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Geeitha S, Ravishankar K, Cho J, Easwaramoorthy SV. Integrating cat boost algorithm with triangulating feature importance to predict survival outcome in recurrent cervical cancer. Sci Rep 2024; 14:19828. [PMID: 39191808 DOI: 10.1038/s41598-024-67562-0] [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: 03/21/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
Cervical cancer is one of the most dangerous malignancies in women. Prolonged survival times are made possible by breakthroughs in early recognition and efficient treatment of a disease.The existing methods are lagging on finding the important attributes to predict the survival outcome. The main objective of this study is to find individuals with cervical cancer who are at greater risk of death from recurrence by predicting the survival.A novel approach in a proposed technique is Triangulating feature importance to find the important risk factors through which the treatment may vary to improve the survival outcome.Five algorithms Support vector machine, Naive Bayes, supervised logistic regression, decision tree algorithm, Gradient boosting, and random forest are used to build the concept. Conventional attribute selection methods like information gain (IG), FCBF, and ReliefFare employed. The recommended classifier is evaluated for Precision, Recall, F1, Mathews Correlation Coefficient (MCC), Classification Accuracy (CA), and Area under curve (AUC) using various methods. Gradient boosting algorithm (CAT BOOST) attains the highest accuracy value of 0.99 to predict survival outcome of recurrence cervical cancer patients. The proposed outcome of the research is to identify the important risk factors through which the survival outcome of the patients improved.
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Affiliation(s)
- S Geeitha
- Department of Information Technology, M. Kumarasamy College of Engineering, Thalavapalayam, Karur, Tamil Nadu, India
| | - K Ravishankar
- Department of Computer Science and Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Jaehyuk Cho
- Department of Software Engineering and Division of Electronics and Information Engineering, Jeonbuk National University, Jeonju-Si, Republic of Korea.
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Welsh A, Matshitse R, Khan SF, Nyokong T, Prince S, Smith GS. Trinuclear ruthenium(II) polypyridyl complexes: Evaluation as photosensitizers for enhanced cervical cancer treatment. J Inorg Biochem 2024; 256:112545. [PMID: 38581803 DOI: 10.1016/j.jinorgbio.2024.112545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Trinuclear ruthenium(II) polypyridyl complexes anchored to benzimidazole-triazine / trisamine scaffolds were investigated as photosensitizers for photodynamic therapy. The trinuclear complexes were noted to produce a significant amount of singlet oxygen in both DMF and aqueous media, are photostable and show appreciable emission quantum yields (ɸem). In our experimental setting, despite the moderate phototoxic activity in the HeLa cervical cancer cell line, the phototoxic indices (PI) of the trinuclear complexes are superior relative to the PIs of a clinically approved photosensitizer, Photofrin®, and the pro-drug 5-aminolevulinic acid (PI: >7 relative to PI: >1 and PI: 4.4 for 5-aminolevulinic acid and Photofrin®, respectively). Furthermore, the ruthenium complexes were noted to show appreciable long-term cytotoxicity upon light irradiation in HeLa cells in a concentration-dependent manner. Consequently, this long-term activity of the ruthenium(II) polypyridyl complexes embodies their ability to reduce the probability of the recurrence of cervical cancer. Taken together, this presents a strong motivation for the development of polymetallic complexes as anticancer agents.
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Affiliation(s)
- Athi Welsh
- Department of Chemistry, University of Cape Town, Rondebosch 7700, ,South Africa
| | - Refilwe Matshitse
- Institute for Nanotechnology Innovation, Rhodes University, Makhanda 6140, South Africa
| | - Saif F Khan
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Faculty of Health Science, Observatory, 7925, South Africa
| | - Tebello Nyokong
- Institute for Nanotechnology Innovation, Rhodes University, Makhanda 6140, South Africa
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Faculty of Health Science, Observatory, 7925, South Africa
| | - Gregory S Smith
- Department of Chemistry, University of Cape Town, Rondebosch 7700, ,South Africa.
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Li N, Yu K, Huang D, Li S, Zeng D, Li J, Fan L. Molecular Characterization of Cuproptosis-related lncRNAs: Defining Molecular Subtypes and a Prognostic Signature of Ovarian Cancer. Biol Trace Elem Res 2024; 202:1428-1445. [PMID: 37528285 DOI: 10.1007/s12011-023-03780-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Cuproptosis, a newly discovered form of programmed cell death, relies on mitochondrial respiration, the chain of which has been found to be altered in ovarian cancer (OC). The current work probed into the effects of Cuproptosis on the prognosis, immune microenvironment and therapeutic response of OC based on Cuproptosis-related lncRNAs. Data on OC gene expression and clinical characteristics were collected from TCGA, ICGC and GEO databases, and mRNA and lncRNA were distinguished. Cuproptosis-related lncRNAs were screened for consensus clustering analysis. Differentially expressed lncRNAs (DElncRNAs) were identified between clusters, and least absolute shrinkage and selection operator (LASSO) and Cox regression analysis were performed to establish a prognostic signature. Its potential value in OC was evaluated by Gene Set Enrichment Analysis (GSEA), tumor cell mutation and immune microenvironment analysis, and response to immunotherapy and antineoplastic drugs. According to the classification scheme of Cuproptosis-related lncRNAs, OC was divided into four molecular subtypes, which were different in survival time, immune characteristics and somatic mutation. The prognostic signature between subtypes included 10 lncRNAs, which were significantly correlated with the prognosis, immune microenvironment related indexes, the expression of immune checkpoint molecules and the sensitivity of antineoplastic drug Paclitaxel and Gefitinib of OC. We examined the expression of ten LncRNAs in OC cell lines and found that LINC00189, ZFHX4-AS1, RPS6KA2-IT1 and C9orf106 were expressed elevated in OC cell lines, and LINC00861, LINC00582, DEPDC1-AS1, LINC01556, LEMD1-AS1, TYMSOS expression was decreased in OC cell lines. The results of CCK8 showed that the cell viability of OC cells decreased after inhibition of C9orf106, whereas the cell viability of OC cells increased after inhibition of LEMD1-AS1. This work revealed new Cuproptosis-related lncRNA molecular subtypes exhibiting tumor microenvironment (TME) heterogeneity for OC and proposed a prognostic signature that may have benefits in understanding the prognosis, pathological features and immune microenvironment of OC patients.
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Affiliation(s)
- Nan Li
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China
| | - Kai Yu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Delun Huang
- Department of Physiology, Guangxi University of Chinese Medicine, Nanning, 530001, China
| | - Shu Li
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China
| | - Dingyuan Zeng
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China
- The Department of Obstetrics and Gynecology, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China
| | - Jingjing Li
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China.
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China.
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China.
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China.
| | - Li Fan
- Reproductive Medicine Center, Liuzhou Maternity and Child Health Care Hospital, Liuzhou, 545001, China.
- Liuzhou Institute of Reproduction and Genetics, Liuzhou, 545001, China.
- Affiliated Maternity Hospital and Affiliated Children's Hospital of Guangxi, University of Science and Technology, Liuzhou, 545001, China.
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, 545001, China.
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Ju L, Liu B, Fan Z, Zhang W, Shi X. Adaptive optimization technology of a conformal infrared dome based on the Von Karman surface under hypersonic conditions. OPTICS EXPRESS 2023; 31:22323-22342. [PMID: 37475346 DOI: 10.1364/oe.492866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/17/2023] [Indexed: 07/22/2023]
Abstract
With the advent of the hypersonic era, diverse combat methods of hypersonic precision-guided weapons have been gradually developed. This study focuses on the precise design of a conformal infrared dome to accommodate different working conditions. To achieve this, an adaptive optimization technology for configuring conformal infrared domes is proposed, employing a multi-objective genetic algorithm. The technology enables the dome to dynamically balance its aerodynamic and imaging performance, taking into account the specific characteristics of each working condition. Moreover, it streamlines the design process of the conformal infrared domes. By optimizing the design with von Karman surfaces, we can overcome the limitations associated with the traditional quadric configuration. In order to evaluate its performance, a comparison was made with a conventional ellipsoid dome. The results indicate that, under the same working conditions, the air drag coefficient of the optimized infrared dome is reduced by 34.29% and that the peak signal-to-noise ratio of the distorted image from the infrared detection system is increased by 1.7%. We have demonstrated the effectiveness of the optimization method to balance aerodynamic performance and optical performance. Hopefully, our new method will improve the comprehensive performance of the infrared dome as well as the guidance capability of infrared detection technology.
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Gao K, Lian W, Zhao R, Huang W, Xiong J. The joint role of methylation and immune-related lncRNAs in ovarian cancer: Defining molecular subtypes and developing prognostic signature. Transl Oncol 2023; 34:101704. [PMID: 37257331 DOI: 10.1016/j.tranon.2023.101704] [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: 03/10/2023] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023] Open
Abstract
INTRODUCTION Complex outcome of ovarian cancer (OC) stems from the tumor immune microenvironment (TIME) influenced by genetic and epigenetic factors. This study aimed to comprehensively explored the subclasses of OC through lncRNAs related to both N6-methyladenosine (m6A)/N1-methyladenosine (m1A)/N7-methylguanosine (m7G)/5-methylcytosine (m5C) in terms of epigenetic variability and immune molecules and develop a new set of risk predictive systems. MATERIAL AND METHODS The lncRNA data of OC were collected from TCGA. Spearman correlation analysis on lncRNA data of OC with immune-related gene expression and with m6A/m5C/m1A/m7G were respectively conducted. The m6A/m5C/m1A/m7G-related m6A/m5C/m1A/m7G related immune lncRNA subtypes were identified on the basis of the prognostic lncRNAs. Heterogeneity among subtypes was evaluated by tumor mutation analysis, tumor microenvironment (TME) component analysis, response to immune checkpoint blocked (ICB) and chemotherapeutic drugs. A risk predictive system was developed based on the results of Cox regression analysis and random survival forest analysis of the differences between each specific cluster and other clusters. RESULTS Three m6A/m5C/m1A/m7G-related immune lncRNA subtypes of OC showing distinct differences in prognosis, mutation pattern, TIME components, immunotherapy and chemotherapy response were identified. A set of risk predictive system consisting of 10 lncRNA for OC was developed, according to which the risk score of samples in each OC dataset was calculated and risk type was defined. CONCLUSIONS This study classified three m6A/m5C/m1A/m7G-related immune lncRNA subtypes with distinct heterogeneous mutation patterns, TME components, ICB therapy and immune response, and provided a set of risk predictive system consisted of 10 lncRNA for OC.
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Affiliation(s)
- Kefei Gao
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Wenqin Lian
- Department of Burns and Plastic & Wound Repair Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361100, China
| | - Rui Zhao
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Weiming Huang
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
| | - Jian Xiong
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
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Nelson TM, Ghosh S, Postler TS. L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data. Int J Mol Sci 2022; 23:15851. [PMID: 36555493 PMCID: PMC9781625 DOI: 10.3390/ijms232415851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Long-read sequencing (LRS) has been adopted to meet a wide variety of research needs, ranging from the construction of novel transcriptome annotations to the rapid identification of emerging virus variants. Amongst other advantages, LRS preserves more information about RNA at the transcript level than conventional high-throughput sequencing, including far more accurate and quantitative records of splicing patterns. New studies with LRS datasets are being published at an exponential rate, generating a vast reservoir of information that can be leveraged to address a host of different research questions. However, mining such publicly available data in a tailored fashion is currently not easy, as the available software tools typically require familiarity with the command-line interface, which constitutes a significant obstacle to many researchers. Additionally, different research groups utilize different software packages to perform LRS analysis, which often prevents a direct comparison of published results across different studies. To address these challenges, we have developed the Long-Read Analysis Pipeline for Transcriptomics (L-RAPiT), a user-friendly, free pipeline requiring no dedicated computational resources or bioinformatics expertise. L-RAPiT can be implemented directly through Google Colaboratory, a system based on the open-source Jupyter notebook environment, and allows for the direct analysis of transcriptomic reads from Oxford Nanopore and PacBio LRS machines. This new pipeline enables the rapid, convenient, and standardized analysis of publicly available or newly generated LRS datasets.
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Long Intergenic Non-Protein Coding RNA 173 in Human Cancers. Cancers (Basel) 2022; 14:cancers14235923. [PMID: 36497407 PMCID: PMC9737410 DOI: 10.3390/cancers14235923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Long non-coding RNAs belong to non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides and limited protein-coding ability. Growing research has clarified that dysregulated lncRNAs are correlated with the development of various complex diseases, including cancer. LINC00173 has drawn researchers' attention as one of the recently discovered lncRNAs. Aberrant expression of LINC00173 affects the initiation and progression of human cancers. In the present review, we summarize the recent considerable research on LINC00173 in 11 human cancers. Through the summary of the abnormal expression of LINC00173 and its potential molecular regulation mechanism in cancers, this article indicates that LINC00173 may serve as a potential diagnostic biomarker and a target for drug therapy, thus providing novel clues for future related research.
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Kyrgiafini MA, Sarafidou T, Mamuris Z. The Role of Long Noncoding RNAs on Male Infertility: A Systematic Review and In Silico Analysis. BIOLOGY 2022; 11:biology11101510. [PMID: 36290414 PMCID: PMC9598197 DOI: 10.3390/biology11101510] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022]
Abstract
Male infertility is a complex disorder affecting many couples worldwide. Long noncoding RNAs (lncRNAs) regulate important cellular processes; however, a comprehensive understanding of their role in male infertility is limited. This systematic review investigates the differential expressions of lncRNAs in male infertility or variations in lncRNA regions associated with it. The PRISMA guidelines were used to search Pubmed and Web of Science (1 June 2022). Inclusion criteria were human participants, patients diagnosed with male infertility, and English language speakers. We also performed an in silico analysis investigating lncRNAs that are reported in many subtypes of male infertility. A total of 625 articles were found, and after the screening and eligibility stages, 20 studies were included in the final sample. Many lncRNAs are deregulated in male infertility, and interactions between lncRNAs and miRNAs play an important role. However, there is a knowledge gap regarding the impact of variants found in lncRNA regions. Furthermore, eight lncRNAs were identified as differentially expressed in many subtypes of male infertility. After in silico analysis, gene ontology (GO) and KEGG enrichment analysis of the genes targeted by them revealed their association with bladder and prostate cancer. However, pathways involved in general in tumorigenesis and cancer development of all types, such as p53 pathways, apoptosis, and cell death, were also enriched, indicating a link between cancer and male infertility. This evidence, however, is preliminary. Future research is needed to explore the exact mechanism of action of the identified lncRNAs and investigate the association between male infertility and cancer.
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Lin Z, Zou J, Sui X, Yao S, Lin L, Wang J, Zhao J. Necroptosis-related lncRNA signature predicts prognosis and immune response for cervical squamous cell carcinoma and endocervical adenocarcinomas. Sci Rep 2022; 12:16285. [PMID: 36175606 PMCID: PMC9523019 DOI: 10.1038/s41598-022-20858-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 09/20/2022] [Indexed: 12/24/2022] Open
Abstract
Necroptosis, a programmed form of necrotic cell death, plays critical regulatory roles in the progression and metastatic spread of cancers such as cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). However, there are few articles systematically analyzing the necroptosis-related long non-coding RNAs (NRlncRNAs) correlated with CESC patients. Both RNA-sequencing and clinical data of CESC patients are downloaded from TCGA database in this study. Pearson correlation analysis, least absolute shrinkage, operator algorithm selection and Cox regression model are employed to screen and create a risk score model of eleven-NRlncRNAs (MIR100HG, LINC00996, SNHG30, LINC02688, HCG15, TUBA3FP, MIAT, DBH-AS1, ERICH6-AS1SCAT1, LINC01702) prognostic. Thereafter, a series of tests are carried out in sequence to evaluate the model for independent prognostic value. Gene set enrichment analytic paper, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analytic paper make it clear that immune-related signaling pathways are very rich in the high-risk subgroup. Additionally, the prognostic risk score model is correlated to immune cell infiltration, potential immune checkpoint, immune function, immune micro-environmental and m6A-related gene. Mutation frequency in mutated genes and survival probability trend are higher in the low-risk subgroup in most of test cases when compared to the high-risk subgroup. This study constructs a renewed prognostic model of eleven-NRlncRNAs, which may make some contribution to accurately predicting the prognosis and the immune response from CESC patients, and improve the recognition of CESC patients and optimize customized treatment regimens to some extent.
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Affiliation(s)
- Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China.
| | - Jiani Zou
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Xiaohui Sui
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Shujuan Yao
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Lidong Lin
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Jiuling Wang
- Office of Medical Insurance Management, Qilu Hospital of Shandong University, Jinan, 250012, China.
| | - Junde Zhao
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China.
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May-Hau DI, Bárcenas-López DA, Núñez-Enríquez JC, Bekker-Méndez VC, Beltrán-Anaya FO, Jiménez-Hernández E, Ortíz-Maganda MP, Guerra-Castillo FX, Medina-Sanson A, Flores-Lujano J, Martín-Trejo JA, Peñaloza-González JG, Velázquez-Aviña MM, Torres-Nava JR, Hernández-Echáurregui GA, Espinosa-Elizondo RM, Gutiérrez-Rivera MDL, Sanchez-Hernandez R, Pérez-Saldívar ML, Flores-Villegas LV, Merino-Pasaye LE, Duarte-Rodríguez DA, Mata-Rocha M, Sepúlveda-Robles OA, Rosas-Vargas H, Hidalgo-Miranda A, Mejía-Aranguré JM, Jiménez-Morales S. Underexpression of LINC00173 in TCF3/PBX1-Positive Cases Is Associated With Poor Prognosis in Children With B-Cell Precursor Acute Lymphoblastic Leukemia. Front Oncol 2022; 12:887766. [PMID: 35719952 PMCID: PMC9201104 DOI: 10.3389/fonc.2022.887766] [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: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most frequent pediatric cancer worldwide. Despite improvements in treatment regimens, approximately 20% of the cases cannot be cured, highlighting the necessity for identifying new biomarkers to improve the current clinical and molecular risk stratification schemes. We aimed to investigate whether LINC00173 is a biomarker in ALL and to explore its expression level in other human cancer types. Methods A nested case-control study including Mexican children with BCP-ALL was conducted. LINC00173 expression was evaluated by qRT-PCR using hydrolysis probes. To validate our findings, RNA-seq expression data from BCP-ALL and normal tissues were retrieved from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Genotype-Tissue Expression (GTEx) repositories, respectively. LINC00173 expression was also evaluated in solid tumors by downloading available data from The Cancer Genome Atlas (TCGA). Results A lower expression of LINC00173 in BCP-ALL cases compared to normal subjects was observed (p < 0.05). ALL patients who carry the TCF3/PBX1 fusion gene displayed lower expression of LINC00173 in contrast to other BCP-ALL molecular subtypes (p < 0.04). LINC00173 underexpression was associated with a high risk to relapse (HR = 1.946, 95% CI = 1.213-3.120) and die (HR = 2.073, 95% CI = 1.211-3.547). Patients with TCF3/PBX1 and underexpression of LINC00173 had the worst prognosis (DFS: HR = 12.24, 95% CI = 5.04-29.71; OS: HR = 11.19, 95% CI = 26-32). TCGA data analysis revealed that underexpression of LINC00173 is also associated with poor clinical outcomes in six new reported tumor types. Conclusion Our findings suggest that LINC00173 is a biomarker of poor prognosis in BCP-ALL and other types of cancer. We observed an association between the expression of LINC00173 and TCF3/PBX1 and the risk to relapse and die in BCP-ALL, which is worse in TCF3/PBX1-positive cases displaying underexpression of LINC00173. Experimental studies are needed to provide insight into the LINC00173 and TCF3/PBX relationship.
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Affiliation(s)
- Didier Ismael May-Hau
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Maestría en Investigación Clínica Experimental en Salud, Universidad Nacional Autónoma de Mexico, México City, Mexico
| | - Diego Alberto Bárcenas-López
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Fredy Omar Beltrán-Anaya
- Laboratorio de Epidemiología Clínica y Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Mónica Patricia Ortíz-Maganda
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Francisco Xavier Guerra-Castillo
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México, Mexico City, Mexico
| | | | | | - María de Lourdes Gutiérrez-Rivera
- Servicio de Oncología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rodrigo Sanchez-Hernandez
- Servicio de Oncología Pediátrica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional "20 de Noviembre", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional "20 de Noviembre", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Medicine Faculty, Universidad Autónoma de México, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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11
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Tian J, Luo B. Identification of Three Prognosis-Related Differentially Expressed lncRNAs Driven by Copy Number Variation in Thyroid Cancer. J Immunol Res 2022; 2022:9203796. [PMID: 35642209 PMCID: PMC9148411 DOI: 10.1155/2022/9203796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 02/07/2023] Open
Abstract
Thyroid cancer as the malignant tumor with the highest incidence in the endocrine system also shows a fast growth and development. In this work, we developed a new method to identify copy number variation- (CNV-) driven differentially expressed lncRNAs in thyroid cancer for predicting cancer prognosis. The data of RNA sequencing, CNV, methylation, mutation, and clinical details of thyroid cancer were obtained from the Cancer Genome Atlas database (TCGA). Molecular subtypes were clustered by iClusterPlus. Weighted gene co-expression network analysis (WGCNA) was employed to show co-expression modules. DEseq2 was conducted to identify protein coding genes (PCGs) and differentially expressed lncRNAs. CNV was detected using GISTIC 2.0. Three molecular subtypes were identified, and 68 differentially expressed lncRNAs (DElncRNAs) related to cancer were found among different molecular subtypes. CNV of FOXD2-AS1, FAM181A-AS1, and RNF157-AS1 was associated with overall survival and was involved in cancer-related pathways. These three DElncRNAs discovered based on CNV could serve as prognostic biomarkers to predict prognosis for thyroid cancer and new targets to explore molecular drugs.
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Affiliation(s)
- Jinyi Tian
- Department of General Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, 168 Litang Road, Changping District, Beijing, China
| | - Bin Luo
- Department of General Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, 168 Litang Road, Changping District, Beijing, China
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12
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LINC00852 Regulates Cell Proliferation, Invasion, Migration and Apoptosis in Hepatocellular Carcinoma Via the miR-625/E2F1 Axis. Cell Mol Bioeng 2021; 15:207-217. [DOI: 10.1007/s12195-021-00714-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
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13
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Li Q, Li X, Yang X, Zhang B, Gu Y, Gu G, Xiong J, Li Y, Qian Z. Long Intergenic Nonprotein Coding RNA 173 Inhibits Tumor Growth and Promotes Apoptosis by Repressing Sphingosine Kinase 1 Protein Expression in Pancreatic Cancer. DNA Cell Biol 2021; 40:757-775. [PMID: 33978457 DOI: 10.1089/dna.2020.6103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is a common malignant tumor worldwide. Extensive studies have been conducted on the functional role of long noncoding RNAs in pancreatic cancer. In this study, long intergenic nonprotein coding RNA 173 (LINC00173) was highly expressed in pancreatic cancer tissues. In vitro functional experiments showed that LINC00173 overexpression inhibited the proliferation and invasion of pancreatic cancer cells and promoted cell apoptosis in MIA PaCa-2 and PANC-1 cells. RNA sequencing analysis and Western blot assays demonstrated that LINC00173 reduced the expression of sphingosine kinase 1 (SPHK1) and then inhibited the protein expression of activated phospho-protein kinase B (AKT) and NF-κB. In vivo functional assays also revealed that LINC00173 inhibited the growth of pancreatic cancer xenografts, repressed cell proliferation, promoted cell apoptosis, and inhibited SPHK1 expression. The combined results of this study indicate that LINC00173 inhibits pancreatic cancer progression by repressing SPHK1 expression. Improving LINC00173 may represent a therapeutic strategy for pancreatic cancer in the future.
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Affiliation(s)
- Qian Li
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xingxing Li
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaojun Yang
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bin Zhang
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuqing Gu
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guangliang Gu
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiageng Xiong
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanan Li
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhuyin Qian
- Pancreas Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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14
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Yang H, Gao L, Zhang M, Ning N, Wang Y, Wu D, Li X. Identification and Analysis of An Epigenetically Regulated Five-lncRNA Signature Associated With Outcome and Chemotherapy Response in Ovarian Cancer. Front Cell Dev Biol 2021; 9:644940. [PMID: 33708773 PMCID: PMC7940383 DOI: 10.3389/fcell.2021.644940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
The deregulation of long non-coding RNAs (lncRNAs) by epigenetic alterations has been implicated in cancer initiation and progression. However, the epigenetically regulated lncRNAs and their association with clinical outcome and therapeutic response in ovarian cancer (OV) remain poorly investigated. This study performed an integrative analysis of DNA methylation data and transcriptome data and identified 419 lncRNAs as potential epigenetically regulated lncRNAs. Using machine-learning and multivariate Cox regression analysis methods, we identified and developed an epigenetically regulated lncRNA expression signature (EpiLncRNASig) consisting of five lncRNAs from the list of 17 epigenetically regulated lncRNAs significantly associated with outcome. The EpiLncRNASig could stratify patients into high-risk groups and low-risk groups with significantly different survival and chemotherapy response in different patient cohorts. Multivariate Cox regression analyses, after adjusted by other clinical features and treatment response, demonstrated the independence of the DEpiLncSig in predicting survival. Functional analysis for relevant protein-coding genes of the DEpiLncSig indicated enrichment of known immune-related or cancer-related biological pathways. Taken together, our study not only provides a promising prognostic biomarker for predicting outcome and chemotherapy response but also will improve our understanding of lncRNA epigenetic regulation mechanisms in OV.
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Affiliation(s)
- Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital and The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Lin Gao
- Institute for Endemic Fluorosis Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, China
| | - Meiling Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ning Ning
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Di Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaomei Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
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15
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Chao X, Song X, Wu H, You Y, Wu M, Li L. Selection of Treatment Regimens for Recurrent Cervical Cancer. Front Oncol 2021; 11:618485. [PMID: 33604304 PMCID: PMC7884815 DOI: 10.3389/fonc.2021.618485] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/11/2021] [Indexed: 12/09/2022] Open
Abstract
OBJECTIVE The selection of individualized treatment for recurrent cervical cancer is challenging. This study aimed to investigate the impact of various therapies on survival outcomes after recurrence. METHODS Eligible patients were diagnosed with recurrent cervical cancer between March 2012 and April 2018. Postrecurrence progression-free survival (PFS) and overall survival (OS) were investigated in the whole cohort and in subgroups, categorized by recurrence site and prior radiotherapy history, using a multivariate model that incorporated treatment for primary and recurrent tumors, histological pathology, and FIGO staging. RESULTS Two hundred and sixty recurrent cervical cancer patients were included. As of March 1, 2020, the median postrecurrence PFS and OS were 7.0 (range 0-94) and 24.0 (1.8-149.1) months, respectively. In a multivariate model measured by PFS, radiotherapy was superior to other therapies for the whole cohort (p=0.029) and recurrence only within the pelvic cavity (p=0.005), but the advantages of radiotherapy disappeared in patients with a history of radiotherapy (p values >0.05). For recurrence only beyond the pelvic cavity, combination therapy resulted in improved PFS (p=0.028). For recurrence both within and beyond the pelvic cavity, no therapy regimen provided additional PFS benefits (p values >0.05). Radiotherapy and combination therapy were also associated with improved postrecurrence OS for recurrence within the pelvic cavity (p=0.034) and only beyond the pelvic cavity (p=0.017), respectively. CONCLUSIONS In cervical cancer patients, postrecurrence radiotherapy can improve PFS and OS for patients with recurrence within the pelvic cavity and without prior radiotherapy. For recurrence beyond the pelvic cavity or cases with a history of radiotherapy, combination or individualized therapy may provide potential survival benefits.
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Affiliation(s)
- Xiaopei Chao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Xiaochen Song
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Yan You
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Ming Wu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
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16
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Gu X, Chu Q, Zheng Q, Wang J, Zhu H. The dual functions of the long noncoding RNA CASC15 in malignancy. Biomed Pharmacother 2021; 135:111212. [PMID: 33433353 DOI: 10.1016/j.biopha.2020.111212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/05/2020] [Accepted: 12/26/2020] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) play vital roles in tumorigenesis and progression. LncRNAs can participate in various biological processes, such as cell growth, anti-apoptosis functions, migration, and invasion. Cancer susceptibility candidate 15 (CASC15) is a cancer-related lncRNA that has been reported to play opposite roles in the pathogenesis of different types of cancers. Studies have shown that CASC15 is downregulated in ovarian cancer and neuroblastoma, acting mainly as a tumour suppressor, while it is highly expressed and carcinogenic in hepatocellular carcinoma (HCC), lung cancer, tongue squamous cell carcinoma, gastric cancer, colorectal cancer, cervical cancer, and breast cancer. Furthermore, aberrant CASC15 expression is associated with tumorigenesis, progression, and patient outcomes via regulation of target genes and signalling pathways. In this review, we summarize current data concerning the regulatory functions and underlying mechanisms of CASC15 in tumour development. We also highlight its potential clinical utility as a biomarker for early detection or as a therapeutic target in human cancers.
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Affiliation(s)
- Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Qiuxian Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Haihong Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China.
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17
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Adiga D, Eswaran S, Pandey D, Sharan K, Kabekkodu SP. Molecular landscape of recurrent cervical cancer. Crit Rev Oncol Hematol 2020; 157:103178. [PMID: 33279812 DOI: 10.1016/j.critrevonc.2020.103178] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer (CC) is a major gynecological problem in developing and underdeveloped countries. Despite the significant advancement in early detection and treatment modalities, several patients recur. Moreover, the molecular mechanisms responsible for CC recurrence remains obscure. The patients with CC recurrence often show poor prognosis and significantly high mortality rates. The clinical management of recurrent CC depends on treatment history, site, and extent of the recurrence. Owing to poor prognosis and limited treatment options, recurrent CC often presents a challenge to the clinicians. Several in vitro, in vivo, and patient studies have led to the identification of the critical molecular changes responsible for CC recurrence. Both aberrant genetic and epigenetic modifications leading to altered cell signaling pathways have been reported to impact CC recurrence. Researchers are currently trying to dissect the molecular pathways in CC and translate these findings for better management of disease. This article attempts to review the existing knowledge of disease relapse, accompanying challenges, and associated molecular players in CC.
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Affiliation(s)
- Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Deeksha Pandey
- Department of OBGYN, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Krishna Sharan
- Department of Radiotherapy and Oncology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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18
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Fan G, Jiao J, Shen F, Ren Q, Wang Q, Chu F. Long non-coding RNA HCG11 sponging miR-522-3p inhibits the tumorigenesis of non-small cell lung cancer by upregulating SOCS5. Thorac Cancer 2020; 11:2877-2886. [PMID: 32844573 PMCID: PMC7529553 DOI: 10.1111/1759-7714.13624] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Numerous studies have shown that long non-coding RNA (lncRNA) is involved in various human diseases including non-small cell lung cancer (NSCLC). The aim of this study was to explore the potential role of lncRNA HCG11 in the pathogenesis of NSCLC. METHODS The mRNA expression of HCG11, miR-522-3p and SOCS5 was detected by RT-qPCR. The regulatory mechanism of lncRNA HCG11 was investigated by CCK-8, transwell and dual luciferase reporter assays. RESULTS Downregulation of lncRNA HCG11 and upregulation of miR-522-3p were found in NSCLC tissues and cells, and abnormal expressions of lncRNA HCG11 and miR-522-3p were related to adverse clinical outcomes of NSCLC patients. LncRNA HCG11 acted as a molecular sponge for miR-522-3p. Functionally, lncRNA HCG11 inhibited cell viability, migration and invasion in NSCLC by downregulating miR-522-3p. Further, miR-522-3p directly targeted SOCS5. lncRNA HCG11 could positively regulate SOCS5 expression in NSCLC. In addition, HCG11 downregulation or miR-522-3p overexpression abolished the inhibitory effect of SOCS5 on cell viability, migration and invasion in NSCLC. CONCLUSIONS LncRNA HCG11 inhibits cell viability, migration and invasion in NSCLC by functioning as a ceRNA of miR-522-3p to upregulate SOCS5.
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Affiliation(s)
- Gang Fan
- Department of Clinical LaboratoryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Jin Jiao
- Department of Clinical LaboratoryShandong Maternal and Child Health Care HospitalJinanChina
| | - Feng Shen
- Department of Clinical LaboratoryShandong Maternal and Child Health Care HospitalJinanChina
| | - Qingxia Ren
- Department of Clinical LaboratoryPeople's Hospital of RizhaoRizhaoChina
| | - Qing Wang
- Department of ImagingThe People's Hospital of Zhangqiu AreaJinanChina
| | - Fulu Chu
- Department of Clinical LaboratoryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
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19
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Xu D, Dang W, Wang S, Hu B, Yin L, Guan B. An optimal prognostic model based on gene expression for clear cell renal cell carcinoma. Oncol Lett 2020; 20:2420-2434. [PMID: 32782559 PMCID: PMC7400162 DOI: 10.3892/ol.2020.11780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/06/2020] [Indexed: 12/11/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent type of RCC; however, prognostic prediction tools for ccRCC are scant. Developing mRNA or long non-coding RNA (lncRNA)-based risk assessment tools may improve the prognosis in patients with ccRCC. RNA-sequencing and prognostic data from patients with ccRCC were downloaded from The Cancer Genome Atlas and the European Bioinformatics Institute Array database at the National Center for Biotechnology Information. Differentially expressed (DE) RNAs (DERs) and prognostic DERs were screened between less favorable and favorable prognoses using the limma package in R 3.4.1, and analyzed using univariate and multivariate Cox regression analyses, respectively. Risk score models were constructed using optimal combinations of DEmRNAs and DElncRNAs identified using the Least Absolute Shrinkage And Selection Operator Cox regression model of the penalized package. Associations between risk score models and overall survival time were evaluated. Independent prognostic clinical factors were screened using univariate and multivariate Cox regression analyses, and nomogram models were constructed. Gene Ontology biological processes and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted using the clusterProfiler package in R3.4.1. A total of 451 DERs were identified, including 404 mRNAs and 47 lncRNAs, between less favorable and favorable prognoses, and 269 DERs, including 233 mRNAs and 36 lncRNAs, were identified as independent prognostic factors. Optimal combinations including 10 DEmRNAs or 10 DElncRNAs were screened using four risk score models based on the status or expression levels of the 10 DEmRNAs or 10 DElncRNAs. The model based on the expression levels of the 10 DEmRNAs had the highest prognostic power. These prognostic DEmRNAs may be involved in biological processes associated with the inflammatory response, complement and coagulation cascades and neuroactive ligand-receptor interaction pathways. The present validated risk assessment tool based on the expression levels of these 10 DEmRNAs may help to identify patients with ccRCC at a high risk of mortality. These 10 DEmRNAs in optimal combinations may serve as prognostic biomarkers and help to elucidate the pathogenesis of ccRCC.
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Affiliation(s)
- Dan Xu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China.,Department of Nephrology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Wantai Dang
- Department of Rheumatology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Shaoqing Wang
- Department of Nephrology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, P.R. China
| | - Bo Hu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Baozhang Guan
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
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