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Mégret L, Mendoza C, Arrieta Lobo M, Brouillet E, Nguyen TTY, Bouaziz O, Chambaz A, Néri C. Precision machine learning to understand micro-RNA regulation in neurodegenerative diseases. Front Mol Neurosci 2022; 15:914830. [PMID: 36157078 PMCID: PMC9500540 DOI: 10.3389/fnmol.2022.914830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Micro-RNAs (miRNAs) are short (∼21 nt) non-coding RNAs that regulate gene expression through the degradation or translational repression of mRNAs. Accumulating evidence points to a role of miRNA regulation in the pathogenesis of a wide range of neurodegenerative (ND) diseases such as, for example, Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis and Huntington disease (HD). Several systems level studies aimed to explore the role of miRNA regulation in NDs, but these studies remain challenging. Part of the problem may be related to the lack of sufficiently rich or homogeneous data, such as time series or cell-type-specific data obtained in model systems or human biosamples, to account for context dependency. Part of the problem may also be related to the methodological challenges associated with the accurate system-level modeling of miRNA and mRNA data. Here, we critically review the main families of machine learning methods used to analyze expression data, highlighting the added value of using shape-analysis concepts as a solution for precisely modeling highly dimensional miRNA and mRNA data such as the ones obtained in the study of the HD process, and elaborating on the potential of these concepts and methods for modeling complex omics data.
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Affiliation(s)
- Lucile Mégret
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
- *Correspondence: Lucile Mégret,
| | - Cloé Mendoza
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
| | - Maialen Arrieta Lobo
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
| | - Emmanuel Brouillet
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
| | - Thi-Thanh-Yen Nguyen
- Université Paris Cité, MAP5 (Centre National de la Recherche Scientifique UMR 8145), Paris, France
| | - Olivier Bouaziz
- Université Paris Cité, MAP5 (Centre National de la Recherche Scientifique UMR 8145), Paris, France
| | - Antoine Chambaz
- Université Paris Cité, MAP5 (Centre National de la Recherche Scientifique UMR 8145), Paris, France
| | - Christian Néri
- Sorbonne Université, Centre National de la Recherche Scientifique UMR 8256, Paris, France
- Christian Néri,
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Zhou X, Ao X, Jia Z, Li Y, Kuang S, Du C, Zhang J, Wang J, Liu Y. Non-coding RNA in cancer drug resistance: Underlying mechanisms and clinical applications. Front Oncol 2022; 12:951864. [PMID: 36059609 PMCID: PMC9428469 DOI: 10.3389/fonc.2022.951864] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/02/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is one of the most frequently diagnosed malignant diseases worldwide, posing a serious, long-term threat to patients’ health and life. Systemic chemotherapy remains the first-line therapeutic approach for recurrent or metastatic cancer patients after surgery, with the potential to effectively extend patient survival. However, the development of drug resistance seriously limits the clinical efficiency of chemotherapy and ultimately results in treatment failure and patient death. A large number of studies have shown that non-coding RNAs (ncRNAs), particularly microRNAs, long non-coding RNAs, and circular RNAs, are widely involved in the regulation of cancer drug resistance. Their dysregulation contributes to the development of cancer drug resistance by modulating the expression of specific target genes involved in cellular apoptosis, autophagy, drug efflux, epithelial-to-mesenchymal transition (EMT), and cancer stem cells (CSCs). Moreover, some ncRNAs also possess great potential as efficient, specific biomarkers in diagnosis and prognosis as well as therapeutic targets in cancer patients. In this review, we summarize the recent findings on the emerging role and underlying mechanisms of ncRNAs involved in cancer drug resistance and focus on their clinical applications as biomarkers and therapeutic targets in cancer treatment. This information will be of great benefit to early diagnosis and prognostic assessments of cancer as well as the development of ncRNA-based therapeutic strategies for cancer patients.
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Affiliation(s)
- Xuehao Zhou
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xiang Ao
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Zhaojun Jia
- College of New Materials and Chemical Engineering, Beijing Key Laboratory of Enze Biomass Fine Chemicals, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Yiwen Li
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Shouxiang Kuang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chengcheng Du
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jinyu Zhang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Ying Liu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, China.,Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, China
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103
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Non-Coding RNAs in Hepatocellular Carcinoma. LIVERS 2022. [DOI: 10.3390/livers2030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver cancer ranks as the fourth leading cause of cancer-related deaths. Despite extensive research efforts aiming to evaluate the biological mechanisms underlying hepatocellular carcinoma (HCC) development, little has been translated towards new diagnostic and treatment options for HCC patients. Historically, the focus has been centered on coding RNAs and their respective proteins. However, significant advances in sequencing and RNA detection technologies have shifted the research focus towards non-coding RNAs (ncRNA), as well as their impact on HCC development and progression. A number of studies reported complex post-transcriptional interactions between various ncRNA and coding RNA molecules. These interactions offer insights into the role of ncRNAs in both the known pathways leading to oncogenesis, such as dysregulation of p53, and lesser-known mechanisms, such as small nucleolar RNA methylation. Studies investigating these mechanisms have identified prevalent ncRNA changes in microRNAs, snoRNAs, and long non-coding RNAs that can both pre- and post-translationally regulate key factors in HCC progression. In this review, we present relevant publications describing ncRNAs to summarize the impact of different ncRNA species on liver cancer development and progression and to evaluate recent attempts at clinical translation.
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104
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Hu Q, Zhang X, Sun M, jiang B, Zhang Z, Sun D. Potential epigenetic molecular regulatory networks in ocular neovascularization. Front Genet 2022; 13:970224. [PMID: 36118885 PMCID: PMC9478661 DOI: 10.3389/fgene.2022.970224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Neovascularization is one of the many manifestations of ocular diseases, including corneal injury and vascular diseases of the retina and choroid. Although anti-VEGF drugs have been used to effectively treat neovascularization, long-term use of anti-angiogenic factors can cause a variety of neurological and developmental side effects. As a result, better drugs to treat ocular neovascularization are urgently required. There is mounting evidence that epigenetic regulation is important in ocular neovascularization. DNA methylation and histone modification, non-coding RNA, and mRNA modification are all examples of epigenetic mechanisms. In order to shed new light on epigenetic therapeutics in ocular neovascularization, this review focuses on recent advances in the epigenetic control of ocular neovascularization as well as discusses these new mechanisms.
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105
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Song D, Ha CZ, Xu Q, Hu YH. mRNA expression profiling of the cancellous bone in patients with idiopathic osteonecrosis of the femoral head by whole-transcriptome sequencing. Medicine (Baltimore) 2022; 101:e30213. [PMID: 36107565 PMCID: PMC9439785 DOI: 10.1097/md.0000000000030213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Idiopathic osteonecrosis of the femoral head (INFH) seriously affects patients' activities and is a heavy burden to society and patients' families. Therefore, the early diagnosis and treatment of INFH is essential in reducing pain and burden. In the present study, the cancellous bone under the cartilage of the femoral head was isolated from patients with INFH and femoral neck fracture (FNF). Histological examination revealed that the bone trabecular and the medullary cavity in the INFH group compared with those in the FNF group. Whole-transcriptome sequencing (WTS), a recently applied technology, plays a significant role in the screening of risk factors associated with the onset of femoral head necrosis. Herein, WTS was used to obtain the mRNA expression profile in the cancellous bone of the femoral head isolated from 5 patients with INFH and 5 patients with FNF. Compared with the FNF group, a total of 155 differentially expressed genes were identified in the INFH group. Among these genes, 96 and 59 were upregulated and downregulated, respectively. Reverse transcription-quantitative PCR and western blot analyses revealed that leucine-rich repeat-containing 17 (LRRC17) displayed the most significantly decreased mRNA and protein expression levels between the INFH and FNF groups. The expression profile of the differentially expressed genes and LRRC17 protein in the INFH and FNF groups was consistent with that obtained by WTS. LRRC17, a leucine repeat sequence, plays a significant role in regulating bone metabolism, thus indicating that LRRC17 downregulation could affect bone metabolism and could be considered a key factor in the pathogenesis of INFH.
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Affiliation(s)
- Da Song
- Department of Orthopedics, Liaocheng People’s Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Cheng-Zhi Ha
- Department of Orthopedics, Liaocheng People’s Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Qi Xu
- Department of Orthopedics, Liaocheng People’s Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Yan-Hui Hu
- Department of Orthopedics, Liaocheng People’s Hospital, Liaocheng, Shandong 252000, P.R. China
- * Correspondence: Yan-hui Hu, Department of Orthopedics, Liaocheng People’s Hospital, No. 67 Dongchang West Road, Liaocheng, Shandong 252000, P.R. China (e-mail: )
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Mutual regulation of noncoding RNAs and RNA modifications in psychopathology: Potential therapeutic targets for psychiatric disorders? Pharmacol Ther 2022; 237:108254. [DOI: 10.1016/j.pharmthera.2022.108254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022]
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Wang Y, Feng YC, Gan Y, Teng L, Wang L, La T, Wang P, Gu Y, Yan L, Li N, Zhang L, Wang L, Thorne RF, Zhang XD, Cao H, Shao FM. LncRNA MILIP links YBX1 to translational activation of Snai1 and promotes metastasis in clear cell renal cell carcinoma. J Exp Clin Cancer Res 2022; 41:260. [PMID: 36028903 PMCID: PMC9414127 DOI: 10.1186/s13046-022-02452-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/28/2022] [Indexed: 12/25/2022] Open
Abstract
Abstract
Background
Distant metastasis is the major cause of clear cell renal cell carcinoma (ccRCC)-associated mortality. However, molecular mechanisms involved in ccRCC metastasis remain to be fully understood. With the increasing appreciation of the role of long non-coding RNAs (lncRNAs) in cancer development, progression, and treatment resistance, the list of aberrantly expressed lncRNAs contributing to ccRCC pathogenesis is expanding rapidly.
Methods
Bioinformatics analysis was carried out to interrogate publicly available ccRCC datasets. In situ hybridization and qRT-PCR assays were used to test lncRNA expression in human ccRCC tissues and cell lines, respectively. Chromatin immunoprecipitation and luciferase reporter assays were used to examine transcriptional regulation of gene expression. Wound healing as well as transwell migration and invasion assays were employed to monitor ccRCC cell migration and invasion in vitro. ccRCC metastasis was also examined using mouse models in vivo. RNA pulldown and RNA immunoprecipitation were performed to test RNA–protein associations, whereas RNA-RNA interactions were tested using domain-specific chromatin isolation by RNA purification.
Results
MILIP expression was upregulated in metastatic compared with primary ccRCC tissues. The increased MILIP expression in metastatic ccRCC cells was driven by the transcription factor AP-2 gamma (TFAP2C). Knockdown of MILIP diminished the potential of ccRCC cell migration and invasion in vitro and reduced the formation of ccRCC metastatic lesions in vivo. The effect of MILIP on ccRCC cells was associated with alterations in the expression of epithelial-to-mesenchymal transition (EMT) hallmark genes. Mechanistically, MILIP formed an RNA-RNA duplex with the snail family transcriptional repressor 1 (Snai1) mRNA and bound to Y-box binding protein 1 (YBX1). This promoted the association between the YBX1 protein and the Snai1 mRNA, leading to increased translation of the latter. Snai1 in turn played an important role in MILIP-driven ccRCC metastasis.
Conclusions
The TFAP2C-responsive lncRNA MILIP drives ccRCC metastasis. Targeting MILIP may thus represent a potential avenue for ccRCC treatment.
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Chen S, Zhang C, Shen L, Hu J, Chen X, Yu Y. Noncoding RNAs in cataract formation: star molecules emerge in an endless stream. Pharmacol Res 2022; 184:106417. [PMID: 36038044 DOI: 10.1016/j.phrs.2022.106417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
For decades, research on the pathological mechanism of cataracts has usually focused on the abnormal protein changes caused by a series of risk factors. However, an entire class of molecules, termed non-coding RNA (ncRNA), was discovered in recent years and proven to be heavily involved in cataract formation. Recent studies have recognized the key regulatory roles of ncRNAs in cataracts by shaping cellular activities such as proliferation, apoptosis, migration and epithelial-mesenchymal transition (EMT). This review summarizes our current insight into the biogenesis, properties and functions of ncRNAs and then discusses the development of research on ncRNAs in cataracts. Considering the significant role of ncRNA in cataract formation, research on novel associated regulatory mechanisms is urgently needed, and the development of therapeutic alternatives for the treatment of cataracts seems promising.
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Affiliation(s)
- Silong Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Chengshou Zhang
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Lifang Shen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Jianghua Hu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Department of Ophthalmology, Jiande Branch, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, China.
| | - Yibo Yu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China.
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Integrative analysis of the roles of lncRNAs and mRNAs in ischaemic preconditioning to alleviate liver ischaemia-reperfusion injury in mice. Biochem Biophys Res Commun 2022; 627:30-38. [PMID: 36007332 DOI: 10.1016/j.bbrc.2022.08.041] [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: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022]
Abstract
The objective of our study was to elucidate the possible underlying mechanism for the protective effect of ischaemic preconditioning (IPC) against ischaemia-reperfusion (I/R) injury and to provide new research perspectives of long non-coding RNAs (lncRNAs). In this study, serum and liver tissue samples were collected to measure indexes of liver injury from a mouse liver model in sham, I/R injury and I/R + IPC groups. Furthermore, liver samples from 5 randomly selected mice per group were extracted and subjected to the microarray and subsequent bioinformatics analysis. IPC ameliorated liver damage by lowered liver transaminase levels and pro-inflammatory cytokines. A total of 167 lncRNAs and 108 messenger RNAs (mRNAs) were significantly differentially expressed genes (DEGs) between the I/R + IPC and I/R groups. Gene Ontology (GO) analysis revealed that these genes were mainly related to unfolded proteins, responses to topologically incorrect proteins, responses to temperature stimuli, protein folding and protein refolding. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the DEGs were enriched in the following pathways: protein processing in the endoplasmic reticulum; antigen processing and presentation; and fructose and mannose metabolism. Additionally, the 7 selected DEGs (Hspa1ab, Chka, Clec2h, Mvd, Adra1a, AK085737 and AK088966) were validated in modules of the lncRNA-mRNA weighted coexpression network, which agreed with the qRT-PCR and chip data. And the identified differentially expressed lncRNAs and mRNAs may provide new clues to understand the pivotal pathophysiological mechanism by which IPC alleviates I/R-caused liver damage.
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Song Z, He C, Wen J, Yang J, Chen P. Long Non-coding RNAs: Pivotal Epigenetic Regulators in Diabetic Retinopathy. Curr Genomics 2022; 23:246-261. [PMID: 36777876 PMCID: PMC9875540 DOI: 10.2174/1389202923666220531105035] [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: 04/04/2022] [Revised: 05/07/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
Diabetic retinopathy (DR) is a severe complication of diabetes; however, its mechanism is not fully understood. Evidence has recently revealed that long non-coding RNAs (lncRNAs) are abnormally expressed in DR, and lncRNAs may function as pivotal regulators. LncRNAs are able to modulate gene expression at the epigenetic level by acting as scaffolds of histone modification complexes and sponges of binding with microRNAs (miRNAs). LncRNAs are believed to be important epigenetic regulators, which may become beneficial in the diagnosis and therapy of DR. However, the mechanisms of lncRNAs in DR are still unclear. In this review, we summarize the possible functions and mechanisms of lncRNAs in epigenetic regulation to target genes in the progression of DR.
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Affiliation(s)
- Zhaoxia Song
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Chang He
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Jianping Wen
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Jianli Yang
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Peng Chen
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, China;,Address correspondence to this author at the Department of Medical Genetics, College of Basic Medical Sciences, Jilin University. Address: Room 413, 126 Xinmin Street, Changchun, Jilin 130021, China; Tel/Fax: 0086-18584362191; E-mail:
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Denham AN, Drake J, Gavrilov M, Taylor ZN, Bacanu SA, Vladimirov VI. Long Non-Coding RNAs: The New Frontier into Understanding the Etiology of Alcohol Use Disorder. Noncoding RNA 2022; 8:ncrna8040059. [PMID: 36005827 PMCID: PMC9415279 DOI: 10.3390/ncrna8040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022] Open
Abstract
Alcohol use disorder (AUD) is a complex, chronic, debilitating condition impacting millions worldwide. Genetic, environmental, and epigenetic factors are known to contribute to the development of AUD. Long non-coding RNAs (lncRNAs) are a class of regulatory RNAs, commonly referred to as the “dark matter” of the genome, with little to no protein-coding potential. LncRNAs have been implicated in numerous processes critical for cell survival, suggesting that they play important functional roles in regulating different cell processes. LncRNAs were also shown to display higher tissue specificity than protein-coding genes and have a higher abundance in the brain and central nervous system, demonstrating a possible role in the etiology of psychiatric disorders. Indeed, genetic (e.g., genome-wide association studies (GWAS)), molecular (e.g., expression quantitative trait loci (eQTL)) and epigenetic studies from postmortem brain tissues have identified a growing list of lncRNAs associated with neuropsychiatric and substance use disorders. Given that the expression patterns of lncRNAs have been associated with widespread changes in the transcriptome, including methylation, chromatin architecture, and activation or suppression of translational activity, the regulatory nature of lncRNAs may be ubiquitous and an innate component of gene regulation. In this review, we present a synopsis of the functional impact that lncRNAs may play in the etiology of AUD. We also discuss the classifications of lncRNAs, their known functional roles, and therapeutic advancements in the field of lncRNAs to further clarify the functional relationship between lncRNAs and AUD.
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Affiliation(s)
- Allie N. Denham
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Correspondence:
| | - John Drake
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- MSCI Program, Texas A&M University, Bryan, TX 77807, USA
| | - Matthew Gavrilov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
| | - Zachary N. Taylor
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
- Texas A&M Institute for Neuroscience, College Station, Texas A&M University, College Station, TX 77843, USA
- Genetics Interdisciplinary Program, College Station, Texas A&M University, College Station, TX 77843, USA
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
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112
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Zhao X, Feng B, Wang Q, Tang L, Liu Q, Ma W, Li C, Shao C. Cloning of the Maternal Effector Gene org and Its Regulation by lncRNA ORG-AS in Chinese Tongue Sole (Cynoglossus semilaevis). Int J Mol Sci 2022; 23:ijms23158605. [PMID: 35955739 PMCID: PMC9369028 DOI: 10.3390/ijms23158605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Maternal effector genes (MEGs) encode maternal RNA and protein, accumulating in the cytoplasm of oocytes. During oocyte development, MEGs participate in oocyte meiosis and promote oocyte development. And MEGs can also regulate maternal transcriptome stability and promote maternal–zygotic transition (MTZ) in early embryonic development. Long noncoding RNAs (lncRNAs), as new epigenetic regulators, can regulate gene expression at both the transcriptional and post-transcriptional levels through cis- or trans-regulation. The oogenesis-related gene org is a germ-cell-specific gene in fish, but the role of org in embryonic development and oogenesis has rarely been studied, and the knowledge of the lncRNA-mediated regulation of org is limited. In this study, we cloned and identified the org gene of Chinese tongue sole (Cynoglossus semilaevis), and we identified a lncRNA named lncRNA ORG-anti-sequence (ORG-AS), located at the reverse overlapping region of org. The results of qRT-PCR and FISH demonstrated that org was highly expressed during the early stages of embryonic development and oogenesis and was located in the cytoplasm of oocytes. ORG-AS was expressed at low levels in the ovary and colocalized with org in the cytoplasm of oocytes. In vitro experiments showed that overexpression of ORG-AS inhibited org expression. These results suggest that org, as a MEG in C. semilaevis, participates in the MTZ and the oogenesis. The lncRNA ORG-AS negatively regulates the gene expression of org through trans-regulation. These new findings broaden the function of MEGs in embryonic development and the oogenesis of bony fish and prove that lncRNAs are important molecular factors regulating org.
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Affiliation(s)
- Xiaona Zhao
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (X.Z.); (C.L.)
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
| | - Bo Feng
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
| | - Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
| | - Qian Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
| | - Wenxiu Ma
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (X.Z.); (C.L.)
| | - Changwei Shao
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (X.Z.); (C.L.)
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (B.F.); (Q.W.); (L.T.); (Q.L.); (W.M.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Correspondence: ; Tel.: +86-139-6962-5483
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Yu J, Liu M, Fang Q, Zhang X. Polycyclic aromatic hydrocarbons, long non-coding RNA expression, and DNA damage in coke oven workers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:57277-57286. [PMID: 35349071 DOI: 10.1007/s11356-022-19828-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Exposure to polycyclic aromatic hydrocarbons (PAHs) was associated with DNA damage, while the roles of long non-coding RNAs (lncRNAs) in the associations were unclear. We aimed to assess the association of lncRNA NR_024564 with urinary monohydroxy PAHs (OH-PAHs) and DNA damage among 332 coke oven workers. We determined 12 OH-PAHs by gas chromatography-mass spectrometry, and the expression level of NR_024564 by droplet digital RT-PCR and DNA damage by the comet assay. In total participants, we found that NR_024564 was not significantly associated with OH-PAHs or comet parameters. However, among workers with ≥ 20 working years, multiple OH-PAHs including urinary 1-hydroxyphenanthrene (1-OHPh), 2-OHPh, 3-OHPh, 9-OHPh, 1‑hydroxypyrene, and total PAH metabolites were related to increased comet parameters. Moreover, NR_024564 was significantly associated with 2-OHPh and four comet parameters. Each 1% increase in 2-OHPh was associated with 0.35% reduction (95% CI: 0.16%, 0.55%) in NR_024564 (P-FDR = 0.005), and 2-OHPh was marginally interacted with working years in relation to NR_024564 decrease. Also, each 1% increment of NR_024564 was related to 0.04-0.13% decrease of Olive tail moment, percent DNA in the comet tail, tail length, and tail moment (all P-FDR < 0.05). Furthermore, low NR_024564 level combined with high levels of 1-OHPh and 2-OHPh or ≥ 20 working years was positively associated with the comet parameters among the total participants. Our results indicated that NR_024564 might be linked to the adverse associations of PAHs with the DNA damage of coke oven workers who worked for ≥ 20 years.
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Affiliation(s)
- Jie Yu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd., Wuhan, 430030, Hubei, China
| | - Miao Liu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd., Wuhan, 430030, Hubei, China
| | - Qin Fang
- Department of Medical Affairs, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, 519000, Guangdong, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd., Wuhan, 430030, Hubei, China.
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114
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Peña-Flores JA, Bermúdez M, Ramos-Payán R, Villegas-Mercado CE, Soto-Barreras U, Muela-Campos D, Álvarez-Ramírez A, Pérez-Aguirre B, Larrinua-Pacheco AD, López-Camarillo C, López-Gutiérrez JA, Garnica-Palazuelos J, Estrada-Macías ME, Cota-Quintero JL, Barraza-Gómez AA. Emerging role of lncRNAs in drug resistance mechanisms in head and neck squamous cell carcinoma. Front Oncol 2022; 12:965628. [PMID: 35978835 PMCID: PMC9376329 DOI: 10.3389/fonc.2022.965628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) originates in the squamous cell lining the mucosal surfaces of the head and neck region, including the oral cavity, nasopharynx, tonsils, oropharynx, larynx, and hypopharynx. The heterogeneity, anatomical, and functional characteristics of the patient make the HNSCC a complex and difficult-to-treat disease, leading to a poor survival rate and a decreased quality of life due to the loss of important physiologic functions and aggressive surgical injury. Alteration of driver-oncogenic and tumor-suppressing lncRNAs has recently been recently in HNSCC to obtain possible biomarkers for diagnostic, prognostic, and therapeutic approaches. This review provides current knowledge about the implication of lncRNAs in drug resistance mechanisms in HNSCC. Chemotherapy resistance is a major therapeutic challenge in HNSCC in which lncRNAs are implicated. Lately, it has been shown that lncRNAs involved in autophagy induced by chemotherapy and epithelial–mesenchymal transition (EMT) can act as mechanisms of resistance to anticancer drugs. Conversely, lncRNAs involved in mesenchymal–epithelial transition (MET) are related to chemosensitivity and inhibition of invasiveness of drug-resistant cells. In this regard, long non-coding RNAs (lncRNAs) play a pivotal role in both processes and are important for cancer detection, progression, diagnosis, therapy response, and prognostic values. As the involvement of more lncRNAs is elucidated in chemoresistance mechanisms, an improvement in diagnostic and prognostic tools could promote an advance in targeted and specific therapies in precision oncology.
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Affiliation(s)
- José A. Peña-Flores
- Faculty of Odontology, Autonomous University of Chihuahua, Chihuahua, Mexico
| | - Mercedes Bermúdez
- Faculty of Odontology, Autonomous University of Chihuahua, Chihuahua, Mexico
- *Correspondence: Mercedes Bermúdez,
| | - Rosalío Ramos-Payán
- Faculty of Biological and Chemical Sciences, Autonomous University of Sinaloa, Culiacán, Mexico
| | | | - Uriel Soto-Barreras
- Faculty of Odontology, Autonomous University of Chihuahua, Chihuahua, Mexico
| | | | | | | | | | | | - Jorge A. López-Gutiérrez
- Faculty of Biological and Chemical Sciences, Autonomous University of Sinaloa, Culiacán, Mexico
- Faculty of Biology, Autonomous University of Sinaloa, Culiacán, Mexico
| | | | | | - Juan L. Cota-Quintero
- Faculty of Biology, Autonomous University of Sinaloa, Culiacán, Mexico
- Faculty of Odontology , Autonomous University of Sinaloa, Culiacán, Mexico
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115
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Regulation of the Cancer Stem Phenotype by Long Non-Coding RNAs. Cells 2022; 11:cells11152352. [PMID: 35954194 PMCID: PMC9367355 DOI: 10.3390/cells11152352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer stem cells are a cell population within malignant tumors that are characterized by the ability to self-renew, the presence of specific molecules that define their identity, the ability to form malignant tumors in vivo, resistance to drugs, and the ability to invade and migrate to other regions of the body. These characteristics are regulated by various molecules, such as lncRNAs, which are transcripts that generally do not code for proteins but regulate multiple biological processes through various mechanisms of action. LncRNAs, such as HOTAIR, H19, LncTCF7, LUCAT1, MALAT1, LINC00511, and FMR1-AS1, have been described as key regulators of stemness in cancer, allowing cancer cells to acquire this phenotype. It has been proposed that cancer stem cells are clinically responsible for the high recurrence rates after treatment and the high frequency of metastasis in malignant tumors, so understanding the mechanisms that regulate the stem phenotype could have an impact on the improvement of cancer treatments.
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116
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Schell G, Roy B, Prall K, Dwivedi Y. miR-218: A Stress-Responsive Epigenetic Modifier. Noncoding RNA 2022; 8:ncrna8040055. [PMID: 35893238 PMCID: PMC9326663 DOI: 10.3390/ncrna8040055] [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: 06/16/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding the epigenetic role of microRNAs (miRNAs) has been a critical development in the field of neuropsychiatry and in understanding their underlying pathophysiology. Abnormalities in miRNA expression are often seen as key to the pathogenesis of many stress-associated mental disorders, including major depressive disorder (MDD). Recent advances in omics biology have further contributed to this understanding and expanded the role of miRNAs in networking a diverse array of molecular pathways, which are essentially related to the stress adaptivity of a healthy brain. Studies have highlighted the role of many such miRNAs in causing maladaptive changes in the brain's stress axis. One such miRNA is miR-218, which is debated as a critical candidate for increased stress susceptibility. miR-218 is expressed throughout the brain, notably in the hippocampus and prefrontal cortex (PFC). It is expressed at various levels through life stages, as seen by adolescent and adult animal models. Until now, a minimal number of studies have been conducted on human subjects to understand its role in stress-related abnormalities in brain circuits. However, several studies, including animal and cell-culture models, have been used to understand the impact of miR-218 on stress response and hypothalamic-pituitary-adrenal (HPA) axis function. So far, expression changes in this miRNA have been found to regulate signaling pathways such as glucocorticoid signaling, serotonergic signaling, and glutamatergic signaling. Recently, the developmental role of miR-218 has generated interest, given its increasing expression from adolescence to adulthood and targeting the Netrin-1/DCC signaling pathway. Since miR-218 expression affects neuronal development and plasticity, it is expected that a change in miR-218 expression levels over the course of development may negatively impact the process and make individuals stress-susceptible in adulthood. In this review, we describe the role of miR-218 in stress-induced neuropsychiatric conditions with an emphasis on stress-related disorders.
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Toma I, Porfire AS, Tefas LR, Berindan-Neagoe I, Tomuță I. A Quality by Design Approach in Pharmaceutical Development of Non-Viral Vectors with a Focus on miRNA. Pharmaceutics 2022; 14:pharmaceutics14071482. [PMID: 35890377 PMCID: PMC9322860 DOI: 10.3390/pharmaceutics14071482] [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: 05/20/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 12/10/2022] Open
Abstract
Cancer is the leading cause of death worldwide. Tumors consist of heterogeneous cell populations that have different biological properties. While conventional cancer therapy such as chemotherapy, radiotherapy, and surgery does not target cancer cells specifically, gene therapy is attracting increasing attention as an alternative capable of overcoming these limitations. With the advent of gene therapy, there is increasing interest in developing non-viral vectors for genetic material delivery in cancer therapy. Nanosystems, both organic and inorganic, are the most common non-viral vectors used in gene therapy. The most used organic vectors are polymeric and lipid-based delivery systems. These nanostructures are designed to bind and protect the genetic material, leading to high efficiency, prolonged gene expression, and low toxicity. Quality by Design (QbD) is a step-by-step approach that investigates all the factors that may affect the quality of the final product, leading to efficient pharmaceutical development. This paper aims to provide a new perspective regarding the use of the QbD approach for improving the quality of non-viral vectors for genetic material delivery and their application in cancer therapy.
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Affiliation(s)
- Ioana Toma
- Department of Pharmaceutical Technology and Biopharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.T.); (L.R.T.); (I.T.)
| | - Alina Silvia Porfire
- Department of Pharmaceutical Technology and Biopharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.T.); (L.R.T.); (I.T.)
- Correspondence:
| | - Lucia Ruxandra Tefas
- Department of Pharmaceutical Technology and Biopharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.T.); (L.R.T.); (I.T.)
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
| | - Ioan Tomuță
- Department of Pharmaceutical Technology and Biopharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (I.T.); (L.R.T.); (I.T.)
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118
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Parashar D, Singh A, Gupta S, Sharma A, Sharma MK, Roy KK, Chauhan SC, Kashyap VK. Emerging Roles and Potential Applications of Non-Coding RNAs in Cervical Cancer. Genes (Basel) 2022; 13:genes13071254. [PMID: 35886037 PMCID: PMC9317009 DOI: 10.3390/genes13071254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/06/2022] Open
Abstract
Cervical cancer (CC) is a preventable disease using proven interventions, specifically prophylactic vaccination, pervasive disease screening, and treatment, but it is still the most frequently diagnosed cancer in women worldwide. Patients with advanced or metastatic CC have a very dismal prognosis and current therapeutic options are very limited. Therefore, understanding the mechanism of metastasis and discovering new therapeutic targets are crucial. New sequencing tools have given a full visualization of the human transcriptome's composition. Non-coding RNAs (NcRNAs) perform various functions in transcriptional, translational, and post-translational processes through their interactions with proteins, RNA, and even DNA. It has been suggested that ncRNAs act as key regulators of a variety of biological processes, with their expression being tightly controlled under physiological settings. In recent years, and notably in the past decade, significant effort has been made to examine the role of ncRNAs in a variety of human diseases, including cancer. Therefore, shedding light on the functions of ncRNA will aid in our better understanding of CC. In this review, we summarize the emerging roles of ncRNAs in progression, metastasis, therapeutics, chemo-resistance, human papillomavirus (HPV) regulation, metabolic reprogramming, diagnosis, and as a prognostic biomarker of CC. We also discussed the role of ncRNA in the tumor microenvironment and tumor immunology, including cancer stem cells (CSCs) in CC. We also address contemporary technologies such as antisense oligonucleotides, CRISPR-Cas9, and exosomes, as well as their potential applications in targeting ncRNAs to manage CC.
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Affiliation(s)
- Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, MI 53226, USA
- Correspondence: (D.P.); (V.K.K.); Tel.: +1-414-439-8089 (D.P.); +1-956-296-1738 (V.K.K.)
| | - Anupam Singh
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India; (A.S.); (S.G.)
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India; (A.S.); (S.G.)
| | - Aishwarya Sharma
- Sri Siddhartha Medical College and Research Center, Tumkur 572107, Karnataka, India;
| | - Manish K. Sharma
- Department of Biotechnology, IP College, Bulandshahr 203001, Uttar Pradesh, India;
| | - Kuldeep K. Roy
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun 248007, Uttarakhand, India;
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA;
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Vivek K. Kashyap
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA;
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- Correspondence: (D.P.); (V.K.K.); Tel.: +1-414-439-8089 (D.P.); +1-956-296-1738 (V.K.K.)
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119
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Bartolucci D, Pession A, Hrelia P, Tonelli R. Precision Anti-Cancer Medicines by Oligonucleotide Therapeutics in Clinical Research Targeting Undruggable Proteins and Non-Coding RNAs. Pharmaceutics 2022; 14:pharmaceutics14071453. [PMID: 35890348 PMCID: PMC9315662 DOI: 10.3390/pharmaceutics14071453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer incidence and mortality continue to increase, while the conventional chemotherapeutic drugs confer limited efficacy and relevant toxic side effects. Novel strategies are urgently needed for more effective and safe therapeutics in oncology. However, a large number of proteins are considered undruggable by conventional drugs, such as the small molecules. Moreover, the mRNA itself retains oncological functions, and its targeting offers the double advantage of blocking the tumorigenic activities of the mRNA and the translation into protein. Finally, a large family of non-coding RNAs (ncRNAs) has recently emerged that are also dysregulated in cancer, but they could not be targeted by drugs directed against the proteins. In this context, this review describes how the oligonucleotide therapeutics targeting RNA or DNA sequences, are emerging as a new class of drugs, able to tackle the limitations described above. Numerous clinical trials are evaluating oligonucleotides for tumor treatment, and in the next few years some of them are expected to reach the market. We describe the oligonucleotide therapeutics targeting undruggable proteins (focusing on the most relevant, such as those originating from the MYC and RAS gene families), and for ncRNAs, in particular on those that are under clinical trial evaluation in oncology. We highlight the challenges and solutions for the clinical success of oligonucleotide therapeutics, with particular emphasis on the peculiar challenges that render it arduous to treat tumors, such as heterogeneity and the high mutation rate. In the review are presented these and other advantages offered by the oligonucleotide as an emerging class of biotherapeutics for a new era of precision anti-cancer medicine.
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Affiliation(s)
| | - Andrea Pession
- Pediatric Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | - Roberto Tonelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
- Correspondence:
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120
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Erfanparast L, Taghizadieh M, Shekarchi AA. Non-Coding RNAs and Oral Cancer: Small Molecules With Big Functions. Front Oncol 2022; 12:914593. [PMID: 35898889 PMCID: PMC9309727 DOI: 10.3389/fonc.2022.914593] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022] Open
Abstract
Oral cancer remains a major public concern with considerable socioeconomic impact in the world. Despite substantial advancements have been made in treating oral cancer, the five-year survival rate for oral cancer remained undesirable, and the molecular mechanisms underlying OSCC carcinogenesis have not been fully understood. Noncoding RNAs (ncRNAs) include transfer RNAs (tRNAs), as well as small RNAs such as microRNAs, and the long ncRNAs such as HOTAIR are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including cancer cell development. Cell death, such as apoptosis, necrosis, and autophagy, plays a vital role in the progression of cancer. A better understanding of the regulatory relationships between ncRNAs and these various types of cancer cell death is therefore urgently required. The occurrence and development of oral cancer can be controlled by increasing or decreasing the expression of ncRNAs, a method which confers broad prospects for oral cancer treatment. Therefore, it is urgent for us to understand the influence of ncRNAs on the development of different modes of oral tumor death, and to evaluate whether ncRNAs have the potential to be used as biological targets for inducing cell death and recurrence of chemotherapy. The purpose of this review is to describe the impact of ncRNAs on cell apoptosis and autophagy in oral cancer in order to explore potential targets for oral cancer therapy.
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Affiliation(s)
- Leila Erfanparast
- Department of Pediatric Dentistry, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- *Correspondence: Mohammad Taghizadieh,
| | - Ali Akbar Shekarchi
- Department of Pathology, Tabriz University of Medical Sciences, Tabriz, Iran
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Zhang P, Wu S, He Y, Li X, Zhu Y, Lin X, Chen L, Zhao Y, Niu L, Zhang S, Li X, Zhu L, Shen L. LncRNA-Mediated Adipogenesis in Different Adipocytes. Int J Mol Sci 2022; 23:ijms23137488. [PMID: 35806493 PMCID: PMC9267348 DOI: 10.3390/ijms23137488] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/01/2023] Open
Abstract
Long-chain noncoding RNAs (lncRNAs) are RNAs that do not code for proteins, widely present in eukaryotes. They regulate gene expression at multiple levels through different mechanisms at epigenetic, transcription, translation, and the maturation of mRNA transcripts or regulation of the chromatin structure, and compete with microRNAs for binding to endogenous RNA. Adipose tissue is a large and endocrine-rich functional tissue in mammals. Excessive accumulation of white adipose tissue in mammals can cause metabolic diseases. However, unlike white fat, brown and beige fats release energy as heat. In recent years, many lncRNAs associated with adipogenesis have been reported. The molecular mechanisms of how lncRNAs regulate adipogenesis are continually investigated. In this review, we discuss the classification of lncRNAs according to their transcriptional location. lncRNAs that participate in the adipogenesis of white or brown fats are also discussed. The function of lncRNAs as decoy molecules and RNA double-stranded complexes, among other functions, is also discussed.
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Affiliation(s)
- Peiwen Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuang Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxu He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinrong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong 637009, China;
| | - Xutao Lin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Z.); (L.S.); Tel.: +86-28-8629-1133 (L.Z. & L.S.)
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Z.); (L.S.); Tel.: +86-28-8629-1133 (L.Z. & L.S.)
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Ai C, Yang H, Ding Y, Tang J, Guo F. A multi-layer multi-kernel neural network for determining associations between non-coding RNAs and diseases. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2022.04.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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123
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Gholami A, Farhadi K, Sayyadipour F, Soleimani M, Saba F. Long noncoding RNAs (lncRNAs) in human lymphomas. Genes Dis 2022; 9:900-914. [PMID: 35685474 PMCID: PMC9170579 DOI: 10.1016/j.gendis.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 01/17/2023] Open
Abstract
Lymphomas are a diverse group of haematologic malignancies, which occur in infection-fighting cells of the lymphatic system. Long non-coding RNAs (lncRNAs) are non-coding RNAs, which have recently received significant attention as the main mediators of gene expression. In this review, we summarize the current knowledge on lncRNAs involved in lymphomas, their molecular functions, as well as their potential clinical value. Relevant literature was identified by a PubMed search of English language papers using the following terms: Lymphoma, LncRNA, leukemia, proliferation, apoptosis, and prognosis. LncRNAs are imperative for lymphoma carcinogenesis through affecting apoptosis, cell proliferation, invasion, and response to chemotherapy. The expression level of lncRNAs can affect chemotherapy-induced apoptosis. Taken together, lncRNA dysregulation in lymphoma cells is not only an epiphenomenon but also lncRNA transcription is critically related to the initiation and progression of lymphomas. Aberrant expression of lncRNAs can lead to the transformation of normal lymphocytes into lymphoma cells.
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Affiliation(s)
- Ali Gholami
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| | - Khosro Farhadi
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| | - Fatemeh Sayyadipour
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
| | - Masoud Soleimani
- Department of Haematology, Tarbiat Modares University, Tehran 146899-5513, Iran
| | - Fakhredin Saba
- Department of Medical Laboratory Science, School of Paramedical, Kermanshah University of Medical Sciences, Kermanshah 671568-5420, Iran
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Mampre D, Mehkri Y, Rajkumar S, Sriram S, Hernandez J, Lucke-Wold B, Chandra V. Treatment of breast cancer brain metastases: radiotherapy and emerging preclinical approaches. DIAGNOSTICS AND THERAPEUTICS 2022; 1:25-38. [PMID: 35782783 PMCID: PMC9249118 DOI: 10.55976/dt.1202216523-36] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The breast is one of the common primary sites of brain metastases (BM). Radiotherapy for BM from breast cancer may include whole brain radiation therapy (WBRT), stereotactic radiosurgery (SRS), and stereotactic radiotherapy (SRT), but a consensus is difficult to reach because of the wide and varied protocols, indications, and outcomes of these interventions. Overall, dissemination of disease, patient functional status, and tumor size are all important factors in the decision of treatment with WBRT or SRS. Thus far, previous studies indicate that WBRT can improve tumor control compared to SRS, but increase side effects, however no randomized trials have compared the efficacy of these therapies in BM from breast cancer. Therapies targeting long non-coding RNAs and transcription factors, such as MALAT1, HOTAIR, lnc-BM, TGL1, and ATF3, have the potential to both prevent metastatic spread and treat BM with improved radiosensitivity. Given the propensity for HER2+ breast cancer to develop BM, the above-mentioned cell lines may represent an important target for future investigations, and the development of everolimus and pyrotinib are equally important.
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Affiliation(s)
- David Mampre
- Department of Neurosurgery, University of Florida, Gainesville, FL
| | - Yusuf Mehkri
- Department of Neurosurgery, University of Florida, Gainesville, FL
| | | | - Sai Sriram
- Department of Neurosurgery, University of Florida, Gainesville, FL
| | - Jairo Hernandez
- Department of Neurosurgery, University of Florida, Gainesville, FL
| | | | - Vyshak Chandra
- Department of Neurosurgery, University of Florida, Gainesville, FL
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125
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Zakutansky PM, Feng Y. The Long Non-Coding RNA GOMAFU in Schizophrenia: Function, Disease Risk, and Beyond. Cells 2022; 11:1949. [PMID: 35741078 PMCID: PMC9221589 DOI: 10.3390/cells11121949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Neuropsychiatric diseases are among the most common brain developmental disorders, represented by schizophrenia (SZ). The complex multifactorial etiology of SZ remains poorly understood, which reflects genetic vulnerabilities and environmental risks that affect numerous genes and biological pathways. Besides the dysregulation of protein-coding genes, recent discoveries demonstrate that abnormalities associated with non-coding RNAs, including microRNAs and long non-coding RNAs (lncRNAs), also contribute to the pathogenesis of SZ. lncRNAs are an actively evolving family of non-coding RNAs that harbor greater than 200 nucleotides but do not encode for proteins. In general, lncRNA genes are poorly conserved. The large number of lncRNAs specifically expressed in the human brain, together with the genetic alterations and dysregulation of lncRNA genes in the SZ brain, suggests a critical role in normal cognitive function and the pathogenesis of neuropsychiatric diseases. A particular lncRNA of interest is GOMAFU, also known as MIAT and RNCR2. Growing evidence suggests the function of GOMAFU in governing neuronal development and its potential roles as a risk factor and biomarker for SZ, which will be reviewed in this article. Moreover, we discuss the potential mechanisms through which GOMAFU regulates molecular pathways, including its subcellular localization and interaction with RNA-binding proteins, and how interruption to GOMAFU pathways may contribute to the pathogenesis of SZ.
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Affiliation(s)
- Paul M. Zakutansky
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, USA;
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yue Feng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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126
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Xu X, Zhang Y. Regulation of Oxidative Stress by Long Non-coding RNAs in Central Nervous System Disorders. Front Mol Neurosci 2022; 15:931704. [PMID: 35782387 PMCID: PMC9241987 DOI: 10.3389/fnmol.2022.931704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Central nervous system (CNS) disorders, such as ischemic stroke, Alzheimer’s disease, Parkinson’s disease, spinal cord injury, glioma, and epilepsy, involve oxidative stress and neuronal apoptosis, often leading to long-term disability or death. Emerging studies suggest that oxidative stress may induce epigenetic modifications that contribute to CNS disorders. Non-coding RNAs are epigenetic regulators involved in CNS disorders and have attracted extensive attention. Long non-coding RNAs (lncRNAs) are non-coding RNAs more than 200 nucleotides long and have no protein-coding function. However, these molecules exert regulatory functions at the transcriptional, post-transcriptional, and epigenetic levels. However, the major role of lncRNAs in the pathophysiology of CNS disorders, especially related to oxidative stress, remains unclear. Here, we review the molecular functions of lncRNAs in oxidative stress and highlight lncRNAs that exert positive or negative roles in oxidation/antioxidant systems. This review provides novel insights into the therapeutic potential of lncRNAs that mediate oxidative stress in CNS disorders.
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Affiliation(s)
- Xiaoman Xu
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Yi Zhang,
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Lu Y, Ying D, Tian Y, Ruan Y, Cheng G, Lv K, Zhou X, Han S. LncRNA LINC01857 drives pancreatic adenocarcinoma progression via modulating miR-19a-3p/SMOC2. Clinics (Sao Paulo) 2022; 77:100047. [PMID: 35662010 PMCID: PMC9168480 DOI: 10.1016/j.clinsp.2022.100047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Emerging evidence has demonstrated that LINC01857 exerts a pivotal function in many cancers. However, its function in Pancreatic Ductal Adenocarcinoma (PDAC) still remains unclear. This study was designed to investigate the regulatory character of LINC01857 in PDAC. METHODS Bioinformatic tools and databases were used to seek potential miRNAs and mRNAs. Gene expression was evaluated by Reverse Transcription quantitative real-time Polymerase Chain Reaction (RT-qPCR), and western blot was used for protein level detection. A subcellular fraction assay was done to ascertain the location of LINC01857 in PANC-1 and BxPC-3 human pancreatic cancer cells. CCK-8, EdU, wound healing and Transwell assays were performed to inquire into the influence of LINC01857, and SPARC -related Modular Calcium-binding protein-2 (SMOC2) on cell viability, proliferation, migration, and invasion, respectively. The interaction between LINC01857 and its downstream genes was explored by RNA immunoprecipitation and luciferase reporter assays. RESULTS LINC01857 levels were significantly elevated in PDAC. Knockdown of LINC01857 significantly restrained the proliferation, migration, invasion, and Epithelial-Mesenchymal Transition (EMT) process of PDAC cells. MiR-19a-3p was a downstream target of LINC01857, and miR-19a-3p levels were significantly decreased in PDAC cells. In addition, SMOC2 expression had a negative correlation with that of miR-19a-3p, and SMOC2 was a downstream target of miR-19a-3p. Furthermore, SMOC2 upregulation partially abolished the inhibitive influence of LINC01857 downregulation on cell proliferation, migration, invasion, and the EMT process. CONCLUSION LINC01857 promotes malignant phenotypes of PDAC cells via upregulation of SMOC2 by interacting with miR-19a-3p.
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Affiliation(s)
- Yeting Lu
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Dongjian Ying
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Yuan Tian
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Yi Ruan
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Gong Cheng
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Kaiji Lv
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Xinhua Zhou
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Shuo Han
- Department of Healthcare Security and Price Management, The Affiliated Lihuili Hospital, Ningbo University (Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China.
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128
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Long non-coding RNAs involved in different steps of cancer metastasis. Clin Transl Oncol 2022; 24:997-1013. [PMID: 35119654 DOI: 10.1007/s12094-021-02761-z] [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: 10/18/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
Non-proteincoding transcripts bearing 200 base pairs known as long non-coding RNAs (lncRNAs) play a role in a variety of molecular mechanisms, including cell differentiation, apoptosis and metastasis. Previous studies have suggested that frequently dysregulated lncRNAs play a crucial role in various aspects of cancer metastasis. Metastasis is the main leading cause of death in cancer. The role of lncRNAs in different stages of metastasis is the subject of this review. Based on in vitro and in vivo investigations on metastasis, we categorized lncRNAs into distinct stages of metastasis including angiogenesis, invasion, intravasation, survival in circulation, and extravasation. The involvement of lncRNAs in angiogenesis and invasion has been extensively studied. Here, we comprehensively discuss the role and functions of these lncRNAs with a particular focus on the molecular mechanisms.
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129
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Non-Coding RNA Networks as Potential Novel Biomarker and Therapeutic Target for Sepsis and Sepsis-Related Multi-Organ Failure. Diagnostics (Basel) 2022; 12:diagnostics12061355. [PMID: 35741168 PMCID: PMC9222180 DOI: 10.3390/diagnostics12061355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
According to “Sepsis-3” consensus, sepsis is a life-threatening clinical syndrome caused by a dysregulated inflammatory host response to infection. A rapid identification of sepsis is mandatory, as the extent of the organ damage triggered by both the pathogen itself and the host’s immune response could abruptly evolve to multiple organ failure and ultimately lead to the death of the patient. The most commonly used therapeutic strategy is to provide hemodynamic and global support to the patient and to rapidly initiate broad-spectrum empiric antibiotic therapy. To date, there is no gold standard diagnostic test that can ascertain the diagnosis of sepsis. Therefore, once sepsis is suspected, the presence of organ dysfunction can be assessed using the Sepsis-related Organ Failure Assessment (SOFA) score, although the diagnosis continues to depend primarily on clinical judgment. Clinicians can now rely on several serum biomarkers for the diagnosis of sepsis (e.g., procalcitonin), and promising new biomarkers have been evaluated, e.g., presepsin and adrenomedullin, although their clinical relevance in the hospital setting is still under discussion. Non-codingRNA, including long non-codingRNAs (lncRNAs), circularRNAs (circRNAs) and microRNAs (miRNAs), take part in a complex chain of events playing a pivotal role in several important regulatory processes in humans. In this narrative review we summarize and then analyze the function of circRNAs-miRNA-mRNA networks as putative novel biomarkers and therapeutic targets for sepsis, focusing only on data collected in clinical settings in humans.
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130
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Wiedemann GM. Localization Matters: Epigenetic Regulation of Natural Killer Cells in Different Tissue Microenvironments. Front Immunol 2022; 13:913054. [PMID: 35707540 PMCID: PMC9191276 DOI: 10.3389/fimmu.2022.913054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Natural Killer cells (NK cells) are cytotoxic innate lymphoid cells (ILCs), which play a key role in the early protection against viral infection and cancer. In addition to mounting rapid effector responses, NK cells possess the capacity to generate long-lived memory cells in response to certain stimuli, thus blurring the lines between innate and adaptive immunity and making NK cells an ideal candidate for tumor immunotherapy. NK cell development, activation and memory formation are regulated by epigenetic alterations driven by a complex interplay of external and internal signals. These epigenetic modifications can convey long-lasting functional and phenotypic changes and critically modify their response to stimulation. Here, we review how NK cell functionality and plasticity are regulated at the epigenetic level in different tissue microenvironments and within tumor microenvironments. An in-depth understanding of the epigenetic modifications underlying NK cell functional diversity in different environments is an essential step in the development of NK cell-based cancer therapies.
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131
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Pinho JD, Silva GEB, Teixeira-Júnior AAL, Rocha TMS, Batista LL, de Sousa AM, Calixto JDRR, Burbano RR, de Souza CRT, Khayat AS. Non-Coding RNA in Penile Cancer. Front Oncol 2022; 12:812008. [PMID: 35651809 PMCID: PMC9150447 DOI: 10.3389/fonc.2022.812008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022] Open
Abstract
Penile cancer (PC) still presents a health threat for developing countries, in particular Brazil. Despite this, little progress has been made on the study of markers, including molecular ones, that can aid in the correct management of the patient, especially concerning lymphadenectomy. As in other neoplasms, non-coding RNAs (ncRNAs) have been investigated for penile cancer, with emphasis on microRNAs, piRNAs (PIWI-interacting small RNAs), and long non-coding RNAs (LncRNAs). In this context, this review aims to assemble the available knowledge on non-coding RNA linked in PC, contributing to our understanding of the penile carcinogenesis process and addressing their clinical relevance. ncRNAs are part of the novel generation of biomarkers, with high potential for diagnosis and prognosis, orientating the type of treatment. Furthermore, its versatility regarding the use of paraffin samples makes it possible to carry out retrospective studies.
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Affiliation(s)
- Jaqueline Diniz Pinho
- Zé Doca Center for Higher Studies, State University of Maranhão, Zé Doca, Brazil
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- Oncology Research Center, João de Barros Barreto University Hospital, Federal University of Pará, Belém, Brazil
- *Correspondence: Jaqueline Diniz Pinho,
| | - Gyl Eanes Barros Silva
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | - Antonio Augusto Lima Teixeira-Júnior
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
- Department of Genetics, University of Sao Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thalita Moura Silva Rocha
- Laboratory of Immunofluorescence and Electron Microscopy, University Hospital of the Federal University of Maranhão, São Luís, Brazil
| | - Lecildo Lira Batista
- Oncology Research Center, João de Barros Barreto University Hospital, Federal University of Pará, Belém, Brazil
- Coordination of Medicine, Federal University of Amapá, Macapá, Brazil
| | - Amanda Marques de Sousa
- Oncology Research Center, João de Barros Barreto University Hospital, Federal University of Pará, Belém, Brazil
| | | | | | | | - André Salim Khayat
- Oncology Research Center, João de Barros Barreto University Hospital, Federal University of Pará, Belém, Brazil
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Wang S, Wang R, Gao F, Huang J, Zhao X, Li D. Pan-cancer analysis of the DNA methylation patterns of long non-coding RNA. Genomics 2022; 114:110377. [PMID: 35513292 DOI: 10.1016/j.ygeno.2022.110377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 11/04/2022]
Abstract
Long non-coding RNA (lncRNA) regulated by abnormal DNA methylation (ADM-lncRNA) emerges as a biomarker for cancer diagnosis and treatment. This study comprehensively described the methylation patterns of lncRNA in pan-cancer using the cancer data set in The Cancer Genome Atlas (TCGA). Based on the cancer heterogeneity of ADM-lncRNA in pan-cancer, we constructed a co-expression network of pan-cancer ADM-lncRNA (pADM-lncRNA) in 10 cancers, highlighting the combined action mode of abnormal DNA methylation, and indicating the internal connection among different cancers. Functional analysis revealed the pan-carcinogenic pathway of pADM-lncRNA and suggested potential factors for cancer heterogeneity and tumor immune microenvironment changes. Survival analysis showed the potential of pADM-lncRNA-mRNA co-expression pair as cancer biomarkers. Revealing the action mode of lncRNA and DNA methylation in cancer may help understand the key molecular mechanisms of cell carcinogenesis.
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Affiliation(s)
- Shijia Wang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Rendong Wang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Fang Gao
- Health Management Center, Binzhou People's Hospital, Shandong Province, China
| | - Jun Huang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Xiaoxiao Zhao
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Dongguo Li
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China.
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Ghafouri-Fard S, Shoorei H, Mohaqiq M, Majidpoor J, Moosavi MA, Taheri M. Exploring the role of non-coding RNAs in autophagy. Autophagy 2022; 18:949-970. [PMID: 33525971 PMCID: PMC9196749 DOI: 10.1080/15548627.2021.1883881] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/13/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
As a self-degradative mechanism, macroautophagy/autophagy has a role in the maintenance of energy homeostasis during critical periods in the development of cells. It also controls cellular damage through the eradication of damaged proteins and organelles. This process is accomplished by tens of ATG (autophagy-related) proteins. Recent studies have shown the involvement of non-coding RNAs in the regulation of autophagy. These transcripts mostly modulate the expression of ATG genes. Both long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been shown to modulate the autophagy mechanism. Levels of several lncRNAs and miRNAs are altered in this process. In the present review, we discuss the role of lncRNAs and miRNAs in the regulation of autophagy in diverse contexts such as cancer, deep vein thrombosis, spinal cord injury, diabetes and its complications, acute myocardial infarction, osteoarthritis, pre-eclampsia and epilepsy.Abbreviations: AMI: acute myocardial infarction; ATG: autophagy-related; lncRNA: long non-coding RNA; miRNA: microRNA.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Mahdi Mohaqiq
- Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Moosavi
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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134
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Almatroudi A. Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter. Int J Mol Sci 2022; 23:ijms23084430. [PMID: 35457250 PMCID: PMC9024992 DOI: 10.3390/ijms23084430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 02/07/2023] Open
Abstract
A growing amount of information about the different types, functions, and roles played by non-coding RNAs (ncRNAs) is becoming available, as more and more research is done. ncRNAs have been identified as potential therapeutic targets in the treatment of tuberculosis (TB), because they may be essential regulators of the gene network. ncRNA profiling and sequencing has recently revealed significant dysregulation in tuberculosis, primarily due to aberrant processes of ncRNA synthesis, including amplification, deletion, improper epigenetic regulation, or abnormal transcription. Despite the fact that ncRNAs may have a role in TB characteristics, the detailed mechanisms behind these occurrences are still unknown. The dark matter of the genome can only be explored through the development of cutting-edge bioinformatics and molecular technologies. In this review, ncRNAs' synthesis and functions are discussed in detail, with an emphasis on the potential role of ncRNAs in tuberculosis. We also focus on current platforms, experimental strategies, and computational analyses to explore ncRNAs in TB. Finally, a viewpoint is presented on the key challenges and novel techniques for the future and for a wide-ranging therapeutic application of ncRNAs.
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Affiliation(s)
- Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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135
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Saltarella I, Apollonio B, Lamanuzzi A, Desantis V, Mariggiò MA, Desaphy JF, Vacca A, Frassanito MA. The Landscape of lncRNAs in Multiple Myeloma: Implications in the "Hallmarks of Cancer", Clinical Perspectives and Therapeutic Opportunities. Cancers (Basel) 2022; 14:cancers14081963. [PMID: 35454868 PMCID: PMC9032822 DOI: 10.3390/cancers14081963] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Multiple myeloma (MM) is an aggressive hematological neoplasia caused by the uncontrolled proliferation of aberrant plasmacells. Neoplastic transformation and progression are driven by a number of biological processes, called ‘hallmarks of cancer’, which are regulated by different molecules, including long non-coding RNAs. A deeper understanding of the mechanisms that regulate MM development and progression will help to improve patients stratification and management, and promote the identification of new therapeutic targets. Abstract Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that are not translated into proteins. Nowadays, lncRNAs are gaining importance as key regulators of gene expression and, consequently, of several biological functions in physiological and pathological conditions, including cancer. Here, we point out the role of lncRNAs in the pathogenesis of multiple myeloma (MM). We focus on their ability to regulate the biological processes identified as “hallmarks of cancer” that enable malignant cell transformation, early tumor onset and progression. The aberrant expression of lncRNAs in MM suggests their potential use as clinical biomarkers for diagnosis, patient stratification, and clinical management. Moreover, they represent ideal candidates for therapeutic targeting.
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Affiliation(s)
- Ilaria Saltarella
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine “Guido Baccelli”, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy; (I.S.); (B.A.); (A.L.); (V.D.); (A.V.)
- Department of Biomedical Sciences and Human Oncology, Pharmacology Section, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy;
| | - Benedetta Apollonio
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine “Guido Baccelli”, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy; (I.S.); (B.A.); (A.L.); (V.D.); (A.V.)
| | - Aurelia Lamanuzzi
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine “Guido Baccelli”, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy; (I.S.); (B.A.); (A.L.); (V.D.); (A.V.)
| | - Vanessa Desantis
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine “Guido Baccelli”, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy; (I.S.); (B.A.); (A.L.); (V.D.); (A.V.)
- Department of Biomedical Sciences and Human Oncology, Pharmacology Section, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy;
| | - Maria Addolorata Mariggiò
- Department of Biomedical Sciences and Human Oncology, Unit of General Pathology, University of Bari Aldo Moro, I-70124 Bari, Italy;
| | - Jean-François Desaphy
- Department of Biomedical Sciences and Human Oncology, Pharmacology Section, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy;
| | - Angelo Vacca
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine “Guido Baccelli”, University of Bari Medical School, Piazza Giulio Cesare 11, I-70124 Bari, Italy; (I.S.); (B.A.); (A.L.); (V.D.); (A.V.)
| | - Maria Antonia Frassanito
- Department of Biomedical Sciences and Human Oncology, Unit of General Pathology, University of Bari Aldo Moro, I-70124 Bari, Italy;
- Correspondence:
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Chen X, Liu Y, Liu H, Wang ZW, Zhu X. Unraveling diverse roles of noncoding RNAs in various human papillomavirus negative cancers. Pharmacol Ther 2022; 238:108188. [PMID: 35421419 DOI: 10.1016/j.pharmthera.2022.108188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 12/17/2022]
Abstract
Human papillomavirus (HPV)-negative tumors distinguish from cancers associated with HPV infection. Due to its high rate of lymph node metastasis and difficulty in inchoate discover and diagnosis, the treatment efficacy of HPV-negative cancers is unsatisfactory. Epidemiological evidence suggests that HPV-negative tumor patients have a poor prognosis, and the mortality is higher than that of cancer patients caused by HPV infection. Evidence has demonstrated that noncoding RNAs (ncRNAs) play a crucial role in regulation of physiological and developmental processes. Therefore, dysregulated ncRNAs are involved in the occurrence of diversified diseases, including cancer. In cumulative studies, ncRNAs are concerned with pathogenetic mechanisms of HPV-negative tumors via regulating gene expression and signal transduction. It is important to decipher the functions of ncRNAs in HPV-negative cancers and identify the potential biomarkers, which will bring new treatment strategies for improving outcome of cancer therapy. In this review, we demonstrated the effects of ncRNAs via regulating the development and progression of HPV- negative tumors by directly or indirectly acting on target molecules, which provide a basis for future tumor targeted therapy by targeting ncRNAs for HPV-negative cancers.
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Affiliation(s)
- Xin Chen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Hejing Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhi-Wei Wang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China; Department of Research and Development, Beijing Zhongwei Research Center of Biological and Translational Medicine, Beijing 100161, China.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China.
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Yang X, Cao D, Ma W, Gao S, Wen G, Zhong J. Wnt signaling in triple-negative breast cancers: Its roles in molecular subtyping and cancer cell stemness and its crosstalk with non-coding RNAs. Life Sci 2022; 300:120565. [DOI: 10.1016/j.lfs.2022.120565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
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Caponnetto A, Battaglia R, Ferrara C, Vento ME, Borzì P, Paradiso M, Scollo P, Purrello M, Longobardi S, D’Hooghe T, Valerio D, Di Pietro C. Down-regulation of long non-coding RNAs in reproductive aging and analysis of the lncRNA-miRNA-mRNA networks in human cumulus cells. J Assist Reprod Genet 2022; 39:919-931. [PMID: 35247118 PMCID: PMC9050988 DOI: 10.1007/s10815-022-02446-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/23/2022] [Indexed: 02/02/2023] Open
Abstract
PURPOSE Long non-coding RNAs (lncRNAs) control gene expression at multiple levels. By interacting with microRNAs (miRNAs), they regulate their mRNA targets creating dynamic regulatory networks involved in different cellular processes. Their role in follicle development and oocyte maturation has recently emerged. lncRNA deregulation has been found associated with different pathological conditions. In this study, we identified differentially expressed lncRNAs in cumulus cells (CCs) isolated from MII oocytes of advanced maternal age women and proposed ceRNA-networks involved in signaling pathways crucial in ovarian folliculogenesis and female germ cell maturation. METHODS We performed a high-throughput analysis of the expression profile of 68 lncRNAs from CCs of aged and young women by using NanoString technology. By miRNet, TarPmiR, miRTarBase, OKdb, and KEGG we predicted some ceRNA-networks involving the differentially expressed (DE) lncRNAs, miRNA interactors, and their mRNA target genes. RESULTS We identified 28 lncRNAs down-regulated in CC samples from aged women. The analysis revealed that the miRNAs binding 11 of the DE lncRNAs and their mRNA targets are included in ceRNA-networks involved in the regulation of the PI3K-Akt, FOXO, and p53 signaling pathways. CONCLUSION We proposed that the lncRNA down-regulation in CCs from aged women could influence the expression of genes encoding proteins deregulated in reproductive aging. A better understanding of the interplay of lncRNA-miRNA-mRNA networks in human CCs could increase our knowledge about the mechanisms of regulation of gene expression involved in aging, lead to the development of novel therapeutics, and improve reproductive outcomes in aged women.
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Affiliation(s)
- Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “Giovanni Sichel, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “Giovanni Sichel, University of Catania, 95123 Catania, Italy
| | - Carmen Ferrara
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “Giovanni Sichel, University of Catania, 95123 Catania, Italy
| | | | | | | | | | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “Giovanni Sichel, University of Catania, 95123 Catania, Italy
| | | | - Thomas D’Hooghe
- Global Medical Affairs Fertility, R&D Healthcare, the Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | | | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “Giovanni Sichel, University of Catania, 95123 Catania, Italy
| | - Italian Society of Embryology, Reproduction, Research (SIERR)
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “Giovanni Sichel, University of Catania, 95123 Catania, Italy
- IVF Unit, Cannizzaro Hospital, Catania, Italy
- Global Clinical Development, Merck Serono SpA, Rome, Italy
- Global Medical Affairs Fertility, R&D Healthcare, the Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
- Institute of Genetic Research (IRG), 80143 Naples, Italy
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Sun P, Hamblin MH, Yin KJ. Non-coding RNAs in the regulation of blood–brain barrier functions in central nervous system disorders. Fluids Barriers CNS 2022; 19:27. [PMID: 35346266 PMCID: PMC8959280 DOI: 10.1186/s12987-022-00317-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 12/26/2022] Open
Abstract
The blood–brain barrier (BBB) is an essential component of the neurovascular unit that controls the exchanges of various biological substances between the blood and the brain. BBB damage is a common feature of different central nervous systems (CNS) disorders and plays a vital role in the pathogenesis of the diseases. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNA (lncRNAs), and circular RNAs (circRNAs), are important regulatory RNA molecules that are involved in almost all cellular processes in normal development and various diseases, including CNS diseases. Cumulative evidences have demonstrated ncRNA regulation of BBB functions in different CNS diseases. In this review, we have summarized the miRNAs, lncRNAs, and circRNAs that can be served as diagnostic and prognostic biomarkers for BBB injuries, and demonstrated the involvement and underlying mechanisms of ncRNAs in modulating BBB structure and function in various CNS diseases, including ischemic stroke, hemorrhagic stroke, traumatic brain injury (TBI), spinal cord injury (SCI), multiple sclerosis (MS), Alzheimer's disease (AD), vascular cognitive impairment and dementia (VCID), brain tumors, brain infections, diabetes, sepsis-associated encephalopathy (SAE), and others. We have also discussed the pharmaceutical drugs that can regulate BBB functions via ncRNAs-related signaling cascades in CNS disorders, along with the challenges, perspective, and therapeutic potential of ncRNA regulation of BBB functions in CNS diseases.
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Sayad A, Najafi S, Hussen BM, Abdullah ST, Movahedpour A, Taheri M, Hajiesmaeili M. The Emerging Roles of the β-Secretase BACE1 and the Long Non-coding RNA BACE1-AS in Human Diseases: A Focus on Neurodegenerative Diseases and Cancer. Front Aging Neurosci 2022; 14:853180. [PMID: 35386116 PMCID: PMC8978056 DOI: 10.3389/fnagi.2022.853180] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/07/2022] [Indexed: 01/18/2023] Open
Abstract
The β-Secretase (BACE1) is widely studied to be particularly involved in amyloid deposition, a process known as the pathogenic pathway in neurodegenerative diseases. Therefore, BACE1 expression is frequently reported to be upregulated in brain samples of the patients with Alzheimer’s disease (AD). BACE1 expression is regulated by BACE1-AS, a long non-coding RNA (lncRNA), which is transcribed in the opposite direction to its locus. BACE1-AS positively regulates the BACE1 expression, and their expression levels are regulated in physiological processes, such as brain and vascular homeostasis, although their roles in the regulation of amyloidogenic process have been studied further. BACE1-AS dysregulation is reported consistent with BACE1 in a number of human diseases, such as AD, Parkinson’s disease (PD), heart failure (HF), and mild cognitive impairment. BACE1 or less BACE1-AS inhibition has shown therapeutic potentials particularly in decreasing manifestations of amyloid-linked neurodegenerative diseases. Here, we have reviewed the role of lncRNA BACE1 and BACE1-AS in a number of human diseases focusing on neurodegenerative disorders, particularly, AD.
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Affiliation(s)
- Arezou Sayad
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | | | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- *Correspondence: Mohammad Taheri,
| | - Mohammadreza Hajiesmaeili
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Critical Care Quality Improvement Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Mohammadreza Hajiesmaeili,
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Salehi S, Afzali S, Shahi A, Amirzargar AA, Mansoori Y. Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Organ Transplantation. Front Immunol 2022; 13:835746. [PMID: 35359941 PMCID: PMC8962195 DOI: 10.3389/fimmu.2022.835746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Organ transplantation is the most preferred treatment option for end-stage organ diseases; however, allograft rejection is the major hurdle in successful long-term transplant survival. In spite of developing better HLA matching and more effective immunosuppressive regimen, one-year graft survival has been increased by nearly 90% and the incidence of acute rejection by one-year post-transplantation has been decreased by 12.2% in the last decades, chronic allograft rejection has remained as one of the major obstacles to the long-lasting survival of the transplanted allograft. Therefore, seemingly preventing the allograft rejection and inducing immunological tolerance against transplanted allografts is one of the primary goals in transplantation research to enable long-lasting graft survival. Various mechanisms such as long noncoding RNAs (lncRNAs) have been proposed that induce immune tolerance by modulating the gene expression and regulating innate and adaptive immune responses during transplantation. Besides, because of involvement in regulating epigenetic, transcriptional, and post-translational mechanisms, lncRNAs could affect allograft status. Therefore, these molecules could be considered as the potential targets for prediction, prognosis, diagnosis, and treatment of graft rejection. It is suggested that the noninvasive predictive biomarkers hold promise to overcome the current limitations of conventional tissue biopsy in the diagnosis of rejection. Hence, this review aims to provide a comprehensive overview of lncRNAs and their function to facilitate diagnosis, prognosis, and prediction of the risk of graft rejection, and the suggestive therapeutic choices after transplantation.
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Affiliation(s)
- Saeedeh Salehi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Afzali
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shahi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Ali Akbar Amirzargar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
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Lozano-Velasco E, Garcia-Padilla C, del Mar Muñoz-Gallardo M, Martinez-Amaro FJ, Caño-Carrillo S, Castillo-Casas JM, Sanchez-Fernandez C, Aranega AE, Franco D. Post-Transcriptional Regulation of Molecular Determinants during Cardiogenesis. Int J Mol Sci 2022; 23:ijms23052839. [PMID: 35269981 PMCID: PMC8911333 DOI: 10.3390/ijms23052839] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/19/2022] [Accepted: 02/26/2022] [Indexed: 12/15/2022] Open
Abstract
Cardiovascular development is initiated soon after gastrulation as bilateral precardiac mesoderm is progressively symmetrically determined at both sides of the developing embryo. The precardiac mesoderm subsequently fused at the embryonic midline constituting an embryonic linear heart tube. As development progress, the embryonic heart displays the first sign of left-right asymmetric morphology by the invariably rightward looping of the initial heart tube and prospective embryonic ventricular and atrial chambers emerged. As cardiac development progresses, the atrial and ventricular chambers enlarged and distinct left and right compartments emerge as consequence of the formation of the interatrial and interventricular septa, respectively. The last steps of cardiac morphogenesis are represented by the completion of atrial and ventricular septation, resulting in the configuration of a double circuitry with distinct systemic and pulmonary chambers, each of them with distinct inlets and outlets connections. Over the last decade, our understanding of the contribution of multiple growth factor signaling cascades such as Tgf-beta, Bmp and Wnt signaling as well as of transcriptional regulators to cardiac morphogenesis have greatly enlarged. Recently, a novel layer of complexity has emerged with the discovery of non-coding RNAs, particularly microRNAs and lncRNAs. Herein, we provide a state-of-the-art review of the contribution of non-coding RNAs during cardiac development. microRNAs and lncRNAs have been reported to functional modulate all stages of cardiac morphogenesis, spanning from lateral plate mesoderm formation to outflow tract septation, by modulating major growth factor signaling pathways as well as those transcriptional regulators involved in cardiac development.
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Affiliation(s)
- Estefania Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
| | - Carlos Garcia-Padilla
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Department of Anatomy, Embryology and Zoology, School of Medicine, University of Extremadura, 06006 Badajoz, Spain
| | - Maria del Mar Muñoz-Gallardo
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Francisco Jose Martinez-Amaro
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Sheila Caño-Carrillo
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Juan Manuel Castillo-Casas
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
| | - Cristina Sanchez-Fernandez
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
| | - Amelia E. Aranega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (E.L.-V.); (C.G.-P.); (M.d.M.M.-G.); (F.J.M.-A.); (S.C.-C.); (J.M.C.-C.); (C.S.-F.); (A.E.A.)
- Fundación Medina, 18007 Granada, Spain
- Correspondence:
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LncRNA MALAT1 functions as a biomarker of no-reflow phenomenon in ST-segment elevation myocardial infarction patients receiving primary percutaneous coronary intervention. Sci Rep 2022; 12:3294. [PMID: 35228564 PMCID: PMC8885644 DOI: 10.1038/s41598-022-06923-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/21/2022] [Indexed: 11/20/2022] Open
Abstract
MALAT1 was reported to sponge miR-30e, miR-126 and miR-155 in the pathogenesis of many diseases. Plasma miR-30e can indicate the risk of no-reflow during primary percutaneous coronary intervention (pPCI), while miR-126 can be used as a predictor of coronary slow flow phenomenon. In this study, we compared the diagnostic value of above genes in the prediction of no-reflow phenomenon in ST-segment elevation myocardial infarction (STEMI) subjects receiving pPCI. Quantitative real-time PCR, ELISA, Western blot and luciferase assays were performed to explore the regulatory relationship of MALAT1/miR-30e, MALAT1/miR-126, MALAT1/miR-155, miR-126/HPSE, and miR-155/EDN1. ROC analysis was carried out to evaluate the potential value of MALAT1, miRNAs and target genes in differentiating normal reflow and no-reflow in STEMI patients receiving pPCI. Elevated MALAT1, CRP, HPSE, and EDN1 expression and suppressed miR-30e, miR-155 and miR-126 expression was found in the plasma of STEMI patients receiving pPCI who were diagnosed with no-reflow phenomenon. ROC analysis showed that the expression of MALAT1, miR-30e, miR-126 and CRP could be used as predictive biomarkers to differentiate normal reflow and no-reflow in STEMI patients receiving pPCI. MALAT1 was found to suppress the expression of miR-30e, miR-126 and miR-155, and HPSE and EDN1 were respectively targeted by miR-126 and miR-155. This study demonstrated that MALAT1 could respectively sponge the expression of miR-30e, miR-126 and miR-155. And miR-30e, miR-126 and miR-155 respectively targeted CRP, HPSE and EDN1 negatively. Moreover, MALAT1 could function as an effective biomarker of no-reflow phenomenon in STEMI patients receiving pPCI.
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Romano R, Cillo F, Moracas C, Pignata L, Nannola C, Toriello E, De Rosa A, Cirillo E, Coppola E, Giardino G, Brunetti-Pierri N, Riccio A, Pignata C. Epigenetic Alterations in Inborn Errors of Immunity. J Clin Med 2022; 11:jcm11051261. [PMID: 35268351 PMCID: PMC8910960 DOI: 10.3390/jcm11051261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
The epigenome bridges environmental factors and the genome, fine-tuning the process of gene transcription. Physiological programs, including the development, maturation and maintenance of cellular identity and function, are modulated by intricate epigenetic changes that encompass DNA methylation, chromatin remodeling, histone modifications and RNA processing. The collection of genome-wide DNA methylation data has recently shed new light into the potential contribution of epigenetics in pathophysiology, particularly in the field of immune system and host defense. The study of patients carrying mutations in genes encoding for molecules involved in the epigenetic machinery has allowed the identification and better characterization of environment-genome interactions via epigenetics as well as paving the way for the development of new potential therapeutic options. In this review, we summarize current knowledge of the role of epigenetic modifications in the immune system and outline their potential involvement in the pathogenesis of inborn errors of immunity.
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Affiliation(s)
- Roberta Romano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Francesca Cillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Cristina Moracas
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Chiara Nannola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Elisabetta Toriello
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Antonio De Rosa
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emma Coppola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Nicola Brunetti-Pierri
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
- Correspondence: (A.R.); (C.P.)
| | - Claudio Pignata
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
- Correspondence: (A.R.); (C.P.)
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Gkoutsias A, Makis A. The role of epigenetics in childhood autoimmune diseases with hematological manifestations. Pediatr Investig 2022; 6:36-46. [PMID: 35382418 PMCID: PMC8960932 DOI: 10.1002/ped4.12309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/22/2021] [Indexed: 11/18/2022] Open
Abstract
Autoimmune diseases with hematological manifestations are often characterized by chronicity and relapses despite treatment, and the underlying pathogenetic mechanisms remain unknown. Epigenetic alterations play a vital role in the deregulation of immune tolerance and the development of autoimmune diseases. In recent years, study of epigenetic mechanisms in both adult and childhood autoimmune disorders has been seeking to explain the pathophysiology of these heterogeneous diseases and to elucidate the interaction between genetic and environmental factors. Various mechanisms, including DNA methylation, histone modifications (chromatin remodeling), and noncoding RNAs (ncRNAs), have been studied extensively in the context of autoimmune diseases. This paper summarizes the epigenetic patterns in some of the most common childhood autoimmune disorders with hematological manifestations, based on epigenetic studies in children with primary immune thrombocytopenia (ITP), systemic lupus erythematosus (SLE), and juvenile idiopathic arthritis (JIA). Research findings indicate that methylation changes in genes expressed on T cells, modifications at a variety of histone sites, and alterations in the expression of several ncRNAs are involved in the pathogenesis of these diseases. These mechanisms not only determine the development of these diseases but also affect the severity of the clinical presentation and biochemical markers. Further studies will provide new tools for the prevention and diagnosis of childhood autoimmune disorders, and possible novel treatment options.
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Affiliation(s)
- Athanasios Gkoutsias
- Department of Pediatrics Faculty of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Alexandros Makis
- Department of Pediatrics Faculty of Medicine School of Health Sciences University of Ioannina Ioannina Greece
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A Non-Canonical Link between Non-Coding RNAs and Cardiovascular Diseases. Biomedicines 2022; 10:biomedicines10020445. [PMID: 35203652 PMCID: PMC8962294 DOI: 10.3390/biomedicines10020445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
Cardiovascular diseases (CVDs) are among the top leading causes of mortality worldwide. Besides canonical environmental and genetic changes reported so far for CVDs, non-coding RNAs (ncRNAs) have emerged as key regulators of genetic and epigenetic mechanisms involved in CVD progression. High-throughput and sequencing data revealed that almost 80% of the total genome not only encodes for canonical ncRNAs, such as micro and long ncRNAs (miRNAs and lncRNAs), but also generates novel non-canonical sub-classes of ncRNAs, such as isomiRs and miRNA- and lncRNA-like RNAs. Moreover, recent studies reveal that canonical ncRNA sequences can influence the onset and evolution of CVD through novel “non-canonical” mechanisms. However, a debate exists over the real existence of these non-canonical ncRNAs and their concrete biochemical functions, with most of the dark genome being considered as “junk RNA”. In this review, we report on the ncRNAs with a scientifically validated canonical and non-canonical biogenesis. Moreover, we report on canonical ncRNAs that play a role in CVD through non-canonical mechanisms of action.
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147
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Non-Coding RNAs in the Crosstalk between Breast Cancer Cells and Tumor-Associated Macrophages. Noncoding RNA 2022; 8:ncrna8010016. [PMID: 35202089 PMCID: PMC8874851 DOI: 10.3390/ncrna8010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a pivotal role in regulating the tumor microenvironment (TME) by controlling gene expression at multiple levels. In tumors, ncRNAs can mediate the crosstalk between cancer cells and other cells in the TME, such as immune cells, stromal cells, and endothelial cells, influencing tumor development and progression. Tumor-associated macrophages (TAMs) are among the most abundant inflammatory cells infiltrating solid cancers that promote tumorigenesis, and their infiltration correlates with a poor prognosis in many tumors. Cancer cells produce different ncRNAs that orchestrate TAM recruitment and polarization toward a tumor-promoting phenotype. Tumor-reprogrammed macrophages shape the TME by promoting angiogenesis and tissue remodeling, and suppressing the anti-tumor activity of adaptive immune cells. TAMs can also produce ncRNA molecules that boost cancer cell proliferation and direct their phenotype and metabolic changes facilitating cancer progression and metastasis. This review will focus on the crosstalk between cancer cells and TAMs mediated by microRNAs and long non-coding RNAs during breast cancer (BC) initiation and progression.
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148
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Sasa GBK, Xuan C, Chen M, Jiang Z, Ding X. Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review. Transl Cancer Res 2022; 10:5406-5429. [PMID: 35116387 PMCID: PMC8799054 DOI: 10.21037/tcr-21-1607] [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: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 11/06/2022]
Abstract
Objective To explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in lung squamous cell carcinoma (LUSC), emphasizing their exact roles in carcinogenesis and modes of action. Background LUSC is the second most prevalent form, accounting for around 30% of non-small cell lung cancer (NSCLC). To date, molecular-targeted treatments have significantly improved overall survival in lung adenocarcinoma patients but have had little effect on LUSC therapy. As a result, there is an urgent need to discover new treatments for LUSC that are based on existing genomic methods. Methods In this review, we summarized and analyzed recent research on the biological activities and processes of lncRNA, immunotherapy, and DNA methylation in the formation of LUSC. The relevant studies were retrieved using a thorough search of Pubmed, Web of Science, Science Direct, Google Scholar, and the university's online library, among other sources. Conclusions LncRNAs are the primary components of the mammalian transcriptome and are emerging as master regulators of a number of cellular processes, including the cell cycle, differentiation, apoptosis, and growth, and are implicated in the pathogenesis of a variety of cancers, including LUSC. Understanding their role in LUSC in detail may help develop innovative treatment methods and tactics for LUSC. Meanwhile, immunotherapy has transformed the LUSC treatment and is now considered the new standard of care. To get a better knowledge of LUSC biology, it is critical to develop superior modeling systems. Preclinical models, particularly those that resemble human illness by preserving the tumor immune environment, are essential for studying cancer progression and evaluating novel treatment targets. DNA methylation, similarly, is a component of epigenetic alterations that regulate cellular function and contribute to cancer development. By methylating the promoter regions of tumor suppressor genes, abnormal DNA methylation silences their expression. DNA methylation indicators are critical in the early detection of lung cancer, predicting therapy efficacy, and tracking treatment resistance. As such, this review seeks to explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in LUSC, emphasizing their exact roles in carcinogenesis and modes of action.
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Affiliation(s)
- Gabriel B K Sasa
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Xuan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Meiyue Chen
- The fourth affiliated hospital, Zhejiang University of Medicine, Hangzhou, China
| | - Zhenggang Jiang
- Department of Science Research and Information Management, Zhejiang Provincial Centers for Disease Control and Prevention, Hangzhou, China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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149
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Park HJ, Jung C, Yoo TH. Development of one-step isothermal methods to detect RNAs using hairpin-loop signal converters and proximity proteolysis reaction. Biosens Bioelectron 2022; 197:113769. [PMID: 34773751 DOI: 10.1016/j.bios.2021.113769] [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: 08/27/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Ribonucleic acids (RNAs) provide valuable information for biological systems and act as important indicators of disease states. RNAs are diverse in size and structure, and various strategies have been proposed for the detection of nucleic acids; however, developing them into point-of-care (POC) tests has been challenging as most of them consist of complex time-consuming steps. Here, we propose a strategy to assay RNAs using a hairpin-loop (HP) converter and proximity proteolysis reaction (PPR). Interaction between the loop part of HP and its target exposes a single strand of nucleotides, which acts as the template for PPR. A pair of protease and zymogen-conjugated nucleic acids associates with the adjacent regions of the template, resulting in an enhanced proteolysis reaction between protease and zymogen. The activated zymogen then generates a color signal through the hydrolysis of a chromogenic substrate. The combination of HP converter and PPR allowed the same pair of protease- and zymogen-nucleic acids to be used for different RNAs. Guidelines were provided for designing HP converters based on computational analyses and experimental characterizations. This strategy using an HP converter and PPR has been successfully applied to develop simple isothermal methods for the detection of various RNAs, including several microRNAs and KRAS mRNA, in the picomolar range in 1 h. The simplicity of designing HP converters and the beneficial properties of PPR as POC tests would enable the development of novel methods to detect RNAs under low-resource conditions.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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Crosstalk between Long Non Coding RNAs, microRNAs and DNA Damage Repair in Prostate Cancer: New Therapeutic Opportunities? Cancers (Basel) 2022; 14:cancers14030755. [PMID: 35159022 PMCID: PMC8834032 DOI: 10.3390/cancers14030755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Non-coding RNAs are a type of genetic material that doesn’t make protein, but performs diverse regulatory functions. In prostate cancer, most treatments target proteins, and resistance to such therapies is common, leading to disease progression. Targeting non-coding RNAs may provide alterative treatment options and potentially overcome drug resistance. Major types of non-coding RNAs include tiny ‘microRNAs’ and much longer ‘long non-coding RNAs’. Scientific studies have shown that these form a major part of the human genome, and play key roles in altering gene activity and determining the fate of cells. Importantly, in cancer, their activity is altered. Recent evidence suggests that microRNAs and long non-coding RNAs play important roles in controlling response to DNA damage. In this review, we explore how different types of non-coding RNA interact to control cell DNA damage responses, and how this knowledge may be used to design better prostate cancer treatments and tests. Abstract It is increasingly appreciated that transcripts derived from non-coding parts of the human genome, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of biological processes both in normal physiology and disease. Their dysregulation during tumourigenesis has attracted significant interest in their exploitation as novel cancer therapeutics. Prostate cancer (PCa), as one of the most diagnosed malignancies and a leading cause of cancer-related death in men, continues to pose a major public health problem. In particular, survival of men with metastatic disease is very poor. Defects in DNA damage response (DDR) pathways culminate in genomic instability in PCa, which is associated with aggressive disease and poor patient outcome. Treatment options for metastatic PCa remain limited. Thus, researchers are increasingly targeting ncRNAs and DDR pathways to develop new biomarkers and therapeutics for PCa. Increasing evidence points to a widespread and biologically-relevant regulatory network of interactions between lncRNAs and miRNAs, with implications for major biological and pathological processes. This review summarises the current state of knowledge surrounding the roles of the lncRNA:miRNA interactions in PCa DDR, and their emerging potential as predictive and diagnostic biomarkers. We also discuss their therapeutic promise for the clinical management of PCa.
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