriminate between doRNA, C-doRNA, mutated and precursor sequences, can accurately detect as low as 240 copies and is quantitatively linear over a range of 7 logs. This method provides a unique tool to expand and facilitate studies exploring the molecular and cellular biology of RNA species shorter than microRNAs.
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227
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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228
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Ren J, Xu N, Zhou R, Huang F, Zhang H, Li W. Long non-coding RNA PCED1B antisense RNA 1 promotes gastric cancer progression via modulating microRNA-215-3p / C-X-C motif chemokine receptor 1 axis. Bioengineered 2021; 12:6083-6095. [PMID: 34516330 PMCID: PMC8806612 DOI: 10.1080/21655979.2021.1971503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) emerge as vital modulators and tissue-specific biomarkers of multiple cancers, including gastric cancer (GC). Instead, the expression characteristics, biological function and molecular mechanism of lncRNA PCED1B antisense RNA 1 (PCED1B-AS1) in GC await more elaboration. In this study, 48 cases of GC tissues and matched non-cancerous tissues were collected, and PCED1B-AS1, microRNA-215-3p (miR-215-3p) and C-X-C motif chemokine receptor 1 (CXCR1) expression levels were detected by qRT-PCR. Besides, CCK-8, EdU, Transwell and Western blot assays were conducted to assess the impact of PCED1B-AS1 or miR-215-3p on cell growth, migration, invasion and epithelial-mesenchymal transition (EMT). The interaction between genes was verified by bioinformatics analysis, rna immunoprecitipation (RIP) and dual-luciferase reporter gene assays. We demonstrated that, PCED1B-AS1 expression level was raised in GC tissues and cell lines, and increased expression of PCED1B-AS1 was in association with tumor size, TNM stage and lymph node metastasis in GC patients. Additionally, PCED1B-AS1 overexpression promoted GC cells proliferation, migration, invasion and EMT, and miR-215-3p overexpression counteracted the biological effects of PCED1B-AS1. Mechanistically, PCED1B-AS1 specifically inhibited miR-215-3p expressions, thus up-regulating CXCR1 expressions. In conclusion, PCED1B-AS1 accelerates GC progression via adsorbing miR-215-3p and up-regulating CXCR1, indicating that PCED1B-AS1 is a novel therapeutic target for treating GC.
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Affiliation(s)
- Junyu Ren
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ning Xu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruize Zhou
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fengchang Huang
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hongbin Zhang
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wenliang Li
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
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229
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Liu W, Yu M, Chen F, Wang L, Ye C, Chen Q, Zhu Q, Xie D, Shao M, Yang L. A novel delivery nanobiotechnology: engineered miR-181b exosomes improved osteointegration by regulating macrophage polarization. J Nanobiotechnology 2021; 19:269. [PMID: 34493305 PMCID: PMC8424816 DOI: 10.1186/s12951-021-01015-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background Many patients suffer from implant loosening after the implantation of titanium alloy caused by immune response to the foreign bodies and this could inhibit the following osteogenesis, which could possibly give rise to aseptic loosening and poor osteointegration while there is currently no appropriate solution in clinical practice. Exosome (Exo) carrying miRNA has been proven to be a suitable nanocarrier for solving this problem. In this study, we explored whether exosomes overexpressing miR-181b (Exo-181b) could exert beneficial effect on promoting M2 macrophage polarization, thus inhibiting inflammation as well as promoting osteogenesis and elaborated the underlying mechanism in vitro. Furthermore, we aimed to find whether Exo-181b could enhance osteointegration. Results In vitro, we firstly verified that Exo-181b significantly enhanced M2 polarization and inhibited inflammation by suppressing PRKCD and activating p-AKT. Then, in vivo, we verified that Exo-181b enhanced M2 polarization, reduced the inflammatory response and enhanced osteointegration. Also, we verified that the enhanced M2 polarization could indirectly promote the migration and osteogenic differentiation by secreting VEGF and BMP-2 in vitro. Conclusions Exo-181b could suppress inflammatory response by promoting M2 polarization via activating PRKCD/AKT signaling pathway, which further promoting osteogenesis in vitro and promote osteointegration in vivo. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-01015-y.
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Affiliation(s)
- Wei Liu
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China
| | - Muyu Yu
- Department of Endocrinology and Metabolism, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Medical Centre of Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Key Clinic Centre of Metabolism Disease, Shanghai Institute for Diabetes, Shanghai, China
| | - Feng Chen
- Department of Orthopaedics, Shanghai Fengxian Central Hospital, Branch of the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, 201400, People's Republic of China.,College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Longqing Wang
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China
| | - Cheng Ye
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China
| | - Qing Chen
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China
| | - Qi Zhu
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China
| | - Dong Xie
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China
| | - Mingzhe Shao
- Department of Vascular Surgery, Multidisciplinary Collaboration Group of Diabetic Foot, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Lili Yang
- Spine Center, Department of Orthopaedics, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, 200003, Shanghai, China.
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230
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Wu W, Klockow JL, Zhang M, Lafortune F, Chang E, Jin L, Wu Y, Daldrup-Link HE. Glioblastoma multiforme (GBM): An overview of current therapies and mechanisms of resistance. Pharmacol Res 2021; 171:105780. [PMID: 34302977 PMCID: PMC8384724 DOI: 10.1016/j.phrs.2021.105780] [Citation(s) in RCA: 219] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 12/21/2022]
Abstract
Glioblastoma multiforme (GBM) is a WHO grade IV glioma and the most common malignant, primary brain tumor with a 5-year survival of 7.2%. Its highly infiltrative nature, genetic heterogeneity, and protection by the blood brain barrier (BBB) have posed great treatment challenges. The standard treatment for GBMs is surgical resection followed by chemoradiotherapy. The robust DNA repair and self-renewing capabilities of glioblastoma cells and glioma initiating cells (GICs), respectively, promote resistance against all current treatment modalities. Thus, durable GBM management will require the invention of innovative treatment strategies. In this review, we will describe biological and molecular targets for GBM therapy, the current status of pharmacologic therapy, prominent mechanisms of resistance, and new treatment approaches. To date, medical imaging is primarily used to determine the location, size and macroscopic morphology of GBM before, during, and after therapy. In the future, molecular and cellular imaging approaches will more dynamically monitor the expression of molecular targets and/or immune responses in the tumor, thereby enabling more immediate adaptation of tumor-tailored, targeted therapies.
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Affiliation(s)
- Wei Wu
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Jessica L Klockow
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Michael Zhang
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA; Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Famyrah Lafortune
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Edwin Chang
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Linchun Jin
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL 32611, USA
| | - Yang Wu
- Department of Neuropathology, Institute of Pathology, Technical University of Munich, Munich, Bayern 81675, Germany
| | - Heike E Daldrup-Link
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA.
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231
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Zhao S, Kong X, Wu X. RNAi-based immunity in insects against baculoviruses and the strategies of baculoviruses involved in siRNA and miRNA pathways to weaken the defense. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104116. [PMID: 33991532 DOI: 10.1016/j.dci.2021.104116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Protection against viral infection in hosts concerns diverse cellular and molecular mechanisms, among which RNA interference (RNAi) response is a vital one. Small interfering RNAs (siRNAs), microRNAs (miRNAs) and PIWI interacting RNAs (piRNAs) are primary categories of small RNAs involved in RNAi response, playing significant roles in restraining viral invasion. However, during a long-term coevolution, viruses have gained the ability to evade, avoid, or suppress antiviral immunity to ensure efficient replication and transmission. Baculoviruses are enveloped, insect-pathogenic viruses with double-stranded circular DNA genomes, which encode suppressors of siRNA pathway and miRNAs targeting immune-related genes to mask the antiviral activity of their hosts. This review summarized recent findings for the RNAi-based antiviral immunity in insects as well as the strategies that baculoviruses exploit to break the shield of host siRNA pathway, and hijack cellular miRNAs or encode their own miRNAs that regulate both viral and cellular gene expression to create a favorable environment for viral infection.
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Affiliation(s)
- Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Xiangshuo Kong
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China.
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232
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Karimi H, Boroujeni PB, Sabbaghian M, Meybodi AM. Gene Alterations and Expression Spectrum of NANOS3 in Nonobstructive Azoospermia. Reprod Sci 2021; 29:92-99. [PMID: 34417763 DOI: 10.1007/s43032-021-00680-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/22/2021] [Indexed: 10/20/2022]
Abstract
Nanos3, a zinc finger RNA-binding protein, suppresses the apoptosis in primordial germ cells (PGCs) during migration to gonads and maintains the PGC population. The genetic variations and expression of NANOS3 in patients with non-obstructive azoospermia (NOA) were evaluated in this study. The study included 100 idiopathic infertile men with NOA and 100 fertile men as the as the case and control groups, respectively. NANOS3 gene variations were analyzed using the standard polymerase chain reaction (PCR) and sequencing. For mRNA and protein expression analysis, testicular biopsy specimens from 27 patients including 9 obstructive azoospermia (OA), 9 maturation arrest (MA), and 9 Sertoli cell-only syndromes (SCOS) were collected and evaluated using the real-time PCR technique and immunohistochemistry. Although the evaluation of the 5`UTR regulatory region has shown the significant difference in the numbers of TG repeats in rs11182456 between groups, the odd ratio was not strong enough to consider that as a certain risk factor lead to azoospermia and infertility. Meanwhile, NANOS3 expression at mRNA level had a significant difference among OA, SCOS, and MA groups.
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Affiliation(s)
- Hamideh Karimi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Parnaz Borjian Boroujeni
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Marjan Sabbaghian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. .,Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, 12 Hafez St, Banihashem St, Resalat St, PO Box 19395-4644, Tehran, Iran.
| | - Anahita Mohseni Meybodi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. .,Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, 12 Hafez St, Banihashem St, Resalat St, PO Box 19395-4644, Tehran, Iran. .,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada. .,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.
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233
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Leo L, Colonna Romano N. Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease. Int J Mol Sci 2021; 22:ijms22168809. [PMID: 34445507 PMCID: PMC8395756 DOI: 10.3390/ijms22168809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation.
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234
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Molecular epigenetic dynamics in breast carcinogenesis. Arch Pharm Res 2021; 44:741-763. [PMID: 34392501 DOI: 10.1007/s12272-021-01348-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Breast cancer has become one of the most common dreadful diseases that target women across the globe. The most obvious reasons we associate with it are either genetic mutations or dysregulation of pathways. However, there is yet another domain that has a significant role in influencing the genetic mutations and pathways. Epigenetic mechanisms influence these pathways either independently or in association with genetic mutations, thereby expediting the process of breast carcinogenesis. Breast cancer is governed by various transduction pathways such as PI3K/AKT/mTOR, NOTCH, β Catenin, NF-kB, Hedgehog, etc. There are many proteins as well that serve to be tumor suppressors but somehow lose their ability to function. This may be because of either genetic mutation or a process that represses their function. Apart from these, there are a lot of individual factors like puberty, breastfeeding, abortion, parity, circadian rhythm, alcohol consumption, pollutants, and obesity that drive these mutations and hence alter the pathways. Epigenetic mechanisms like DNA methylation, histone modifications, and lncRNAs directly or indirectly bring alterations in the proteins that are involved in the pathways. They do this by either promoting the transcription of genes or by repressing it at the ground genetic level that advances breast carcinogenesis. Epigenetics precedes genetic mutation in driving carcinogenesis and so, it needs to be explored further to diversify the possibilities of target specific treatments. In this review, the general role of DNA methylation, histone modification, and lncRNAs in breast cancer and their role in influencing the oncogenic signaling pathways along with the various factors governing them have been discussed for a better understanding of the role of epigenetics in breast carcinogenesis.
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235
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Akbari B, Ghahri-Saremi N, Soltantoyeh T, Hadjati J, Ghassemi S, Mirzaei HR. Epigenetic strategies to boost CAR T cell therapy. Mol Ther 2021; 29:2640-2659. [PMID: 34365035 DOI: 10.1016/j.ymthe.2021.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/19/2021] [Accepted: 07/31/2021] [Indexed: 02/08/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy has led to a paradigm shift in cancer immunotherapy, but still several obstacles limit CAR T cell efficacy in cancers. Advances in high-throughput technologies revealed new insights into the role that epigenetic reprogramming plays in T cells. Mechanistic studies as well as comprehensive epigenome maps revealed an important role for epigenetic remodeling in T cell differentiation. These modifications shape the overall immune response through alterations in T cell phenotype and function. Here, we outline how epigenetic modifications in CAR T cells can overcome barriers limiting CAR T cell effectiveness, particularly in immunosuppressive tumor microenvironments. We also offer our perspective on how selected epigenetic modifications can boost CAR T cells to ultimately improve the efficacy of CAR T cell therapy.
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Affiliation(s)
- Behnia Akbari
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Navid Ghahri-Saremi
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Tahereh Soltantoyeh
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Jamshid Hadjati
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Saba Ghassemi
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran.
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236
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Zeng C, Tsoi LC, Gudjonsson JE. Dysregulated epigenetic modifications in psoriasis. Exp Dermatol 2021; 30:1156-1166. [PMID: 33756010 DOI: 10.1111/exd.14332] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/08/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The observed incidence of psoriasis has been gradually increasing over time (J Am Acad Dermatol, 03, 2009, 394), but the underlying pathogenic factors have remained unclear. Recent studies suggest the importance of epigenetic modification in the pathogenesis of psoriasis. Aberrant epigenetic patterns including changes in DNA methylation, histone modifications and non-coding RNA expression are observed in psoriatic skin. Reversing these epigenetic mechanisms has showed improvement in psoriatic phenotypes, making epigenetic therapy a potential avenue for psoriasis treatment. Here, we summarize relevant evidence for epigenetic dysregulation contributing to psoriasis susceptibility and pathogenesis, and the factors responsible for epigenetic modifications, providing directions for potential future clinical avenues.
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Affiliation(s)
- Chang Zeng
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics and Department of Biostatistics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
- A. Alfred Taubman Medical Research Institute, Ann Arbor, MI, USA
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237
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Jiang ZF, Shao Y, Zhang L, Shen J. Lung-derived exosomes regulate the function of mesenchymal stem cells and alleviate phosgene-induced lung injury via miR-34c-3p. J Biochem Mol Toxicol 2021; 35:e22851. [PMID: 34331784 DOI: 10.1002/jbt.22851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/29/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022]
Abstract
Phosgene may induce acute lung injury (ALI) when a person is exposed to it. Mesenchymal stem cells (MSCs) were affirmed to have therapeutic effects on phosgene-induced ALI. In a previous study, ALI exosomes have been confirmed to promote the proliferation and migration of MSCs. However, the mechanism of this phenomenon is still unclear. MicroRNAs (miRNAs) are essential in the physiological process of cells. In this study, lung-derived exosomes were isolated from phosgene-exposed and normal rats, respectively, through ultracentrifugation and cultured MSCs with these exosomes. We found that rno-miR-34c-3p was downregulated in MSCs cocultured with ALI exosomes. MiR-34c-3p inhibitor promoted the proliferation and migration of MSCs. Moreover, the dual-luciferase reporter assay demonstrated that miR-34c-3p regulated Janus kinase 1 (JAK1) expression. The miR-34c-3p inhibitor also significantly activated the JAK1/signal transducer and activator of transcription 3 (STAT3) signaling pathway. In conclusion, ALI exosomes decrease the miR-34c-3p expression levels, influencing MSCs via the JAK1/STAT3 signaling pathway.
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Affiliation(s)
- Zhi-Feng Jiang
- Department of Intensive Care Unit, Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Chemical Injury, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Radiation Injury, Jinshan Hospital, Fudan University, Shanghai, China
| | - Yiru Shao
- Department of Intensive Care Unit, Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Chemical Injury, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Radiation Injury, Jinshan Hospital, Fudan University, Shanghai, China
| | - Lin Zhang
- Department of Intensive Care Unit, Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Chemical Injury, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Radiation Injury, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jie Shen
- Department of Intensive Care Unit, Center of Emergency and Intensive Care Unit, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Chemical Injury, Jinshan Hospital, Fudan University, Shanghai, China.,Department of Intensive Care Unit, Medical Research Center of Radiation Injury, Jinshan Hospital, Fudan University, Shanghai, China
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238
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Brocato E, Wolstenholme JT. Neuroepigenetic consequences of adolescent ethanol exposure. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2021; 160:45-84. [PMID: 34696879 DOI: 10.1016/bs.irn.2021.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Adolescence is a critical developmental period characterized by ongoing brain maturation processes including myelination and synaptic pruning. Adolescents experience heightened reward sensitivity, sensation seeking, impulsivity, and diminished inhibitory self-control, which contribute to increased participation in risky behaviors, including the initiation of alcohol use. Ethanol exposure in adolescence alters memory and cognition, anxiety-like behavior, and ethanol sensitivity as well as brain myelination and dendritic spine morphology, with effects lasting into adulthood. Emerging evidence suggests that epigenetic modifications may explain these lasting effects. Focusing on the amygdala, prefrontal cortex and hippocampus, we review studies investigating the epigenetic consequences of adolescent ethanol exposure. Ethanol metabolism globally increases donor substrates for histone acetylation and histone and DNA methylation, and this chapter discusses how this can further impact epigenetic programming of the adolescent brain. Elucidation of the mechanisms through which ethanol can alter the epigenetic code at specific transcripts may provide therapeutic targets for intervention.
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Affiliation(s)
- Emily Brocato
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Jennifer T Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States; VCU-Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States.
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239
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Ju X, Tang Y, Qu R, Hao S. The Emerging Role of Circ-SHPRH in Cancer. Onco Targets Ther 2021; 14:4177-4188. [PMID: 34285509 PMCID: PMC8286153 DOI: 10.2147/ott.s317403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Circ-SHPRH is a circular RNA that can regulate the expression of target genes by sponging microRNAs (miRNAs) or translating tumor suppressor proteins. Recent studies have suggested that circ-SHPRH may play a role in the development of tumors and cancers. Hence, this paper aimed to review the biological characteristics, molecular mechanisms, and potential clinical significance of circ-SHPRH in a variety of tumors and to evaluate its potential as a new diagnostic and prognostic biomarker. METHODS Numerous experiments were performed regarding the abnormal expression of circ-SHPRH in a variety of tumors, including hepatocellular carcinoma, gastric carcinoma, non-small cell lung cancer, osteosarcoma, colorectal cancer, cholangiocarcinoma, pancreatic ductal adenocarcinoma, retinoblastoma, and glioblastoma. RESULTS Upregulation of circ-SHPRH reportedly inhibits tumor cell proliferation, migration, and invasion, leading to the inhibition of tumor development. The clinicopathological parameters and the functional characteristics of circ-SHPRH in multiple human tumors and cancers were summarized. Circ-SHPRH functions as a tumor suppressor gene and has great potential as a diagnostic and prognostic biomarker for different types of cancer.
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Affiliation(s)
- Xinyue Ju
- Department of Hematology and Oncology, The Second Bethune Clinical Medical College of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Yan Tang
- Department of Hematology and Oncology, The Second Bethune Clinical Medical College of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Rongfeng Qu
- Department of Hematology and Oncology, The Second Bethune Clinical Medical College of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Shuhong Hao
- Department of Hematology and Oncology, The Second Bethune Clinical Medical College of Jilin University, Changchun, Jilin, People’s Republic of China
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240
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Sellitto A, Pecoraro G, Giurato G, Nassa G, Rizzo F, Saggese P, Martinez CA, Scafoglio C, Tarallo R. Regulation of Metabolic Reprogramming by Long Non-Coding RNAs in Cancer. Cancers (Basel) 2021; 13:cancers13143485. [PMID: 34298698 PMCID: PMC8308086 DOI: 10.3390/cancers13143485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 01/10/2023] Open
Abstract
Metabolic reprogramming is a well described hallmark of cancer. Oncogenic stimuli and the microenvironment shape the metabolic phenotype of cancer cells, causing pathological modifications of carbohydrate, amino acid and lipid metabolism that support the uncontrolled growth and proliferation of cancer cells. Conversely, metabolic alterations in cancer can drive changes in genetic programs affecting cell proliferation and differentiation. In recent years, the role of non-coding RNAs in metabolic reprogramming in cancer has been extensively studied. Here, we review this topic, with a focus on glucose, glutamine, and lipid metabolism and point to some evidence that metabolic alterations occurring in cancer can drive changes in non-coding RNA expression, thus adding an additional level of complexity in the relationship between metabolism and genetic programs in cancer cells.
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Affiliation(s)
- Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
| | - Pasquale Saggese
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.S.); (C.A.M.); (C.S.)
| | - Cesar A. Martinez
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.S.); (C.A.M.); (C.S.)
| | - Claudio Scafoglio
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.S.); (C.A.M.); (C.S.)
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
- Correspondence: ; Tel.: +39-089-965067
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241
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Moreira L, Costa C, Pires J, Teixeira JP, Fraga S. How can exposure to engineered nanomaterials influence our epigenetic code? A review of the mechanisms and molecular targets. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108385. [PMID: 34893164 DOI: 10.1016/j.mrrev.2021.108385] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 06/14/2023]
Abstract
Evidence suggests that engineered nanomaterials (ENM) can induce epigenetic modifications. In this review, we provide an overview of the epigenetic modulation of gene expression induced by ENM used in a variety of applications: titanium dioxide (TiO2), silver (Ag), gold (Au), silica (SiO2) nanoparticles and carbon-based nanomaterials (CNM). Exposure to these ENM can trigger alterations in cell patterns of DNA methylation, post-transcriptional histone modifications and expression of non-coding RNA. Such effects are dependent on ENM dose and physicochemical properties including size, shape and surface chemistry, as well as on the cell/organism sensitivity. The genes affected are mostly involved in the regulation of the epigenetic machinery itself, as well as in apoptosis, cell cycle, DNA repair and inflammation related pathways, whose long-term alterations might lead to the onset or progression of certain pathologies. In addition, some DNA methylation patterns may be retained as a form of epigenetic memory. Prenatal exposure to ENM may impair the normal development of the offspring by transplacental effects and/or putative transmission of epimutations in imprinting genes. Thus, understanding the impact of ENM on the epigenome is of paramount importance and epigenetic evaluation must be considered when assessing the risk of ENM to human health.
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Affiliation(s)
- Luciana Moreira
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
| | - Carla Costa
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
| | - Joana Pires
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS-UP), Porto, Portugal.
| | - João Paulo Teixeira
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
| | - Sónia Fraga
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal; EPIUnit - Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
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242
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Zeng Z, Teng Q, Xiao J. Long noncoding RNA ILF3-AS1 aggravates papillary thyroid carcinoma progression via regulating the miR-4306/PLAGL2 axis. Cancer Cell Int 2021; 21:322. [PMID: 34176471 PMCID: PMC8237480 DOI: 10.1186/s12935-021-01950-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It have been proven that long non-coding RNAs (lncRNAs) serve as regulators in carcinogenesis. Interleukin enhancer binding factor 3 antisense RNA 1 (ILF3-AS1) has been illuminated as a prognostic factor in some cancers. Nevertheless, its expression pattern and possible functions in papillary thyroid carcinoma (PTC) have not been studied. METHODS The expression of ILF3-AS1 was measured by RT-qPCR and ISH. Colony formation assay and EdU assay were used to probe cell proliferation. TUNEL assay was used for analysis of cell apoptosis. Immunofluorescence and western blot were conducted to evaluate the expression change of E-cadherin and N-cadherin. The RNA interaction was demonstrated by mechanism experiments, including pull down assay and dual luciferase reporter assay. RESULTS ILF3-AS1 expression was evidently upregulated in PTC cell lines. ILF3-AS1 knockdown restrained the proliferation, migration and invasion of PTC cells. Mechanical investigation revealed that miR-4306 could interact with ILF3-AS1. PLAGL2 was a downstream target of miR-4306. The effects of ILF3-AS1 knockdown on the cellular processes were abrogated by miR-4306 downregulation or pleiomorphic adenoma gene-like 2 (PLAGL2) overexpression. CONCLUSION ILF3-AS1 plays tumor-promoting role in PTC via targeting miR-4306/PLAGL2 axis.
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Affiliation(s)
- Zhaohui Zeng
- Department of Nuclear Medicine, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Qiangfeng Teng
- Department of Nuclear Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, Nanning, 530021, Guangxi, China.
| | - Jinhong Xiao
- Department of Laboratory, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
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243
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Li T, Wei Y, Qu M, Mou L, Miao J, Xi M, Liu Y, He R. Formaldehyde and De/Methylation in Age-Related Cognitive Impairment. Genes (Basel) 2021; 12:genes12060913. [PMID: 34199279 PMCID: PMC8231798 DOI: 10.3390/genes12060913] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/31/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
Formaldehyde (FA) is a highly reactive substance that is ubiquitous in the environment and is usually considered as a pollutant. In the human body, FA is a product of various metabolic pathways and participates in one-carbon cycle, which provides carbon for the synthesis and modification of bio-compounds, such as DNA, RNA, and amino acids. Endogenous FA plays a role in epigenetic regulation, especially in the methylation and demethylation of DNA, histones, and RNA. Recently, epigenetic alterations associated with FA dysmetabolism have been considered as one of the important features in age-related cognitive impairment (ARCI), suggesting the potential of using FA as a diagnostic biomarker of ARCI. Notably, FA plays multifaceted roles, and, at certain concentrations, it promotes cell proliferation, enhances memory formation, and elongates life span, effects that could also be involved in the aetiology of ARCI. Further investigation of and the regulation of the epigenetics landscape may provide new insights about the aetiology of ARCI and provide novel therapeutic targets.
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Affiliation(s)
- Ting Li
- Bayannur Hospital, Bayannur 015000, China;
| | - Yan Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Meihua Qu
- Translational Medical Center, Weifang Second People’s Hospital, The Second Affiliated Hospital of Weifang Medical University, Weifang 261041, China;
| | - Lixian Mou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Junye Miao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Mengqi Xi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China; (M.X.); (Y.L.)
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China; (M.X.); (Y.L.)
| | - Rongqiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
- Correspondence:
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244
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Yu J, An Y, Zou M, Li X, Dong X. Mechanism of Circular RNA RAD23B for Regulating Glycolysis and Proliferation of Ovarian Cancer Cells by Targeting MicroRNA-519b-3p. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We investigated whether circRAD23B regulates glycolysis and proliferation of ovarian cancer cells by targeting miRNA-519b-3p. circRAD23B expression in ovarian cancer tissues was significantly higher than that in paracancerous tissues, and miRNA-519b-3p expression in ovarian cance tissues
was significantly lower than that in paracancerous tissues (P < 0.05). Transfection sicircRAD23B or miRNA-519b-3p mimics can greatly attenuate cell viability, glucose consumption, lactic acid level, and CyclinD1 protein level (P < 0.05), and increase p21 protein level (P
< 0.05). Double luciferase reporter experiment confirmed that circRAD23B could function as a miRNA-519b-3p sponge molecule. Co-transfection of si-circRAD23B and anti-miRNA-519b-3p could greatly decrease cell viability, glucose consumption, lactic acid level, and CyclinD1 protein level (P
< 0.05), and increase p21 protein level by comparison with si-circRAD23B+anti-miRNA-NC group (P < 0.05). Inhibiting circRAD23B expression can, in turn, inhibit glycolysis and the proliferation of ovarian cancer cells by up-regulating miRNA-519b-3p expression.
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Affiliation(s)
- Jinmei Yu
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, PR China
| | - Yunting An
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, PR China
| | - Meiyan Zou
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, PR China
| | - Xia Li
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, PR China
| | - Xiaoyuan Dong
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, PR China
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245
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Zivarpour P, Asemi Z, Jamilian H, Hallajzadeh J. PiRNAs and PIWI proteins as new biomarkers for diagnosis and treatment of liver cancer. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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246
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Keyvani-Ghamsari S, Khorsandi K, Rasul A, Zaman MK. Current understanding of epigenetics mechanism as a novel target in reducing cancer stem cells resistance. Clin Epigenetics 2021; 13:120. [PMID: 34051847 PMCID: PMC8164819 DOI: 10.1186/s13148-021-01107-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
At present, after extensive studies in the field of cancer, cancer stem cells (CSCs) have been proposed as a major factor in tumor initiation, progression, metastasis, and recurrence. CSCs are a subpopulation of bulk tumors, with stem cell-like properties and tumorigenic capabilities, having the abilities of self-renewal and differentiation, thereby being able to generate heterogeneous lineages of cancer cells and lead to resistance toward anti-tumor treatments. Highly resistant to conventional chemo- and radiotherapy, CSCs have heterogeneity and can migrate to different organs and metastasize. Recent studies have demonstrated that the population of CSCs and the progression of cancer are increased by the deregulation of different epigenetic pathways having effects on gene expression patterns and key pathways connected with cell proliferation and survival. Further, epigenetic modifications (DNA methylation, histone modifications, and RNA methylations) have been revealed to be key drivers in the formation and maintenance of CSCs. Hence, identifying CSCs and targeting epigenetic pathways therein can offer new insights into the treatment of cancer. In the present review, recent studies are addressed in terms of the characteristics of CSCs, the resistance thereof, and the factors influencing the development thereof, with an emphasis on different types of epigenetic changes in genes and main signaling pathways involved therein. Finally, targeted therapy for CSCs by epigenetic drugs is referred to, which is a new approach in overcoming resistance and recurrence of cancer.
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Affiliation(s)
| | - Khatereh Khorsandi
- Department of Photodynamic, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran.
| | - Azhar Rasul
- Department of Zoology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Khatir Zaman
- Department of Biotechnology, Abdul Wali Khan University Mardan (AWKUM), Mardan, 23200, Pakistan
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247
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Sieber KR, Dorman T, Newell N, Yan H. (Epi)Genetic Mechanisms Underlying the Evolutionary Success of Eusocial Insects. INSECTS 2021; 12:498. [PMID: 34071806 PMCID: PMC8229086 DOI: 10.3390/insects12060498] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022]
Abstract
Eusocial insects, such as bees, ants, and wasps of the Hymenoptera and termites of the Blattodea, are able to generate remarkable diversity in morphology and behavior despite being genetically uniform within a colony. Most eusocial insect species display caste structures in which reproductive ability is possessed by a single or a few queens while all other colony members act as workers. However, in some species, caste structure is somewhat plastic, and individuals may switch from one caste or behavioral phenotype to another in response to certain environmental cues. As different castes normally share a common genetic background, it is believed that much of this observed within-colony diversity results from transcriptional differences between individuals. This suggests that epigenetic mechanisms, featured by modified gene expression without changing genes themselves, may play an important role in eusocial insects. Indeed, epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs, have been shown to influence eusocial insects in multiple aspects, along with typical genetic regulation. This review summarizes the most recent findings regarding such mechanisms and their diverse roles in eusocial insects.
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Affiliation(s)
- Kayli R. Sieber
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (K.R.S.); (T.D.); (N.N.)
| | - Taylor Dorman
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (K.R.S.); (T.D.); (N.N.)
| | - Nicholas Newell
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (K.R.S.); (T.D.); (N.N.)
| | - Hua Yan
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; (K.R.S.); (T.D.); (N.N.)
- Center for Smell and Taste, University of Florida, Gainesville, FL 32611, USA
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248
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Bacolod MD. The Epigenetic Factors that Drive Cancer Drug Resistance. Curr Cancer Drug Targets 2021; 21:269-273. [PMID: 34112067 DOI: 10.2174/156800962104210527150438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, United States
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249
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Bure IV, Nemtsova MV. Methylation and Noncoding RNAs in Gastric Cancer: Everything Is Connected. Int J Mol Sci 2021; 22:ijms22115683. [PMID: 34073603 PMCID: PMC8199097 DOI: 10.3390/ijms22115683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Despite recent progress, gastric cancer remains one of the most common cancers and has a high mortality rate worldwide. Aberrant DNA methylation pattern and deregulation of noncoding RNA expression appear in the early stages of gastric cancer. Numerous investigations have confirmed their significant role in gastric cancer tumorigenesis and their high potential as diagnostic and prognostic biomarkers. Currently, it is clear that these epigenetic regulators do not work alone but interact with each other, generating a complex network. The aim of our review was to summarize the current knowledge of this interaction in gastric cancer and estimate its clinical potential for the diagnosis, prognosis, and treatment of the disease.
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Affiliation(s)
- Irina V. Bure
- Laboratory of Medical Genetics, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
- Correspondence: ; Tel.: +49-915-069-2721
| | - Marina V. Nemtsova
- Laboratory of Medical Genetics, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
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Yang Z, Xu F, Wang H, Teschendorff AE, Xie F, He Y. Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation. EBioMedicine 2021; 68:103399. [PMID: 34044218 PMCID: PMC8245911 DOI: 10.1016/j.ebiom.2021.103399] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Disruption of DNA methylation (DNAm) is one of the key signatures of cancer, however, detailed mechanisms that alter the DNA methylome in cancer remain to be elucidated. METHODS Here we present a novel integrative analysis framework, called MeLncTRN (Methylation mediated LncRNA Transcriptional Regulatory Network), that integrates genome-wide transcriptome, DNA methylome and copy number variation profiles, to systematically identify the epigenetically-driven lncRNA-gene regulation circuits across 18 cancer types. FINDING We show that a significant fraction of the aberrant DNAm and gene expression landscape in cancer is associated with long noncoding RNAs (lncRNAs). We reveal distinct types of regulation between lncRNA modulators and target genes that are operative in either only specific cancers or across cancers. Functional studies identified a common theme of cancer hallmarks that lncRNA modulators may participate in. The coupled lncRNA gene interactions via DNAm also serve as markers for classifications of cancer subtypes with different prognoses. INTERPRETATION Our study reveals a vital layer of DNAm and associated expression regulation for many cancer-related genes and we also provide a valuable database resource for interrogating epigenetically mediated lncRNA-gene interactions in cancer. FUNDING National Natural Science Foundation of China [91959106, 31871255].
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Feng Xu
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Haizhou Wang
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Andrew E Teschendorff
- CAS Key Lab of Computational Biology, Shanghai Institute for Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Feng Xie
- Soochow University, 8 Jixue Road, Suzhou 215131, Jiangsu Province, China
| | - Yungang He
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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