1
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Wang F, Zhou C, Zhu Y, Keshavarzi M. The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers. Cell Biol Toxicol 2024; 40:42. [PMID: 38836981 PMCID: PMC11153289 DOI: 10.1007/s10565-024-09884-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
Many types of gynecological cancer (GC) are often silent until they reach an advanced stage, and are therefore often diagnosed too late for effective treatment. Hence, there is a real need for more efficient diagnosis and treatment for patients with GC. During recent years, researchers have increasingly studied the impact of microRNAs cancer development, leading to a number of applications in detection and treatment. MicroRNAs are a particular group of tiny RNA molecules that regulate regular gene expression by affecting the translation process. The downregulation of numerous miRNAs has been observed in human malignancies. Let-7 is an example of a miRNA that controls cellular processes as well as signaling cascades to affect post-transcriptional gene expression. Recent research supports the hypothesis that enhancing let-7 expression in those cancers where it is downregulated may be a potential treatment option. Exosomes are tiny vesicles that move through body fluids and can include components like miRNAs (including let-7) that are important for communication between cells. Studies proved that exosomes are able to enhance tumor growth, angiogenesis, chemoresistance, metastasis, and immune evasion, thus suggesting their importance in GC management.
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Affiliation(s)
- Fei Wang
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Chundi Zhou
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Yanping Zhu
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China.
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Tehran, Iran.
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2
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Cai Y, Liu Y, Sun Y, Ren Y. LncRNA DLG5-AS1 facilitates breast cancer cell proliferation and invasion by promoting EZH2-mediated transcriptional silencing of SFRP1. Arch Biochem Biophys 2024; 756:110018. [PMID: 38677505 DOI: 10.1016/j.abb.2024.110018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
Rapid proliferation and metastasis of breast cancer contributed to poor clinical prognosis. Accumulating evidence revealed that the dysregulation of long noncoding RNAs (lncRNAs) was associated with breast cancer progression. However, the role of lncRNA DLG5-AS1 in breast cancer has not been established. Here, we investigated the mechanisms of DLG5-AS1 in the development of breast cancer. We found that the expression of DLG5-AS1 was significantly upregulated in breast cancer tissues and cell lines. DLG5-AS1 interference markedly restrained AU565 cell proliferation, invasion, the expression of apoptosis related (caspase3 and caspase8) and Wnt/β-catenin pathway related proteins (wnt5a, β-Catenin and c-Myc), as well as promoted cell apoptosis, whereas DLG5-AS1 overexpression showed an opposite effects. In addition, DLG5-AS1 could directly bind with miR-519 b-3p. We also found that enhancer of zeste homolog 2 (EZH2) is a direct target of miR-519 b-3p, and DLG5-AS1 upregulated EZH2 expression by inhibiting the expression of miR-519 b-3p. EZH2 restrained secreted frizzled related protein 1 (SFRP1) expression through inducing H3 histone methylation in its promoter. MiR-519 b-3p overexpression or SFRP1 knockdown memorably reversed the effects of DLG5-AS1 overexpression on cell functions and Wnt/β-Catenin pathway related protein expression. Finally, in vivo experiments demonstrated that silencing of DLG5-AS1 inhibited xenograft tumor development in mice. Taken together, these findings demonstrated that DLG5-AS1 facilitated cell proliferation and invasion by promoting EZH2-mediated transcriptional silencing of SFRP1 in breast cancer.
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Affiliation(s)
- Yun Cai
- Department of Traditional Chinese Medicine (TCM), The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Yi Liu
- Department of Traditional Chinese Medicine (TCM), The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Ye Sun
- Department of Traditional Chinese Medicine (TCM), The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Yu Ren
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
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3
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Azwar S, Ng CT, Zahari Sham SY, Seow HF, Chai M, Ghazali MF, Jabar MF. Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes. Noncoding RNA 2024; 10:25. [PMID: 38668383 PMCID: PMC11054952 DOI: 10.3390/ncrna10020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/28/2023] [Accepted: 10/07/2023] [Indexed: 04/29/2024] Open
Abstract
A growing number of studies have suggested the involvement of long non-coding RNAs as the key players in not just the initiation and progression of the tumor microenvironment, but also in chemotherapy tolerance. In the present study, generated 5-FU-resistant SW480/DR cells were analyzed via cDNA microarray for its aberrant lncRNAs and mRNAs expression in comparison with the 5-FU-susceptible SW480/DS cells. Among the 126 lncRNAs described, lncRNAs GNAS-AS1, MIR205HG, and LOC102723721 have been identified to be significantly upregulated, while lncRNs lnc-RP11-597K23.2.1-2, LOC100507639, and CCDC144NL-AS1 have been found to be significantly downregulated. In the meantime, bioinformatic analysis through gene ontology studies of aberrantly expressed mRNAs revealed "regulated exocytosis", among others, as the biological process most impacted in SW480/DR cells. To investigate, exosome purification was then carried out and its characterization were validated via transmission electron microscopy and nanoparticle tracking analysis. Interestingly, it was determined that the 5-FU-resistant SW480/DR cells secretes significantly higher concentration of extracellular vesicles, particularly, exosomes when compared to the 5-FU-susceptible SW480/DS cells. Based on the lncRNA-mRNA interaction network analysis generated, lncRNA GNAS-AS1 and MIR205HG have been identified to be potentially involved in the incidence of 5-FU resistance in SW480 colon cancer cells through promoting increased release of exosomes into the intercellular matrix. Our study hopes not only to provide insights on the list of involved candidate lncRNAs, but also to elucidate the role exosomes play in the initiation and development of 5-FU chemotherapy resistance in colon cancer cells.
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Affiliation(s)
- Shamin Azwar
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.Y.Z.S.)
| | - Chin Tat Ng
- Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Malaysia;
| | - Siti Yazmin Zahari Sham
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.Y.Z.S.)
| | - Heng Fong Seow
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.Y.Z.S.)
| | - Minhian Chai
- School of Animal, Aquatic and Environmental Sciences, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut 22200, Malaysia; (M.C.); (M.F.G.)
| | - Mohd Faizal Ghazali
- School of Animal, Aquatic and Environmental Sciences, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut 22200, Malaysia; (M.C.); (M.F.G.)
| | - Mohd Faisal Jabar
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
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4
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Davodabadi F, Mirinejad S, Malik S, Dhasmana A, Ulucan-Karnak F, Sargazi S, Sargazi S, Fathi-Karkan S, Rahdar A. Nanotherapeutic approaches for delivery of long non-coding RNAs: an updated review with emphasis on cancer. NANOSCALE 2024; 16:3881-3914. [PMID: 38353296 DOI: 10.1039/d3nr05656b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The long noncoding RNAs (lncRNAs) comprise a wide range of RNA species whose length exceeds 200 nucleotides, which regulate the expression of genes and cellular functions in a wide range of organisms. Several diseases, including malignancy, have been associated with lncRNA dysregulation. Due to their functions in cancer development and progression, lncRNAs have emerged as promising biomarkers and therapeutic targets in cancer diagnosis and treatment. Several studies have investigated the anti-cancer properties of lncRNAs; however, only a few lncRNAs have been found to exhibit tumor suppressor properties. Furthermore, their length and poor stability make them difficult to synthesize. Thus, to overcome the instability of lncRNAs, poor specificity, and their off-target effects, researchers have constructed nanocarriers that encapsulate lncRNAs. Recently, translational medicine research has focused on delivering lncRNAs into tumor cells, including cancer cells, through nano-drug delivery systems in vivo. The developed nanocarriers can protect, target, and release lncRNAs under controlled conditions without appreciable adverse effects. To deliver lncRNAs to cancer cells, various nanocarriers, such as exosomes, microbubbles, polymer nanoparticles, 1,2-dioleyl-3-trimethylammoniumpropane chloride nanocarriers, and virus-like particles, have been successfully developed. Despite this, every nanocarrier has its own advantages and disadvantages when it comes to delivering nucleic acids effectively and safely. This article examines the current status of nanocarriers for lncRNA delivery in cancer therapy, focusing on their potential to enhance cancer treatment.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran.
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi-834002, India.
| | - Archna Dhasmana
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, 248140, India.
| | - Fulden Ulucan-Karnak
- Department of Medical Biochemistry, Institute of Health Sciences, Ege University, İzmir 35100, Turkey.
| | - Sara Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166, Iran
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd 9414974877, Iran.
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, P. O. Box. 98613-35856, Iran.
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5
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Gonzales LR, Blom S, Henriques R, Bachem CWB, Immink RGH. LncRNAs: the art of being influential without protein. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00021-9. [PMID: 38368122 DOI: 10.1016/j.tplants.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/19/2024]
Abstract
The plant long noncoding (lnc)RNA field is on the brink of transitioning from large-scale identification of lncRNAs to their functional characterization. Due to the cross-kingdom conservation of interaction types and molecular functions, there is much to be learned from mammalian lncRNA research. Here, we discuss the different molecular processes involving lncRNAs from the regulation of chromatin to splicing. Furthermore, we discuss the lncRNA interactome, which includes proteins, other RNAs, and DNA. We explore and discuss how mammalian lncRNA functionalities could be reflected in similar pathways in plants and hypothesize that several breakthroughs in mammalian research could lead to the discovery of novel plant lncRNA molecular functions. Expanding our knowledge of the biological role of lncRNAs and their multiple applications paves the way for future agricultural applications.
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Affiliation(s)
| | - Suze Blom
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rossana Henriques
- School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Christian W B Bachem
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands.
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6
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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7
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Bonilauri B, Ribeiro AL, Spangenberg L, Dallagiovanna B. Unveiling Polysomal Long Non-Coding RNA Expression on the First Day of Adipogenesis and Osteogenesis in Human Adipose-Derived Stem Cells. Int J Mol Sci 2024; 25:2013. [PMID: 38396700 PMCID: PMC10888724 DOI: 10.3390/ijms25042013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/25/2024] Open
Abstract
Understanding the intricate molecular mechanisms governing the fate of human adipose-derived stem cells (hASCs) is essential for elucidating the delicate balance between adipogenic and osteogenic differentiation in both healthy and pathological conditions. Long non-coding RNAs (lncRNAs) have emerged as key regulators involved in lineage commitment and differentiation of stem cells, operating at various levels of gene regulation, including transcriptional, post-transcriptional, and post-translational processes. To gain deeper insights into the role of lncRNAs' in hASCs' differentiation, we conducted a comprehensive analysis of the lncRNA transcriptome (RNA-seq) and translatome (polysomal-RNA-seq) during a 24 h period of adipogenesis and osteogenesis. Our findings revealed distinct expression patterns between the transcriptome and translatome during both differentiation processes, highlighting 90 lncRNAs that are exclusively regulated in the polysomal fraction. These findings underscore the significance of investigating lncRNAs associated with ribosomes, considering their unique expression patterns and potential mechanisms of action, such as translational regulation and potential coding capacity for microproteins. Additionally, we identified specific lncRNA gene expression programs associated with adipogenesis and osteogenesis during the early stages of cell differentiation. By shedding light on the expression and potential functions of these polysome-associated lncRNAs, we aim to deepen our understanding of their involvement in the regulation of adipogenic and osteogenic differentiation, ultimately paving the way for novel therapeutic strategies and insights into regenerative medicine.
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Affiliation(s)
- Bernardo Bonilauri
- Stem Cell Basic Biology Laboratory (LABCET), Carlos Chagas Institute—Fiocruz/PR, Curitiba 81350-010, PR, Brazil;
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Annanda Lyra Ribeiro
- Stem Cell Basic Biology Laboratory (LABCET), Carlos Chagas Institute—Fiocruz/PR, Curitiba 81350-010, PR, Brazil;
| | - Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;
| | - Bruno Dallagiovanna
- Stem Cell Basic Biology Laboratory (LABCET), Carlos Chagas Institute—Fiocruz/PR, Curitiba 81350-010, PR, Brazil;
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8
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Özdemir S, Çomaklı S, Küçükler S, Aksungur N, Altundaş N, Kara S, Korkut E, Aydın Ş, Bağcı B, Çulha MH, Öztürk G. Integrative analysis of serum-derived exosomal lncRNA profiles of alveolar echinococcosis patients. Gene 2024; 892:147884. [PMID: 37813208 DOI: 10.1016/j.gene.2023.147884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
Alveolar echinococcosis is a severe zoonotic disease caused by the pseudotumoral intrahepatic development of the larval stage of the tapeworm Echinococcus multilocularis. The diagnosis of alveolar echinococcosis is hard since it has features of liver cancer. LncRNAs are among the non-coding RNAs that have received the most attention in recent biomarker studies. Here, we aimed to identify the serum-derived exosomal lncRNAs associated with alveolar echinococcosis in humans with RNA-seq. After RNA isolation from exosomes, we performed RNA-seq to determine the lncRNAs. We found 8 target genes in the cis direction and a total of 6468 gene targets for lncRNAs were identified in the trans direction. Totally 621 mRNA transcripts were found as differentially expressed between the controls and patients. 278 of them were up-regulated and 343 were down-regulated. Moreover, 234 lncRNAs were found as differentially expressed between the controls and patients. 58 of them were up-regulated, and 176 of them were down-regulated. The top five biological pathways regulated by identified lncRNAs were detected in this study. As a result, it is thought that these results will contribute to lncRNA-based biomarker studies that can be used in the early diagnosis of alveolar echinococcosis in humans.
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Affiliation(s)
- Selçuk Özdemir
- Atatürk University, Faculty of Veterinary Medicine, Department of Genetics, Erzurum, Turkey; German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany.
| | - Selim Çomaklı
- Atatürk University, Faculty of Veterinary Medicine, Department of Pathology, Erzurum, Turkey
| | - Sefa Küçükler
- Atatürk University, Faculty of Veterinary Medicine, Department of Biochemistry, Erzurum, Turkey
| | - Nurhak Aksungur
- Atatürk University, Faculty of Medicine, Department of General Surgery, Erzurum, Turkey
| | - Necip Altundaş
- Atatürk University, Faculty of Medicine, Department of General Surgery, Erzurum, Turkey
| | - Salih Kara
- Atatürk University, Faculty of Medicine, Department of General Surgery, Erzurum, Turkey
| | - Ercan Korkut
- Atatürk University, Faculty of Medicine, Department of General Surgery, Erzurum, Turkey
| | - Şeyma Aydın
- Atatürk University, Faculty of Veterinary Medicine, Department of Genetics, Erzurum, Turkey
| | - Betül Bağcı
- Atatürk University, Faculty of Veterinary Medicine, Department of Genetics, Erzurum, Turkey
| | - Muhammed Hüdai Çulha
- Selçuk University, Faculty of Veterinary Medicine, Department of Genetics, Konya, Turkey
| | - Gürkan Öztürk
- Atatürk University, Faculty of Medicine, Department of General Surgery, Erzurum, Turkey
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9
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Yan Q, Su X, Chen Y, Wang Z, Han W, Xia Q, Mao Y, Si J, Li H, Duan S. LINC00941: a novel player involved in the progression of human cancers. Hum Cell 2024; 37:167-180. [PMID: 37995050 DOI: 10.1007/s13577-023-01002-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
LINC00941, also known as lncRNA-MUF, is an intergenic non-coding RNA located on chromosome 12p11.21. It actively participates in a complex competing endogenous RNA network, regulating the expression of microRNA and its downstream proteins. Through transcriptional and post-transcriptional regulation, LINC00941 plays a vital role in multiple signaling pathways, influencing cell behaviors such as tumor cell proliferation, epithelial-mesenchymal transition, migration, and invasion. Noteworthy is its consistently high expression in various tumor types, closely correlating with clinicopathological features and cancer prognoses. Elevated LINC00941 levels are associated with adverse clinical outcomes, including increased tumor size, extensive lymphatic metastasis, and distant metastasis, leading to poorer survival rates across different cancers. Additionally, LINC00941 and its associated genes are linked to various targeted drugs available in the market. In this comprehensive review, we systematically summarize existing studies, detailing LINC00941's differential expression, clinicopathological and prognostic implications, regulatory mechanisms, and associated therapeutic drugs. Our analysis includes relevant charts and incorporates bioinformatics analyses to verify LINC00941's differential expression in pan-cancer and explore potential transcriptional regulation patterns of downstream targets. This work not only establishes a robust data foundation but also guides future research directions. Given its potential as a significant cancer biomarker and therapeutic target, further investigation into LINC00941's differential expression and regulatory mechanisms is essential.
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Affiliation(s)
- Qibin Yan
- Institute of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Department of Pharmacy, Hangzhou City University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinming Su
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yunzhu Chen
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zehua Wang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Wenbo Han
- Department of Pharmacy, Hangzhou City University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qing Xia
- Institute of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yunan Mao
- Department of Pharmacy, Hangzhou City University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiahua Si
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Hanbing Li
- Institute of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China.
| | - Shiwei Duan
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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10
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Ismail NH, Mussa A, Al-Khreisat MJ, Mohamed Yusoff S, Husin A, Al-Jamal HAN, Johan MF, Islam MA. Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma. Noncoding RNA 2023; 9:68. [PMID: 37987364 PMCID: PMC10660696 DOI: 10.3390/ncrna9060068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
The dysregulation of non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), leads to the development and advancement of multiple myeloma (MM). miRNAs, in particular, are paramount in post-transcriptional gene regulation, promoting mRNA degradation and translational inhibition. As a result, miRNAs can serve as oncogenes or tumor suppressors depending on the target genes. In MM, miRNA disruption could result in abnormal gene expression responsible for cell growth, apoptosis, and other biological processes pertinent to cancer development. The dysregulated miRNAs inhibit the activity of tumor suppressor genes, contributing to disease progression. Nonetheless, several miRNAs are downregulated in MM and have been identified as gene regulators implicated in extracellular matrix remodeling and cell adhesion. miRNA depletion potentially facilitates the tumor advancement and resistance of therapeutic drugs. Additionally, lncRNAs are key regulators of numerous cellular processes, such as gene expression, chromatin remodeling, protein trafficking, and recently linked MM development. The lncRNAs are uniquely expressed and influence gene expression that supports MM growth, in addition to facilitating cellular proliferation and viability via multiple molecular pathways. miRNA and lncRNA alterations potentially result in anomalous gene expression and interfere with the regular functioning of MM. Thus, this review aims to highlight the dysregulation of these ncRNAs, which engender novel therapeutic modalities for the treatment of MM.
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Affiliation(s)
- Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman 11111, Sudan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Shafini Mohamed Yusoff
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azlan Husin
- Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hamid Ali Nagi Al-Jamal
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin (UniSZA), Kuala Nerus 21300, Terengganu, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Md Asiful Islam
- WHO Collaborating Centre for Global Women’s Health, Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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11
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Kalmatte A, Rekha PD, Ratnacaram CK. Emerging cell cycle related non-coding RNA biomarkers from saliva and blood for oral squamous cell carcinoma. Mol Biol Rep 2023; 50:9479-9496. [PMID: 37717257 DOI: 10.1007/s11033-023-08791-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023]
Abstract
The unnotified or undifferentiable early stages of oral squamous cell carcinoma (OSCC) progression are the prime reasons for late-stage detection and poor survival outcomes of oral cancer. This review summarizes the prior research and recent advancements on the influence of dysregulated non-coding RNA (ncRNA) on cell cycle and their employability as diagnostic and prognostic biomarkers of oral cancer. The literature search was performed using the following keywords: 'serum/saliva non-coding RNAs' and 'serum/saliva non-coding RNAs and cell cycle', 'serum/saliva dysregulated ncRNAs and cell cycle', 'Cdk/CKI and ncRNAs', 'tissue ncRNAs' concerning 'oral cancer''. The compiled data focuses mainly on the diagnostic and prognostic significance of MicroRNAs (miRNAs), Circular RNAs (circRNAs), and Long noncoding RNAs (lncRNAs) on oral cancer and all other cancers as well as subject-relevant articles published in languages other than English are beyond the scope of this review and excluded from the study. Moreover, articles focusing on DNA, protein, and metabolite markers are eliminated from the study. While there exist various potential biomolecules such as DNA, RNA, proteins, metabolites, and specific antigens representing predictive biomarkers in body fluids for oral cancer, this review completely focuses on non-coding RNAs restricted to saliva and blood, picking out a few of the reliable ones amongst the recent investigations based on the sophisticated techniques, cohort, and sensitivity as well as specificity, i.e., salivary miR-1307-5p, miR-3928, hsa_circ_0001874 and ENST00000412740, NR_131012, ENST00000588803, NR_038323, miR-21 in circulation. Thus, further studies are required to clinically confirm the usage of these non-invasive biomarkers in oral cancer.
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Affiliation(s)
- Asrarunissa Kalmatte
- Srinivas College Of Physiotherapy, City Campus, Pandeshwar, Mangaluru, Karnataka, 575001, India
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Punchappady Devasya Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Chandrahas Koumar Ratnacaram
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangaluru, Karnataka, 575018, India.
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12
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Zhao J, Li G, Ren Y, Zhang Z, Chen H, Zhang H, Zhao X, Li W, Jia Y, Guan X, Liu M. Ellagic acid inhibits human colon cancer HCT-116 cells by regulating long noncoding RNAs. Anticancer Drugs 2023; 34:1112-1121. [PMID: 36847079 PMCID: PMC10569677 DOI: 10.1097/cad.0000000000001513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 03/01/2023]
Abstract
The natural phenolic compound ellagic acid exerts anti-cancer effects, including activity against colorectal cancer (CRC). Previously, we reported that ellagic acid can inhibit the proliferation of CRC, and can induce cell cycle arrest and apoptosis. This study investigated ellagic acid-mediated anticancer effects using the human colon cancer HCT-116 cell line. After 72 h of ellagic acid treatment, a total of 206 long noncoding RNAs (lncRNAs) with differential expression greater than 1.5-fold were identified (115 down-regulated and 91 up-regulated). Furthermore, the co-expression network analysis of differentially expressed lncRNA and mRNA showed that differential expressed lncRNA might be the target of ellagic acid activity in inhibiting CRC.
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Affiliation(s)
- Jinlu Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Yi Ren
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Zhicheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Hongsheng Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Haopeng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Xingyu Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Wang Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Yucheng Jia
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Xue Guan
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
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Kyrgiafini MA, Giannoulis T, Chatziparasidou A, Christoforidis N, Mamuris Z. Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility. Int J Mol Sci 2023; 24:15002. [PMID: 37834450 PMCID: PMC10573971 DOI: 10.3390/ijms241915002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Male infertility is a global health issue, affecting over 20 million men worldwide. Genetic factors are crucial in various male infertility forms, including teratozoospermia. Nonetheless, the genetic causes of male infertility remain largely unexplored. In this study, we employed whole-genome sequencing and RNA expression analysis to detect differentially expressed (DE) long-noncoding RNAs (lncRNAs) in teratozoospermia, along with mutations that are exclusive to teratozoospermic individuals within these DE lncRNAs regions. Bioinformatic tools were used to assess variants' impact on lncRNA structure, function, and lncRNA-miRNA interactions. Our analysis identified 1166 unique mutations in teratozoospermic men within DE lncRNAs, distinguishing them from normozoospermic men. Among these, 64 variants in 23 lncRNAs showed potential regulatory roles, 7 variants affected 4 lncRNA structures, while 37 variants in 17 lncRNAs caused miRNA target loss or gain. Pathway Enrichment and Gene Ontology analyses of the genes targeted by the affected miRNAs revealed dysregulated pathways in teratozoospermia and a link between male infertility and cancer. This study lists novel variants and lncRNAs associated for the first time with teratozoospermia. These findings pave the way for future studies aiming to enhance diagnosis and therapy in the field of male infertility.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Alexia Chatziparasidou
- Embryolab IVF Unit, St. 173-175 Ethnikis Antistaseos, Kalamaria, 55134 Thessaloniki, Greece
| | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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Farzaneh M, Abouali Gale Dari M, Anbiyaiee A, Najafi S, Dayer D, Mousavi Salehi A, Keivan M, Ghafourian M, Uddin S, Azizidoost S. Emerging roles of the long non-coding RNA NEAT1 in gynecologic cancers. J Cell Commun Signal 2023; 17:531-547. [PMID: 37310654 PMCID: PMC10409959 DOI: 10.1007/s12079-023-00746-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/10/2023] [Indexed: 06/14/2023] Open
Abstract
Gynecologic cancers are a worldwide problem among women. Recently, molecular targeted therapy opened up an avenue for cancer diagnosis and treatment. Long non-coding RNAs (lncRNAs) are RNA molecules (> 200 nt) that are not translated into protein, and interact with DNA, RNA, and proteins. LncRNAs were found to play pivotal roles in cancer tumorigenesis and progression. Nuclear paraspeckle assembly transcript 1 (NEAT1) is a lncRNA that mediates cell proliferation, migration, and EMT in gynecologic cancers by targeting several miRNAs/mRNA axes. Therefore, NEAT1 may function as a potent biomarker for the prediction and treatment of breast, ovarian, cervical, and endometrial cancers. In this narrative review, we summarized various NEAT1-related signaling pathways that are critical in gynecologic cancers. Long non-coding RNA (lncRNA) by targeting various signaling pathways involved in its target genes can regulate the occurrence of gynecologic cancers.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahrokh Abouali Gale Dari
- Department of Obstetrics and Gynecology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Anbiyaiee
- Department of Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Dian Dayer
- Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abdolah Mousavi Salehi
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mona Keivan
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehri Ghafourian
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, 3050, Doha, Qatar
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh 22602 India
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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15
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Orak G, Rezaei HB, Ameli F, Maghsoodi F, Cheraghzade M, Adelipour M. The expression of lncRNAs CASC2, NEAT1, LINC00299 in breast cancer tissues and their relationship with the XBP1 splicing rate in Iranian patients during 2014-2019: A cross-sectional study. Health Sci Rep 2023; 6:e1552. [PMID: 37706018 PMCID: PMC10495808 DOI: 10.1002/hsr2.1552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/29/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Background and Aims Breast cancer is a leading cause of incidence and mortality in women globally. Identifying new molecular markers can aid in cancer diagnosis, targeted therapy, and treatment monitoring. This study aimed to measure the expression of the X-box binding protein 1 (XBP1) gene, an index of the unfolded protein response (UPR), and long noncoding RNAs (lncRNAs), including Nuclear Enriched Abundant Transcript 1 (NEAT1), Cancer Susceptibility Candidate 2 (CASC2), and Long Intergenic Nonprotein Coding RNA 299 (LINC00299), as possible regulators of the UPR pathway. Methods Total RNA was extracted from 40 samples of breast tumor tissues and their respective controls. The expression level of lncRNAs CASC2, NEAT1, and LINC00299 was quantified using reverse transcription-polymerase chain reaction (RT-PCR). The ratio of the spliced form of XBP1 to its unspliced form (XBP1u) was determined by PCR and electrophoresis. Results The results showed a 2.8-fold increase in the ratio of XBP1s/u in breast cancer tissues compared to adjacent nonmalignant samples (p < 0.05). Additionally, the level of lncRNAs NEAT1, CASC2, and LINC00299 in breast tumor tissues increased significantly by twofold, 1.5-fold, and 2.3-fold, respectively, compared to adjacent nonmalignant samples (p < 0.05). Conclusions Based on the association between the expression of lncRNAs CASC2, LINC00299, and NEAT1 and the XBP1s/u ratio, these lncRNAs could be potential regulators of the UPR pathway. Also, CASC2 and NEAT1 genes could be suggested as suitable biomarkers to distinguish cancerous tissue from noncancerous breast tissue due to their significant increase in expression in cancerous samples compared to adjacent noncancerous.
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Affiliation(s)
- Ghazal Orak
- Department of Clinical Biochemistry, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Hossein Babaahmadi Rezaei
- Department of Clinical Biochemistry, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
- Hyperlipidemia Research CenterAhvaz Jundishapur University of Medical ScienceAhvazIran
| | - Fereshteh Ameli
- Department of Pathology, School of MedicineTehran University of Medical ScienceTehranIran
| | - Fatemeh Maghsoodi
- Department of Public HealthAbadan University of Medical SciencesAbadanIran
| | - Maryam Cheraghzade
- Department of Clinical Biochemistry, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Maryam Adelipour
- Department of Clinical Biochemistry, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
- Cellular and Molecular Research Center, Medical Basic Science Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
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Bakr M, Abd-Elmawla MA, Elimam H, Gamal El-Din H, Fawzy A, Abulsoud AI, Rizk SM. Telomerase RNA component lncRNA as potential diagnostic biomarker promotes CRC cellular migration and apoptosis evasion via modulation of β-catenin protein level. Noncoding RNA Res 2023; 8:302-314. [PMID: 37032720 PMCID: PMC10074408 DOI: 10.1016/j.ncrna.2023.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Aim Long non-coding RNA (LncRNA) telomerase RNA component (TERC) has telomerase-dependent and independent activity in numerous cancer types. The present study purposes to demonstrate the role of lncRNA TERC as a diagnostic serum biomarker in colorectal cancer (CRC) patients and the molecular mechanism of lncRNA TERC in inducing tumor in CRC cell lines. Materials and methods PCR array was performed to examine lncRNAs dysregulated in CRC. LncRNA TERC expression level was evaluated in 70 CRC patients and 35 control subjects using RT-qPCR. Then transfection was performed to build down-expression models of lncRNA TERC. ROC curve analysis was applied to assess the diagnostic value of serum LncRNA CRC. In addition, RT-qPCR was used to detect expression level of lncRNA TERC and β-catenin mRNA. Moreover, ELISA and Western blot were used to detect the level of β-catenin protein in sera of CRC patients and cell lines. The biological functions such as cell growth and migration of CRC cells were assessed using a wound healing assay. Cell cycle analysis and apoptosis analysis were performed using flow cytometry. Results The lncRNA TERC is overexpressed in the sera of CRC patients with high diagnostic and stage discrimination accuracy. Furthermore, lncRNA TERC expression was upregulated in CRC cell lines and lncRNA TERC silencing induced cell arrest and apoptosis and inhibited cell migration. Furthermore, inhibition of lncRNA TERC reduces β-catenin protein levels. Conclusion The lncRNA TERC could be considered as an early stages CRC diagnostic biomarker with a good ability to discriminate between CRC stages. lncRNA TERC induces CRC by promoting cell migration and evading apoptosis by elevating the level of β-catenin protein.
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Kałafut J, Czerwonka A, Czapla K, Przybyszewska-Podstawka A, Hermanowicz JM, Rivero-Müller A, Borkiewicz L. Regulation of Notch1 Signalling by Long Non-Coding RNAs in Cancers and Other Health Disorders. Int J Mol Sci 2023; 24:12579. [PMID: 37628760 PMCID: PMC10454443 DOI: 10.3390/ijms241612579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Notch1 signalling plays a multifaceted role in tissue development and homeostasis. Currently, due to the pivotal role of Notch1 signalling, the relationship between NOTCH1 expression and the development of health disorders is being intensively studied. Nevertheless, Notch1 signalling is not only controlled at the transcriptional level but also by a variety of post-translational events. First is the ligand-dependent mechanical activation of NOTCH receptors and then the intracellular crosstalk with other signalling molecules-among those are long non-coding RNAs (lncRNAs). In this review, we provide a detailed overview of the specific role of lncRNAs in the modulation of Notch1 signalling, from expression to activity, and their connection with the development of health disorders, especially cancers.
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Affiliation(s)
- Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Arkadiusz Czerwonka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Karolina Czapla
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Alicja Przybyszewska-Podstawka
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Justyna Magdalena Hermanowicz
- Department of Pharmacodynamics, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland;
- Department of Clinical Pharmacy, Medical University of Bialystok, Waszyngtona 15, 15-274 Bialystok, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
| | - Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Aleje Raławickie 1, 20-059 Lublin, Poland; (J.K.); (A.C.); (K.C.); (A.P.-P.)
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Jaiswal A, Kaushik N, Choi EH, Kaushik NK. Functional impact of non-coding RNAs in high-grade breast carcinoma: Moving from resistance to clinical applications: A comprehensive review. Biochim Biophys Acta Rev Cancer 2023; 1878:188915. [PMID: 37196783 DOI: 10.1016/j.bbcan.2023.188915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/08/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Despite the recent advances in cancer therapy, triple-negative breast cancers (TNBCs) are the most relapsing cancer sub-type. It is partly due to their propensity to develop resistance against the available therapies. An intricate network of regulatory molecules in cellular mechanisms leads to the development of resistance in tumors. Non-coding RNAs (ncRNAs) have gained widespread attention as critical regulators of cancer hallmarks. Existing research suggests that aberrant expression of ncRNAs modulates the oncogenic or tumor suppressive signaling. This can mitigate the responsiveness of efficacious anti-tumor interventions. This review presents a systematic overview of biogenesis and down streaming molecular mechanism of the subgroups of ncRNAs. Furthermore, it explains ncRNA-based strategies and challenges to target the chemo-, radio-, and immunoresistance in TNBCs from a clinical standpoint.
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Affiliation(s)
- Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Suwon 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
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Tang L, Liu QM, Zhang S, Zhou J. LncRNA NR2F1-AS1 as a potential biomarker for prognosis in cancer patients: meta and bioinformatics analysis. Expert Rev Mol Diagn 2023; 23:1263-1272. [PMID: 37902251 DOI: 10.1080/14737159.2023.2277521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023]
Abstract
BACKGROUND Previous studies have shown that the differential expression of lncRNA NR2F1-AS1 is closely related to the prognosis of cancer, but the conclusion is still controversial. Therefore, we conducted a meta-analysis and bioinformatics analysis to explore the correlation between LncRNA NR2F1-AS1 and cancer prognosis. METHODS From the beginning to January 25, 2023, we searched for correlational studies on PubMed, Embase, the Cochrane Library, and Web of Science. We used pooled hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs) to determine the importance of LncRNA NR2F1-AS1 for survival and clinicopathological features of human cancers. RESULTS The meta-analysis of 637 patients in the 11 included articles showed that upregulation of LncRNA NR2F1-AS1 was associated with shorter overall survival (HR = 1.46,95%Cl 1.06-2.01, p = 0.02) in cancer patients. In addition, overexpression of LncRNA NR2F1-AS1 predicted TNM tumor stage (OR = 3.37, 95%Cl 2.07-5.48, p < 0.00001), and Distant metastasis (OR = 0.18, 95%Cl 0.06-0.48, p = 0.0007). However, the difference in age (OR = 1.10,95%Cl 0.71-1.71, p = 0.67), gender (OR = 1.26,95%Cl 0.79-2.00, p = 0.34), Lymph node metastasis (OR = 1.44,95%Cl 0.27-7.80, p = 0.67) or larger tumor size (OR = 1.56,95%Cl 0.48-5.08, p = 0.46) was not statistically significant. CONCLUSION Upregulation of LncRNA NR2F1-AS1 was associated with poor prognosis and advanced clinicopathologic features of tumor patients.
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Affiliation(s)
- Lu Tang
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Qing-Mei Liu
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Shuang Zhang
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jun Zhou
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, Southwest Medical University, Luzhou, Sichuan Province, China
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Wang Q, Xie Z. GAS5 silencing attenuates hypoxia-induced cardiomyocytes injury by targeting miR-21/PTEN. Immun Inflamm Dis 2023; 11:e945. [PMID: 37506155 PMCID: PMC10373574 DOI: 10.1002/iid3.945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
INTRODUCTION Myocardial hypoxia is an important factor causing myocardial infarction (MI). Interestingly, many unknown factors in the molecular mechanism of MI remain unclear. Our study explored the role of lncRNA growth arrest-specific 5 (GAS5) in cell injury under hypoxia. METHODS AS5 expression was assessed in MI and human cardiomyocytes under hypoxia through RT-qPCR assay. Methyl thiazolyl tetrazolium assay, flow cytometry assay, and transwell assay was carried out for cell viability, cell apoptosis, cell migration, and invasion, respectively. The regulatory target of GAS5 was explored through a dual-luciferase reporter assay. RESULTS Our findings indicated that the upregulation of GAS5 was related to hypoxia. Downregulation of GAS5 expression could decrease hypoxia-induced cell apoptosis and increase cell migration and invasion. Moreover, GAS 5 targeted miR-21, which regulated the phosphatase and tension homology deleted on chromosome ten gene (PTEN) expression. Furthermore, the knockdown of miR-21 eliminated the effect of GAS5 silencing on cell injury. CONCLUSION These results indicated that lncRNA GAS5 silencing decreased cardiomyocyte injury by hypoxia-induced through regulating miR-21/PTEN.
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Affiliation(s)
- Qianli Wang
- Cardiovascular Surgery Intensive Care Unit, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, P.R. China
| | - Zan Xie
- Department of Cardiology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong, P.R. China
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Fonseca-Montaño MA, Vázquez-Santillán KI, Hidalgo-Miranda A. The current advances of lncRNAs in breast cancer immunobiology research. Front Immunol 2023; 14:1194300. [PMID: 37342324 PMCID: PMC10277570 DOI: 10.3389/fimmu.2023.1194300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related death in women worldwide. Breast cancer development and progression are mainly associated with tumor-intrinsic alterations in diverse genes and signaling pathways and with tumor-extrinsic dysregulations linked to the tumor immune microenvironment. Significantly, abnormal expression of lncRNAs affects the tumor immune microenvironment characteristics and modulates the behavior of different cancer types, including breast cancer. In this review, we provide the current advances about the role of lncRNAs as tumor-intrinsic and tumor-extrinsic modulators of the antitumoral immune response and the immune microenvironment in breast cancer, as well as lncRNAs which are potential biomarkers of tumor immune microenvironment and clinicopathological characteristics in patients, suggesting that lncRNAs are potential targets for immunotherapy in breast cancer.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Fonseca-Montaño MA, Cisneros-Villanueva M, Coales I, Hidalgo-Miranda A. LINC00426 is a potential immune phenotype-related biomarker and an overall survival predictor in PAM50 luminal B breast cancer. Front Genet 2023; 14:1034569. [PMID: 37260772 PMCID: PMC10228735 DOI: 10.3389/fgene.2023.1034569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets). Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression. Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Isabelle Coales
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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23
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Spirito L, Maturi R, Credendino SC, Manfredi C, Arcaniolo D, De Martino M, Esposito F, Napolitano L, Di Bello F, Fusco A, Pallante P, De Sio M, De Vita G. Differential Expression of LncRNA in Bladder Cancer Development. Diagnostics (Basel) 2023; 13:diagnostics13101745. [PMID: 37238229 DOI: 10.3390/diagnostics13101745] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Bladder cancer (BC) is the tenth most common cancer, with urothelial carcinoma representing about 90% of all BC, including neoplasms and carcinomas of different grades of malignancy. Urinary cytology has a significant role in BC screening and surveillance, although it has a low detection rate and high dependence on the pathologist's experience. The currently available biomarkers are not implemented into routine clinical practice due to high costs or low sensitivity. In recent years, the role of lncRNAs in BC has emerged, even though it is still poorly explored. We have previously shown that the lncRNAs Metallophosphoesterase Domain-Containing 2 Antisense RNA 1 (MPPED2-AS1), Rhabdomyosarcoma-2 Associated Transcript (RMST), Kelch-like protein 14 antisense (Klhl14AS) and Prader Willi/Angelman region RNA 5 (PAR5) are involved in the progression of different types of cancers. Here, we investigated the expression of these molecules in BC, first by interrogating the GEPIA database and observing a different distribution of expression levels between normal and cancer specimens. We then measured them in a cohort of neoplastic bladder lesions, either benign or malignant, from patients with suspicion of BC undergoing transurethral resection of bladder tumor (TURBT). The total RNA from biopsies was analyzed using qRT-PCR for the expression of the four lncRNA genes, showing differential expression of the investigated lncRNAs between normal tissue, benign lesions and cancers. In conclusion, the data reported here highlight the involvement of novel lncRNAs in BC development, whose altered expression could potentially affect the regulatory circuits in which these molecules are involved. Our study paves the way for testing lncRNA genes as markers for BC diagnosis and/or follow-up.
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Affiliation(s)
- Lorenzo Spirito
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Rufina Maturi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Sara Carmela Credendino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Celeste Manfredi
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Davide Arcaniolo
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Marco De Martino
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Napoli, Italy
| | - Francesco Esposito
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
| | - Luigi Napolitano
- Urology Unit, Department of Neurosciences, Reproductive Sciences, and Odontostomatology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Francesco Di Bello
- Urology Unit, Department of Neurosciences, Reproductive Sciences, and Odontostomatology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Alfredo Fusco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
| | - Pierlorenzo Pallante
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
| | - Marco De Sio
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Gabriella De Vita
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
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24
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Arman K, Dalloul Z, Bozgeyik E. Emerging role of microRNAs and long non-coding RNAs in COVID-19 with implications to therapeutics. Gene 2023; 861:147232. [PMID: 36736508 PMCID: PMC9892334 DOI: 10.1016/j.gene.2023.147232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection which is commonly known as COVID-19 (COronaVIrus Disease 2019) has creeped into the human population taking tolls of life and causing tremendous economic crisis. It is indeed crucial to gain knowledge about their characteristics and interactions with human host cells. It has been shown that the majority of our genome consists of non-coding RNAs. Non-coding RNAs including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs) display significant roles in regulating gene expression in almost all cancers and viral diseases. It is intriguing that miRNAs and lncRNAs remarkably regulate the function and expression of major immune components of SARS-CoV-2. MiRNAs act via RNA interference mechanism in which they bind to the complementary sequences of the viral RNA strand, inducing the formation of silencing complex that eventually degrades or inhibits the viral RNA and viral protein expression. LncRNAs have been extensively shown to regulate gene expression in cytokine storm and thus emerges as a critical target for COVID-19 treatment. These lncRNAs also act as competing endogenous RNAs (ceRNAs) by sponging miRNAs and thus affecting the expression of downstream targets during SARS-CoV-2 infection. In this review, we extensively discuss the role of miRNAs and lncRNAs, describe their mechanism of action and their different interacting human targets cells during SARS-CoV-2 infection. Finally, we discuss possible ways how an interference with their molecular function could be exploited for new therapies against SARS-CoV-2.
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Affiliation(s)
- Kaifee Arman
- Institut de recherches cliniques de Montréal, Montréal, QC H2W 1R7, Canada.
| | - Zeinab Dalloul
- Institut de recherches cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Esra Bozgeyik
- Department of Medical Services and Techniques, Vocational School of Health Services, Adiyaman University, Adiyaman, Turkey
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25
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Yin X, Wang S, Ge R, Chen J, Gao Y, Xu S, Yang T. Long non-coding RNA DNMBP-AS1 promotes prostate cancer development by regulating LCLAT1. Syst Biol Reprod Med 2023; 69:142-152. [PMID: 36602957 DOI: 10.1080/19396368.2022.2129520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/22/2022] [Indexed: 01/06/2023]
Abstract
Prostate cancer (PCa) is as a serious threat to male's health around the world. Recent studies have indicated that long non-coding RNAs (lncRNAs) occupy an important position in various human cancers. However, the function and mechanism of lncRNA DNMBP antisense RNA 1 (DNMBP-AS1) in PCa is rarely investigated. RT-qPCR analysis was used to test gene expression. CCK-8, colony formation, EdU staining and transwell assays were conducted to assess the function of DNMBP-AS1 on PCa cell behaviors. RNA pull down, RIP and luciferase reporter assays were implemented to verify the mechanism of DNMBP-AS1. DNMBP-AS1 was obviously up-regulated in PCa cell lines. Functionally, DNMBP-AS1 knockdown weakened cell proliferation, migration and invasion of PCa. Mechanistically, DNMBP-AS1 sponged microRNA-6766-3p (miR-6766-3p) to regulate lysocardiolipin acyltransferase 1 (LCLAT1) expression. Furthermore, DNMBP-AS1 could stabilize LCLAT1 expression by recruiting ELAV like RNA binding protein 1 (ELAVL1). Consequently, rescue assays demonstrated that DNMBP-AS1 regulated PCa cell proliferation, migration and invasion through enhancing LCLAT1 expression. Collectively, we elucidated the function and regulatory mechanism of DNMBP-AS1 and provided the first evidence of DNMBP-AS1 as a driver for PCa.
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Affiliation(s)
- Xiangang Yin
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Suying Wang
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Rong Ge
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Jinping Chen
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Youliang Gao
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Shanshan Xu
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
| | - Ting Yang
- Beijing Jinglai Huake Biotechnology Co., Ltd, Beijing, China
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26
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Islam S, Mukherjee C. Molecular regulation of hypoxia through the lenses of noncoding RNAs and epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1750. [PMID: 35785444 DOI: 10.1002/wrna.1750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Cells maintain homeostasis in response to environmental stress through specific cell stress responses. Hypoxic stress, well known to be associated with diverse solid tumors, is one of the main reasons for cancer-related mortality. Although cells can balance themselves well during hypoxic stress, the underlying molecular mechanisms are not well understood. The enhanced appreciation of diverse roles played by noncoding transcriptome and epigenome in recent years has brought to light the involvement of noncoding RNAs and epigenetic modifiers in hypoxic regulation. The emergence of techniques like deep sequencing has facilitated the identification of large numbers of long noncoding RNAs (lncRNAs) that are differentially regulated in various cancers. Similarly, proteomic studies have identified diverse epigenetic modifiers such as HATs, HDACs, DNMTs, polycomb groups of proteins, and their possible roles in the regulation of hypoxia. The crosstalk between lncRNAs and epigenetic modifiers play a pivotal role in hypoxia-induced cancer initiation and progression. Besides the lncRNAs, several other noncoding RNAs like circular RNAs, miRNAs, and so forth are also expressed during hypoxic conditions. Hypoxia has a profound effect on the expression of noncoding RNAs and epigenetic modifiers. Conversely, noncoding RNAs/epigenetic modifies can regulate the hypoxia signaling axis by modulating the stability of the hypoxia-inducible factors (HIFs). The focus of this review is to illustrate the molecular orchestration underlying hypoxia biology, especially in cancers, which can help in identifying promising therapeutic targets in hypoxia-induced cancers. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Safirul Islam
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
| | - Chandrama Mukherjee
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
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27
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Behnia M, Bradfute SB. The Host Non-Coding RNA Response to Alphavirus Infection. Viruses 2023; 15:v15020562. [PMID: 36851776 PMCID: PMC9967650 DOI: 10.3390/v15020562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Alphaviruses are important human and animal pathogens that can cause a range of debilitating symptoms and are found worldwide. These include arthralgic diseases caused by Old-World viruses and encephalitis induced by infection with New-World alphaviruses. Non-coding RNAs do not encode for proteins, but can modulate cellular response pathways in a myriad of ways. There are several classes of non-coding RNAs, some more well-studied than others. Much research has focused on the mRNA response to infection against alphaviruses, but analysis of non-coding RNA responses has been more limited until recently. This review covers what is known regarding host cell non-coding RNA responses in alphavirus infections and highlights gaps in the knowledge that future research should address.
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28
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Sharma T, Nisar S, Masoodi T, Macha MA, Uddin S, Akil AAS, Pandita TK, Singh M, Bhat AA. Current and emerging biomarkers in ovarian cancer diagnosis; CA125 and beyond. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:85-114. [PMID: 36707207 DOI: 10.1016/bs.apcsb.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ovarian cancer (OC) is one of the most common causes of cancer-related death in women worldwide. Its five-year survival rates are worse than the two most common gynecological cancers, cervical and endometrial. This is because it is asymptomatic in the early stages and usually detected in the advanced metastasized stage. Thus, survival is increasingly dependent on timely diagnosis. The delay in detection is contributed partly by the occurrence of non-specific clinical symptoms in the early stages and the lack of effective biomarkers and detection approaches. This underlines the need for biomarker identification and clinical validation, enabling earlier diagnosis, effective prognosis, and response to therapy. Apart from the traditional diagnostic biomarkers for OC, several new biomarkers have been delineated using advanced high-throughput molecular approaches in recent years. They are currently being clinically evaluated for their true diagnostic potential. In this chapter, we document the commonly utilized traditional screening markers and recently identified emerging biomarkers in OC diagnosis, focusing on secretory and protein biomarkers. We also briefly reviewed the recent advances and prospects in OC diagnosis.
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Affiliation(s)
- Tarang Sharma
- Department of Medical Oncology, Dr. B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sabah Nisar
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Tariq Masoodi
- Laboratory of Cancer immunology and genetics, Sidra Medicine, Doha, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Jammu and Kashmir, India
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Ammira Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Tej K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX, United States
| | - Mayank Singh
- Department of Medical Oncology, Dr. B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar.
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29
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Sabeena S. Role of noncoding RNAs with emphasis on long noncoding RNAs as cervical cancer biomarkers. J Med Virol 2023; 95:e28525. [PMID: 36702772 DOI: 10.1002/jmv.28525] [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: 10/18/2022] [Revised: 12/28/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Cervical cancer is a significant public health problem in developing countries, as most cases present at an advanced stage. This review aimed to analyze the role of noncoding RNAs as diagnostic and prognostic biomarkers in cervical cancers. Published studies on specific microRNA signatures in body fluids and cervical cancer tissues are highly heterogeneous, and there are no validated assays. The precision of the various immune-associated long noncoding (lncRNA) signatures should be assessed in clinical samples. Even though lncRNAs are tissue and cancer-specific, safe and appropriate methods for delivery to tumor tissues, toxicities and side effects are to be explored. Few studies have evaluated deregulated lncRNA expression levels with clinicopathological factors in a limited number of clinical samples. Prospective studies assessing the diagnostic and prognostic roles of circulating lncRNAs and P-Element-induced wimpy testis interacting PIWI RNAs (Piwil RNAs) in cervical cancer cases are essential. For the clinical application of lnc-RNA-based biomarkers, comprehensive research is needed as the impact of noncoding transcripts on molecular pathways is complex. The standardization and validation of deregulated ncRNAs in noninvasive samples of cervical cancer cases are needed.
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30
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Hyttinen JMT, Blasiak J, Kaarniranta K. Non-Coding RNAs Regulating Mitochondrial Functions and the Oxidative Stress Response as Putative Targets against Age-Related Macular Degeneration (AMD). Int J Mol Sci 2023; 24:ijms24032636. [PMID: 36768958 PMCID: PMC9917342 DOI: 10.3390/ijms24032636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Age-related macular degeneration (AMD) is an ever-increasing, insidious disease which reduces the quality of life of millions of elderly people around the world. AMD is characterised by damage to the retinal pigment epithelium (RPE) in the macula region of the retina. The origins of this multi-factorial disease are complex and still not fully understood. Oxidative stress and mitochondrial imbalance in the RPE are believed to be important factors in the development of AMD. In this review, the regulation of the mitochondrial function and antioxidant stress response by non-coding RNAs (ncRNAs), newly emerged epigenetic factors, is discussed. These molecules include microRNAs, long non-coding RNAs, and circular non-coding RNAs. They act mainly as mRNA suppressors, controllers of other ncRNAs, or by interacting with proteins. We include here examples of these RNA molecules which affect various mitochondrial processes and antioxidant signaling of the cell. As a future prospect, the possibility to manipulate these ncRNAs to strengthen mitochondrial and antioxidant response functions is discussed. Non-coding RNAs could be used as potential diagnostic markers for AMD, and in the future, also as therapeutic targets, either by suppressing or increasing their expression. In addition to AMD, it is possible that non-coding RNAs could be regulators in other oxidative stress-related degenerative diseases.
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Affiliation(s)
- Juha M. T. Hyttinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- Correspondence:
| | - Janusz Blasiak
- Department of Molecular Genetics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- Department of Ophthalmology, Kuopio University Hospital, P.O. Box 100, FI-70029 Kuopio, Finland
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31
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Firat H, Zhang L, Baksi S, Leszek P, Schordan E, Ounzain S, Kottwitz J, Patriki D, Heidecker B, Lüscher TF, Pedrazzini T, Devaux Y. FIMICS: A panel of long noncoding RNAs for cardiovascular conditions. Heliyon 2023; 9:e13087. [PMID: 36747920 PMCID: PMC9898641 DOI: 10.1016/j.heliyon.2023.e13087] [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: 09/07/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Cardiovascular disorders such as heart failure are leading causes of mortality. Patient stratification via identification of novel biomarkers could improve management of cardiovascular diseases of complex etiologies. Long-noncoding RNAs (lncRNAs) are highly tissue-specific in nature and have emerged as important biomarkers in human diseases. In this study, we aimed to identify cardiac-enriched lncRNAs as potential biomarkers for cardiovascular conditions. Deep RNA sequencing and quantitative PCR identified differentially expressed lncRNAs between failing and non-failing hearts. An independent dataset was used to evaluate the enrichment of lncRNAs in normal hearts. We identified a panel of 2906 lncRNAs, named FIMICS, that were either cardiac-enriched or differentially expressed between failing and non-failing hearts. Expression of lncRNAs in blood samples differentiated patients with myocarditis and acute myocardial infarction. We hereby present the FIMICS panel, a readily available tool to provide insights into cardiovascular pathologies and which could be helpful for diagnosis, monitoring and prognosis purposes.
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Affiliation(s)
| | - Lu Zhang
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Shounak Baksi
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Przemyslaw Leszek
- The Heart Failure and Transplantology Department, Institute of Cardiology, Warsaw, Poland
| | | | | | - Jan Kottwitz
- Division of Anesthesiology, Intensive Care, Rescue and Pain Medicine, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Dimitri Patriki
- Department of Cardiology, University Hospital of Zurich, Raemistrasse 100, 8091 Zurich, Switzerland
| | | | - Thomas F. Lüscher
- Royal Brompton & Harefield Hospitals GSTT, Imperial College and Kings College London, U.K. and Center for Molecular Cardiology, University of Zurich, Switzerland
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg,Corresponding author. Cardiovascular Research Unit, Luxembourg Institute of Health, L1445, Luxembourg.
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32
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Long Noncoding RNA: A Novel Insight into the Pathogenesis of Acute Lung Injury. J Clin Med 2023; 12:jcm12020604. [PMID: 36675533 PMCID: PMC9861694 DOI: 10.3390/jcm12020604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), represent an acute stage of lung inflammation where the alveolar epithelium loses its functionality. ALI has a devastating impact on the population as it not only has a high rate of incidence, but also has high rates of morbidity and mortality. Due to the involvement of multiple factors, the pathogenesis of ALI is complex and is not fully understood yet. Long noncoding RNAs (lncRNAs) are a group of non-protein-coding transcripts longer than 200 nucleotides. Growing evidence has shown that lncRNAs have a decisive role in the pathogenesis of ALI. LncRNAs can either promote or hinder the development of ALI in various cell types in the lungs. Mechanistically, current studies have found that lncRNAs play crucial roles in the pathogenesis of ALI via the regulation of small RNAs (e.g., microRNAs) or downstream proteins. Undoubtedly, lncRNAs not only have the potential to reveal the underlying mechanisms of ALI pathogenesis but also serve as diagnostic and therapeutic targets for the therapy of ALI.
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33
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Schynkel T, van Snippenberg W, Van Hecke C, Vandekerckhove L, Trypsteen W. Evaluating lncRNA Expression Patterns during HIV-1 Treatment Interruption. Int J Mol Sci 2023; 24:ijms24021031. [PMID: 36674541 PMCID: PMC9866393 DOI: 10.3390/ijms24021031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Lately, the interest in long non-coding RNAs (lncRNAs) as potential drug targets and predictive markers in the context of HIV-1 has peaked, but their in vivo expression and regulation remains largely unexplored. Therefore, the present study examined lncRNA expression patterns during a clinical antiretroviral treatment interruption (ATI) trial. Peripheral blood mononuclear cells were isolated from ten patients at four timepoints: prior to ATI, 7-15 days after stop, at viral rebound and 3 months post antiretroviral therapy re-initiation. RNA was extracted and RT-qPCR on five known HIV-1-related lncRNAs (HEAL, MALAT1, NEAT1, GAS5 and NRON) was performed and correlated with HIV-1 and host marker expression. All lncRNAs correlated stronger with interferon stimulated genes (ISGs) than with HIV-1 reservoir and replication markers. However, one lncRNA, HEAL, showed significant upregulation at viral rebound during ATI compared to baseline and re-initiation of therapy (p = 0.0010 and p = 0.0094, respectively), following a similar viral-load-driven expression pattern to ISGs. In vitro knockdown of HEAL caused a significant reduction in HIV-1 infection levels, validating HEAL's importance for HIV-1 replication. We conclude that the HIV-1-promoting lncRNA HEAL is upregulated at viral rebound during ATI, most likely induced by viral cues.
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34
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Zhu D, Ouyang X, Zhang Y, Yu X, Su K, Li L. A promising new cancer marker: Long noncoding RNA EGFR-AS1. Front Oncol 2023; 13:1130472. [PMID: 36910672 PMCID: PMC9999470 DOI: 10.3389/fonc.2023.1130472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Cancer consists of a group of diseases with the salient properties of an uncontrolled cell cycle, metastasis, and evasion of the immune response, mainly driven by the genomic instability of somatic cells and the physicochemical environment. Long noncoding RNAs (lncRNAs) are defined as noncoding RNAs with a length of more than 200 nucleotides. LncRNA dysregulation participates in diverse disease types and is tightly associated with patient clinical features, such as age, disease stage, and prognosis. In addition, an increasing number of lncRNAs have been confirmed to regulate a series of biological and pathological processes through numerous mechanisms. The lncRNA epidermal growth factor receptor antisense RNA 1 (EGFR-AS1) was recently discovered to be aberrantly expressed in many types of diseases, particularly in cancers. A high level of EGFR-AS1 was demonstrated to correlate with multiple patient clinical characteristics. More importantly, EGFR-AS1 was found to be involved in the mediation of various cellular activities, including cell proliferation, invasion, migration, chemosensitivity, and stemness. Therefore, EGFR-AS1 is a promising marker for cancer management. In this review, we introduce the expression profile, molecular mechanisms, biological functions, and clinical value of EGFR-AS1 in cancers.
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Affiliation(s)
- Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxi Ouyang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanhong Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaopeng Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kunkai Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Basu K, Dey A, Kiran M. Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse. RNA Biol 2023; 20:563-572. [PMID: 37543950 PMCID: PMC10405767 DOI: 10.1080/15476286.2023.2242649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA splice variants are the product of the alternative last exon and exon skipping. LncRNAs and mRNAs with higher transcript complexity have shorter intron lengths. Longer exon length and GC/AG at 5'/3' splice sites are associated with higher transcript complexity in lncRNAs. Lastly, our results indicate that inefficient splicing of lncRNAs may facilitate multiple introns splicing and, thus, more spliced products per exon.
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Affiliation(s)
- Koushiki Basu
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Anubha Dey
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
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36
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Xia Q, Shen J, Wang Q, Ke Y, Yan Q, Li H, Zhang D, Duan S. LINC00324 in cancer: Regulatory and therapeutic implications. Front Oncol 2022; 12:1039366. [PMID: 36620587 PMCID: PMC9815511 DOI: 10.3389/fonc.2022.1039366] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
LINC00324 is a 2082 bp intergenic noncoding RNA. Aberrant expression of LINC00324 was associated with the risk of 11 tumors and was closely associated with clinicopathological features and prognostic levels of 7 tumors. LINC00324 can sponge multiple miRNAs to form complex ceRNA networks, and can also recruit transcription factors and bind RNA-binding protein HuR, thereby regulating the expression of a number of downstream protein-coding genes. LINC00324 is involved in 4 signaling pathways, including the PI3K/AKT signaling pathway, cell cycle regulatory pathway, Notch signaling pathway, and Jak/STAT3 signaling pathway. High expression of LINC00324 was associated with larger tumors, a higher degree of metastasis, a higher TNM stage and clinical stage, and shorter OS. Currently, four downstream genes in the LINC00324 network have targeted drugs. In this review, we summarize the molecular mechanisms and clinical value of LINC00324 in tumors and discuss future directions and challenges for LINC00324 research.
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Affiliation(s)
- Qing Xia
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China,College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China,Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China
| | - Qurui Wang
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China
| | - Yufei Ke
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China
| | - Qibin Yan
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China
| | - Hanbing Li
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Dayong Zhang
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China,*Correspondence: Dayong Zhang, ; Shiwei Duan,
| | - Shiwei Duan
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, Zhejiang, China,*Correspondence: Dayong Zhang, ; Shiwei Duan,
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Yuan S, Yuan X, Li L. Long non-coding RNA HOXA11-AS protects the barrier function of corneal endothelial cells by sponging microRNA-155 to alleviate corneal endothelial injury. Am J Transl Res 2022; 14:8489-8503. [PMID: 36628203 PMCID: PMC9827337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/31/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Corneal endothelial cells (CECs) are extremely vulnerable to injury. In this study, the role and mechanism of action of the long non-coding RNA HOXA11-AS during corneal endothelial injury (CEI) were evaluated in vivo and in vitro. METHODS Scratch wounds were made to induce CEI in the corneal endothelium of rats and mice. Homeobox A11 (HOXA11)-AS expression was determined at different time points using quantitative real-time PCR. Human CECs with HOXA11-AS overexpression or downregulation were examined for survival, ferroptosis, and migration. Bioinformatics and dual-luciferase reporter assays were used to investigate the correlation between HOXA11-AS and microRNA (miR)-155. RESULTS HOXA11-AS expression was reduced in the corneal endothelium in a time-dependent manner. Scratch wounds triggered high rates of ferroptosis and migration in CECs and impaired cell proliferation. HOXA11-AS overexpression partially attenuated the scratch wound-induced changes in proliferation, ferroptosis, and migration, whereas silencing HOXA11-AS had the opposite effects. Moreover, HOXA11-AS served as a competing endogenous RNA of miR-155. Levels of miR-155 were upregulated in the corneal endothelium following the scratch injury, and this upregulation abolished the effect of HOXA11-AS overexpression on the behavior of CECs after injury; miR-155 inhibition counteracted the effect of HOXA11-AS silencing. CONCLUSIONS HOXA11-AS exerts protective effects against CEI by sponging miR-155, suggesting that these loci are treatment targets for corneal endothelial disorders.
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Affiliation(s)
- Shuyi Yuan
- Clinical College of Ophthalmology, Tianjin Medical UniversityTianjin 300070, China,Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye HospitalNo. 4 Gansu Road, He-ping District, Tianjin 300000, China
| | - Xiaoyong Yuan
- Clinical College of Ophthalmology, Tianjin Medical UniversityTianjin 300070, China,Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye HospitalNo. 4 Gansu Road, He-ping District, Tianjin 300000, China
| | - Lihua Li
- Clinical College of Ophthalmology, Tianjin Medical UniversityTianjin 300070, China,Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye HospitalNo. 4 Gansu Road, He-ping District, Tianjin 300000, China
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Liang W, Lu Y, Pan X, Zeng Y, Zheng W, Li Y, Nie Y, Li D, Wang D. Decreased Expression of a Novel lncRNA FAM181A-AS1 is Associated with Poor Prognosis and Immune Infiltration in Lung Adenocarcinoma. Pharmgenomics Pers Med 2022; 15:985-998. [PMID: 36482943 PMCID: PMC9724578 DOI: 10.2147/pgpm.s384901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/18/2022] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND There is no clear information regarding the role of FAM181A antisense RNA 1 (FAM181A-AS1) in lung adenocarcinoma (LUAD). We explored the relationship between FAM181A-AS1 and LUAD using bioinformatics analysis and experimental validation in this study. METHODS Statistics and databases were used to evaluate the relationship between clinical features in LUAD patients and FAM181A-AS1 expression, prognostic factors, regulation network, and immune infiltration of FAM181A-AS1 in function. LUAD cell lines were tested for FAM181A-AS1 expression using qRT-PCR. RESULTS FAM181A-AS1 showed significantly low expression in LUAD patients. Low FAM181A-AS1 expression predicted a poorer overall survival (OS) (HR: 0.66; 95% CI: 0.49-0.88; P=0.005) and disease specific survival (DSS) (HR: 0.64; 95% CI: 0.44-0.92; P=0.017) of LUAD patients. There was also an independent correlation between low FAM181A-AS1 expression (HR: 0.547; 95% CI: 0.350-0.857; P=0.008) and OS in LUAD patients. The FAM181A-AS1 high-expression phenotype was differentially enriched for M phase, cellular senescence, cell cycle checkpoints, chromatin modifying enzymes, ESR-mediated signaling, DNA repair, G2/M checkpoints, HCMV infection, and DNA double-strand break repair. A correlation was found between the expression of FAM181A-AS1 and immune infiltrating cells. A significant decrease in FAM181A-AS1 expression was observed in LUAD cell lines compared to Beas-2B. CONCLUSION There was a significant association between low FAM181A-AS1 expression in LUAD patients and poor survival and immune infiltration. The FAM181A-AS1 gene may provide a useful biomarker for LUAD prognosis and immunotherapy response.
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Affiliation(s)
- Weiquan Liang
- Department of Respiratory and Critical Care Medicine, The Second People’s Hospital of Foshan (Affiliated Foshan Hospital of Southern Medical University), Foshan, 528200, People’s Republic of China
| | - Yiyu Lu
- Department of Oncology, The Sixth Affiliated Hospital, South China University of Technology, Foshan, 528200, People’s Republic of China
| | - Xingxi Pan
- Department of Oncology, The Sixth Affiliated Hospital, South China University of Technology, Foshan, 528200, People’s Republic of China
| | - Yunxiang Zeng
- Department of Respiratory and Critical Care Medicine, The Second People’s Hospital of Foshan (Affiliated Foshan Hospital of Southern Medical University), Foshan, 528200, People’s Republic of China
| | - Weiqiang Zheng
- Department of Respiratory and Critical Care Medicine, The Second People’s Hospital of Foshan (Affiliated Foshan Hospital of Southern Medical University), Foshan, 528200, People’s Republic of China
| | - Yiran Li
- Department of Respiratory and Critical Care Medicine, The Second People’s Hospital of Foshan (Affiliated Foshan Hospital of Southern Medical University), Foshan, 528200, People’s Republic of China
| | - Yuanhang Nie
- Department of Respiratory and Critical Care Medicine, The Second People’s Hospital of Foshan (Affiliated Foshan Hospital of Southern Medical University), Foshan, 528200, People’s Republic of China
| | - Dongbing Li
- ChosenMed Technology Beijing Co., Ltd, Beijing, 100853, People’s Republic of China
| | - Dongliang Wang
- ChosenMed Technology Beijing Co., Ltd, Beijing, 100853, People’s Republic of China
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Agrawal D, Kumari R, Ratre P, Rehman A, Srivastava RK, Reszka E, Goryacheva IY, Mishra PK. Cell-free circulating miRNAs-lncRNAs-mRNAs as predictive markers for breast cancer risk assessment in women exposed to indoor air pollution. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100267. [DOI: 10.1016/j.cscee.2022.100267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
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40
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Lu Z, Feng Y. Foreboding lncRNA markers of low-grade gliomas dependent on metabolism. Medicine (Baltimore) 2022; 101:e31302. [PMID: 36343057 PMCID: PMC9646492 DOI: 10.1097/md.0000000000031302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
At present, there is no systematic study on the signature of long-chain noncoding RNAs (lncRNAs) involved in metabolism that can fully predict the prognosis in patients with low-grade gliomas (LGGs). Therefore, consistent metabolic-related lncRNA signatures need to be established. The Cancer Genome Atlas (TCGA) was used to identify the expression profile of lncRNAs containing 529 LGGs samples. LncRNAs and genes related to metabolism are used to establish a network in the form of coexpression to screen lncRNAs related to metabolism. LncRNA was more clearly described by univariate Cox regression. Moreover, lncRNA signatures were explored by multivariate Cox regression and lasso regression. The risk score was established according to the signature and it was an unattached prognostic marker according to Cox regression analysis. Functional enrichment of lncRNAs was shown by employing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Univariate Cox retrospective analysis showed that 543 metabolism-related lncRNAs were independent prognostic factors of LGG, and multivariate Cox regression analysis confirmed that 19 metabolism-related lncRNAs were prognostic genes of LGG. In the risk model, the low-risk group had a higher Overall survival (OS) than the high-risk group (P < .001). Univariate Cox regression analysis of risk score and clinical factors showed that risk score was an independent prognostic factor (P < .001, HR = 1.047, 95% CI: 1.038-1.056). Multivariate Cox results showed that risk score could predict the prognosis of LGG (P < .001, HR = 1.036, 95% CI: 1.026-1.045). ROC curve analysis showed that risk score could predict the prognosis of LGG. The areas of 1-year, 3-years, and 5 years are 0.891, 0.904 and 0.832. GO and KEGG analysis showed that metabolism-related lncRNAs was mainly concentrated in the pathways related to tumor metabolism. In order to find a more stable and reliable target for the treatment of LGG, we established 19 metabolic-related lncRNAs prognostic model, and determined that it can predict the prognosis of LGG patients. This provides a new solution approach to the poor prognosis of patients with LGG and may reverse the trend of LGG's transformation to high-grade gliomas.
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Affiliation(s)
- Zhuangzhuang Lu
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yugong Feng
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- * Correspondence: Yugong Feng, Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, China (e-mail: )
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Tang J, Wu Z, Wang X, Hou Y, Bai Y, Tian Y. Hypoxia-Regulated lncRNA USP2-AS1 Drives Head and Neck Squamous Cell Carcinoma Progression. Cells 2022; 11:3407. [PMID: 36359803 PMCID: PMC9655520 DOI: 10.3390/cells11213407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/16/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
The role of hypoxia-regulated long non-coding RNA (lncRNA) in the development of head and neck squamous cell carcinoma (HNSCC) remains to be elucidated. In the current study, we initially screened hypoxia-regulated lncRNA in HNSCC cells by RNA-seq, before focusing on the rarely annotated lncRNA USP2 antisense RNA 1 (USP2-AS1). We determined that USP2-AS1 is a direct target of HIF1α and is remarkably elevated in HNSCC compared with matched normal tissues. Patients with a higher level of USP2-AS1 suffered a poor prognosis. Next, loss- and gain-of-function assays revealed that USP2-AS1 promoted cell proliferation and invasion in vitro and in vivo. Mechanically, RNA pulldown and LC-MS/MS demonstrated that the E3 ligase DDB1- and CUL4-associated factor 13 (DCAF13) is one of the binding partners to USP2-AS1 in HNSCC cells. In addition, we assumed that USP2-AS1 regulates the activity of DCAF13 by targeting its substrate ATR. Moreover, the knockdown of DCAF13 restored the elevated cell proliferation and growth levels achieved by USP2-AS1 overexpression. Altogether, we found that lncRNA USP2-AS1 functions as a HIF1α-regulated oncogenic lncRNA and promotes HNSCC cell proliferation and growth by interacting and modulating the activity of DCAF13.
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Affiliation(s)
- Jianmin Tang
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Institute of Radiotherapy and Oncology, Soochow University, Suzhou 215004, China
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Zheng Wu
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Xiaohang Wang
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Yanli Hou
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Yongrui Bai
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Ye Tian
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Institute of Radiotherapy and Oncology, Soochow University, Suzhou 215004, China
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Soghala S, Harsiny K, Momeni P, Hatami M, Kholghi Oskooei V, Hussen BM, Taheri M, Ghafouri-Fard S. Down-regulation of LINC-ROR, HOXA-AS2 and MEG3 in gastric cancer. Heliyon 2022; 8:e11155. [PMID: 36299522 PMCID: PMC9589166 DOI: 10.1016/j.heliyon.2022.e11155] [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: 06/04/2021] [Revised: 10/16/2021] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been identified as modulators of gastric carcinogenesis. Evaluation of expression amounts of these transcripts is a primary but essential step for recognition of the role of lncRNAs in the carcinogenesis. Therefore, we compared expressions of LINC-ROR, HOXA-AS2, MEG3 and HOTTIP lncRNAs in gastric cancer samples and nearby non-cancerous samples. Expression levels of LINC-ROR, HOXA-AS2 and MEG3 lncRNAs have been lower in gastric cancer samples compared with nearby non-cancerous samples (Expression ratios = 0.26, 0.37 and 0.36; P values = 0.021, 0.015 and 0.032, respectively). However, expression levels of HOTTIP were not significantly different between gastric cancer tissues and nearby tissues (P value = 0.43). HOTTIP expression was associated with tumor size (P value = 0.04). In addition, MEG3 expression was associated with site of primary tumor (P = 0.0003). Expressions of LINC-ROR and HOXA-AS2 were not associated with any clinical or pathological parameter. ROC curve analysis revealed that HOXA-AS2 and LINC-ROR could significantly differentiate between gastric cancer samples and nearby non-cancerous tissues (AUC values = 0.68 and 0.64; P values = 0.01 and 0.04, respectively). Taken together, the current investigation provides clues for contribution of LINC-ROR, HOXA-AS2 and MEG3 lncRNAs in gastric carcinogenesis and warrants further mechanistical assays.
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Affiliation(s)
- Shahrad Soghala
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kiana Harsiny
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parto Momeni
- Department of Cellular and Molecular Biology-Molecular Cellular Science, Faculty of Basic Science, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mahsa Hatami
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi Oskooei
- Department of Medical Biotechnology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran,Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq,Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Institute of Human Genetics, Jena University Hospital, Jena, Germany,Corresponding author.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author.
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Ngongang NN, Mezajou CF, Kameni C, Ngum JA, Simo USF, Tatang FJ, Ngate Nguengo S, Chakam Nouthio AP, Wandji Pajiep MA, Toumeni MH, Takou Madjoumo ES, Tchinda MF, Ngangue RJEM, Dongmo FFD, Wade A, Akami M, Ngane Ngono AR, Tamgue O. TNF and HNRNPL Related Immunoregulatory Long non-coding RNA (THRIL) and long intergenic noncoding RNA-p21 (lincRNA-p21) as potential useful biomarkers for the diagnosis of tuberculosis. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.969307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Early diagnosis is crucial in controlling tuberculosis globally and in developing countries with the emergence of drug-resistant Mycobacterium tuberculosis strains. Long non-coding RNAs (lncRNAs) are promising tuberculosis diagnostic biomarkers. Two lncRNA diagnostic markers, lncRNA THRIL and lincRNA-p21, were studied as tuberculosis diagnostic biomarkers. This cross-sectional study was conducted at the Center of Respiratory Diseases of LAQUINTINIE hospital and the National Veterinary Laboratory of Douala from December 2020 to August 2021. The ability of lncRNAs to distinguish between 19 healthy controls, 15 latent tuberculosis, and 21 active tuberculosis was estimated using quantitative polymerase chain reaction and Receiver Operating Characteristic curve analysis. Our analysis showed that lncRNA THRIL and lincRNA-p21 were significantly upregulated (P <0.05) in active and latent tuberculosis compared with healthy controls. LincRNA-p21 expression was significantly increased (P <0.05) in active tuberculosis compared with latent tuberculosis, whereas lncRNA THRIL was not significantly affected (P ≥0.05). Both lncRNA THRIL and lincRNA-p21 showed excellent performance in classifying latent tuberculosis and healthy controls (AUC = 92.86%). Furthermore, lncRNA THRIL was good at discriminating active tuberculosis from healthy controls (AUC = 89.79%), while lincRNA-p21 showed excellent discriminating performance (AUC = 100%). LncRNA THRIL was identified as a poor discriminator of latent tuberculosis from active tuberculosis (AUC = 64.28%), while lincRNA-p21 showed excellent diagnostic performance in this distinction (AUC = 92.86%). Our cross-sectional study suggests that lncRNA THRIL and lincRNA-p21 are promising tuberculosis diagnostic biomarkers that can differentiate between latent and active infection.
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A novel lncRNA MTAR1 promotes cancer development through IGF2BPs mediated post-transcriptional regulation of c-MYC. Oncogene 2022; 41:4736-4753. [DOI: 10.1038/s41388-022-02464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
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Li S, Xie X, Peng F, Du J, Peng C. Regulation of temozolomide resistance via lncRNAs: Clinical and biological properties of lncRNAs in gliomas (Review). Int J Oncol 2022; 61:101. [PMID: 35796022 PMCID: PMC9291250 DOI: 10.3892/ijo.2022.5391] [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: 04/11/2022] [Accepted: 06/10/2022] [Indexed: 11/05/2022] Open
Abstract
Gliomas are a primary types of intracranial malignancies and are characterized by a poor prognosis due to aggressive recurrence profiles. Temozolomide (TMZ) is an auxiliary alkylating agent that is extensively used in conjunction with surgical resection and forms the mainstay of clinical treatment strategies for gliomas. However, the frequent occurrence of TMZ resistance in clinical practice limits its therapeutic efficacy. Accumulating evidence has demonstrated that long non‑coding RNAs (lncRNAs) can play key and varied roles in glioma progression. lncRNAs have been reported to inhibit glioma progression by targeting various signaling pathways. In addition, the differential expression of lncRNAs has also been found to mediate the resistance of glioma to several chemotherapeutic agents, particularly to TMZ. The present review article therefore summarizes the findings of previous studies in an aim to report the significance and function of lncRNAs in regulating the chemoresistance of gliomas. The present review may provide further insight into the clinical treatment of gliomas.
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Affiliation(s)
- Sui Li
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of The Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaofang Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P.R. China
| | - Fu Peng
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of The Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Correspondence to: Dr Fu Peng or Professor Junrong Du, Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of The Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, 17 Renmin South Road, Chengdu, Sichuan 610041, P.R. China, E-mail: , E-mail:
| | - Junrong Du
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of The Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
- Correspondence to: Dr Fu Peng or Professor Junrong Du, Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of The Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, 17 Renmin South Road, Chengdu, Sichuan 610041, P.R. China, E-mail: , E-mail:
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P.R. China
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Integrated Analysis of the lncRNA-Associated ceRNA Network in Wilms Tumor via TARGET and GEO Databases. Genet Res (Camb) 2022; 2022:2365991. [PMID: 36101743 PMCID: PMC9452976 DOI: 10.1155/2022/2365991] [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: 06/18/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Wilms tumor (WT) is the most common genitourinary renal tumor that typically occurs in children under 15 and is thought to be linked to somatic and germline mutations. However, the specific functional role of competing endogenous RNAs (ceRNAs) and their potential implications in WT remain unclear. In this study, we developed an lncRNA-mediated (long noncoding RNA-mediated) ceRNA network via the R packages for WT with expression data obtained from the tumor alterations relevant for genomics-driven therapy (TARGET) database. Unsupervised hierarchical clustering analysis revealed that the WT specimens could be clearly distinguished from healthy specimens with respect to the expression of disordered RNAs. A total of 1,607 differentially expressed (DE) lncRNAs, 116 DE microRNAs (DEmiRNAs), and 3,262 DE messenger RNAs (DEmRNAs) were identified as WT-specific RNAs, and a lncRNA-miRNA-mRNA ceRNA network with 159 DElncRNAs, 18 DEmiRNAs, 131 DEmRNAs, and 792 interactions was constructed. According to the clinical survival data, 12 DElncRNAs, 5 DEmRNAs, and 2 DEmiRNAs were selected from the ceRNA network that could significantly impact the overall survival of WT patients (P < 0.05). Functional enrichment analysis showed that the biological processes and pathways of DEmRNAs, such as cell cycle and virus infection, may be associated with WT. The present study constructed a dysregulated lncRNA-mediated ceRNA network in WT and discovered that lncRNA-mediated ceRNAs may serve as important regulators in WT development and progression. Survival-associated RNAs may serve as new potential biomarkers, suggesting that the constructed ceRNA network in WT might be important for determining optimal therapeutic strategies.
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Bigagli E, Maggiore G, Cinci L, D'Ambrosio M, Locatello LG, Nardi C, Palomba A, Leopardi G, Orlando P, Licci G, Gallo O, Luceri C. Low levels of miR-34c in nasal washings as a candidate marker of aggressive disease in wood and leather exposed workers with sinonasal intestinal-type adenocarcinomas (ITACs). Transl Oncol 2022; 25:101507. [PMID: 35998435 PMCID: PMC9421288 DOI: 10.1016/j.tranon.2022.101507] [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: 04/21/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022] Open
Abstract
MiR-34c targeting MUC2 is higher in ITACs compared to the corresponding normal mucosa. MiR-34c is higher in differentiated compared to mucinous ITACs. Low nasal washings miR-34c correlates with higher disease extension. Mir-34c targets critical targetable cancer and inflammatory related pathways. Mir-34c is a noninvasive candidate biomarker for ITAC patients and exposed workers.
Introduction Sinonasal intestinal-type adenocarcinomas (ITACs) are rare and aggressive tumors, closely related to professional exposure to wood dusts or leather. Here we explored the role of non-coding RNAs controlling MUC2 in liquid biopsies and tumors from ITAC patients with the aim of identifying biomarkers and molecular mechanisms to improve early diagnosis, prognosis, and therapeutic approaches for this rare cancer. Methods MiR-34c-3p, lncRNA AF147447 and MUC2 were measured in tumors and normal mucosa, in nasal washings (NW) from the affected and non-affected nostril and in plasma from 17 ITAC patients. The Apparent Diffusion Coefficient (ADC) was also evaluated by Magnetic Resonance Imaging. Results MiR-34c was higher in ITACs compared to the corresponding normal mucosa (p = 0.021). Differentiated tumors exhibited higher miR-34c levels (p = 0.025) and lower ADC values (p<0.001) compared to mucinous ones and these parameters were also inversely correlated (r = 0.87; p = 0.001). High MUC2 tumor expression was associated with orbital extension (p = 0.010). Low miR-34c levels in NW were associated with orbital (p = 0.009) and intracranial (p = 0.031) extension and with advanced TNM stage (p = 0.054). Functional analysis identified Wnt, Focal adhesion, MAPK and inflammatory signalings among the pathways most enriched in mir-34c targets. Discussion Our results suggest measuring miR-34c in NW as a biomarker for early diagnosis and monitoring of ITAC patients and for the surveillance of wood and leather exposed workers. Further research on the involvement of miR-34c regulated pathways in ITAC tumorigenesis may also allow the development of new therapeutic approaches for this rare cancer.
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Affiliation(s)
- Elisabetta Bigagli
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) Section of Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Giandomenico Maggiore
- Department of Otorhinolaryngology, Careggi University Hospital, University of Florence, Florence, Italy
| | - Lorenzo Cinci
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, Careggi University Hospital, Florence, Italy
| | - Mario D'Ambrosio
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) Section of Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Luca Giovanni Locatello
- Department of Otorhinolaryngology, Careggi University Hospital, University of Florence, Florence, Italy.
| | - Cosimo Nardi
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, Careggi University Hospital, Florence, Italy
| | - Annarita Palomba
- Section of Pathological Anatomy, Department of Health Sciences, Azienda Ospedaliero-Universitaria Careggi, University of Florence, Italy
| | | | - Pietro Orlando
- Department of Otorhinolaryngology, Careggi University Hospital, University of Florence, Florence, Italy
| | - Giuseppe Licci
- Department of Otorhinolaryngology, Careggi University Hospital, University of Florence, Florence, Italy
| | - Oreste Gallo
- Department of Otorhinolaryngology, Careggi University Hospital, University of Florence, Florence, Italy
| | - Cristina Luceri
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA) Section of Pharmacology and Toxicology, University of Florence, Florence, Italy.
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48
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Piergentili R, Basile G, Nocella C, Carnevale R, Marinelli E, Patrone R, Zaami S. Using ncRNAs as Tools in Cancer Diagnosis and Treatment-The Way towards Personalized Medicine to Improve Patients' Health. Int J Mol Sci 2022; 23:ijms23169353. [PMID: 36012617 PMCID: PMC9409241 DOI: 10.3390/ijms23169353] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 12/06/2022] Open
Abstract
Although the first discovery of a non-coding RNA (ncRNA) dates back to 1958, only in recent years has the complexity of the transcriptome started to be elucidated. However, its components are still under investigation and their identification is one of the challenges that scientists are presently facing. In addition, their function is still far from being fully understood. The non-coding portion of the genome is indeed the largest, both quantitatively and qualitatively. A large fraction of these ncRNAs have a regulatory role either in coding mRNAs or in other ncRNAs, creating an intracellular network of crossed interactions (competing endogenous RNA networks, or ceRNET) that fine-tune the gene expression in both health and disease. The alteration of the equilibrium among such interactions can be enough to cause a transition from health to disease, but the opposite is equally true, leading to the possibility of intervening based on these mechanisms to cure human conditions. In this review, we summarize the present knowledge on these mechanisms, illustrating how they can be used for disease treatment, the current challenges and pitfalls, and the roles of environmental and lifestyle-related contributing factors, in addition to the ethical, legal, and social issues arising from their (improper) use.
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Affiliation(s)
- Roberto Piergentili
- Institute of Molecular Biology and Pathology, Italian National Research Council (CNR-IBPM), 00185 Rome, Italy
| | - Giuseppe Basile
- Trauma Unit and Emergency Department, IRCCS Galeazzi Orthopedics Institute, 20161 Milan, Italy
- Head of Legal Medicine Unit, Clinical Institute San Siro, 20148 Milan, Italy
| | - Cristina Nocella
- Department of Clinical Internal, Anaesthesiological and Cardiovascular Sciences, “Sapienza” University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Roberto Carnevale
- Department of Medico-Surgical Sciences and Biotechnologies, “Sapienza” University of Rome, 04100 Latina, Italy
- Mediterranea Cardiocentro-Napoli, Via Orazio, 80122 Naples, Italy
| | - Enrico Marinelli
- Department of Medico-Surgical Sciences and Biotechnologies, “Sapienza” University of Rome, 04100 Latina, Italy
- Correspondence:
| | - Renato Patrone
- PhD ICTH, University of Federico II, HPB Department INT F. Pascale IRCCS of Naples, Via Mariano Semmola, 80131 Naples, Italy
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Section of Forensic Medicine, “Sapienza” University of Rome, 00161 Rome, Italy
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lncRNA MIR4435-2HG Accelerates the Development of Bladder Cancer through Enhancing IQGAP3 and CDCA5 Expression. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3858249. [PMID: 35993042 PMCID: PMC9391195 DOI: 10.1155/2022/3858249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/10/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Background. Bladder cancer (BCa) is one of the most prevalent cancers occurring in the urinary system. Long noncoding RNAs (lncRNAs), in recent years, have emerged as crucial regulators in various biological processes of tumors. Aim. To identify the role of MIR4435-2 host gene (MIR4435-2HG) and uncover its molecular mechanism in BCa. Methods. Firstly, quantitative real-time PCR (RT-qPCR) analysis was used to examine MIR4435-2HG expression in BCa cells. Cell Counting Kit-8 (CCK-8), 5-ethynyl-2
-deoxyuridine (EdU), wound healing, and transwell assays were implemented to identify the role of MIR4435-2HG in BCa. RNA-binding protein immunoprecipitation (RIP), RNA pull down, and luciferase reporter assays were applied to explore the potential mechanism of MIR4435-2HG in BCa. Results. MIR4435-2HG was highly expressed in BCa. Moreover, MIR4435-2HG silencing abrogated BCa cell proliferation, migration, and invasion. In terms of underlying mechanism, MIR44352HG acted as a microRNA-2467-3p (miR-2467-3p) sponge to control the expression of IQ motif containing GTPase activating protein 3 (IQGAP3) and cell division cycle associated 5 (CDCA5), resulting in activation of the rat sarcoma virus (Ras)/rapidly accelerated fibrosarcoma (Raf)/mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) and PI3K/AKT/mTOR signaling pathways. Conclusion. MIR4435-2HG involves in the progression of BCa, which might provide novel insights for BCa treatment.
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Dey SS, Sharma PK, Munshi AD, Jaiswal S, Behera TK, Kumari K, G. B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884476. [PMID: 35991462 PMCID: PMC9383263 DOI: 10.3389/fpls.2022.884476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2-3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10-15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.
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Affiliation(s)
- Shyam S. Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A. D. Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T. K. Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Boopalakrishnan G.
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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