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Hutarew G, Alinger-Scharinger B, Sotlar K, Kraus TFJ. Genome-Wide Methylation Analysis in Two Wild-Type Non-Small Cell Lung Cancer Subgroups with Negative and High PD-L1 Expression. Cancers (Basel) 2024; 16:1841. [PMID: 38791918 PMCID: PMC11119885 DOI: 10.3390/cancers16101841] [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: 03/27/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
We conducted a pilot study to analyze the differential methylation status of 20 primary acinar adenocarcinomas of the lungs. These adenocarcinomas had to be wild type in mutation analysis and had either high (TPS > 50%; n = 10) or negative (TPS < 1%; n = 10) PD-L1 status to be integrated into our study. To examine the methylation of 866,895 specific sites, we utilized the Illumina Infinium EPIC bead chip array. Both hypermethylation and hypomethylation play significant roles in tumor development, progression, and metastasis. They also impact the formation of the tumor microenvironment, which plays a decisive role in tumor differentiation, epigenetics, dissemination, and immune evasion. The gained methylation patterns were correlated with PD-L1 expression. Our analysis has identified distinct methylation patterns in lung adenocarcinomas with high and negative PD-L1 expression. After analyzing the correlation between the methylation results of genes and promoters with their pathobiology, we found that tumors with high expression of PD-L1 tend to exhibit oncogenic effects through hypermethylation. On the other hand, tumors with negative PD-L1 expression show loss of their suppressor functions through hypomethylation. The suppressor functions of hypermethylated genes and promoters are ineffective compared to simultaneously activated dominant oncogenic mechanisms. The tumor microenvironment supports tumor growth in both groups.
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Affiliation(s)
- Georg Hutarew
- Institute of Pathology, University Hospital Salzburg, Paracelsus Medical University, Müllner Hauptstr. 48, A-5020 Salzburg, Austria; (B.A.-S.); (K.S.); (T.F.J.K.)
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2
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Ahmad S, Zhang XL, Ahmad A. Epigenetic regulation of pulmonary inflammation. Semin Cell Dev Biol 2024; 154:346-354. [PMID: 37230854 PMCID: PMC10592630 DOI: 10.1016/j.semcdb.2023.05.003] [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: 10/31/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
Pulmonary disease such as chronic obstructive pulmonary disease (COPD), asthma, pulmonary fibrosis and pulmonary hypertension are the leading cause of deaths. More importantly, lung diseases are on the rise and environmental factors induced epigenetic modifications are major players on this increased prevalence. It has been reported that dysregulation of genes involved in epigenetic regulation such as the histone deacetylase (HDACs) and histone acetyltransferase (HATs) play important role in lung health and pulmonary disease pathogenesis. Inflammation is an essential component of respiratory diseases. Injury and inflammation trigger release of extracellular vesicles that can act as epigenetic modifiers through transfer of epigenetic regulators such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), proteins and lipids, from one cell to another. The immune dysregulations caused by the cargo contents are important contributors of respiratory disease pathogenesis. N6 methylation of RNA is also emerging to be a critical mechanism of epigenetic alteration and upregulation of immune responses to environmental stressors. Epigenetic changes such as DNA methylation are stable and often long term and cause onset of chronic lung conditions. These epigenetic pathways are also being utilized for therapeutic intervention in several lung conditions.
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Affiliation(s)
- Shama Ahmad
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xiao Lu Zhang
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aftab Ahmad
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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3
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Hussain MS, Altamimi ASA, Afzal M, Almalki WH, Kazmi I, Alzarea SI, Saleem S, Prasher P, Oliver B, Singh SK, MacLoughlin R, Dua K, Gupta G. From carcinogenesis to therapeutic avenues: lncRNAs and mTOR crosstalk in lung cancer. Pathol Res Pract 2024; 253:155015. [PMID: 38103364 DOI: 10.1016/j.prp.2023.155015] [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: 10/24/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to have a crucial function in the modulation of the activity of genes, impacting a variety of homeostatic processes involving growth, survival, movement, and genomic consistency. Certain lncRNAs' aberrant expression has been linked to carcinogenesis, tumor growth, and therapeutic resistance. They are beneficial for the management of malignancies since they can function as cancer-causing or cancer-suppressing genes and behave as screening or prognosis indicators. The modulation of the tumor microenvironment, metabolic modification, and spread have all been linked to lncRNAs in lung cancer. Recent research has indicated that lncRNAs may interact with various mTOR signalling systems to control expression in lung cancer. Furthermore, the route can affect how lncRNAs are expressed. Emphasizing the function of lncRNAs as crucial participants in the mTOR pathway, the current review intends to examine the interactions between the mTOR cascade and the advancement of lung cancer. The article will shed light on the roles and processes of a few lncRNAs associated with the development of lung cancer, as well as their therapeutic prospects.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017 Jaipur, Rajasthan, India
| | - Abdulmalik S A Altamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- ōDepartment of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Energy Acres, Dehradun 248007, India
| | - Brian Oliver
- Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia; Woolcock Institute of Medical Research, Macquarie university, Sydney, NSW, 2137
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ronan MacLoughlin
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Leinster D02 YN77, Ireland; School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, Leinster D02 PN40, Ireland; Research and Development, Science and Emerging Technologies, Aerogen Ltd., Galway Business Park, H91 HE94 Galway, Ireland
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India.
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4
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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5
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Solati A, Thvimi S, Khatami SH, Shabaninejad Z, Malekzadegan Y, Alizadeh M, Mousavi P, Taheri-Anganeh M, Razmjoue D, Bahmyari S, Ghasemnejad-Berenji H, Vafadar A, Soltani Fard E, Ghasemi H, Movahedpour A. Non-coding RNAs in gynecologic cancer. Clin Chim Acta 2023; 551:117618. [PMID: 38375624 DOI: 10.1016/j.cca.2023.117618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 02/21/2024]
Abstract
The term "gynecologic cancer" pertains to neoplasms impacting the reproductive tissues and organs of women encompassing the endometrium, vagina, cervix, uterus, vulva, and ovaries. The progression of gynecologic cancer is linked to various molecular mechanisms. Historically, cancer research primarily focused on protein-coding genes. However, recent years have unveiled the involvement of non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs (LncRNAs), and circular RNAs, in modulating cellular functions within gynecological cancer. Substantial evidence suggests that ncRNAs may wield a dual role in gynecological cancer, acting as either oncogenic or tumor-suppressive agents. Numerous clinical trials are presently investigating the roles of ncRNAs as biomarkers and therapeutic agents. These endeavors may introduce a fresh perspective on the diagnosis and treatment of gynecological cancer. In this overview, we highlight some of the ncRNAs associated with gynecological cancers.
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Affiliation(s)
- Arezoo Solati
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sina Thvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mehdi Alizadeh
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Damoun Razmjoue
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran; Department of Pharmacognosy, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sedigheh Bahmyari
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hojat Ghasemnejad-Berenji
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Asma Vafadar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
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6
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Mollazadeh S, Abdolahzadeh N, Moghbeli M, Arab F, Saburi E. The crosstalk between non-coding RNA polymorphisms and resistance to lung cancer therapies. Heliyon 2023; 9:e20652. [PMID: 37829813 PMCID: PMC10565774 DOI: 10.1016/j.heliyon.2023.e20652] [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: 04/03/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
Lung cancer (LC) is one of the most common cancer-related mortality in the world. Even with intensive multimodality therapies, lung cancer has a poor prognosis and a high morbidity rate. This review focused on the role of non-coding RNA polymorphisms such as lncRNAs and miRNAs in the resistance to LC therapies, which could open promising avenue for better therapeutic response. Of note, there is currently no valid biomarker to predict lung cancer sensitivity in patients during treatment. Since genetic variations cause many challenges in treating patients, genotyping of known polymorphisms must be thoroughly explored to find desirable treatment platforms. With this knowledge, individualized treatments could become more possible in management of LC.
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Affiliation(s)
- Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Negar Abdolahzadeh
- Department of Advanced Sciences and Technologies, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Meysam Moghbeli
- Medical Genetics and Molecular Medicine Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Arab
- Medical Genetics and Molecular Medicine Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- Medical Genetics and Molecular Medicine Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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7
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Khaliefa AK, Desouky EM, Hozayen WG, Shaaban SM, Hasona NA. miRNA-1246, HOTAIR, and IL-39 signature as potential diagnostic biomarkers in breast cancer. Noncoding RNA Res 2023; 8:205-210. [PMID: 36865390 PMCID: PMC9972401 DOI: 10.1016/j.ncrna.2023.02.002] [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: 12/28/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
The molecular alterations in noncoding RNA can lead to a cellular storm that is correlated to higher mortality and morbidity rates and contributes to the progression and metastasis of cancer. Herein, we aim to evaluate the expression levels and correlations of microRNA-1246 (miR-1246), HOX transcript antisense RNA (HOTAIR), and interleukin-39 (IL-39) in patients with breast cancer (BC). In this study, 130 participants were recruited, including 90 breast cancer patients and 40 healthy control participants. Serum levels of miR-1246 and HOTAIR expression were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). Also, the level of IL-39 expression was evaluated using a Western blot. All BC participants demonstrated a remarkable elevation in miR-1246 and HOTAIR expression levels. Moreover, IL-39 expression levels demonstrated a noticeable decline in BC patients. Furthermore, the differential expression fold of miR-1246 and HOTAIR revealed a strong positive correlation among breast cancer patients. In addition, a negative relationship between the IL-39 and the miR-1246 and HOTAIR differential expression was also noticed. This study revealed that HOTAIR/miR-1246 exerts an oncogenic impact in patients with breast cancer. The expression levels of circulation miR-1246, HOTAIR, and IL-39 could be considered early diagnostic biomarkers in BC patients.
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Affiliation(s)
- Amal K. Khaliefa
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Salah Salim St., 62511, Beni-Suef, Egypt
| | - Ekram M. Desouky
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Salah Salim St., 62511, Beni-Suef, Egypt
| | - Walaa G. Hozayen
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Salah Salim St., 62511, Beni-Suef, Egypt
| | - Saeed M. Shaaban
- Oncology Department, Faculty of Medicine, Beni-Suef University, 62511, Beni-Suef, Egypt
| | - Nabil A. Hasona
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Salah Salim St., 62511, Beni-Suef, Egypt,Beni Suef National University, Faculty of Science, Biochemistry Department, Beni Suef, 62511, Egypt,Corresponding author. Department of Biochemistry, Faculty of Science, Beni-Suef University, Salah Salim St., 62511, Beni-Suef, Egypt.
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8
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Azizidoost S, Ghaedrahmati F, Sheykhi-Sabzehpoush M, Uddin S, Ghafourian M, Mousavi Salehi A, Keivan M, Cheraghzadeh M, Nazeri Z, Farzaneh M, Khoshnam SE. The role of LncRNA MCM3AP-AS1 in human cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:33-47. [PMID: 36002764 DOI: 10.1007/s12094-022-02904-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/18/2022] [Indexed: 01/07/2023]
Abstract
Long noncoding RNAs (lncRNA) play pivotal roles in every level of gene and genome regulation. MCM3AP-AS1 is a lncRNA that has an oncogenic role in several kinds of cancers. Aberrant expression of MCM3AP-AS1 has been reported to be involved in the progression of diverse malignancies, including colorectal, cervical, prostate, lymphoma, lung, ovary, liver, bone, and breast cancers. It is generally believed that MCM3AP-AS1 expression is associated with cancer cell growth, proliferation, angiogenesis, and metastasis. MCM3AP-AS1 by targeting various signaling pathways and microRNAs (miRNAs) presents an important role in cancer pathogenesis. MCM3AP-AS1 as a competitive endogenous RNA has the ability to sponge miRNA, inhibit their expressions, and bind to different target mRNAs related to cancer development. Therefore, MCM3AP-AS1 by targeting several signaling pathways, including the FOX family, Wnt, EGF, and VEGF can be a potent target for cancer prediction and diagnosis. In this review, we will summarize the role of MCM3AP-AS1 in various human cancers.
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Affiliation(s)
- Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Mehri Ghafourian
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abdolah Mousavi Salehi
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mona Keivan
- Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Maryam Cheraghzadeh
- Department of Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Nazeri
- Department of Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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9
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Yang CZ, Yang T, Liu XT, He CF, Guo W, Liu S, Yao XH, Xiao X, Zeng WR, Lin LZ, Huang ZY. Comprehensive analysis of somatic mutator-derived and immune infiltrates related lncRNA signatures of genome instability reveals potential prognostic biomarkers involved in non-small cell lung cancer. Front Genet 2022; 13:982030. [PMID: 36226174 PMCID: PMC9548567 DOI: 10.3389/fgene.2022.982030] [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: 06/30/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The function and features of long non-coding RNAs (lncRNAs) are already attracting attention and extensive research on their role as biomarkers of prediction in lung cancer. However, the signatures that are both related to genomic instability (GI) and tumor immune microenvironment (TIME) have not yet been fully explored in previous studies of non-small cell lung cancer (NSCLC). Method: The clinical characteristics, RNA expression profiles, and somatic mutation information of patients in this study came from The Cancer Genome Atlas (TCGA) database. Cox proportional hazards regression analysis was performed to construct genomic instability-related lncRNA signature (GIrLncSig). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to predict the potential functions of lncRNAs. CIBERSORT was used to calculate the proportion of immune cells in NSCLC. Result: Eleven genomic instability-related lncRNAs in NSCLC were identified, then we established a prognostic model with the GIrLncSig ground on the 11 lncRNAs. Through the computed GIrLncSig risk score, patients were divided into high-risk and low-risk groups. By plotting ROC curves, we found that patients in the low-risk group in the test set and TCGA set had longer overall survival than those in the high-risk group, thus validating the survival predictive power of GIrLncSig. By stratified analysis, there was still a significant difference in overall survival between high and low risk groups of patients after adjusting for other clinical characteristics, suggesting the prognostic significance of GIrLncSig is independent. In addition, combining GIrLncSig with TP53 could better predict clinical outcomes. Besides, the immune microenvironment differed significantly between the high-risk and the low-risk groups, patients with low risk scores tend to have upregulation of immune checkpoints and chemokines. Finally, we found that high-risk scores were associated with increased sensitivity to chemotherapy. Conclusion: we provided a new perspective on lncRNAs related to GI and TIME and revealed the worth of them in immune infiltration and immunotherapeutic response. Besides, we found that the expression of AC027288.1 is associated with PD-1 expression, which may be a potential prognostic marker in immune checkpoint inhibitor response to improve the prediction of clinical survival in NSCLC patients.
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Affiliation(s)
- Cai-Zhi Yang
- The First School of Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ting Yang
- The First School of Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue-Ting Liu
- The First School of Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Can-Feng He
- The First School of Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Guo
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shan Liu
- The First School of Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Hui Yao
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xi Xiao
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei-Ran Zeng
- Oncology Department, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhong-Yu Huang, ; Li-Zhu Lin, ; Wei-Ran Zeng,
| | - Li-Zhu Lin
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhong-Yu Huang, ; Li-Zhu Lin, ; Wei-Ran Zeng,
| | - Zhong-Yu Huang
- Guangzhou First People’s Hospital School of Medicine, South China University of Technology, Guangzhou, China
- Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
- *Correspondence: Zhong-Yu Huang, ; Li-Zhu Lin, ; Wei-Ran Zeng,
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10
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Ji Y, Zhang G, Zhang X. Identification of LncRNA CARD8-AS1 as a Potential Prognostic Biomarker Associated With Progression of Lung Adenocarcinoma. Br J Biomed Sci 2022; 79:10498. [PMID: 35996500 PMCID: PMC9302548 DOI: 10.3389/bjbs.2022.10498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022]
Abstract
Introduction: Long non-coding RNAs (lncRNAs) exhibit crucial roles in human tumors. However, the role of lncRNA CARD8-AS1 in lung adenocarcinoma remains elusive. This study investigated the role of CARD8-AS1 in lung adenocarcinoma.Materials and Methods: The expression of CARD8-AS1 was detected by RT-qPCR analysis and confirmed using an online database. The clinical value of CARD8-AS1 was evaluated using the Kaplan-Meier curve and multivariate Cox regression analyses. The effects of CARD8-AS1 on cancer cell proliferation, migration, and invasion potential were assessed through several cellular experiments. Western blot assay was used to measure Bcl-2 and Bax protein levels. The interaction among CARD8-AS1, miR-650, and Bax, was assessed using a dual-luciferase reporter assay.Results: The expression of CARD8-AS1 was decreased in lung adenocarcinoma tissues and cell lines (p < 0.001). Low expression of CARD8-AS1 was related to tumor size (p = 0.042), TNM stage (p = 0.021), lymph node metastasis (p = 0.025), and poor overall survival (p < 0.05). Elevated expression of CARD8-AS1 could suppress cellular viability, migration potential, and invasion ability (p < 0.05). The Bcl-2 protein levels were decreased while Bax levels were increased by overexpression of CARD8-AS1 (p < 0.001). miR-650 may thus be a direct target of CARD8-AS1 and Bax may be a direct target of miR-650.Discussion: CARD8-AS1 expression was downregulated in lung adenocarcinoma and associated with several clinical parameters. CARD8-AS1 exerted tumor-suppressive effects by targeting the miR-650 and then regulating Bax expression. CARD8-AS1/miR-650 may serve as novel prognostic biomarkers and potential therapeutic targets for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Yong Ji
- Department of Respiratory, Shanghai General Hospital - Songjiang South Campus, Shanghai, China
| | - Guoqing Zhang
- Department of Respiratory, Shanghai General Hospital - Jiading Campus, Shanghai, China
- *Correspondence: Xingyi Zhang, ; Guoqing Zhang,
| | - Xingyi Zhang
- Department of Respiratory, Shanghai General Hospital - Songjiang South Campus, Shanghai, China
- *Correspondence: Xingyi Zhang, ; Guoqing Zhang,
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