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Lin Y, Zhao W, Pu R, Lv Z, Xie H, Li Y, Zhang Z. Long non‑coding RNAs as diagnostic and prognostic biomarkers for colorectal cancer (Review). Oncol Lett 2024; 28:486. [PMID: 39185489 PMCID: PMC11342420 DOI: 10.3892/ol.2024.14619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the 3rd most common cancer globally and is the 2nd leading cause of cancer-related death. Owing to the lack of specific early symptoms and the limitations of existing early diagnostic methods, most patients with CRC are diagnosed at advanced stages. To overcome these challenges, researchers have increasingly focused on molecular biomarkers, with particular interest in long non-coding RNAs (lncRNAs). These non-protein-coding RNAs, which exceed 200 nucleotides in length, play critical roles in the development and progression of CRC. The stability and detectability of lncRNAs in the circulatory system make them promising candidate biomarkers. The analysis of circulating lncRNAs in peripheral blood represents a potential option for minimally invasive diagnostic tests based on liquid biopsy samples. The present review aimed to evaluate the efficacy of lncRNAs with altered expression levels in peripheral blood as diagnostic markers for CRC. Additionally, the clinical significance of lncRNAs as prognostic markers for this disease were summarized.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Ruonan Pu
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Ying Li
- Department of Ultrasonography, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
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Wei P, Wang Y, Feng H, Zhang F, Ji Z, Zhang K, Zhang Q, Jiang L, Qian Y, Fu Y. Gene-Engineered Cerium-Exosomes Mediate Atherosclerosis Therapy Through Remodeling of the Inflammatory Microenvironment and DNA Damage Repair. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404463. [PMID: 39235409 DOI: 10.1002/smll.202404463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/10/2024] [Indexed: 09/06/2024]
Abstract
The pro-inflammatory immune microenvironment in the localized lesion areas and the absence of DNA damage repair mechanisms in endothelial cells serve as essential accelerating factors in the development of atherosclerosis. The lack of targeted therapeutic strategies represents a significant limitation in the efficacy of therapeutic agents for atherosclerosis. In this study, Genetically engineered SNHG12-loaded cerium-macrophage exosomes (Ce-Exo) are designed as atherosclerosis-targeting agents. In vivo studies demonstrated that Ce-Exo exhibited multivalent targeting properties for macrophages, with a 4.1-fold higher atherosclerotic plaque-aggregation ability than that of the control drugs. This suggests that Ce-Exo has a higher homing capacity and deeper penetration into the atherosclerotic plaque. In apolipoprotein E-deficient mice, Ce-Exo found to effectively remodel the immune microenvironment in the lesion area, repair endothelial cell damage, and inhibit the development of atherosclerosis. This study provides a novel approach to the treatment of atherosclerosis and demonstrates the potential of cell-derived drug carriers in biomedicine.
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Affiliation(s)
- Peng Wei
- Department of Cardiology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
| | - Yifan Wang
- Department of Emergency Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
| | - Haiyan Feng
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, P. R. China
| | - Fan Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, P. R. China
| | - Zhenyan Ji
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Kai Zhang
- Department of Ultrasound in Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
| | - Qiang Zhang
- Institute of Diagnostic and Interventional Radiology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
| | - Lixian Jiang
- Department of Ultrasound in Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
| | - Yuxuan Qian
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
| | - Yimu Fu
- Department of Emergency Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, P. R. China
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Wang L, Wang P, Liu B, Zhang H, Wei CC, Xiong M, Luo G, Wang M. LncRNA MEG3 Inhibits the Epithelial-mesenchymal Transition of Bladder Cancer Cells through the Snail/E-cadherin Axis. Curr Med Sci 2024; 44:726-734. [PMID: 38990449 DOI: 10.1007/s11596-024-2895-x] [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: 07/26/2023] [Accepted: 04/28/2024] [Indexed: 07/12/2024]
Abstract
OBJECTIVE This study aimed to investigate the role of the long noncoding RNA (lncRNA) maternally expressed gene 3 (MEG3) in the epithelial-mesenchymal transition (EMT) of bladder cancer cells and the potential mechanisms. METHODS Cell invasion, migration, and wound healing assays were conducted to assess the effects of MEG3 on the invasive and migratory capabilities of bladder cancer cells. The expression levels of E-cadherin were measured using Western blotting, RT-qPCR, and dual luciferase reporter assays. RNA immunoprecipitation and pull-down assays were performed to investigate the interactions between MEG3 and its downstream targets. RESULTS MEG3 suppressed the invasion and migration of bladder cancer cells and modulated the transcription of E-cadherin. The binding of MEG3 to the zinc finger region of the transcription factor Snail prevented its ability to transcriptionally repress E-cadherin. Additionally, MEG3 suppressed the phosphorylation of extracellular regulated protein kinase (ERK), c-Jun N-terminal kinase (JNK), and P38, thereby decreasing the expression of Snail and stimulating the expression of E-cadherin. CONCLUSION MEG3 plays a vital role in suppressing the EMT in bladder cancer cells, indicating its potential as a promising therapeutic target for the treatment of bladder cancer.
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Affiliation(s)
- Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ping Wang
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bing Liu
- Department of Urology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Cheng-Cheng Wei
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ming Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Gang Luo
- Department of Urology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China.
| | - Miao Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Lin Y, Zhao W, Lv Z, Xie H, Li Y, Zhang Z. The functions and mechanisms of long non-coding RNA in colorectal cancer. Front Oncol 2024; 14:1419972. [PMID: 39026978 PMCID: PMC11254705 DOI: 10.3389/fonc.2024.1419972] [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: 04/19/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
CRC poses a significant challenge in the global health domain, with a high number of deaths attributed to this disease annually. If CRC is detected only in its advanced stages, the difficulty of treatment increases significantly. Therefore, biomarkers for the early detection of CRC play a crucial role in improving patient outcomes and increasing survival rates. The development of a reliable biomarker for early detection of CRC is particularly important for timely diagnosis and treatment. However, current methods for CRC detection, such as endoscopic examination, blood, and stool tests, have certain limitations and often only detect cases in the late stages. To overcome these constraints, researchers have turned their attention to molecular biomarkers, which are considered a promising approach to improving CRC detection. Non-invasive methods using biomarkers such as mRNA, circulating cell-free DNA, microRNA, LncRNA, and proteins can provide more reliable diagnostic information. These biomarkers can be found in blood, tissue, stool, and volatile organic compounds. Identifying molecular biomarkers with high sensitivity and specificity for the early and safe, economic, and easily measurable detection of CRC remains a significant challenge for researchers.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Ying Li
- Ultrasonography Department, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
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Zetzsche J, Fallet M. To live or let die? Epigenetic adaptations to climate change-a review. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae009. [PMID: 39139701 PMCID: PMC11321362 DOI: 10.1093/eep/dvae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/05/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
Anthropogenic activities are responsible for a wide array of environmental disturbances that threaten biodiversity. Climate change, encompassing temperature increases, ocean acidification, increased salinity, droughts, and floods caused by frequent extreme weather events, represents one of the most significant environmental alterations. These drastic challenges pose ecological constraints, with over a million species expected to disappear in the coming years. Therefore, organisms must adapt or face potential extinctions. Adaptations can occur not only through genetic changes but also through non-genetic mechanisms, which often confer faster acclimatization and wider variability ranges than their genetic counterparts. Among these non-genetic mechanisms are epigenetics defined as the study of molecules and mechanisms that can perpetuate alternative gene activity states in the context of the same DNA sequence. Epigenetics has received increased attention in the past decades, as epigenetic mechanisms are sensitive to a wide array of environmental cues, and epimutations spread faster through populations than genetic mutations. Epimutations can be neutral, deleterious, or adaptative and can be transmitted to subsequent generations, making them crucial factors in both long- and short-term responses to environmental fluctuations, such as climate change. In this review, we compile existing evidence of epigenetic involvement in acclimatization and adaptation to climate change and discuss derived perspectives and remaining challenges in the field of environmental epigenetics. Graphical Abstract.
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Affiliation(s)
- Jonas Zetzsche
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
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Chini A, Guha P, Rishi A, Obaid M, Udden SN, Mandal SS. Discovery and functional characterization of LncRNAs associated with inflammation and macrophage activation. Methods 2024; 227:1-16. [PMID: 38703879 DOI: 10.1016/j.ymeth.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024] Open
Abstract
Long noncoding RNAs (lncRNA) are emerging players in regulation of gene expression and cell signaling and their dysregulation has been implicated in a multitude of human diseases. Recent studies from our laboratory revealed that lncRNAs play critical roles in cytokine regulation, inflammation, and metabolism. We demonstrated that lncRNA HOTAIR, which is a well-known regulator of gene silencing, plays critical roles in modulation of cytokines and proinflammatory genes, and glucose metabolism in macrophages during inflammation. In addition, we recently discovered a series of novel lncRNAs that are closely associated with inflammation and macrophage activation. We termed these as long-noncoding inflammation associated RNAs (LinfRNAs). We are currently engaged in the functional characterization of these hLinfRNAs (human LinfRNAs) with a focus on their roles in inflammation, and we are investigating their potential implications in chronic inflammatory human diseases. Here, we have summarized experimental methods that have been utilized for the discovery and functional characterization of lncRNAs in inflammation and macrophage activation.
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Affiliation(s)
- Avisankar Chini
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Prarthana Guha
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Ashcharya Rishi
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Monira Obaid
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sm Nashir Udden
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA.
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Fu W, Cao Y, Liu J, Huang C, Shu K, Zhu N. Xinfeng Capsule Inhibits Pyroptosis and Ameliorates Myocardial Injury in Rats with Adjuvant Arthritis via the GAS5/miR-21/TLR4 Axis. Drug Des Devel Ther 2024; 18:2421-2433. [PMID: 38915862 PMCID: PMC11195676 DOI: 10.2147/dddt.s456783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Purpose This study probed the mechanism of action of Xinfeng Capsule (XFC) in myocardial injury in rats with adjuvant arthritis (AA) via the growth arrest-specific transcript 5 (GAS5)/microRNA-21 (miR-21)/Toll-like receptor 4 (TLR4) axis. Methods Rats were injected with Freund's complete adjuvant to establish a rat model of AA. Then, some modeled rats were given normal saline or drugs only, and some modeled rats were injected with adeno-associated viruses or necrosulfonamide (NSA; a pyroptosis inhibitor) before drug administration. Toe swelling and arthritis index (AI) were calculated. Pathological and morphological changes in synovial and myocardial tissues were analyzed with hematoxylin-eosin staining, and pyroptotic vesicles and the ultrastructural changes of myocardial tissues were observed with transmission electron microscopy. The serum levels of interleukin (IL)-1β, IL-18, IL-6, and tumor necrosis factor (TNF)-α were detected, and lactate dehydrogenase (LDH) release was measured in myocardial tissues, accompanied by the examination of GAS5, miR-21, TLR4, nuclear factor-kB (NF-κB) p65, nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3), Caspase-1, and Gasdermin D (GSDMD) expression in myocardial tissues. Results After AA modeling, rats presented with significantly increased toe swelling and AI scores, synovial and myocardial tissue damage, elevated pyroptotic vesicles, and markedly enhanced serum levels of IL-1β, IL-18, IL-6, and TNF-α, accompanied by significantly diminished GAS5 expression, substantially augmented miR-21, TLR4, NF-κB p65, NLRP3, Caspase-1, and GSDMD expression, greatly increased LDH release in myocardial tissues. XFC treatment significantly declined toe swelling, AI scores, synovial and myocardial tissue damage, and the serum levels of IL-1β, IL-18, IL-6, and TNF-α in AA rats. Additionally, XFC treatment markedly elevated GAS5 expression and substantially lowered LDH release and miR-21, TLR4, NF-κB p65, NLRP3, Caspase-1, and GSDMD expression in myocardial tissues of AA rats. Moreover, the above effects of XFC in AA rats were further promoted by GAS5 overexpression or NSA treatment. Conclusion XFC alleviated myocardial injury in AA rats by regulating the GAS5/miR-21/TLR4 axis and inhibiting pyroptosis and pro-inflammatory cytokine secretion.
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Affiliation(s)
- Wanlan Fu
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, People’s Republic of China
| | - Yunxiang Cao
- Department of Rheumatology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, 230031, People’s Republic of China
| | - Jian Liu
- Department of Rheumatology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, 230031, People’s Republic of China
| | - Chuanbing Huang
- Department of Rheumatology, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, 230031, People’s Republic of China
| | - Kaiyan Shu
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, People’s Republic of China
| | - Nanfei Zhu
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, People’s Republic of China
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Cheng L, Zhao Y, Ke H. Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network in ischemic stroke. Heliyon 2024; 10:e29651. [PMID: 38698974 PMCID: PMC11064068 DOI: 10.1016/j.heliyon.2024.e29651] [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: 11/23/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024] Open
Abstract
Objective Competitive endogenous RNA (ceRNA) networks have uncovered a novel mode of RNA interaction, and are implicated in various biological processes and the pathogenesis of IS. This study aimed to explore the potential mechanisms underlying the ceRNA network in IS. Methods Four public datasets containing lncRNA and mRNA (GSE22255 and GSE16561) and miRNA (GSE55937 and GSE43618) expression profiles from the GEO database were systematically analyzed to explore the role of RNAs in ischemic stroke (IS). Differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs), and miRNAs (DEmiRNAs) between IS and normal control samples were identified. LncRNA-miRNA and miRNA-mRNA interactions were predicted, and the competing endogenous RNA (ceRNA) regulatory network was constructed using the Cytoscape software. The correlation between the RNAs in the ceRNA network and the clinical features of the samples was evaluated. Finally, principal component analysis was performed on the RNAs that constitute the ceRNA regulatory network, and their differential expression and principal component relationships among different types of samples were observed. Results A total of 224 DEmRNAs, 7 DEmiRNAs, and four DElncRNAs related to IS in four datasets were identified. Then, through target gene prediction, a lncRNA-miRNA-mRNA ceRNA network that contained 3 DElncRNAs, 2 DEmiRNAs, and 24 DEmRNAs was constructed. Correlations of the clinical characteristics showed that PART1 and SERPINH1 were related to clinical diseases, WNK1 was related to lifestyle, and seven RNAs were related to age. PCA results indicate that three principal components of PC1, PC2, and PC3 can clearly distinguish between control and IS samples. Conclusion Overall, we constructed a ceRNA network in IS, which could offer insights into the molecular mechanism and potential prognostic biomarkers for further research.
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Affiliation(s)
- Lin Cheng
- Department of Emergency, Shandong Provincial Third Hospital, Jinan, Shandong, 250031, China
| | - Yun Zhao
- Department of Emergency, Shandong Provincial Third Hospital, Jinan, Shandong, 250031, China
| | - Hong Ke
- Department of Neurology, The Fourth People's Hospital of Jinan, Jinan, Shandong, 250031, China
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Qi J, Wu W, Chen J, Han X, Hao Z, Han Y, Xu Y, Lai J, Chen J. Development and validation of a novel prognostic lncRNA signature based on the APOBEC3 family genes in gastric cancer. Heliyon 2024; 10:e28307. [PMID: 38560679 PMCID: PMC10979227 DOI: 10.1016/j.heliyon.2024.e28307] [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: 12/29/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Gastric Cancer (GC) refers to a prevalent malignant cancer accompanied by a weak prognosis. The APOBEC3 family genes and lncRNAs are linked with cancer progression. Nevertheless, there is still a scarcity of data concerning the prognostic value of APOBEC3-related lncRNAs in GC. Methods We extracted the data from GC samples, including transcriptome as well as clinical data, obtained from the TCGA database. Then, we screened for lncRNAs that were correlated with the APOBEC3 family genes and constructed an APOBEC3-related lncRNA prognostic signature (LPS) by utilizing univariate Cox and lasso regression analysis. Furthermore, we validated our constructed signature and evaluated it thoroughly, including analysis of its function, immunity, mutations, and clinical applications via multiple methods, including Metascape, GSEA, and analyses including TIC and TME, immune checkpoints, CNV and SNPs, Kaplan-Meier survival curves, nomogram, decision tree and drug prediction analysis. Finally, we overexpressed LINC01094 to evaluate the impacts on the proliferation as well as migration with regards to KATO-2 cells. Results We selected eight lncRNAs for our APOBEC3-related LPS, which is demonstrated as a valuable tool in predicting the individual GC patients' prognosis. Subsequently, we segregated the samples into subgroups of high-as well as low-risk relying on the risk score with regards to APOBEC3-related LPS. By performing functional analysis, we have shown that immune-as well as tumor-related pathways were enriched in high- and low-risk GC patients. Furthermore, immune analysis revealed a robust correlation between the APOBEC3-related LPS and immunity. We found that immune checkpoints were significantly associated with the APOBEC3-related LPS and were greatly exhibited in GC tumor and high-risk samples. Mutational analysis suggested that the mutational rate was greater in low-risk samples. Furthermore, we predicted small molecular drugs displayed greater sensitivity in patients categorized as high-risk. Moreover, the immune response was also better in high-risk patients. Of these drugs, dasatinib was significant in both methods and might be considered a potential novel drug for treating high-risk GC patients. Finally, we found that LINC01094 has the potential to enhance the migration, proliferation as well as inhibit apoptosis of KATO-2 in GC cells. And Dasatinib has an inhibitory effect on the migration as well as proliferation in GC cells. Conclusion We created a novel APOBEC3-related LPS in predicting the prognosis with regards to individual GC patients. Importantly, this APOBEC3-related LPS was closely associated with immunity and might guide clinical treatment.
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Affiliation(s)
- Jia Qi
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Wenxuan Wu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Jing Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Xiaying Han
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Zhixing Hao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Yaxuan Han
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Yewei Xu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Jun Lai
- Department of Cardiology Guangdong Second Provincial General Hospital, Guangzhou, 510000, Guangdong, China
| | - Jian Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
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Deb P, Chini A, Guha P, Rishi A, Bhan A, Brady B, Perrotti LI, Mandal SS. Dynamic regulation of BDNF gene expression by estradiol and lncRNA HOTAIR. Gene 2024; 897:148055. [PMID: 38043834 DOI: 10.1016/j.gene.2023.148055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Brain derived neurotrophic factor (BDNF) is a major neurotransmitter that controls growth and maintenance of neurons and its misregulation is linked to neurodegeneration and human diseases. Estradiol (E2) is well-known to regulate the process of differentiation and plasticity of hippocampal neurons. Here we examined the mechanisms of BDNF gene regulation under basal conditions and under stimuli such as E2. Our results demonstrated that BDNF expression is induced by E2 in vitro in HT22 cells (hippocampal neuronal cells) and in vivo (in ovariectomized mouse brain under E2-treatment). Using chromatin immunoprecipitation assay, we demonstrated that estrogen receptors (ERα, ERβ) were enriched at the BDNF promoter in presence of E2. Additionally, ER-coregulators (e.g., CBP/p300, MLL3), histone acetylation, H3K4-trimethylation, and RNA polymerase II levels were also elevated at the BDNF promoter in an E2-dependent manner. Additionally, under the basal conditions (in the absence of E2), the long noncoding RNA HOTAIR and its interacting partners PRC2 and LSD1 complexes binds to the promoter of BDNF and represses its expression. HOTAIR knockdown -relieves the repression resulting in elevation of BDNF expression. Further, levels of HOTAIR-interacting partners, EZH2 and LSD1 were reduced at the BDNF promoter upon HOTAIR-knockdown revealing that HOTAIR plays a regulatory role in BDNF gene expression by modulating promoter histone modifications. Additionally, we showed that E2 induced-BDNF expression is mediated by the displacement of silencing factors, EZH2 and LSD1 at BDNF promoter and subsequent recruitment of active transcription machinery. These results reveal the mechanisms of BDNF gene regulation under the basal condition and in presence of a positive regulator such as E2 in neuronal cells.
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Affiliation(s)
- Paromita Deb
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Avisankar Chini
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Prarthana Guha
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Ashcharya Rishi
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Arunoday Bhan
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Blake Brady
- Department of Psychology, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Linda I Perrotti
- Department of Psychology, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States.
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Rahbar Farzam O, Najafi S, Amini M, Rahimi Z, Dabbaghipour R, Zohdi O, Asemani Shahgoli G, Baradaran B, Akbari B. Interplay of miRNAs and lncRNAs in STAT3 signaling pathway in colorectal cancer progression. Cancer Cell Int 2024; 24:16. [PMID: 38185635 PMCID: PMC10771635 DOI: 10.1186/s12935-023-03202-3] [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: 03/01/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024] Open
Abstract
In recent decades, colorectal cancer (CRC) has turned into one of the most widespread malignancies, and the incidence of this malignancy is expected to increase. Despite considerable improvements in therapeutic approaches, the prognosis, and the management of CRC face many problems. Likely, the main limitation in the successful treatment of CRC is the lack of appropriate clinical therapeutic targets. As an effective target, the signal transducer and activator of transcription 3 (STAT3) are regulated by a wide range of genes and involved in cellular processes, including cell growth, migration, invasion, immunosuppression, and angiogenesis. Aberrant regulation of STAT3 signaling leads to cellular dysfunction, diseases, and malignancies, including CRC. Consequently, targeting this signaling pathway is considered one of the therapeutic strategies used in CRC treatment. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are non-coding RNA molecules with partial or no protein-coding activity that participate in gene regulation at epigenetic, transcriptional, and post-transcriptional levels and regulate multiple signaling pathways, including STAT3 signaling (especially JAK/STAT). Therefore, these regulatory molecules are suggested to be very promising targets to present new insights into overcoming the limitations of conventional therapeutic strategies. Therefore, the current review study aimed to summarize the therapeutic and diagnostic significance of miRNAs and lncRNAs and their therapeutic and diagnostic significance related to the expression and activity of STAT3 in CRC.
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Affiliation(s)
- Omid Rahbar Farzam
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Rahimi
- Department of Clinical Biochemistry, Medical School, Daneshgah Avenue, Kermanshah, Iran
- Medical Biology Research Center, Daneshgah Avenue, Kermanshah, Iran
| | - Reza Dabbaghipour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Zohdi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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12
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Alluli A, Fonseca G, Matthews J, Eidelman DH, Baglole CJ. Regulation of long non-coding RNA expression by aryl hydrocarbon receptor activation. Toxicol Lett 2024; 391:13-25. [PMID: 38036013 DOI: 10.1016/j.toxlet.2023.11.004] [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: 04/13/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor that can be activated by endogenous or xenobiotic ligands. Upon activation, the AhR translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT), and binds to specific DNA sequences called xenobiotic response elements (XRE) to promote target gene transcription, including cytochrome P450 (e.g., CYP1A1) expression. In addition to mRNA, the AhR may also regulate long non-coding RNA (lncRNA) expression. lncRNA are transcripts more than 200 nucleotides in length that do not encode a protein. Herein, we tested whether AhR activation regulates the expression of lncRNA in response to benzo[a]pyrene (B[a]P) using RNA sequencing (RNA-seq). We found that many lncRNA (e.g., SATB1-AS1, MIR4290HG, AC008969.1, LINC01533, VIPR1-AS1) and protein-coding RNA (e.g., CYP1A1, BX005266.2, AQP3, BTG2, DCX, and AhRR) were differentially expressed (DE) in A549 cells treated with B[a]P; many of these genes were dependent on AhR expression including CYP1A1, CYP1B1 and TiPARP. GO analyses indicated that DE protein-coding RNAs in A549WT cells are associated with distinct molecular functions compared to A549KO cells. KEGG analyses showed the hsa01100 pathway was associated with DE lncRNA only in A549WT cells. A549KO cells treated with B[a]P exhibited a distinct set of differentially-regulated lncRNA including upregulation of HOTAIR. We further confirmed that despite AhR activation in A549WT cells, B[a]P did not alter the expression of many well-characterized lncRNA including NEAT1, HOTTIP, SOX2OT, MALAT1, H19, and Linc00673. Thus, there is control over select lncRNA expression in A549 cells exposed to B[a]P, a finding which could yield insight into the molecular function of the AhR.
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Affiliation(s)
- Aeshah Alluli
- Meakins-Christie Laboratories, McGill University, Montreal, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Montreal, Canada; Department of Pathology, McGill University, Montreal, Canada
| | - Gregory Fonseca
- Meakins-Christie Laboratories, McGill University, Montreal, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Montreal, Canada; Department of Medicine, McGill University, Montreal, Canada
| | - Jason Matthews
- Department of Nutrition, University of Oslo, Oslo, Norway; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - David H Eidelman
- Meakins-Christie Laboratories, McGill University, Montreal, Canada; Department of Medicine, McGill University, Montreal, Canada
| | - Carolyn J Baglole
- Meakins-Christie Laboratories, McGill University, Montreal, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Montreal, Canada; Department of Pathology, McGill University, Montreal, Canada; Department of Medicine, McGill University, Montreal, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada.
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13
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Zou F, Zhang ZH, Zou SS, Zhuang ZB, Ji Q, Chang R, Cao JH, Wang B. LncRNA MIR210HG promotes the proliferation, migration, and invasion of lung cancer cells by inhibiting the transcription of SH3GL3. Kaohsiung J Med Sci 2023; 39:1166-1177. [PMID: 37916731 DOI: 10.1002/kjm2.12775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Lung cancer (LCa), the most frequent malignancy worldwide, causes millions of mortalities each year. Overexpression of the long noncoding RNA MIR210HG in LCa has been established; however, a more comprehensive investigation into its biological role within LCa is imperative. This study aimed to validate the MIR210H levels in LCa tissues and cells. The expression of indicated genes was evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) and/or Western blotting. The viability, proliferation, migration, and invasion of LCa cells were measured using the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), colony formation, wound healing, and transwell assays, respectively. The methylation levels of LCa cells were determined via methylation-specific PCR; additionally, chromatin immunoprecipitation or RNA immunoprecipitation assays were performed to determine the targeting relationship between DNA methyltransferase 1 (DNMT1) and the SH3-domain containing CRB2 like 3 (SH3GL3) promoters and the interaction between DNMT1 and MIR210HG, respectively. Our findings revealed the upregulation of MIR210HG, coupled with a diminished expression of SH3GL3 in LCa tissues and cells. Knockdown of MIR210HG or overexpression of SH3GL3 suppressed the proliferative, migratory, and invasive capacities of the cells. DNMT1 bound to the SH3GL3 promoter region, and MIR210HG inhibited the transcription of SH3GL3 by recruiting DNMT1. These findings indicate that MIR210HG facilitates LCa cell growth and metastasis by repressing SH3GL3 transcription via the recruitment of DNMT1 to the SH3GL3 promoter region.
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Affiliation(s)
- Fang Zou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, P.R. China
| | - Zhi-Hua Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, P.R. China
| | - Shuang-Shuang Zou
- Guangzhou Liwan Stomatological Hospital, Guangzhou, Guangdong Province, P.R. China
| | - Zhong-Bao Zhuang
- Department of Pharmacy, Hebei North University, Zhangjiakou, Hebei Province, P.R. China
| | - Qiang Ji
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, P.R. China
| | - Rui Chang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, P.R. China
| | - Jia-Huan Cao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, P.R. China
| | - Bu Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, P.R. China
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14
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Shwani T, Zhang C, Owen LA, Shakoor A, Vitale AT, Lillvis JH, Barr JL, Cromwell P, Finley R, Husami N, Au E, Zavala RA, Graves EC, Zhang SX, Farkas MH, Ammar DA, Allison KM, Tawfik A, Sherva RM, Li M, Stambolian D, Kim IK, Farrer LA, DeAngelis MM. Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration. Cells 2023; 12:2668. [PMID: 38067097 PMCID: PMC10705168 DOI: 10.3390/cells12232668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, and elucidating its underlying disease mechanisms is vital to the development of appropriate therapeutics. We identified differentially expressed genes (DEGs) and differentially spliced genes (DSGs) across the clinical stages of AMD in disease-affected tissue, the macular retina pigment epithelium (RPE)/choroid and the macular neural retina within the same eye. We utilized 27 deeply phenotyped donor eyes (recovered within a 6 h postmortem interval time) from Caucasian donors (60-94 years) using a standardized published protocol. Significant findings were then validated in an independent set of well-characterized donor eyes (n = 85). There was limited overlap between DEGs and DSGs, suggesting distinct mechanisms at play in AMD pathophysiology. A greater number of previously reported AMD loci overlapped with DSGs compared to DEGs between disease states, and no DEG overlap with previously reported loci was found in the macular retina between disease states. Additionally, we explored allele-specific expression (ASE) in coding regions of previously reported AMD risk loci, uncovering a significant imbalance in C3 rs2230199 and CFH rs1061170 in the macular RPE/choroid for normal eyes and intermediate AMD (iAMD), and for CFH rs1061147 in the macular RPE/choroid for normal eyes and iAMD, and separately neovascular AMD (NEO). Only significant DEGs/DSGs from the macular RPE/choroid were found to overlap between disease states. STAT1, validated between the iAMD vs. normal comparison, and AGTPBP1, BBS5, CERKL, FGFBP2, KIFC3, RORα, and ZNF292, validated between the NEO vs. normal comparison, revealed an intricate regulatory network with transcription factors and miRNAs identifying potential upstream and downstream regulators. Findings regarding the complement genes C3 and CFH suggest that coding variants at these loci may influence AMD development via an imbalance of gene expression in a tissue-specific manner. Our study provides crucial insights into the multifaceted genomic underpinnings of AMD (i.e., tissue-specific gene expression changes, potential splice variation, and allelic imbalance), which may open new avenues for AMD diagnostics and therapies specific to iAMD and NEO.
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Affiliation(s)
- Treefa Shwani
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Leah A. Owen
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
| | - Albert T. Vitale
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Julie L. Barr
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Parker Cromwell
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Robert Finley
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Nadine Husami
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Elizabeth Au
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Rylee A. Zavala
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Elijah C. Graves
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
| | - Sarah X. Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Michael H. Farkas
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - David A. Ammar
- Lion’s Eye Institute for Transplant & Research, Tampa, FL 33605, USA;
| | - Karen M. Allison
- Department of Ophthalmology, Flaum Eye Institute, University of Rochester, Rochester, NY 14642, USA;
| | - Amany Tawfik
- Department of Foundational Medical Studies and Eye Research Center, Oakland University William Beaumont School of Medicine, Rochester, MI 48309, USA;
- Eye Research Institute, Oakland University, Rochester, MI 48309, USA
| | - Richard M. Sherva
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; (R.M.S.); (L.A.F.)
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA;
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; (R.M.S.); (L.A.F.)
| | - Margaret M. DeAngelis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA; (T.S.); (C.Z.); (L.A.O.); (J.H.L.); (J.L.B.); (P.C.); (R.F.); (N.H.); (E.A.); (R.A.Z.); (E.C.G.); (S.X.Z.); (M.H.F.)
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA; (A.S.); (A.T.V.)
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
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Zhong S, Chen S, Lin H, Luo Y, He J. Selection of M7G-related lncRNAs in kidney renal clear cell carcinoma and their putative diagnostic and prognostic role. BMC Urol 2023; 23:186. [PMID: 37968670 PMCID: PMC10652602 DOI: 10.1186/s12894-023-01357-9] [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: 06/20/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is a common malignant tumor of the urinary system. This study aims to develop new biomarkers for KIRC and explore the impact of biomarkers on the immunotherapeutic efficacy for KIRC, providing a theoretical basis for the treatment of KIRC patients. METHODS Transcriptome data for KIRC was obtained from the The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Weighted gene co-expression network analysis identified KIRC-related modules of long noncoding RNAs (lncRNAs). Intersection analysis was performed differentially expressed lncRNAs between KIRC and normal control samples, and lncRNAs associated with N(7)-methylguanosine (m7G), resulting in differentially expressed m7G-associated lncRNAs in KIRC patients (DE-m7G-lncRNAs). Machine Learning was employed to select biomarkers for KIRC. The prognostic value of biomarkers and clinical features was evaluated using Kaplan-Meier (K-M) survival analysis, univariate and multivariate Cox regression analysis. A nomogram was constructed based on biomarkers and clinical features, and its efficacy was evaluated using calibration curves and decision curves. Functional enrichment analysis was performed to investigate the functional enrichment of biomarkers. Correlation analysis was conducted to explore the relationship between biomarkers and immune cell infiltration levels and common immune checkpoint in KIRC samples. RESULTS By intersecting 575 KIRC-related module lncRNAs, 1773 differentially expressed lncRNAs, and 62 m7G-related lncRNAs, we identified 42 DE-m7G-lncRNAs. Using XGBoost and Boruta algorithms, 8 biomarkers for KIRC were selected. Kaplan-Meier survival analysis showed significant survival differences in KIRC patients with high and low expression of the PTCSC3 and RP11-321G12.1. Univariate and multivariate Cox regression analyses showed that AP000696.2, PTCSC3 and clinical characteristics were independent prognostic factors for patients with KIRC. A nomogram based on these prognostic factors accurately predicted the prognosis of KIRC patients. The biomarkers showed associations with clinical features of KIRC patients, mainly localized in the cytoplasm and related to cytokine-mediated immune response. Furthermore, immune feature analysis demonstrated a significant decrease in immune cell infiltration levels in KIRC samples compared to normal samples, with a negative correlation observed between the biomarkers and most differentially infiltrating immune cells and common immune checkpoints. CONCLUSION In summary, this study discovered eight prognostic biomarkers associated with KIRC patients. These biomarkers showed significant correlations with clinical features, immune cell infiltration, and immune checkpoint expression in KIRC patients, laying a theoretical foundation for the diagnosis and treatment of KIRC.
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Affiliation(s)
- Shuangze Zhong
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Shangjin Chen
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Hansheng Lin
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
- Department of Urology, Yangjiang People's Hospital affiliated to Guangdong Medical University, Yangjiang, 42 Dongshan Road, Jiangcheng District, Guangdong Province, 529500, China
| | - Yuancheng Luo
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Jingwei He
- Department of Urology, Yangjiang People's Hospital affiliated to Guangdong Medical University, Yangjiang, 42 Dongshan Road, Jiangcheng District, Guangdong Province, 529500, China.
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16
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Ramezani M, Zobeiry M, Abdolahi S, Hatami B, Zali MR, Baghaei K. A crosstalk between epigenetic modulations and non-alcoholic fatty liver disease progression. Pathol Res Pract 2023; 251:154809. [PMID: 37797383 DOI: 10.1016/j.prp.2023.154809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has recently emerged as a major public health concern worldwide due to its rapidly rising prevalence and its potential to progress into end-stage liver disease. While the precise pathophysiology underlying NAFLD remains incompletely understood, it is strongly associated with various environmental triggers and other metabolic disorders. Epigenetics examines changes in gene expression that are not caused by alterations in the DNA sequence itself. There is accumulating evidence that epigenetics plays a key role in linking environmental cues to the onset and progression of NAFLD. Our understanding of how epigenetic mechanisms contribute to NAFLD pathophysiology has expanded considerably in recent years as research on the epigenetics of NAFLD has developed. This review summarizes recent insights into major epigenetic processes that have been implicated in NAFLD pathogenesis including DNA methylation, histone acetylation, and microRNAs that have emerged as promising targets for further investigation. Elucidating epigenetic mechanisms in NAFLD may uncover novel diagnostic biomarkers and therapeutic targets for this disease. However, many questions have remained unanswered regarding how epigenetics promotes NAFLD onset and progression. Additional studies are needed to further characterize the epigenetic landscape of NAFLD and validate the potential of epigenetic markers as clinical tools. Nevertheless, an enhanced understanding of the epigenetic underpinnings of NAFLD promises to provide key insights into disease mechanisms and pave the way for novel prognostic and therapeutic approaches.
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Affiliation(s)
- Meysam Ramezani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Shahrokh Abdolahi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Behzad Hatami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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17
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Zhang X, Xu X, Song J, Xu Y, Qian H, Jin J, Liang ZF. Non-coding RNAs' function in cancer development, diagnosis and therapy. Biomed Pharmacother 2023; 167:115527. [PMID: 37751642 DOI: 10.1016/j.biopha.2023.115527] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
While previous research on cancer biology has focused on genes that code for proteins, in recent years it has been discovered that non-coding RNAs (ncRNAs)play key regulatory roles in cell biological functions. NcRNAs account for more than 95% of human transcripts and are an important entry point for the study of the mechanism of cancer development. An increasing number of studies have demonstrated that ncRNAs can act as tumor suppressor genes or oncogenes to regulate tumor development at the epigenetic level, transcriptional level, as well as post-transcriptional level. Because of the importance of ncRNAs in cancer, most clinical trials have focused on ncRNAs to explore whether ncRNAs can be used as new biomarkers or therapies. In this review, we focus on recent studies of ncRNAs including microRNAs (miRNAs), long ncRNAs (lncRNAs), circle RNAs (circRNAs), PIWI interacting RNAs (piRNAs), and tRNA in different types of cancer and explore the application of these ncRNAs in the development of cancer and the identification of relevant therapeutic targets and tumor biomarkers. Graphical abstract drawn by Fidraw.
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Affiliation(s)
- XinYi Zhang
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Xiaoqing Xu
- Nanjing Renpin ENT Hospital, Nanjing 210000, Jiangsu, China
| | - Jiajia Song
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Yumeng Xu
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Hui Qian
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China
| | - Jianhua Jin
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China.
| | - Zhao Feng Liang
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou 213017, Jiangsu, China; Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu university, Zhenjiang, Jiangsu 212013, China.
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18
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Zhou Q, Xiong J, Gao Y, Yi R, Xu Y, Chen Q, Wang L, Chen Y. Mitochondria-related lncRNAs: predicting prognosis, tumor microenvironment and treatment response in lung adenocarcinoma. Funct Integr Genomics 2023; 23:323. [PMID: 37864709 PMCID: PMC10590301 DOI: 10.1007/s10142-023-01245-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/23/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023]
Abstract
Lung cancer is the most common type of malignant tumor that affects people in China and even across the globe, as it exhibits the highest rates of morbidity and mortality. Lung adenocarcinoma (LUAD) is a type of lung cancer with a very high incidence. The purpose of this study was to identify potential biomarkers that could be used to forecast the prognosis and improve the existing therapy options for treating LUAD. Clinical and RNA sequencing data of LUAD patients were retrieved from the TCGA database, while the mitochondria-associated gene sets were acquired from the MITOMAP database. Thereafter, Pearson correlation analysis was carried out to screen mitochondria-associated lncRNAs. Furthermore, univariate Cox and Lasso regression analyses were used for the initial screening of the target lncRNAs for prognostic lncRNAs before they could be incorporated into a multivariate Cox Hazard ratio model. Then, the clinical data, concordance index, Kaplan-Meier (K-M) curves, and the clinically-relevant subjects that were approved by the Characteristic Curves (ROC) were employed for assessing the model's predictive value. Additionally, the differences in immune-related functions and biological pathway enrichment between high- and low-risk LUAD groups were examined. Nomograms were developed to anticipate the OS rates of the patients within 1-, 3-, and 5 years, and the differences in drug sensitivity and immunological checkpoints were compared. In this study, 2175 mitochondria-associated lncRNAs were screened. Univariate, multivariate, and Lasso Cox regression analyses were carried out to select 13 lncRNAs with an independent prognostic significance, and a prognostic model was developed. The OS analysis of the established prognostic prediction model revealed significant variations between the high- and low-risk patients. The AUC-ROC values after 1, 3, and 5 years were seen to be 0.746, 0.692, and 0.726, respectively. The results suggested that the prognostic model riskscore could be used as an independent prognostic factor that differed from the other clinical characteristics. After analyzing the findings of the study, it was noted that both the risk groups showed significant differences in their immune functioning, immunological checkpoint genes, and drug sensitivity. The prognosis of patients with LUAD could be accurately and independently predicted using a risk prediction model that included 13 mitochondria-associated lncRNAs.
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Affiliation(s)
- Qianhui Zhou
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Jiali Xiong
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Yan Gao
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Rong Yi
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Yuzhu Xu
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Quefei Chen
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Lin Wang
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China
| | - Ying Chen
- Department of Respiratory and Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, 412000, Hunan, China.
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19
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Alluli A, Rijnbout St James W, Eidelman DH, Baglole CJ. Dynamic relationship between the aryl hydrocarbon receptor and long noncoding RNA balances cellular and toxicological responses. Biochem Pharmacol 2023; 216:115745. [PMID: 37597813 DOI: 10.1016/j.bcp.2023.115745] [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: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor activated by endogenous ligands and xenobiotic chemicals. Once the AhR is activated, it translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT) and binds to xenobiotic response elements (XRE) to promote gene transcription, notably the cytochrome P450 CYP1A1. The AhR not only mediates the toxic effects of environmental chemicals, but also has numerous putative physiological functions. This dichotomy in AhR biology may be related to reciprocal regulation of long non-coding RNA (lncRNA). lncRNA are defined as transcripts more than 200 nucleotides in length that do not encode a protein but are implicated in many physiological processes such as cell differentiation, cell proliferation, and apoptosis. lncRNA are also linked to disease pathogenesis, particularly the development of cancer. Recent studies have revealed that AhR activation by environmental chemicals affects the expression and function of lncRNA. In this article, we provide an overview of AhR signaling pathways activated by diverse ligands and highlight key differences in the putative biological versus toxicological response of AhR activation. We also detail the functions of lncRNA and provide current data on their regulation by the AhR. Finally, we outline how overlap in function between AhR and lncRNA may be one way in which AhR can be both a regulator of endogenous functions but also a mediator of toxicological responses to environmental chemicals. Overall, more research is still needed to fully understand the dynamic interplay between the AhR and lncRNA.
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Affiliation(s)
- Aeshah Alluli
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - Willem Rijnbout St James
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - David H Eidelman
- Meakins-Christie Laboratories, McGill University, Canada; Department of Medicine, McGill University, Canada
| | - Carolyn J Baglole
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada; Department of Medicine, McGill University, Canada; Department of Pharmacology and Therapeutics, McGill University, Canada.
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20
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Zhang R, Gao X, Gu X. BBOX1-AS1: A novel oncogenic long non-coding RNA in human cancers. Pathol Res Pract 2023; 250:154810. [PMID: 37696243 DOI: 10.1016/j.prp.2023.154810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts that contain more than 200 nucleotides. Despite the fact that they cannot encode proteins, many studies have identified roles they play in human cancers through diverse mechanisms. BBOX1-AS1, an oncogenic lncRNA, has recently been demonstrated to participate in tumorigenesis and progression of numerous cancers. Experimental evidence has determined that it participates in diverse biological process, including cell proliferation, invasion, migration, and apoptosis. The dysregulation of BBOX1-AS1 exerts its oncogenicity by acting as a competitive endogenous RNA (ceRNA) or by directly impacting downstream molecules and signaling pathways. Here we summarize the current understanding of the biological functions and clinical significance of BBOX1-AS1 for human cancers.
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Affiliation(s)
- Renfang Zhang
- Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xiaohui Gao
- Department of Oncology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471000, Henan, China.
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21
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Singh P, Zhou L, Shah DA, Cejas RB, Crossman DK, Jouni M, Magdy T, Wang X, Sharafeldin N, Hageman L, McKenna DE, Horvath S, Armenian SH, Balis FM, Hawkins DS, Keller FG, Hudson MM, Neglia JP, Ritchey AK, Ginsberg JP, Landier W, Burridge PW, Bhatia S. Identification of novel hypermethylated or hypomethylated CpG sites and genes associated with anthracycline-induced cardiomyopathy. Sci Rep 2023; 13:12683. [PMID: 37542143 PMCID: PMC10403495 DOI: 10.1038/s41598-023-39357-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023] Open
Abstract
Anthracycline-induced cardiomyopathy is a leading cause of late morbidity in childhood cancer survivors. Aberrant DNA methylation plays a role in de novo cardiovascular disease. Epigenetic processes could play a role in anthracycline-induced cardiomyopathy but remain unstudied. We sought to examine if genome-wide differential methylation at 'CpG' sites in peripheral blood DNA is associated with anthracycline-induced cardiomyopathy. This report used participants from a matched case-control study; 52 non-Hispanic White, anthracycline-exposed childhood cancer survivors with cardiomyopathy were matched 1:1 with 52 survivors with no cardiomyopathy. Paired ChAMP (Chip Analysis Methylation Pipeline) with integrated reference-based deconvolution of adult peripheral blood DNA methylation was used to analyze data from Illumina HumanMethylation EPIC BeadChip arrays. An epigenome-wide association study (EWAS) was performed, and the model was adjusted for GrimAge, sex, interaction terms of age at enrollment, chest radiation, age at diagnosis squared, and cardiovascular risk factors (CVRFs: diabetes, hypertension, dyslipidemia). Prioritized genes were functionally validated by gene knockout in human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) using CRISPR/Cas9 technology. DNA-methylation EPIC array analyses identified 32 differentially methylated probes (DMP: 15 hyper-methylated and 17 hypo-methylated probes) that overlap with 23 genes and 9 intergenic regions. Three hundred and fifty-four differential methylated regions (DMRs) were also identified. Several of these genes are associated with cardiac dysfunction. Knockout of genes EXO6CB, FCHSD2, NIPAL2, and SYNPO2 in hiPSC-CMs increased sensitivity to doxorubicin. In addition, EWAS analysis identified hypo-methylation of probe 'cg15939386' in gene RORA to be significantly associated with anthracycline-induced cardiomyopathy. In this genome-wide DNA methylation profile study, we observed significant differences in DNA methylation at the CpG level between anthracycline-exposed childhood cancer survivors with and without cardiomyopathy, implicating differential DNA methylation of certain genes could play a role in pathogenesis of anthracycline-induced cardiomyopathy.
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Affiliation(s)
- Purnima Singh
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Liting Zhou
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Disheet A Shah
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Romina B Cejas
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mariam Jouni
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Tarek Magdy
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
- Department of Pathology and Translational Pathobiology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - Xuexia Wang
- Department of Biostatistics, Florida International University, Miami, FL, USA
| | - Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lindsey Hageman
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donald E McKenna
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Saro H Armenian
- Department of Population Sciences, City of Hope, Duarte, CA, USA
| | - Frank M Balis
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Frank G Keller
- Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | | | | | - A Kim Ritchey
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | - Wendy Landier
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA.
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22
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Li S, Wang X, Liu Y, Xiao J, Yi J. The implication of necroptosis-related lncRNAs in orchestrating immune infiltration and predicting therapeutic efficacy in colon adenocarcinoma: an integrated bioinformatic analysis with preliminarily experimental validation. Front Genet 2023; 14:1170640. [PMID: 37600653 PMCID: PMC10433646 DOI: 10.3389/fgene.2023.1170640] [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: 02/21/2023] [Accepted: 04/17/2023] [Indexed: 08/22/2023] Open
Abstract
Background: Necroptosis contributes significantly to colon adenocarcinoma (COAD). We aim to assess the relationship between immunoinfiltration and stemness in COAD patients through the development of a risk score profile using necroptosis-related long noncoding RNAs (NRLs). Methods: Our study was based on gene expression data and relevant clinical information from The Cancer Genome Atlas (TCGA). Necroptosis-related genes (NRGs) were obtained from the Kyoto Encyclopedia of Genes and Genome (KEGG) database. Pearson correlation analysis, Cox regression, and least absolute shrinkage and selection operator (LASSO) regression were used to determine the NRL prognositic signature (NRLPS). NRLs expression was examined using qRT-PCR method. Several algorithms were used to identify relationships between immune cell infiltration and NRLPS risk scores. Further analysis of somatic mutations, tumor stemness index (TSI), and drug sensitivity were also explored. Results: To construct NRLPS, 15 lncRNAs were investigated. Furthermore, NRLPS patients with high-risk subgroups had lower survival rates than that of patients with low-risk subgroups. Using GSEA analysis, NRL was found to be enriched in Notch, Hedgehog and Smoothened pathways. Immune infiltration analysis showed significant differences in CD8+ T cells, dendritic cell DCs, and CD4+ T cells between the two risk groups. In addition, our NRLPS showed a relevance with the regulation of tumor microenvironment, tumor mutation burden (TMB) and stemness. Finally, NRLPS demonstrated potential applications in predicting the efficacy of immunotherapy and chemotherapy in patients with COAD. Conclusion: Based on NRLs, a prognostic model was developed for COAD patients that allows a personalized tailoring immunotherapy and chemotherapy to be tailored.
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Affiliation(s)
- Shizhe Li
- Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial People’s Hospital, Changsha, Hunan, China
| | - Xiaotong Wang
- Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial People’s Hospital, Changsha, Hunan, China
| | - Yajun Liu
- Hunan Provincial People’s Hospital, Changsha, Hunan, China
| | - Junbo Xiao
- Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial People’s Hospital, Changsha, Hunan, China
| | - Jun Yi
- Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial People’s Hospital, Changsha, Hunan, China
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23
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Arafat M, Sperling R. Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer. Noncoding RNA 2023; 9:42. [PMID: 37624034 PMCID: PMC10459839 DOI: 10.3390/ncrna9040042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Non-coding RNAs (ncRNAs) play diverse roles in regulating cellular processes and have been implicated in pathological conditions, including cancer, where interactions between ncRNAs play a role. Relevant here are (i) microRNAs (miRNAs), mainly known as negative regulators of gene expression in the cytoplasm. However, identification of miRNAs in the nucleus suggested novel nuclear functions, and (ii) long non-coding RNA (lncRNA) regulates gene expression at multiple levels. The recent findings of miRNA in supraspliceosomes of human breast and cervical cancer cells revealed new candidates of lncRNA targets. Here, we highlight potential cases of crosstalk between lncRNA and supraspliceosomal miRNA expressed from the same genomic region, having complementary sequences. Through RNA:RNA base pairing, changes in the level of one partner (either miRNA or lncRNA), as occur in cancer, could affect the level of the other, which might be involved in breast and cervical cancer. An example is spliceosomal mir-7704 as a negative regulator of the oncogenic lncRNA HAGLR. Because the expression of spliceosomal miRNA is cell-type-specific, the list of cis-interacting lncRNA:spliceosomal miRNA presented here is likely just the tip of the iceberg, and such interactions are likely relevant to additional cancers. We thus highlight the potential of lncRNA:spliceosomal miRNA interactions as novel targets for cancer diagnosis and therapies.
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Affiliation(s)
- Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Yang M, Zhang M, Wang Q, Guo X, Geng P, Gu J, Ji W, Zhang L. Six polymorphisms in the lncRNA H19 gene and the risk of cancer: a systematic review and meta-analysis. BMC Cancer 2023; 23:688. [PMID: 37480014 PMCID: PMC10362596 DOI: 10.1186/s12885-023-11164-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Numerous studies have demonstrated long noncoding RNA (lncRNA) play an important role in the occurrence and progression of cancer, and single nucleotide polymorphisms (SNPs) located in lncRNA are considered to affect cancer suspensibility. Herein, a meta-analysis was carried out to better assess the relationship of H19 polymorphisms and cancer susceptibility. METHODS A literature search was conducted through using PubMed, EMBASE, and Web of Science databases to obtain relevant publications before Aug 23, 2022. The reference lists of the retrieved studies were also investigated to identify additional relevant articles. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to appraise the risk of various cancers. RESULTS There appeared to be a remarkable correlation between the rs2107425 variation and decreased cancer risk among Caucasians. Nevertheless, the rs217727 polymorphism was significantly associated with an increased risk of lung cancer, hepatocellular carcinoma and oral squamous cell carcinoma. Also, we found a significant correlation between the rs2839698 polymorphism and increased cancer risk among Asians, gastric cancer, hepatocellular carcinoma, hospital-based control and larger simple size subgroups, respectively. Similarly, the rs3741219 mutation was notably related to cancer risk in higher quality score. As for rs3024270 polymorphism, the homozygous model was markedly linked to cancer risk in overall analysis and population-based controls. There was no significant association between the rs3741216 polymorphism and cancer risk. CONCLUSION H19 rs2839698 and rs3024270 were closely associated with overall cancer risk. H19 rs2107425 was related to lower cancer risk among Caucasians, while the rs2839698 was related to increased cancer risk among Asians. Our results supported that H19 SNPs were significantly correlated with cancer risk.
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Affiliation(s)
- Maoquan Yang
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, No. 2428, Yuhe Road, Weifang, 261031, Shandong, China
| | - Mingwei Zhang
- Department of Pathology, Shandong University School of Basic Medical Sciences, Jinan, Shandong, China
| | - Qiong Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Department of Gastroenterology, Weifang NO.2 People s Hospital, Weifang, Shandong, China
| | - Xiaojing Guo
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Peizhen Geng
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Jinhua Gu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Wansheng Ji
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, No. 2428, Yuhe Road, Weifang, 261031, Shandong, China.
- Experimental Center for Medical Research, Weifang Medical University, Weifang, Shandong, China.
| | - Li Zhang
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, No. 2428, Yuhe Road, Weifang, 261031, Shandong, China.
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25
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Kong X, Xiong Y, Xue M, He J, Lu Q, Chen M, Li L. Identification of cuproptosis-related lncRNA for predicting prognosis and immunotherapeutic response in cervical cancer. Sci Rep 2023; 13:10697. [PMID: 37400520 DOI: 10.1038/s41598-023-37898-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023] Open
Abstract
Patients diagnosed with advanced cervical cancer (CC) have poor prognosis after primary treatment, and there is a lack of biomarkers for predicting patients with an increased risk of recurrence of CC. Cuproptosis is reported to play a role in tumorigenesis and progression. However, the clinical impacts of cuproptosis-related lncRNAs (CRLs) in CC remain largely unclear. Our study attempted to identify new potential biomarkers to predict prognosis and response to immunotherapy with the aim of improving this situation. The transcriptome data, MAF files, and clinical information for CC cases were obtained from the cancer genome atlas, and Pearson correlation analysis was utilized to identify CRLs. In total, 304 eligible patients with CC were randomly assigned to training and test groups. LASSO regression and multivariate Cox regression were performed to construct a cervical cancer prognostic signature based on cuproptosis-related lncRNAs. Afterwards, we generated Kaplan-Meier curves, receiver operating characteristic curves and nomograms to verify the ability to predict prognosis of patients with CC. Genes for assessing differential expression among risk subgroups were also evaluated by functional enrichment analysis. Immune cell infiltration and the tumour mutation burden were analysed to explore the underlying mechanisms of the signature. Furthermore, the potential value of the prognostic signature to predict response to immunotherapy and sensitivity to chemotherapy drugs was examined. In our study, a risk signature containing eight cuproptosis-related lncRNAs (AL441992.1, SOX21-AS1, AC011468.3, AC012306.2, FZD4-DT, AP001922.5, RUSC1-AS1, AP001453.2) to predict the survival outcome of CC patients was developed, and the reliability of the risk signature was appraised. Cox regression analyses indicated that the comprehensive risk score is an independent prognostic factor. Moreover, significant differences were found in progression-free survival, immune cell infiltration, therapeutic response to immune checkpoint inhibitors, and IC50 for chemotherapeutic agents between risk subgroups, suggesting that our model can be well employed to assess the clinical efficacy of immunotherapy and chemotherapy. Based on our 8-CRLs risk signature, we were able to independently assess the outcome and response to immunotherapy of CC patients, and this signature might benefit clinical decision-making for individualized treatment.
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Affiliation(s)
- Xiaoyu Kong
- School of Public Health, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Mei Xue
- School of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Jie He
- Department of Clinical Laboratory, The First Hospital of Nanchang, Nanchang, 330008, Jiangxi, People's Republic of China
| | - Qinsheng Lu
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510632, Guangdong, People's Republic of China
| | - Miaojuan Chen
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510632, Guangdong, People's Republic of China.
| | - Liping Li
- Department of Clinical Laboratory, The First Hospital of Nanchang, Nanchang, 330008, Jiangxi, People's Republic of China.
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26
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Hillman T. The use of plant-derived exosome-like nanoparticles as a delivery system of CRISPR/Cas9-based therapeutics for editing long non-coding RNAs in cancer colon cells. Front Oncol 2023; 13:1194350. [PMID: 37388221 PMCID: PMC10301836 DOI: 10.3389/fonc.2023.1194350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 07/01/2023] Open
Abstract
Colon cancer is one of the leading causes of cancer in the United States. Colon cancer develops from the many gene mutations found in the genomes of colon cancer cells. Long non-coding RNAs (lncRNAs) can cause the development and progression of many cancers, including colon cancer. LncRNAs have been and could be corrected through the gene-editing technology of the clustered repeats of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system to reduce the proliferation of cancer cells in the colon. However, many current delivery systems for transporting CRISPR/Cas9-based therapeutics in vivo need more safety and efficiency. CRISPR/Cas9-based therapeutics require a safe and effective delivery system to more directly and specifically target cancer cells present in the colon. This review will present pertinent evidence for the increased efficiency and safety of using plant-derived exosome-like nanoparticles as nanocarriers for delivering CRISPR/Cas9-based therapeutics to target colon cancer cells directly.
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Petrone I, dos Santos EC, Binato R, Abdelhay E. Epigenetic Alterations in DCIS Progression: What Can lncRNAs Teach Us? Int J Mol Sci 2023; 24:8733. [PMID: 37240077 PMCID: PMC10218364 DOI: 10.3390/ijms24108733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Some transcripts that are not translated into proteins can be encoded by the mammalian genome. Long noncoding RNAs (lncRNAs) are noncoding RNAs that can function as decoys, scaffolds, and enhancer RNAs and can regulate other molecules, including microRNAs. Therefore, it is essential that we obtain a better understanding of the regulatory mechanisms of lncRNAs. In cancer, lncRNAs function through several mechanisms, including important biological pathways, and the abnormal expression of lncRNAs contributes to breast cancer (BC) initiation and progression. BC is the most common type of cancer among women worldwide and has a high mortality rate. Genetic and epigenetic alterations that can be regulated by lncRNAs may be related to early events of BC progression. Ductal carcinoma in situ (DCIS) is a noninvasive BC that is considered an important preinvasive BC early event because it can progress to invasive BC. Therefore, the identification of predictive biomarkers of DCIS-invasive BC progression has become increasingly important in an attempt to optimize the treatment and quality of life of patients. In this context, this review will address the current knowledge about the role of lncRNAs in DCIS and their potential contribution to the progression of DCIS to invasive BC.
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Affiliation(s)
- Igor Petrone
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
| | - Everton Cruz dos Santos
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
| | - Renata Binato
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
| | - Eliana Abdelhay
- Stem Cell Laboratory, Center for Bone Marrow Transplants, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil; (I.P.); (E.C.d.S.); (R.B.)
- Stricto Sensu Graduate Program in Oncology, Brazilian National Cancer Institute—INCA, Rio de Janeiro 20230-240, Brazil
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Liu J, Song S, Zhao R, Zhang HY, Zhang SX. The functions and networks of non-coding RNAs in the pathogenesis of Rheumatoid Arthritis. Biomed Pharmacother 2023; 163:114707. [PMID: 37087979 DOI: 10.1016/j.biopha.2023.114707] [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: 03/09/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023] Open
Abstract
Rheumatoid Arthritis (RA) is a chronic autoimmune disease. Its main feature is inflammation of synovial tissue with irreversible joint damage and severe physical damage. Non-coding RNAs (ncRNAs) are a class of RNAs that do not have the ability to encode proteins but are vital regulators that mediate many fundamental cellular processes and play an essential role in the pathogenesis of RA. Multiple verified ncRNAs have been confirmed as a prospective biomarkers for diagnosing and treating RA. In this paper, we aim to sort out the role of ncRNAs in the pathogenesis of RA and provide new ideas for the diagnosis and treatment of RA.
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Affiliation(s)
- Jia Liu
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, China; Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, China
| | - Shan Song
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, China; Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, China
| | - Rong Zhao
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, China; Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, China
| | - He-Yi Zhang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, China; Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, China.
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Long Non-Coding RNAs in Retinal Ganglion Cell Apoptosis. Cell Mol Neurobiol 2023; 43:561-574. [PMID: 35226226 DOI: 10.1007/s10571-022-01210-x] [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: 12/05/2021] [Accepted: 02/17/2022] [Indexed: 12/19/2022]
Abstract
Traumatic optic neuropathy or other neurodegenerative diseases, including optic nerve transection, glaucoma, and diabetic retinopathy, can lead to progressive and irreversible visual damage. Long non-coding RNAs (lncRNAs), which belong to the family of non-protein-coding transcripts, have been linked to the pathogenesis, progression, and prognosis of these lesions. Retinal ganglion cells (RGCs) are critical for the transmission of visual information to the brain, damage to which results in visual loss. Apoptosis has been identified as one of the most essential modes of RGC death. Emerging evidence suggests that lncRNAs can regulate RGC degeneration by directly or indirectly modulating apoptosis-associated signaling pathways. This review presents a comprehensive overview of the role of lncRNAs in RGC apoptosis at transcriptional, post-transcriptional, translational, and post-translational levels, emphasizing on the potential mechanisms of action. The current limitations and future perspectives of exploring the connection between lncRNAs and RGC apoptosis have been summarized. Understanding the intricate molecular interaction network of lncRNAs and RGC apoptosis will open new avenues for the identification of novel diagnostic biomarkers, therapeutic targets, and molecules for prognostic evaluation of diseases related to RGC injury.
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Lu D, Liao J, Cheng H, Ma Q, Wu F, Xie F, He Y. Construction and systematic evaluation of a machine learning-based cuproptosis-related lncRNA score signature to predict the response to immunotherapy in hepatocellular carcinoma. Front Immunol 2023; 14:1097075. [PMID: 36761763 PMCID: PMC9905126 DOI: 10.3389/fimmu.2023.1097075] [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: 11/13/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is a common malignant cancer with a poor prognosis. Cuproptosis and associated lncRNAs are connected with cancer progression. However, the information on the prognostic value of cuproptosis-related lncRNAs is still limited in HCC. Methods We isolated the transcriptome and clinical information of HCC from TCGA and ICGC databases. Ten cuproptosis-related genes were obtained and related lncRNAs were correlated by Pearson's correlation. By performing lasso regression, we created a cuproptosis-related lncRNA prognostic model based on the cuproptosis-related lncRNA score (CLS). Comprehensive analyses were performed, including the fields of function, immunity, mutation and clinical application, by various R packages. Results Ten cuproptosis-related genes were selected, and 13 correlated prognostic lncRNAs were collected for model construction. CLS was positively or negatively correlated with cancer-related pathways. In addition, cell cycle and immune related pathways were enriched. By performing tumor microenvironment (TME) analysis, we determined that T-cells were activated. High CLS had more tumor characteristics and may lead to higher invasiveness and treatment resistance. Three genes (TP53, CSMD1 and RB1) were found in high CLS samples with more mutational frequency. More amplification and deletion were detected in high CLS samples. In clinical application, a CLS-based nomogram was constructed. 5-Fluorouracil, gemcitabine and doxorubicin had better sensitivity in patients with high CLS. However, patients with low CLS had better immunotherapeutic sensitivity. Conclusion We created a prognostic CLS signature by machine learning, and we comprehensively analyzed the signature in the fields of function, immunity, mutation and clinical application.
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Affiliation(s)
- Dingyu Lu
- Oncology Department, Deyang People’s Hospital, Deyang, China
| | - Jian Liao
- Intensive care Unit, Deyang People’s Hospital, Deyang, China
| | - Hao Cheng
- Oncology Department, Deyang People’s Hospital, Deyang, China
| | - Qian Ma
- Oncology Department, Deyang People’s Hospital, Deyang, China
| | - Fei Wu
- Oncology Department, Deyang People’s Hospital, Deyang, China
| | - Fei Xie
- Oncology Department, Deyang People’s Hospital, Deyang, China
| | - Yingying He
- Oncology Department, Deyang People’s Hospital, Deyang, China
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31
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Qu A, Wang Q, Chang Q, Liu J, Yang Y, Zhang X, Zhang Y, Zhang X, Wang H, Zhang Y. Prognostic and predictive value of a lncRNA signature in patients with stage II colon cancer. Sci Rep 2023; 13:1350. [PMID: 36693876 PMCID: PMC9873786 DOI: 10.1038/s41598-022-25852-5] [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: 04/25/2022] [Accepted: 12/06/2022] [Indexed: 01/26/2023] Open
Abstract
The current staging method is inadequate to identify high-risk recurrence patients with stage II colon cancer (CC). Using a systematic and comprehensive-biomarker discovery and validation method, we aimed to construct a lncRNA-based signature to improve the prognostic prediction of stage II CC. We identified 1,377 differently expressed lncRNAs by analyzing 16 paired stage II CC tumor tissue and adjacent normal mucosal tissue from the TCGA dataset. Subsequently, using a univariable and step multivariable Cox regression model, we trained an 11-lncRNA signature in the training cohort (n = 141), which could divide patients into high-risk and low-risk groups (AUC at 3 years = 0.801, 95% CI: 0.724-0.877; AUC at 5 years = 0.801, 95% CI: 0.718-0.885). Significantly, patients in the high-risk group had poorer recurrence-free survival (RFS) compared with the low-risk group (log-rank test, P < 0.001 in the training cohort). This lncRNA-based signature was further confirmed in the validation cohort (P < 0.001). Multivariate Cox regression and stratified survival analyses showed that the prognostic value of this signature was independent of other clinicopathological risk factors (CEA, T stage, and chemotherapy). Time-dependent receiver operating characteristic (ROC) analysis demonstrated that this signature had better prognostic ability than any other clinical risk factors or single lncRNAs (all P < 0.05). A nomogram was constructed for clinical use, which integrated both the lncRNA-based signature and clinical risk factors (CEA and T stage) and performed well in the calibration plots. Altogether, our lncRNA-based signature was an independent prognostic factor and possessed a stronger predictive power compared with the currently used clinicopathological risk factors when predicting the recurrence of patients with stage II CC. Collectively, this lncRNA-based signature might facilitate individualized treatment decisions and postoperative counseling, ultimately contributing to improved survival.
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Affiliation(s)
- Ailin Qu
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China
| | - Qian Wang
- Department of Gastroenterology, Central Hospital, Shandong First Medical University, Jinan, 250011, Shandong Province, People's Republic of China
| | - Qing Chang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China
| | - Jingkang Liu
- Department of Gynecology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong Province, People's Republic of China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China
| | - Yanli Zhang
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan, 250031, Shandong Province, People's Republic of China
| | - Xiaoshi Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China
| | - Hongchun Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China.
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Wenhua Xi Road, Jinan, 250012, Shandong Province, People's Republic of China.
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Deshpande RP. Long Noncoding RNAs: Emerging Biomarkers of Therapy Resistance and Tumor Progression. Technol Cancer Res Treat 2023; 22:15330338221150328. [PMID: 36594227 PMCID: PMC9827516 DOI: 10.1177/15330338221150328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Ravindra P. Deshpande
- Ravindra P. Deshpande, Department of Cancer
Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157,
USA.
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Functions and underlying mechanisms of lncRNA HOTAIR in cancer chemotherapy resistance. Cell Death Dis 2022; 8:383. [PMID: 36100611 PMCID: PMC9470550 DOI: 10.1038/s41420-022-01174-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022]
Abstract
Chemotherapy has been one of the most important treatments for advanced cancer in recent decades. Although the sensitivity rate of initial chemotherapy is high, patients with chemotherapy resistant tumors, experience tumor recurrence. In recent years, many studies have shown that homeobox transcript antisense intergenic RNA (HOTAIR) is involved in many pathological processes including carcinogenesis. The abnormal regulation of a variety of cell functions by HOTAIR, such as apoptosis, the cell cycle, epithelial-mesenchymal transition, autophagy, self-renewal, and metabolism, is associated with chemotherapy resistance. Therefore, there is an urgent need to understand the biology and mechanism underlying the role of HOTAIR in tumor behavior and its potential as a biomarker for predicting the effect of chemotherapy. In this manuscript, we review the mechanisms underlying HOTAIR-related drug resistance and discuss the limitations of current knowledge and propose potential future directions.
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Hu C, Cai D, Zhong ME, Fan D, Li CH, Lv MY, Huang ZP, Wang W, Wu XJ, Gao F. Predicting prognosis and immunotherapy response among colorectal cancer patients based on a tumor immune microenvironment-related lncRNA signature. Front Genet 2022; 13:993714. [PMID: 36159987 PMCID: PMC9489948 DOI: 10.3389/fgene.2022.993714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) remodel the tumor immune microenvironment (TIME) by regulating the functions of tumor-infiltrating immune cells. It remains uncertain the way that TIME-related lncRNAs (TRLs) influence the prognosis and immunotherapy response of colorectal cancer (CRC). Aiming at providing survival and immunotherapy response predictions, a CRC TIME-related lncRNA signature (TRLs signature) was developed and the related potential regulatory mechanisms were explored with a comprehensive analysis on gene expression profiles from 97 immune cell lines, 61 CRC cell lines and 1807 CRC patients. Stratifying CRC patients with the TRLs signature, prolonged survival was observed in the low-risk group, while the patients in the high-risk group had significantly higher pro-tumor immune cells infiltration and higher immunotherapy response rate. Through the complex TRLs-mRNA regulation network, immunoregulation pathways and immunotherapy response pathways were found to be differently activated between the groups. In conclusion, the CRC TRLs signature is capable of making prognosis and immunotherapy response predictions, which may find application in stratifying patients for immunotherapy in the bedside.
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Affiliation(s)
- Chuling Hu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Du Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min-Er Zhong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dejun Fan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng-Hang Li
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min-Yi Lv
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Ping Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiao-Jian Wu, ; Feng Gao,
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Gastroenterology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiao-Jian Wu, ; Feng Gao,
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Yuan C, Liu C, Zhao S, Zhang X, Jia H, Chen B, Zhang M, Zheng Y, Zhou J, Bo Y. The Role of N6-Methyladenosine-Associated lncRNAs in the Immune Microenvironment and Prognosis of Colorectal Cancer. JOURNAL OF ONCOLOGY 2022; 2022:4689396. [PMID: 36111241 PMCID: PMC9470360 DOI: 10.1155/2022/4689396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022]
Abstract
Background The role of N6-methyladenosine long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) is elusive. Materials and Methods We identified m6A-associated lncRNAs by using the data gathered from The Cancer Genome Atlas (TCGA) and stratified CRC patients into different subgroups. Cox regression analysis was performed to construct an m6A-associated lncRNA signature. The role of this signature in the immune microenvironment and prognosis was dissected subsequently. Finally, a gene set enrichment analysis (GSEA) was conducted to predict the possible mechanisms based on the signature. Results Three m6A-associated clusters were constructed from 866 differentially expressed lncRNAs. Cluster 2 had poor prognosis and low immune cell infiltration. An m6A-associated lncRNA signature consisting of 14 lncRNAs was constructed and recognized as an independent prognostic indicator of CRC by using survival analysis and receiver operating characteristic (ROC) curves. The clinical features and immune cell infiltration status were significantly different in patients stratified by the risk score. Furthermore, GSEA showed that the P53 pathway and natural killer cell-mediated cytotoxicity were more enriched in the low-risk group. Conclusion Our data revealed that m6A-associated lncRNAs could be potential prognostic indicators of immunogenicity in CRC.
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Affiliation(s)
- Congfei Yuan
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
| | - Caidong Liu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Shuli Zhao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Xishan Zhang
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
| | - Haifeng Jia
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
| | - Baiyu Chen
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
| | - Maojin Zhang
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
| | - Yuan Zheng
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
| | - Jin Zhou
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Yanzhi Bo
- Department of General Surgery, Lianshui County People's Hospital, Huai'an 223400, China
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Kong W, Yin G, Zheng S, Liu X, Zhu A, Yu P, Zhang J, Shan Y, Ying R, Jin H. Long noncoding RNA (lncRNA) HOTAIR: Pathogenic roles and therapeutic opportunities in gastric cancer. Genes Dis 2022; 9:1269-1280. [PMID: 35873034 PMCID: PMC9293693 DOI: 10.1016/j.gendis.2021.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/21/2021] [Accepted: 07/06/2021] [Indexed: 01/17/2023] Open
Abstract
Gastric cancer is one of the first malignant cancers in the world and a large number of people die every year due to this disease. Many genetic and epigenetic risk factors have been identified that play a major role in gastric cancer. HOTAIR is an effective epigenetic agent known as long noncoding RNA (lncRNA). HOTAIR has been described to have biological functions in biochemical and cellular processes through interactions with many factors, leading to genomic stability, proliferation, survival, invasion, migration, metastasis, and drug resistance. In the present article, we reviewed the prognostic value of the molecular mechanisms underlying the HOTAIR regulation and its function in the development of Gastric Cancer, whereas elucidation of HOTAIR–protein and HOTAIR–DNA interactions can be helpful in the identification of cancer processes, leading to the development of potential therapeutic strategies.
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Affiliation(s)
- Wencheng Kong
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Guang Yin
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Sixin Zheng
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Xinchun Liu
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Akao Zhu
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Panpan Yu
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Jian Zhang
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Yuqiang Shan
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Rongchao Ying
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Huicheng Jin
- Department of Gastroenterological Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
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Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Int J Mol Sci 2022; 23:ijms23179630. [PMID: 36077037 PMCID: PMC9455975 DOI: 10.3390/ijms23179630] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 01/19/2023] Open
Abstract
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.
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Affiliation(s)
- Julita Gumna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Antczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Ryszard W. Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Jun Li
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Laboratory of Computational Biology, Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | | | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sicheng Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- Correspondence: (Z.M.); (A.R.)
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Agnieszka Rybarczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
- Correspondence: (Z.M.); (A.R.)
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Zhang Y, Yang M, Yang S, Hong F. Role of noncoding RNAs and untranslated regions in cancer: A review. Medicine (Baltimore) 2022; 101:e30045. [PMID: 35984196 PMCID: PMC9388041 DOI: 10.1097/md.0000000000030045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023] Open
Abstract
Cancer is one of the most prevalent diseases worldwide, and poses a threat to human health. Noncoding RNAs (ncRNAs) constitute most transcripts, but they cannot be translated into proteins. Studies have shown that ncRNAs can act as tumor suppressors or oncogenes. This review describes the role of several ncRNAs in various cancers, including microRNAs (miRNAs) such as the miR-34 family, let-7, miR-17-92 cluster, miR-210, and long noncoding RNAs (lncRNAs) such as HOX transcript antisense intergenic RNA (HOTAIR), Metastasis associated lung adenocarcinoma transcript 1 (MALAT1), H19, NF-κB-interacting lncRNA (NKILA), as well as circular RNAs (circRNAs) and untranslated regions (UTRs), highlighting their effects on cancer growth, invasion, metastasis, angiogenesis, and apoptosis. They function as tumor suppressors or oncogenes that interfere with different axes and pathways, including p53 and IL-6, which are involved in the progression of cancer. The characteristic expression of some ncRNAs in cancer also allows them to be used as biomarkers for early diagnosis and therapeutic candidates. There is a complex network of interactions between ncRNAs, with some lncRNAs and circRNAs acting as competitive endogenous RNAs (ceRNAs) to decoy miRNAs and repress their expression. The ceRNA network is a part of the ncRNA network and numerous ncRNAs work as nodes or hubs in the network, and disruption of their interactions can cause cancer development. Therefore, the balance and stabilization of this network are important for cancer diagnosis and treatment.
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Affiliation(s)
- Yiping Zhang
- Experimental Centre of Pathogen Biology, Nanchang University, Nanchang, China
- Queen Mary College, School of Medicine, Nanchang University, Nanchang, China
| | - Meiwen Yang
- Department of Surgery, Fuzhou Medical College, Nanchang University, Fuzhou, China
| | - Shulong Yang
- Department of Physiology, Key Research Laboratory of Chronic Diseases, Fuzhou Medical College, Nanchang University, Fuzhou, China
- Department of Physiology, College of Medicine, Nanchang University, Nanchang, China
| | - Fenfang Hong
- Experimental Centre of Pathogen Biology, Nanchang University, Nanchang, China
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Cancer cell-derived exosomal LINC00313 induces M2 macrophage differentiation in non-small cell lung cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 24:2395-2408. [PMID: 35980503 DOI: 10.1007/s12094-022-02907-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/23/2022] [Indexed: 10/15/2022]
Abstract
PURPOSE Non-small cell lung cancer (NSCLC) is the major subtype of lung cancer, which is the leading cause of cancer death worldwide. Tumor-associated macrophages (TAMs) are one of the main non-tumor cells in the tumor microenvironment. Here, we investigated the effect of cancer cell-derived exosomal LINC00313 on the M2 macrophage differentiation in NSCLC and clarified its underlying mechanism. METHODS Flow cytometry, Western blotting, ELISA and immunohistochemical staining were performed to identify the macrophage phenotype by detecting the expression of M2 markers. The expression levels of LINC00313 and miR-135a-3p were measured by qRT-PCR, and luciferase reporter assay was used to validate the binding of lncRNA to miRNA, and miRNA to the target gene STAT6. The mouse-xenograft models were established by subcutaneous injection of the NCl-H1299 cells with stable overexpression or knockdown of LINC00313. GW4869 was injected intra-tumorally after tumor implantation. RESULTS It was found that the cancer cells promoted M2 macrophage differentiation by secreting exosomes. LINC00313 was overexpressed in H1299-derived exosomes, and its knockdown abolished the effect of H1299-induced M2 macrophage differentiation. LINC00313 sponged miR-135a-3p to increase the STAT6 expression, resulting in the M2 macrophage differentiation. LINC00313 promoted tumor progression and promoted the expression of M2 markers in isolated tumor macrophages. A novel regulatory mechanism of M2 macrophage differentiation in NSCLC was revealed. It was found that cancer cell-derived exosomal LINC00313 promoted M2 macrophage differentiation in NSCLC by up-regulating STAT6 as miR-135a-3p sponge. CONCLUSIONS This study provides a new mechanism and direction to prevent the M2 macrophage differentiation in NSCLC.
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Xiao J, Wang X, Liu Y, Liu X, Yi J, Hu J. Lactate Metabolism-Associated lncRNA Pairs: A Prognostic Signature to Reveal the Immunological Landscape and Mediate Therapeutic Response in Patients With Colon Adenocarcinoma. Front Immunol 2022; 13:881359. [PMID: 35911752 PMCID: PMC9328180 DOI: 10.3389/fimmu.2022.881359] [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: 02/24/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
Background Lactate metabolism is critically involved in the tumor microenvironment (TME), as well as cancer progression. It is important to note, however, that lactate metabolism-related long non-coding RNAs (laRlncRNAs) remain incredibly understudied in colon adenocarcinoma (COAD). Methods A gene expression profile was obtained from the Cancer Genome Atlas (TCGA) database to identify laRlncRNA expression in COAD patients. A risk signature with prognostic value was identified from TCGA and Gene Expression Omnibus (GEO) cohort based on laRlncRNA pairs by the least absolute shrinkage and selection operator (LASSO) and Cox regression analyses. Quantitative real-time polymerase chain reaction (qRT-PCR) and functional experiments were carried out to verify the expression of laRlncRNAs in COAD. The relationship of laRlncRNA pairs with immune landscape as well as the sensitivity of different therapies was explored. Results In total, 2378 laRlncRNAs were identified, 1,120 pairs of which were studied to determine their prognostic validity, followed by a risk signature established based on the screened 5 laRlncRNA pairs. The laRlncRNA pairs-based signature provided a better overall survival (OS) prediction than other published signatures and functioned as a prognostic marker for COAD patients. According to the calculated optimal cut-off point, patients were divided into high- and low-risk groups. The OS of COAD patients in the high-risk group were significantly shorter than that of those in the low-risk group (P=4.252e-14 in the TCGA cohort and P=2.865-02 in the GEO cohort). Furthermore, it remained an effective predictor of survival in strata of gender, age, TNM stage, and its significance persisted after univariate and multivariate Cox regressions. Additionally, the risk signature was significantly correlated with immune cells infiltration, tumor mutation burden (TMB), microsatellite instability (MSI) as well as immunotherapeutic efficacy and chemotherapy sensitivity. Finally, one of the laRlncRNA, LINC01315, promotes proliferation and migration capacities of colon cancer cells. Conclusion The newly identified laRlncRNAs pairs-based signature exhibits potential effects in predicting prognosis, deciphering patients’ immune landscape, and mediating sensitivity to immunotherapy and chemotherapy. Findings in our study may provide evidence for the role of laRlncRNAs pairs as novel prognostic biomarkers and potentially individualized therapy targets for COAD patients.
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Affiliation(s)
- Junbo Xiao
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaotong Wang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yajun Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Yi
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Jun Yi, ; Jiuye Hu,
| | - Jiuye Hu
- Department of Gastroenterology, Affiliated Hospital of Xiangnan University, Chenzhou, China
- *Correspondence: Jun Yi, ; Jiuye Hu,
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Kang X, Huo Y, Jia S, He F, Li H, Zhou Q, Chang N, Liu D, Li R, Hu Y, Zhang P, Xu A. Silenced LINC01134 Enhances Oxaliplatin Sensitivity by Facilitating Ferroptosis Through GPX4 in Hepatocarcinoma. Front Oncol 2022; 12:939605. [PMID: 35875091 PMCID: PMC9304856 DOI: 10.3389/fonc.2022.939605] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Purpose Recently, long noncoding RNA LINC01134 has been shown to reduce cell viability and apoptosis via the antioxidant stress pathway, thereby enhancing OXA resistance in hepatocellular carcinoma. However, the association of LINC01134 with ferroptosis and the underlying molecular mechanisms remain to be elucidated. Methods Bioinformatics analysis was employed to screen lncRNAs positively correlated with GPX4 and poor clinical prognosis. And Western blot and RT-PCR analysis in HCC cells confirmed the effect of LINC01134 on GPX4 expression. In addition, LINC01134 siRNA was transfected in HCC cells to detect the changes in cell viability, ROS, lipid peroxidation, MDA levels and GSH/GSSG levels. CCK-8, colony formation and apoptosis assays were performed to determine the effect of LINC01134 on cell death. The effect of LINC01134 and OXA on Nrf2 transcriptional binding to GPX4 was analyzed using dual luciferase reporter assay and CHIP. The expression of GPX4 and Nrf2 in HCC tissues was detected by FISH and IHC. Results LINC01134 is a novel lncRNA positively correlated with GPx4 and associated with poor clinical prognosis. Silenced LINC01134 conferred OXA sensitivity by enhancing total ROS, lipid ROS, MDA levels and decreasing GSH/GSSG ratio. Mechanistically, LINC01134 and OXA could promote Nrf2 recruitment to the GPX4 promoter region to exert transcriptional regulation of GPX4. Clinically, LINC01134 was positively correlated with GPX4 or Nrf2, demonstrating the clinical significance of LINC01134, Nrf2 and GPX4 in OXA resistance of HCC. Conclusions We identified LINC01134/Nrf2/GPX4 as a novel and critical axis to regulate HCC growth and progression. Targeting GPX4, knocking down LINC01134 or Nrf2 could be a potential therapeutic strategy for HCC.
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Affiliation(s)
- Xiaofeng Kang
- Department of Oncology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
- International School of Public Health and One Health, Hainan Medical University, Hainan, China
| | - Yan Huo
- Department of Ophthalmology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Songhao Jia
- Department of Infectious Disease, the Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fuliang He
- Department of Liver Research Center, Beijing Friendship Hospital of Capital Medical University, Beijing, China
| | - Huizi Li
- Department of Ophthalmology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Qing Zhou
- Department of gastroenterology, Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Nijia Chang
- Department of Oncology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Donghui Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Rongkuan Li
- Department of Infectious Disease, the Second Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: An Xu, ; Ping Zhang, ; Yi Hu, ; Rongkuan Li,
| | - Yi Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: An Xu, ; Ping Zhang, ; Yi Hu, ; Rongkuan Li,
| | - Ping Zhang
- International School of Public Health and One Health, Hainan Medical University, Hainan, China
- *Correspondence: An Xu, ; Ping Zhang, ; Yi Hu, ; Rongkuan Li,
| | - An Xu
- Department of Oncology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
- *Correspondence: An Xu, ; Ping Zhang, ; Yi Hu, ; Rongkuan Li,
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Predictive Potentials of ZEB1-AS1 in Colorectal Cancer Prognosis and Their Correlation with Immunotherapy. JOURNAL OF ONCOLOGY 2022; 2022:1084555. [PMID: 35794981 PMCID: PMC9252708 DOI: 10.1155/2022/1084555] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Background CRC is the third most common cancer globally. The tumor immune microenvironment is closely associated with the overexpressed lncRNA ZEB1-AS1. However, in individuals with CRC, the ZEB1-AS1 gene's ability to predict immune response is a mystery. Materials and Methods The ZEB1-AS1 gene's prognostic potential was thoroughly investigated. We analyzed and included into the TCGA database all ZEB1-AS1 and ZEB1-AS1-related genes using LASSO-Cox regression. Researchers examined the link among ZEB1-AS1 and the tumor immune microenvironment, immune checkpoint, and tumor mutation burden (TMB) in CRC through the TCGA database. Using a predictive model, researchers were able to determine the link between ZEB1-AS1 and NUDT3 and CRC prognosis. Result According to our findings, individuals with reduced ZEB1-AS1 expression had a better prognosis in CRC. Based on the expression of two genes in the TCGA database, patients were divided into two cohorts. The B lymphocytes and macrophages are less likely to be recruited by tissues with a low-risk score. TMB and immunological checkpoints were shown to have a connection. Based on these genes, a predictive nomogram was built and confirmed, with a C-index of 0.78. Conclusion Prognostic models based on ZEB1-AS1 and ZEB1-AS1-related genes are more accurate for CRC patients when it comes to the prognosis and immune checkpoint responsiveness.
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Review: RNA-based diagnostic markers discovery and therapeutic targets development in cancer. Pharmacol Ther 2022; 234:108123. [PMID: 35121000 DOI: 10.1016/j.pharmthera.2022.108123] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The present review aimed to outline different types of RNAs in cancer diagnostics and treatment, and to provide novel insights into their clinical applications. RNAs, including mRNA, long non-coding (lnc)RNA, circular (circ)RNA and micro (mi)RNA, are now increasingly utilized in the diagnosis and treatment of various cancers. Each aforementioned type of RNA possess their own unique characteristics and could be aberrantly expressed as diagnostic markers or therapeutic targets in different cancers. In addition to mRNAs, which have become a promising alternative in cancer diagnostics and therapy, the uses of lncRNA, circRNA and miRNA in predictive tumor diagnostics and therapy has rapidly increased in recent years. In the present review, the mechanisms of mRNA, lncRNA, circRNA and miRNA in regulating and participating in the development of different cancers were determined, and their potential capacity in cancer diagnostics and therapy were investigated. In addition, the present review analyzed the assoaciations between different RNAs and their subsequent potential in cancer prediction and treatment.
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Reduced expression of lncRNA DLEU7-AS1 is a novel favorable prognostic factor in acute myeloid leukemia. Biosci Rep 2022; 42:231264. [PMID: 35506368 PMCID: PMC9118369 DOI: 10.1042/bsr20212078] [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: 09/08/2021] [Revised: 04/12/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
The objective of our study was to measure DLEU7-AS1 expression in de novo acute myeloid leukemia (AML) whilst also analyzing its clinical relevance. We used gene expression data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Cancer Cell Line Encyclopedia (CCLE) and Genotype-Tissue Expression project (GTEx) to assess the expression profile of DLEU7-AS1 in pan-cancers, cancer cell lines and normal tissues. Reverse transcription-quantitative PCR was used to measure DLEU7-AS1 expression in bone marrow from 30 normal individuals and 110 patients with de novo AML. DLEU7-AS1 expression was found to be markedly reduced in the AML samples of the TCGA pan-cancer datasets. In our PCR validation, DLEU7-AS1 expression was significantly decreased in the AML samples compared with that in controls (P<0.001). Low DLEU7-AS1 expression (DLEU7-AS1low) correlated positively with lower blood platelet counts (P=0.029). In addition, low DLEU7-AS1 expression was more frequently observed in the intermediate (58%; 44/76) and favorable karyotypes (65%; 15/23) compared with that in the poor karyotype (10%; 1/10; P=0.005). In particular, patients with high expression levels of DLEU7-AS1 (DLEU7-AS1high) showed lower complete remission rates (P=0.002) than patients with DLEU7-AS1low. Survival analysis revealed that patients with DLEU7-AS1low had longer overall survival (OS) than patients with DLEU7-AS1high (P<0.05). Multivariate Cox analysis demonstrated that in patients with non-acute promyelocytic leukemia (non-M3) who were ≤60 years old, DLEU7-AS1 expression was an independent prognostic factor for OS. Furthermore, we found distinct correlations among the expression of DLEU7-AS1, infiltration by immune cells and immune checkpoint genes in AML.
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Li C, Wang X, Chen T, Li W, Yang Q. A Novel lncRNA Panel for Risk Stratification and Immune Landscape in Breast Cancer Patients. Int J Gen Med 2022; 15:5253-5272. [PMID: 35655656 PMCID: PMC9154001 DOI: 10.2147/ijgm.s366335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Purpose In recent years, breast cancer (BC) has been a primary cause of mortality in women. However, the underlying mechanisms remain to be elucidated. Accumulating evidence has supported the hypothesis that long noncoding RNAs (lncRNAs) play central roles in the progression of cancer. We aimed to construct an immune-related lncRNA panel to predict the prognosis of patients with BC and evaluate the immune features. Methods The expression profiles of patients with BC were obtained from The Cancer Genome Atlas (TCGA) database to screen the differentially expressed lncRNAs (DELs). Pearson’s correlation analysis was employed to filter the DELs related to the immune-associated genes. Univariate Cox regression, the LASSO algorithm, and multivariate Cox regression analyses were conducted to establish the model. Functional enrichment analyses and biological experiments were performed to explore the immune activity of the lncRNA panel. Results A four-immune-related lncRNA panel (IRLP) composed of AC022196.1, ARHGAP26-AS1, DPYD-AS1 and PURPL was established in TCGA training cohort. The prognostic accuracy of the predictive model was confirmed in TCGA internal validation cohort, TCGA entire cohort and Qilu external validation cohort. Bioinformatics analyses indicated that the IRLP had a close relationship with tumour infiltrating immune cells and immunomodulatory biomarkers. The biological functions of the four immune-related lncRNAs in BC were first investigated in vitro and in vivo. PURPL was indicated to play a central role in the regulation of macrophage recruitment and polarization via CCL2. Conclusion Our study identified IRLP as a reliable prognostic indicator with great potential for clinical application in personalized immunotherapy.
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Affiliation(s)
- Chen Li
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Tong Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Wenhao Li
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Pathology Tissue Bank, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People’s Republic of China
- Research Institute of Breast Cancer, Shandong University, Jinan, Shandong, People’s Republic of China
- Correspondence: Qifeng Yang, Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People’s Republic of China, Email
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Aminimoghaddam S, Fooladi B, Noori M, Nickhah Klashami Z, Kakavand Hamidi A, M Amoli M. The Effect of Metformin on Expression of Long Non-coding RNA H19 in Endometrial Cancer. Med J Islam Repub Iran 2022; 35:155. [PMID: 35341081 PMCID: PMC8932210 DOI: 10.47176/mjiri.35.155] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Endometrial cancer is the fourth most widespread cancer among females, with a growing prevalence in recent years. Management by combined therapies along with surgery, radiotherapy, and chemotherapy have improved patients' prognoses. Besides, the development of new therapies helps preserve fertility and prognosis in aggressive tumors. The purpose of this research was to identify the efficacy of metformin on the H19 long non-coding RNA expression in endometrial cancer to provide further insight into the pathogenesis and treatment of the disease. Methods: A total of 23 patients with endometrial cancer, diagnosed by biopsy or diagnostic curettage, were recruited and divided into three groups, before and after metformin treatment and placebo. Real-time PCR was used to evaluate the H19 expression in cancer tissue in all patients. Results: : It has been observed that in endometrial tissue of the "after-metformin" treatment group, the H19 expression level was significantly reduced, compared with the "before-metformin" treatment group, but not in comparison with the placebo. These findings indicate that metformin reduced the H19 expression in endometrial cancer. Conclusion: Anti-diabetic drugs, such as metformin, may be beneficial by reducing the H19 expression in endometrial cancer due to the H19 relation to cancer progression.
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Affiliation(s)
- Soheila Aminimoghaddam
- Department of Obstetrics and Gynecology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahareh Fooladi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Noori
- Department of Obstetrics and Gynecology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zeynab Nickhah Klashami
- Metabolic Disorders Research Centre, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Iran
| | - Armita Kakavand Hamidi
- Metabolic Disorders Research Centre, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Iran
| | - Mahsa M Amoli
- Metabolic Disorders Research Centre, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Iran
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Yue Q, Bai J, Wang F, Xue F, Li L, Duan X. Novel classification and risk model based on ferroptosis-related lncRNAs to predict oncologic outcomes for gastric cancer patients. J Biochem Mol Toxicol 2022; 36:e23052. [PMID: 35315178 DOI: 10.1002/jbt.23052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/07/2022] [Accepted: 03/10/2022] [Indexed: 12/24/2022]
Abstract
Gastric cancer (GC) is a highly heterogeneous malignancy, characterized by high mortality and poor prognosis. Ferroptosis is a newly defined nonapoptotic programmed cell death mechanism that has been implicated in the development of various pathological conditions. We aimed to identify ferroptosis-related long noncoding RNA (lncRNAs) that might be used to predict GC prognosis. The data were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus database. Two subtypes, C1 and C2, were identified, which had significant variations in prognosis and immune cell infiltrations. Differentially expressed genes between the subtypes were found to be involved in multiple tumor-associated pathways. Subsequently, a training dataset and a testing dataset were created from the TCGA dataset. A predictive model for GC patients based on six ferroptosis-related lncRNAs (including STX18-AS1, MIR99AHG, LINC01197, LINC00968, LINC00865, and LEF1-AS1) was developed. The model could stratify patients into a high- and low-risk group, showing good predictive performance. The testing dataset, entire TCGA dataset, and GSE62254 cohort both confirmed the predictive value of the model. Compared to the clinical parameters (including gender, age, and grade), the risk model was an independent risk factor for GC patients. Moreover, a nomogram (containing our risk score model and clinical parameters) was constructed, which might provide great potential to improve prediction accuracy. Moreover, the single-sample gene set enrichment analysis revealed that the high-risk group was linked to various signaling pathways involved in the regulation of GC progression. Conclusively, a novel classification and risk model based on ferroptosis-related lncRNAs that can predict oncologic outcomes for GC patients has been developed.
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Affiliation(s)
- Qingfang Yue
- Department of Medical Oncology, Shaanxi Provincial People's Hospital, Affiliated Hospital of Northwestern Polytechnical University, Xi'an, Shaanxi, P. R. China
- Postdoctoral Station, Institute of Medical Research, Northwestern Polytechnic University, Xi'an, Shaanxi, P. R. China
| | - Jun Bai
- Department of Medical Oncology, Shaanxi Provincial People's Hospital, Affiliated Hospital of Northwestern Polytechnical University, Xi'an, Shaanxi, P. R. China
| | - Fei Wang
- Department of Gynecology, Shaanxi Provincial People's Hospital, Affiliated Hospital of Northwestern Polytechnical University, Xi'an, Shaanxi, P. R. China
| | - Fei Xue
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Affiliated Hospital of Northwestern Polytechnical University, Xi'an, Shaanxi, P. R. China
| | - Lianxiang Li
- Department of Gynecology, Shaanxi Provincial People's Hospital, Affiliated Hospital of Northwestern Polytechnical University, Xi'an, Shaanxi, P. R. China
| | - Xianglong Duan
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Affiliated Hospital of Northwestern Polytechnical University, Xi'an, Shaanxi, P. R. China
- Medical College, Xizang Mingzu University, Xianyang, Shaanxi, P. R. China
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48
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Zheng P, Wu Y, Chen Y, Chen Z, Zhang T, Chen Z, Zhang T. Novel insights into the mechanisms by which lncRNA HOTAIR regulates migration and invasion in HeLa cells. Cell Cycle 2022; 21:602-617. [PMID: 35090376 PMCID: PMC8942418 DOI: 10.1080/15384101.2022.2030167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
HOTAIR, as one of the few well-studied oncogenic lncRNAs, is involved in human tumorigenesis and is dys-regulated in most human cancers. The transcription co-activator factor YAP1 is broadly expressed in many tissues, and promotes cancer metastasis and progression. However, the precise biological roles of HOTAIR and YAP1 in cancer cells remain unclear. In this study, we showed that HOTAIR regulates H3K27 histone modification in the promoter of miR-200a to mediate miR-200a expression by recruiting EZH2. YAP1, as a potential target gene of miR-200a, aggravated the effects of miR-200a on the migration and invasion of HeLa cells. YAP1 activated the transcription of RPL23, which is a novel downstream transcriptional-regulator of YAP1. Agreement with this, the expression of YAP1 and RPL23 was dramatically decreased after injecting HeLa cells transfected with siHOTAIR in a xenograft mouse model. Accordingly, we propose a novel model of the molecular mechanism by which HOTAIR promotes the migration and invasion of cancer cells involving the miR-200a-3p/YAP1/RPL23 axis.
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Affiliation(s)
- Peng Zheng
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China,College of Life Science and Healthy, Wuhan University of Science and Technology, Wuhan, China,CONTACT Peng Zheng Institute of Biology and Medicine, College of Life Science and Healthy, Wuhan University of Science and Technology, Wuhan430065, China
| | - Yaoqin Wu
- Third Institute of Oceanography State Administration, XiamenChina
| | - Ying Chen
- College of Life Science, Yangtze University, Jingzhou, China
| | - Zhuo Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China,Zhuo Chen Shangdong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Tongcun Zhang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China,College of Life Science and Healthy, Wuhan University of Science and Technology, Wuhan, China,Tongcun Zhang Institute of Biology and Medicine, College of Life Science and Healthy, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Zhuo Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Tongcun Zhang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China
- College of Life Science and Healthy, Wuhan University of Science and Technology, Wuhan, China
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49
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Lin Z, Ji X, Tian N, Gan Y, Ke L. Mapping Intellectual Structure for the Long Non-Coding RNA in Hepatocellular Carcinoma Development Research. Front Genet 2022; 12:771810. [PMID: 35047004 PMCID: PMC8762053 DOI: 10.3389/fgene.2021.771810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/22/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Emerging research suggests that long non-coding RNAs (lncRNAs) play an important role in a variety of developmental or physiological processes of hepatocellular carcinoma (HCC). Various differentially expressed lncRNAs have been identified in HCC. Thus, a deeper analysis of recent research concerning lncRNA and HCC development could provide scientists with a valuable reference for future studies. Methods: Related publications were retrieved from the Web of Science Core Collection database. CiteSpace version 5.6.R4 was employed to conduct bibliometric analysis. Several network maps were constructed to evaluate the collaborations between different countries, institutions, authors, journals, and keywords. Results: A total of 2,667 records were initially found from the year of 2010–2020. The annual related publications output had increased dramatically during these years. Although China was the most prolific country in terms of research publication, the United States played a leading role in collaborative network. The Nanjing Medical University was the most productive institute in the field of lncRNAs in HCC development. Gang Chen was the most prolific researcher, while Yang F was the most frequently co-cited author. Oncotarget, Cell, and Oncogene were the most highly co-cited journals. The most recent burst keywords were interaction, database, and pathway. Conclusion: This study provides a comprehensive overview for the field of lncRNAs in HCC development based on bibliometric and visualized methods. The results would provide a reference for scholars focusing on this field.
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Affiliation(s)
- Zhifeng Lin
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Medical Record, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaohui Ji
- Department of Obstetrics and Gynaecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nana Tian
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Gan
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ke
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Medical Record, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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50
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Erbe R, Gore J, Gemmill K, Gaykalova DA, Fertig EJ. The use of machine learning to discover regulatory networks controlling biological systems. Mol Cell 2022; 82:260-273. [PMID: 35016036 PMCID: PMC8905511 DOI: 10.1016/j.molcel.2021.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
Abstract
Biological systems are composed of a vast web of multiscale molecular interactors and interactions. High-throughput technologies, both bulk and single cell, now allow for investigation of the properties and quantities of these interactors. Computational algorithms and machine learning methods then provide the tools to derive meaningful insights from the resulting data sets. One such approach is graphical network modeling, which provides a computational framework to explicitly model the molecular interactions within and between the cells comprising biological systems. These graphical networks aim to describe a putative chain of cause and effect between interacting molecules. This feature allows for determination of key molecules in a biological process, accelerated generation of mechanistic hypotheses, and simulation of experimental outcomes. We review the computational concepts and applications of graphical network models across molecular scales for both intracellular and intercellular regulatory biology, examples of successful applications, and the future directions needed to overcome current limitations.
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Affiliation(s)
- Rossin Erbe
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jessica Gore
- Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, USA
| | - Kelly Gemmill
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Daria A Gaykalova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Institute for Genome Sciences, University of Maryland Medical Center, Baltimore, MD, USA; Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland Medical Center, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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