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Zhang T, Fang J, Hu J, Kong Y, Jiang R, Wang H, Yang G, Yao G. Downregulation of CASC15 attenuates the symptoms of polycystic ovary syndrome by affecting granulosa cell proliferation and regulating ovarian follicular development. Mol Cell Endocrinol 2024; 592:112322. [PMID: 38942281 DOI: 10.1016/j.mce.2024.112322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
Polycystic ovary syndrome (PCOS) is a type of follicular dysplasia with an unclear pathogenesis, posing certain challenges in its diagnosis and treatment. Cancer susceptibility candidate 15 (CASC15), a long non-coding RNA closely associated with tumour development, has been implicated in PCOS onset and development. Therefore, this study aimed to investigate the molecular mechanisms underlying PCOS by downregulating CASC15 expression in both in vitro and in vivo models. We explored the potential regulatory relationship between CASC15 expression and PCOS by examining cell proliferation, cell cycle dynamics, cell autophagy, steroid hormone secretion capacity, and overall ovarian function in mice. We found that CASC15 expression in granulosa cells derived from patients with PCOS was significantly higher than those of the normal group (P < 0.001). In vitro experiments revealed that downregulating CASC15 significantly inhibited cell proliferation, promoted apoptosis, induced G1-phase cell cycle arrest, and influenced cellular autophagy levels. Moreover, downregulating CASC15 affected the follicular development process in newborn mouse ovaries. In vivo studies in mice demonstrated that disrupting CASC15 expression improved PCOS-related symptoms such as polycystic changes and hyperandrogenism, and significantly affected ovulation induction and embryo implantation in pregnant mice. Overall, CASC15 was highly expressed in granulosa cells of patients with PCOS and its downregulation improved PCOS-related symptoms by influencing granulosa cell function and follicular development in mice.
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Affiliation(s)
- Tongwei Zhang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junnan Fang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingyi Hu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yue Kong
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ran Jiang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huihui Wang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guang Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guidong Yao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Wang Z, Han H, Zhang C, Wu C, Di J, Xing P, Qiao X, Weng K, Hao H, Yang X, Hou Y, Jiang B, Su X. Copy number amplification-induced overexpression of lncRNA LOC101927668 facilitates colorectal cancer progression by recruiting hnRNPD to disrupt RBM47/p53/p21 signaling. J Exp Clin Cancer Res 2024; 43:274. [PMID: 39350250 PMCID: PMC11440719 DOI: 10.1186/s13046-024-03193-7] [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: 05/28/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Somatic copy number alterations (SCNAs) are pivotal in cancer progression and patient prognosis. Dysregulated long non-coding RNAs (lncRNAs), modulated by SCNAs, significantly impact tumorigenesis, including colorectal cancer (CRC). Nonetheless, the functional significance of lncRNAs induced by SCNAs in CRC remains largely unexplored. METHODS The dysregulated lncRNA LOC101927668, induced by copy number amplification, was identified through comprehensive bioinformatic analyses utilizing multidimensional data. Subsequent in situ hybridization was employed to ascertain the subcellular localization of LOC101927668, and gain- and loss-of-function experiments were conducted to elucidate its role in CRC progression. The downstream targets and signaling pathway influenced by LOC101927668 were identified and validated through a comprehensive approach, encompassing RNA sequencing, RT-qPCR, Western blot analysis, dual-luciferase reporter assay, evaluation of mRNA and protein degradation, and rescue experiments. Analysis of AU-rich elements (AREs) within the mRNA 3' untranslated region (UTR) of the downstream target, along with exploration of putative ARE-binding proteins, was conducted. RNA pull-down, mass spectrometry, RNA immunoprecipitation, and dual-luciferase reporter assays were employed to elucidate potential interacting proteins of LOC101927668 and further delineate the regulatory mechanism between LOC101927668 and its downstream target. Moreover, subcutaneous xenograft and orthotopic liver xenograft tumor models were utilized to evaluate the in vivo impact of LOC101927668 on CRC cells and investigate its correlation with downstream targets. RESULTS Significantly overexpressed LOC101927668, driven by chr7p22.3-p14.3 amplification, was markedly correlated with unfavorable clinical outcomes in our CRC patient cohort, as well as in TCGA and GEO datasets. Moreover, we demonstrated that enforced expression of LOC101927668 significantly enhanced cell proliferation, migration, and invasion, while its depletion impeded these processes in a p53-dependent manner. Mechanistically, nucleus-localized LOC101927668 recruited hnRNPD and translocated to the cytoplasm, accelerating the destabilization of RBM47 mRNA, a transcription factor of p53. As a nucleocytoplasmic shuttling protein, hnRNPD mediated RBM47 destabilization by binding to the ARE motif within RBM47 3'UTR, thereby suppressing the p53 signaling pathway and facilitating CRC progression. CONCLUSIONS The overexpression of LOC101927668, driven by SCNAs, facilitates CRC proliferation and metastasis by recruiting hnRNPD, thus perturbing the RBM47/p53/p21 signaling pathway. These findings underscore the pivotal roles of LOC101927668 and highlight its therapeutic potential in anti-CRC interventions.
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Affiliation(s)
- Zaozao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
| | - Haibo Han
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Clinical Laboratory, Peking University Cancer Hospital and Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Chenghai Zhang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Chenxin Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Jiabo Di
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Pu Xing
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xiaowen Qiao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Kai Weng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Hao Hao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xinying Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Yifan Hou
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Beihai Jiang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xiangqian Su
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
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Abd El Fattah YK, Abulsoud AI, AbdelHamid SG, AbdelHalim S, Hamdy NM. CCDC144NL-AS1/hsa-miR-143-3p/HMGA2 interaction: In-silico and clinically implicated in CRC progression, correlated to tumor stage and size in case-controlled study; step toward ncRNA precision. Int J Biol Macromol 2023; 253:126739. [PMID: 37690651 DOI: 10.1016/j.ijbiomac.2023.126739] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/06/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
Unravel the regulatory mechanism of lncRNA CCDC144NL-AS1 in CRC hsa-miR-143-3p, downstream protein HMGA2 interaction arm, association with clinicopathological characteristics. Using peripheral blood as liquid biopsy from 60 CRC patients and 30 controls. The expression levels of CCDC144NL-AS1 and hsa-miR-143-3p detected by qRT-PCR. CCDC144NL-AS1 expression was significantly upregulated in CRC patients' sera, associated with worse CRC clinicopathological features regarding the depth of tumor invasion and highly significant difference between tumor stages 3 and 4 and tumor stages 2 and 4. While, hsa-miR-143-3p expression was downregulated in CRC patients by 4.5-fold change when compared to the control subjects (p < 0.0001) and HMGA2 increased in CRC patients than controls 19.59 ng/μL and 5.377 ng/μL, respectively (p < 0.0001) with significant difference between tumor stages 3 and 4 as well as tumor stages 2 and 4. CRC patients with large tumor size showed upregulation in CCDC144NL-AS1 expression and HMGA2 levels compared to those with small tumor size (p-value = 0.0365 and 0.013, respectively). CCDC144NL-AS1 and HMGA2 were positively correlated, whereas lncRNA CCDC144NL-AS1 and hsa-miR-143-3p were negatively correlated. Conclusion: As an interaction arm CCDC144NL-AS1/hsa-miR-143-3p/HMGA2 were correlated to CRC stages 2-4. Therefore, this interaction arm expression clinically and in silico approved, would direct treatment precision in the near future.
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Affiliation(s)
- Yasmine K Abd El Fattah
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785, Cairo, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, 11785, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy (Boy's Branch), Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Sherihan G AbdelHamid
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Sherif AbdelHalim
- Department of General surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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Salido-Guadarrama I, Romero-Cordoba SL, Rueda-Zarazua B. Multi-Omics Mining of lncRNAs with Biological and Clinical Relevance in Cancer. Int J Mol Sci 2023; 24:16600. [PMID: 38068923 PMCID: PMC10706612 DOI: 10.3390/ijms242316600] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
In this review, we provide a general overview of the current panorama of mining strategies for multi-omics data to investigate lncRNAs with an actual or potential role as biological markers in cancer. Several multi-omics studies focusing on lncRNAs have been performed in the past with varying scopes. Nevertheless, many questions remain regarding the pragmatic application of different molecular technologies and bioinformatics algorithms for mining multi-omics data. Here, we attempt to address some of the less discussed aspects of the practical applications using different study designs for incorporating bioinformatics and statistical analyses of multi-omics data. Finally, we discuss the potential improvements and new paradigms aimed at unraveling the role and utility of lncRNAs in cancer and their potential use as molecular markers for cancer diagnosis and outcome prediction.
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Affiliation(s)
- Ivan Salido-Guadarrama
- Departamento de Bioinformatìca y Análisis Estadísticos, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City 11000, Mexico
| | - Sandra L. Romero-Cordoba
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
- Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Bertha Rueda-Zarazua
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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Chang B, Wang Z, Ren M, Yao Q, Zhao L, Zhou X. A Novel CASC15-ALK and TFG-ROS1 Fusion Observed in Uterine Inflammatory Myofibroblastic Tumor. Int J Gynecol Pathol 2023; 42:451-459. [PMID: 36730016 DOI: 10.1097/pgp.0000000000000926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The majority of inflammatory myofibroblastic tumors (IMTs) in the gynecologic tract occur in the uterine corpus and harbor anaplastic lymphoma kinase ( ALK ) rearrangement. Herein, we report 1 uterine IMT case with a novel fusion involving ALK and 1 uterine IMT case with ROS1 rearrangement. The ages of the patients were 56 and 57 yr, respectively. The tumor size was 10.0 and 8.0 cm, respectively. Both patients had stage IB disease. Histologically, the 2 IMT cases had classic morphologic features and predominantly comprised bland spindle cells with hypercellular (fascicular/storiform) and hypocellular (myxoid rich) areas admixed with variably prominent lymphoplasmacytic infiltration. Immunohistochemically, the ALK -rearranged case was positive for ALK , and the ROS1 -rearranged case was positive for ROS1 . Both cases were diffusely positive for desmin. The tumor cells were variably positive for estrogen receptor (1/2 cases, 50.0%) and progesterone receptor (1/2 cases, 50.0%). Targeted RNA sequencing revealed one case each with either a novel CASC15-ALK or TFG-ROS 1 fusion. We identified a novel ALK fusion partner CASC15 in IMT and described the first uterine IMT with a TFG-ROS1 fusion. This study improves our understanding of molecular events in IMT.
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Chan DKH, Mandal A, Hester S, Yu Z, Higgins GS, Kessler BM, Fischer R, Buczacki SJA. Biallelic FBXW7 knockout induces AKAP8-mediated DNA damage in neighbouring wildtype cells. Cell Death Discov 2023; 9:200. [PMID: 37386001 DOI: 10.1038/s41420-023-01494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/24/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Colorectal cancer possesses marked intratumoral heterogeneity. While subclonal interactions between Vogelstein driver mutations have been extensively studied, less is known about competitive or cooperative effects between subclonal populations with other cancer driver mutations. FBXW7 is a cancer driver mutation which is present in close to 17% of colorectal cancer cells. In this study, we generated isogenic FBXW7 mutant cells using CRISPR-Cas9. We identified an upregulation of oxidative phosphorylation and DNA damage in FBXW7 mutant cells, which surprisingly proliferated at a decreased rate compared to wildtype cells. To determine subclonal interactions, wildtype and mutant FBXW7 cells were cocultured using a Transwell system. Wildtype cells cocultured with FBXW7 mutant cells similarly developed DNA damage which was not observed when wildtype cells were co-cultured with other wildtype cells, suggesting that FBXW7 mutant cells were inducing DNA damage in neighbouring wildtype cells. Using mass spectrometry, we identified AKAP8 as being secreted by FBXW7 mutant cells into the coculture media. Furthermore, overexpression of AKAP8 in wildtype cells recapitulated the DNA damage phenotype observed during coculture, while co-culture of wildtype cells with double mutant FBXW7-/-/AKAP8-/- cells abrogated the DNA damage phenotype. Here, we describe a hitherto unknown phenomenon of AKAP8-mediated DNA damage from FBXW7 mutant to neighbouring wildtype cells. Our findings demonstrate the importance of elucidating the local effect of cancer driver mutations between subclonal populations.
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Affiliation(s)
- Dedrick Kok Hong Chan
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Amit Mandal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Svenja Hester
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Zhanru Yu
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | | | - Benedikt Mathias Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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Zhu X, Song J, Wang M, Wang X, Lv L. Dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in breast cancer: A comprehensive analysis. J Gene Med 2023; 25:e3471. [PMID: 36525372 DOI: 10.1002/jgm.3471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is a malignancy harmful to physical and mental health in women, with quite high mortality. Copy number variations (CNVs) are vital factors affecting the progression of breast cancer. Detecting CNVs in breast cancer to predict the prognosis of patients has become a promising approach to accurate treatment in recent years. The differential analysis was performed on CNVs of long noncoding RNAs (lncRNAs) as well as the expression of lncRNAs, microRNAs (miRNAs) and mRNAs in normal tissue and breast tumor tissue based on The Cancer Genome Atlas (TCGA) database. The CNV-driven lncRNAs were identified by the Kruskal-Wallis test. Meanwhile, a competitive endogenous RNA (ceRNA) network regulated by CNV-driven lncRNA was constructed. As the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed, the mRNAs in the dysregulated ceRNA network were mainly enriched in the biological functions and signaling pathways, including the Focal Adhesion-PI3K-Akt-mTOR-signaling pathway, the neuronal system, metapathway biotransformation Phase I and II and blood circulation, etc. The relationship between the CNVs of five lncRNAs and their gene expression in the ceRNA network was analyzed via a chi-square test, which confirmed that except for LINC00243, the expression of four lncRNAs was notably correlated with the CNVs. The survival analysis revealed that only the copy number gain of LINC00536 was evidently related to the poor prognosis of patients. The CIBERSORT algorithm showed that five lncRNAs were correlated with the abundance of immune cell infiltration and immune checkpoints. In a word, by analyzing CNV-driven lncRNAs and the ceRNA network regulated by these lncRNAs, this study explored the mechanism of breast cancer and provided novel insights into new biomarkers.
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Affiliation(s)
- Xiaotao Zhu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jialu Song
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mingzheng Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaohui Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Lin Lv
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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Xu G, Wang H, Zhuang Y, Lin Q, Li Y, Cai Z, Lin G, Liu W. Identification of a ceRNA Network Driven by Copy Number Variations in Esophageal Cancer. J NIPPON MED SCH 2023; 90:426-438. [PMID: 38246614 DOI: 10.1272/jnms.jnms.2023_90-611] [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] [Indexed: 01/23/2024]
Abstract
BACKGROUND Copy number variation (CNV) is associated with progression of esophageal cancer (EC), a common gastrointestinal neoplasm. METHODS Using sequencing data, CNV data, and clinical data of EC transcriptome samples obtained from public databases, we performed differential expression analysis on sequencing data. Differentially expressed CNV-driven lncRNAs were screened using the chi-square test, and CNV-driven lncRNA-associated miRNAs and mRNAs were predicted. Cytoscape software was then used to construct ceRNA networks. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to investigate biological functions of mRNAs in the ceRNA network. Survival curves were plotted to explore correlations between lncRNAs in the ceRNA network and overall survival of CNV patients. Multiple databases were used to predict lncRNAs-related drugs. RESULTS A dysregulated lncRNA-associated ceRNA network driven by CNV in EC, including 11 lncRNAs, 11 miRNAs and 159 mRNAs, was constructed. Downstream enrichment of mRNAs was related to biological processes such as extracellular matrix organization, indicating that these mRNAs mainly participate in intercellular exchange between tumor cells. Additionally, expression of all lncRNAs in the ceRNA network, except LINC00950, LINC01270 and MIR181A1HG, was correlated with patients' CNV. In addition, none of the 11 lncRNAs was significantly correlated with overall survival of CNV patients. CH5424802 and PD-033299CNV mainly affected the RTK signaling pathway and the cell cycle of tumor cells via RP11-180N14.1 and RP11-273 G15.2 in the ceRNA network. CONCLUSIONS This study identified 11 CNV-driven lncRNAs that might affect EC development, 2 of which have promising effects if applied to drug treatment. These findings might assist in identifying novel treatments for EC.
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Affiliation(s)
- Guoxi Xu
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Huaishuai Wang
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Yixiang Zhuang
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Qiyi Lin
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Yinlin Li
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Zhicong Cai
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Gaofeng Lin
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
| | - Weibo Liu
- Depertment of Gastrointestinal Surgery, Jinjiang Municipal Hospital
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9
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Fu X, Liu H, Fan Y, Yuan J. Extracellular vesicle-mediated transfer of lncRNA CLDN10-AS1 aggravates low-density lipoprotein-induced vascular endothelial injury. Physiol Genomics 2022; 54:471-485. [PMID: 36250558 DOI: 10.1152/physiolgenomics.00094.2022] [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: 12/15/2022] Open
Abstract
Oxidized low-density lipoprotein (ox-LDL) stimulation impairs the oxidation-reduction equilibrium in vascular endothelial cells (VECs) and contributes to atherosclerosis (AS). This study probed the mechanisms of extracellular vesicle (EV)-mediated transfer of lncRNA CLDN10 antisense RNA 1 (CLDN10-AS1) in ox-LDL-induced VEC injury. Initially, VEC injury models were established by treating human umbilical vein endothelial cells (HUVECs) with ox-LDL. EVs were isolated from HUVECs (HUVECs-EVs) and identified. CLDN10-AS1, microRNA (miR)-186, and Yin Yang 1 (YY1) expressions in ox-LDL-treated HUVECs and EVs derived from these cells (ox-EVs) were measured. HUVECs were incubated with EVs, after which the cell viability, apoptosis, and concentrations of proinflammatory cytokines and oxidative stress markers were measured. We discovered that CLDN10-AS1 and YY1 were upregulated in ox-LDL-treated HUVECs, whereas miR-186 was downregulated. ox-EVs treatment elevated CLDN10-AS1 expression in HUVECs and ox-EVs overexpressing CLDN10-AS1 promoted VEC injury. Besides, CLDN10-AS1 is competitively bound to miR-186 and promoted YY1 expression. Rescue experiments revealed that miR-186 overexpression or YY1 suppression partially reversed the roles of ox-EVs overexpressing CLDN10-AS1 in ox-LDL-induced VEC injury. Lastly, clinical serum samples were collected for verification. Overall, CLDN10-AS1 carried by HUVECs-EVs into HUVECs competitively bound to miR-186 to elevate YY1 expression, thereby aggravating ox-LDL-induced VEC injury.
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Affiliation(s)
- Xiaoyang Fu
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China.,People's Hospital of Zhengzhou University, Zhengzhou, China.,Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China.,School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Heng Liu
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yulong Fan
- Department of Vascular Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ji Yuan
- Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China.,School of Clinical Medicine, Henan University, Zhengzhou, China.,Department of Anaesthesia, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Anaesthesia, Central China Fuwai Hospital, Zhengzhou, China
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10
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Li C, Guo H, Xiong J, Feng B, Zhu P, Jiang W, Jiang P, Su X, Huang X. Exosomal long noncoding RNAs MAGI2-AS3 and CCDC144NL-AS1 in oral squamous cell carcinoma development via the PI3K-AKT-mTOR signaling pathway. Pathol Res Pract 2022; 240:154219. [DOI: 10.1016/j.prp.2022.154219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 11/14/2022]
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11
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Ding J, Huang M, Huang B, Peng X, Wu G, Peng C, Zhang H, Mao C, Wu X. Identification of a dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in lung squamous cell carcinoma. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:351-361. [PMID: 36161731 DOI: 10.1002/em.22509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Lung cancer is primarily responsive for cancer death, and its progression is aggressively affected by copy number variation (CNV). Through bioinformatics approach, a ceRNA network of CNV-driven lncRNAs in lung squamous cell carcinoma (LUSC) patients was constructed. Data on normal and LUSC tumor tissue from The Cancer Genome Atlas (TCGA)-LUSC dataset were subjected to differential analysis, and differentially expressed lncRNAs (DElncRNAs), DEmiRNAs, and DEmRNAs were obtained. Based on TCGA-LUSC, CNVs of normal and tumor tissue samples were then compared using a Chi-square test, and lncRNAs were intersected based on their CNVs and expression alternation. In combination with the Kruskal-Wallis test, CNV-driven lncRNAs were acquired. Afterwards, miRNAs and mRNAs that interacted with CNV-driven lncRNAs were obtained based on databases (LncBase, starBase, miRDB, mirDIP and TargetScan), DElncRNAs, DEmiRNAs and DEmRNAs, and correlation analysis. The acquired lncRNAs, miRNAs and mRNAs were subjected to Cytoscape software to construct a CNV-driven ceRNA network, which involved 5 lncRNAs (MIR143HG, LINC00702, MIR22HG, RP11-180 N14.1, RP11-473 M20.9), 6 miRNAs (miR-3200-3p, miR-1301-3p, miR-93-3p, miR-96-5p, miR-96-5p, miR-130b-5p, miR-205-5p) and 80 mRNAs. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses indicated that downstream mRNAs were mainly correlated with blood vessel development and T cell-mediated immunity. In summary, we devoted to analyzing CNV-related lncRNAs, mRNAs, and miRNAs in LUSC, thus clarifying 5 lncRNAs that may influence the malignant progression of LUSC. The ceRNA network regulated by these lncRNAs may be the novel pathogenesis of LUSC.
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Affiliation(s)
- Jianyang Ding
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Mingjiang Huang
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Bin Huang
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Xuyang Peng
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Gongzhi Wu
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Congxiong Peng
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Huaizhong Zhang
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Chaofan Mao
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Xuhui Wu
- Department of Cardiothoracic Surgery, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China
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12
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Bukhari I, Khan MR, Hussain MA, Thorne RF, Yu Y, Zhang B, Zheng P, Mi Y. PINTology: A short history of the lncRNA LINC-PINT in different diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1705. [PMID: 35019222 DOI: 10.1002/wrna.1705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
LINC-PINT is a p53-induced long intergenic noncoding transcript that plays a crucial role in many diseases, especially cancer. This long noncoding RNA (lncRNA) gene produces in total 102 (LNCipedia) alternatively spliced variants (LINC-PINT:1 to LINC-PINT:102). The functions of known variants include RNA transcripts, host transcripts for circular RNA (circRNA) generation and as sources for the translation of short peptides. In most human tumors, LINC-PINT is down-regulated where it serves as a tumor suppressor. However, the diversity of its functions in other maladies signifies its general clinical importance. Current LINC-PINT molecular functions include RNA-protein interactions, miRNA sponging and epigenetic modulation with these mechanisms operating in different cellular contexts to exert effects on biological processes ranging from DNA damage responses, cell cycle and growth arrest, senescence, cell migration and invasion, and apoptosis. Genetic polymorphisms in LINC-PINT have also been functionally associated with cancer and other pathologies including the autoimmune diseases pemphigus foliaceus and arthritis. Hence, LINC-PINT shows great potential as a clinical biomarker, especially for the diagnosis and prognosis of cancer. In this review, we explore the current knowledge highlighting the distinctive molecular functions of LINC-PINT in specific cancers and other disease states. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Ihtisham Bukhari
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
| | - Muhammad Riaz Khan
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada.,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mohammed Amir Hussain
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.,Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, China.,School of Environmental & Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Yong Yu
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
| | - Bingyong Zhang
- Department of Gastroenterology, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Mi
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
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13
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Zheng H, Liu H, Li H, Dou W, Wang J, Zhang J, Liu T, Wu Y, Liu Y, Wang X. Characterization of stem cell landscape and identification of stemness-relevant prognostic gene signature to aid immunotherapy in colorectal cancer. Stem Cell Res Ther 2022; 13:244. [PMID: 35681225 PMCID: PMC9185878 DOI: 10.1186/s13287-022-02913-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/22/2022] [Indexed: 02/08/2023] Open
Abstract
Background It is generally accepted that colorectal cancer (CRC) originates from cancer stem cells (CSCs), which are responsible for CRC progression, metastasis and therapy resistance. The high heterogeneity of CSCs has precluded clinical application of CSC-targeting therapy. Here, we aimed to characterize the stemness landscapes and screen for certain patients more responsive to immunotherapy. Methods Twenty-six stem cell gene sets were acquired from StemChecker database. Consensus clustering algorithm was applied for stemness subtypes identification on 1,467 CRC samples from TCGA and GEO databases. The differences in prognosis, tumor microenvironment (TME) components, therapy responses were evaluated among subtypes. Then, the stemness-risk model was constructed by weighted gene correlation network analysis (WGCNA), Cox regression and random survival forest analyses, and the most important marker was experimentally verified. Results Based on single-sample gene set enrichment analysis (ssGSEA) enrichments scores, CRC patients were classified into three subtypes (C1, C2 and C3). C3 subtype exhibited the worst prognosis, highest macrophages M0 and M2 infiltrations, immune and stromal scores, and minimum sensitivity to immunotherapies, but was more sensitive to drugs like Bosutinib, Docetaxel, Elesclomol, Gefitinib, Lenalidomide, Methotrexate and Sunitinib. The turquoise module was identified by WGCNA that it was most positively correlated with C3 but most negatively with C2, and five hub genes in turquoise module were identified for stemness model construction. CRC patients with higher stemness scores exhibited worse prognosis, more immunosuppressive components in TME and lower immunotherapeutic responses. Additionally, the model’s immunotherapeutic prediction efficacy was further confirmed from two immunotherapy cohorts (anti-PD-L1 in IMvigor210 cohort and anti-PD-1 in GSE78220 cohort). Mechanistically, Gene Set Enrichment Analysis (GSEA) results revealed high stemness score group was enriched in interferon gamma response, interferon alpha response, P53 pathway, coagulation, apoptosis, KRAS signaling upregulation, complement, epithelial–mesenchymal transition (EMT) and IL6-mediated JAK-STAT signaling gene sets. Conclusions Our study characterized three stemness-related subtypes with distinct prognosis and TME patterns in CRC patients, and a 5-gene stemness-risk model was constructed by comprehensive bioinformatic analyses. We suggest our stemness model has prospective clinical implications for prognosis evaluation and might facilitate physicians selecting prospective responders for preferential use of current immune checkpoint inhibitors. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02913-0.
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Affiliation(s)
- Hang Zheng
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Heshu Liu
- Department of Oncology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Huayu Li
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Weidong Dou
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Jingui Wang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Junling Zhang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Tao Liu
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Yingchao Wu
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Yucun Liu
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Xin Wang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, People's Republic of China.
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14
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Chen Y, Long W, Yang L, Zhao Y, Wu X, Li M, Du F, Chen Y, Yang Z, Wen Q, Yi T, Xiao Z, Shen J. Functional Peptides Encoded by Long Non-Coding RNAs in Gastrointestinal Cancer. Front Oncol 2021; 11:777374. [PMID: 34888249 PMCID: PMC8649637 DOI: 10.3389/fonc.2021.777374] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal cancer is by far the most common malignancy and the most common cause of cancer-related deaths worldwide. Recent studies have shown that long non-coding RNAs (lncRNAs) play an important role in the epigenetic regulation of cancer cells and regulate tumor progression by affecting chromatin modifications, gene transcription, translation, and sponge to miRNAs. In particular, lncRNA has recently been found to possess open reading frame (ORF), which can encode functional small peptides or proteins. These peptides interact with its targets to regulate transcription or the signal axis, thus promoting or inhibiting the occurrence and development of tumors. In this review, we summarize the involvement of lncRNAs and the function of lncRNAs encoded small peptides in gastrointestinal cancer.
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Affiliation(s)
- Yao Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Weili Long
- School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Liqiong Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Zhihui Yang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tao Yi
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Laboratory of Personalised Cell Therapy & Cell Medicines, School of Pharmacy, Southwest Medical University, Luzhou, China
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15
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Zhang L, Chi B, Chai J, Qin L, Zhang G, Hua P, Jin C. LncRNA CCDC144NL-AS1 Serves as a Prognosis Biomarker for Non-small Cell Lung Cancer and Promotes Cellular Function by Targeting miR-490-3p. Mol Biotechnol 2021; 63:933-940. [PMID: 34115289 DOI: 10.1007/s12033-021-00351-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/04/2021] [Indexed: 11/26/2022]
Abstract
This study revealed the prognostic significance of long non-coding RNA (lncRNA) CCDC144NL-AS1 in NSCLC patients and discussed the effect and mechanism of proliferation, migration, and invasion of non-small cell lung cancer (NSCLC) cells. 128 pairs of NSCLC tissues and paracancerous tissues were collected, and qRT-PCR was used to detect the differential expression of lncRNA CCDC144NL-AS1 in all tissues and cells lines. Kaplan-Meier analysis and Cox proportional hazards model analysis were used to estimate the prognostic value of lncRNA CCDC144NL-AS1. CCK-8 and Transwell assays confirmed the effect of lncRNA CCDC144NL-AS1 on the proliferation, migration, and invasion of NSCLC. Bioinformatics was used to predict the microRNAs that lncRNA CCDC144NL-AS1 might bind to miR-490-3p. The regulation of lncRNA CCDC144NL-AS1 on miR-490-3p was verified by luciferase activity assay with wide type or mutation. The expression of lncRNA CCDC144NL-AS1 was enhanced in both NSCLC tissues and cell lines. Patients with overexpression of lncRNA CCDC144NL-AS1 have a poor prognosis, and lncRNA CCDC144NL-AS1 is an independent prognostic factor for NSCLC. Increased the relative expression level of lncRNA CCDC144NL-AS1 can promote the proliferation, migration, and invasion of NSCLC cells. LncRNA CCDC144NL-AS1 might target miR-490-3p. LncRNA CCDC144NL-AS1 can be used as an oncogene of NSCLC to predict patient prognosis and promote tumor proliferation, migration, and invasion by targeting miR-490-3p.
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Affiliation(s)
- Lei Zhang
- First Department of Respiratory and Critical Care Medicine, People's Hospital of Rizhao, Shangdong, 276800, China
| | - Baihong Chi
- Second Department of Respiratory and Critical Care Medicine, People's Hospital of Rizhao, No. 126 Taian Road, Donggang District, Shangdong, 276800, China.
| | - Jin Chai
- Department of Pharmacy, The Second Hospital of Jilin University, Jilin, 130041, China
| | - Li Qin
- Department of Thoracic Surgery, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China
| | - Guangxin Zhang
- Department of Thoracic Surgery, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China
| | - Peiyan Hua
- Department of Thoracic Surgery, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China
| | - Chengyan Jin
- Department of Thoracic Surgery, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China
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16
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Wang B, Xu W, Cai Y, Guo C, Zhou G, Yuan C. CASC15: A Tumor-Associated Long Non-Coding RNA. Curr Pharm Des 2021; 27:127-134. [PMID: 32962611 DOI: 10.2174/1381612826666200922153701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND CASC15, one of long non-coding RNA, is involved in the regulation of many tumor biological processes, and is expected to become a new biological therapeutic target. This paper aims to elucidate the pathophysiological function of CASC15 in various tumors. METHODS The relationship between CASC15 and tumors was analyzed by searching references, and summarized the specific pathophysiological mechanism of CASC15. RESULTS LncRNA CASC15 is closely related to tumor development, and has been shown to be abnormally high expressed in all kinds of tumors, including breast cancer, cervical cancer, lung cancer, hepatocellular carcinoma, gastric cancer, bladder cancer, colon cancer, colorectal cancer, cardiac hypertrophy, intrahepatic cholangiocarcinoma, leukemia, melanoma, tongue squamous cell carcinoma and nasopharyngeal carcinoma. However, CASC15 has been found to be down-expressed abnormally in ovarian cancer, glioma and neuroblastoma. Besides, it is identified that CASC15 can affect the proliferation, invasion and apoptosis of tumors. CONCLUSION LncRNA CASC15 has the potential to become a new therapeutic target or marker for a variety of tumors.
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Affiliation(s)
- Bei Wang
- College of Medical Science, China Three Gorges University, Yichang443002, China
| | - Wen Xu
- College of Medical Science, China Three Gorges University, Yichang443002, China
| | - Yuxuan Cai
- College of Medical Science, China Three Gorges University, Yichang443002, China
| | - Chong Guo
- College of Medical Science, China Three Gorges University, Yichang443002, China
| | - Gang Zhou
- College of Traditional Chinese Medicine, China Three Gorges University, Yichang443002, China
| | - Chengfu Yuan
- College of Medical Science, China Three Gorges University, Yichang443002, China
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17
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Liu Z, Zhang Y, Dang Q, Wu K, Jiao D, Li Z, Sun Z, Han X. Genomic Alteration Characterization in Colorectal Cancer Identifies a Prognostic and Metastasis Biomarker: FAM83A|IDO1. Front Oncol 2021; 11:632430. [PMID: 33959500 PMCID: PMC8093579 DOI: 10.3389/fonc.2021.632430] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/15/2021] [Indexed: 12/24/2022] Open
Abstract
Genomic alterations constitute crucial elements of colorectal cancer (CRC). However, a comprehensive understanding of CRC genomic alterations from a global perspective is lacking. In this study, a total of 2,778 patients in 15 public datasets were enrolled. Tissues and clinical information of 30 patients were also collected. We successfully identified two distinct mutation signature clusters (MSC) featured by massive mutations and dominant somatic copy number alterations (SCNA), respectively. MSC-1 was associated with defective DNA mismatch repair, exhibiting more frequent mutations such as ATM, BRAF, and SMAD4. The mutational co-occurrences of BRAF-HMCN and DNAH17-MDN1 as well as the methylation silence event of MLH-1 were only found in MSC-1. MSC-2 was linked to the carcinogenic process of age and tobacco chewing habit, exhibiting dominant SCNA such as MYC (8q24.21) and PTEN (10q23.31) deletion as well as CCND3 (6p21.1) and ERBB2 (17q12) amplification. MSC-1 displayed higher immunogenicity and immune infiltration. MSC-2 had better prognosis and significant stromal activation. Based on the two subtypes, we identified and validated the expression relationship of FAM83A and IDO1 as a robust biomarker for prognosis and distant metastasis of CRC in 15 independent cohorts and qRT-PCR data from 30 samples. These results advance precise treatment and clinical management in CRC.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kunpeng Wu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dechao Jiao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhen Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Interventional Institute of Zhengzhou University, Zhengzhou, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, China
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18
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Copy number variation: Characteristics, evolutionary and pathological aspects. Biomed J 2021; 44:548-559. [PMID: 34649833 PMCID: PMC8640565 DOI: 10.1016/j.bj.2021.02.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.
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19
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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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20
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Hu H, Xu H, Lu F, Zhang J, Xu L, Xu S, Jiang H, Zeng Q, Chen E, He Z. Exploring the Effect of Differentially Expressed Long Non-coding RNAs Driven by Copy Number Variation on Competing Endogenous RNA Network by Mining Lung Adenocarcinoma Data. Front Cell Dev Biol 2021; 8:627436. [PMID: 33585468 PMCID: PMC7876300 DOI: 10.3389/fcell.2020.627436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the first cause of cancer death, and gene copy number variation (CNV) is a vital cause of lung cancer progression. Prognosis prediction of patients followed by medication guidance by detecting CNV of lung cancer is emerging as a promising precise treatment in the future. In this paper, the differences in CNV and gene expression between cancer tissue and normal tissue of lung adenocarcinoma (LUAD) from The Cancer Genome Atlas Lung Adenocarcinoma data set were firstly analyzed, and greater differences were observed. Furthermore, CNV-driven differentially expressed long non-coding RNAs (lncRNAs) were screened out, and then, a competing endogenous RNA (ceRNA) regulatory network related to the gene CNV was established, which involved 9 lncRNAs, seven microRNAs, and 178 downstream messenger RNAs (mRNAs). Pathway enrichment analyses sequentially performed revealed that the downstream mRNAs were mainly enriched in biological pathways related to cell division, DNA repair, and so on, indicating that these mRNAs mainly affected the replication and growth of tumor cells. Besides, the relationship between lncRNAs and drug effects was explored based on previous studies, and it was found that LINC00511 and LINC00942 in the CNV-associated ceRNA network could be used to determine tumor response to drug treatment. As examined, the drugs affected by these two lncRNAs mainly targeted metabolism, target of rapamycin signaling pathway, phosphatidylinositol-3-kinase signaling pathway, epidermal growth factor receptor signaling pathway, and cell cycle. In summary, the present research was devoted to analyzing CNV, lncRNA, mRNA, and microRNA of lung cancer, and nine lncRNAs that could affect the CNV-associated ceRNA network we constructed were identified, two of which are promising in determining tumor response to drug treatment.
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Affiliation(s)
- Huihui Hu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hangdi Xu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Fen Lu
- Operation Room, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jisong Zhang
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Li Xu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Shan Xu
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hanliang Jiang
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Qingxin Zeng
- Department of Thoracic Surgery, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Enguo Chen
- Department of Respiratory, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Zhengfu He
- Department of Thoracic Surgery, College of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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21
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Abstract
Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases. In recent decades, researchers developed a wide variety of cytogenetic and molecular methods with different detection capabilities to detect clinically relevant CNVs. In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases. Although the recent rapid progress of sequencing methods has enabled precise detection of CNVs, determining their functional effect on cellular and whole-body physiology remains a challenge. Here, we provide a comprehensive list of databases and bioinformatics tools that may serve as useful assets for researchers, laboratory diagnosticians, and clinical geneticists facing the challenge of CNV detection and interpretation.
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22
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Bo H, Zhang W, Zhong X, Chen J, Liu Y, Cheong KL, Fan P, Tang S. LINC00467, Driven by Copy Number Amplification and DNA Demethylation, Is Associated with Oxidative Lipid Metabolism and Immune Infiltration in Breast Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:4586319. [PMID: 34956437 PMCID: PMC8695024 DOI: 10.1155/2021/4586319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/30/2021] [Accepted: 11/10/2021] [Indexed: 02/05/2023]
Abstract
Breast cancer (BRCA) is a malignant tumor with a high incidence and poor prognosis in females. However, its pathogenesis remains unclear. In this study, based on bioinformatic analysis, we found that LINC00467 was highly expressed in BRCA and was associated with tumor metastasis and poor prognosis. The genomic and epigenetic analysis showed that LINC00467 may also be regulated by copy number amplification (CNA), chromatin openness, and DNA methylation. In vitro experiments showed that it could promote the proliferation, migration, and invasion of BRCA cells. Competitive endogenous RNA (ceRNA) regulatory network analysis and weighted gene coexpression network analysis (WGCNA) suggested that LINC00467 may play a role in signaling pathways of peroxisomal lipid metabolism, immunity, and others through microRNAs (miRNAs) targeting transforming growth factor beta 2 (TGFB2). In addition, copy number amplification and high expression of LINC00467 were associated with the low infiltration of CD8+ and CD4+ T cells. In conclusion, we found that LINC00467, driven by copy number amplification and DNA demethylation, may be a potential biomarker for the diagnosis and prognosis of BRCA and a tumor promoter acting as a potential therapeutic target for BRCA as well.
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Affiliation(s)
- Hao Bo
- Department of Plastic and Esthetic Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Institute of Reproductive and Stem Cell Engineering, Basic Medicine College, Central South University, Changsha, Hunan 410078, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan 410078, China
| | - Wancong Zhang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong 515000, China
- Plastic Surgery Institute of Shantou University Medical College, Guangdong 515000, China
| | - Xiaoping Zhong
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong 515000, China
- Plastic Surgery Institute of Shantou University Medical College, Guangdong 515000, China
| | - Jiasheng Chen
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong 515000, China
- Plastic Surgery Institute of Shantou University Medical College, Guangdong 515000, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, China
| | - Kit-Leong Cheong
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, China
| | - Pengju Fan
- Department of Plastic and Esthetic Surgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China
| | - Shijie Tang
- Department of Plastic Surgery and Burn Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong 515000, China
- Plastic Surgery Institute of Shantou University Medical College, Guangdong 515000, China
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23
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Gao Y, Wang JW, Ren JY, Guo M, Guo CW, Ning SW, Yu S. Long noncoding RNAs in gastric cancer: From molecular dissection to clinical application. World J Gastroenterol 2020; 26:3401-3412. [PMID: 32655264 PMCID: PMC7327794 DOI: 10.3748/wjg.v26.i24.3401] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of cell processes that are usually dysregulated in gastric cancer (GC). Based on their high specificity and ease of detection in tissues and body fluids, increasing attention has spurred the study of the roles of lncRNAs in GC patients. Thus, it is necessary to elucidate the molecular mechanisms and further explore the clinical applications of lncRNAs in GC. In this review, we summarize current knowledge to examine dysregulated lncRNAs in GC and their underlying molecular mechanisms and activities in GC, which involve microRNA sponging, mRNA stability, genetic variants, alternative splicing, transcription factor binding, and epigenetic modification. More significantly, the potential of lncRNAs as prognostic, circulating, and drug-resistant biomarkers for GC is also described. This review highlights the method of dissecting molecular mechanisms to explore the clinical application of lncRNAs in GC. Overall, this review offers assistance in using lncRNAs as novel candidates for molecular mechanisms and for the identification of revolutionary biomarkers for GC.
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Affiliation(s)
- Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Jun-Wei Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Jia-Yi Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Mian Guo
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Cheng-Wang Guo
- Department of Gastroenterology and Gastrosurgery, Gansu Wuwei Tumor Hospital, Wuwei 733000, Gansu Province, China
| | - Shang-Wei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Shan Yu
- Department of Pathology, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, Heilongjiang Province, China
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24
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Xue C, Zhao Y, Jiang J, Li L. Expression levels of lncRNAs are prognostic for hepatocellular carcinoma overall survival. Am J Transl Res 2020; 12:1873-1883. [PMID: 32509183 PMCID: PMC7269992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Studies have demonstrated that long non-coding RNAs (lncRNAs) play important roles in cancer development and progression. However, associations between the expression patterns and prognostic roles of lncRNAs in hepatocellular carcinoma (HCC) have not been comprehensively described. In this study, we established a prognostic model of lncRNA expression using public datasets of HCC from The Cancer Genome Atlas (TCGA) and adopted the International Cancer Genome Consortium (ICGC) as an independent cohort to validate the stability of our model. Cox regression analysis was used to explore the independent prognostic factor in both training and validation cohorts. Additionally, we explored the functional roles of lncRNAs using bioinformatic analyses. According to lncRNA consensus clusters, we resolved the distribution of molecular and clinical data and observed that individual lncRNA could function as prognostic biomarkers in HCC. Furthermore, the novel lncRNA molecular subtypes were statistically significant for predicting HCC status, which was validated by nested cross-validation. We found that lncRNA subtypes were partially related to gender, histological grade, and mutations within TP53. The lncRNA subtypes were also consistent with mRNA-based subtypes, and pathway enrichment analysis identified the involvement of multiple signaling pathways. In addition, we observed that upregulated DANCR was significantly associated with poor prognosis in HCC patients. In conclusion, our model based on lncRNA expression is statistically significant as a diagnostic and prognostic indicator for patients with HCC.
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Affiliation(s)
- Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
| | - Yalei Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
| | - Jianwen Jiang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- Health Management Center, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou 310003, China
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