1
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Su Q, Pan Z, Chen H, Chen J, Zhang Y, Zhuang W. RBM47 restrains renal cell carcinoma progression and chemoresistance through interacting with lncRNA HOXB-AS1. Cell Death Discov 2023; 9:329. [PMID: 37660095 PMCID: PMC10475063 DOI: 10.1038/s41420-023-01623-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/11/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023] Open
Abstract
RNA binding proteins have the critical role in renal cell carcinoma (RCC) progression. However, the role of RBM47 in RCC has not been elucidated. In this study, we found that RBM47 was downregulated in RCC tissues and its expression was negatively correlated with the prognosis of RCC patients. Also, we found that the expression of RBM47 was regulated by CBP/P300-mediated H3K27ac in RCC. Functionally, RBM47 restrained RCC cells proliferation and metastasis. Mechanistically, RBM47 interfered with the interaction between HOXB-AS1 and p53 proteins via directly binding with HOXB-AS1, finally promoted the entry of p53 into the nucleus and therefore activated the p53 signaling. Moreover, RBM47 had a synergistic anticancer effect with sunitinib both in vivo and in vitro.
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Affiliation(s)
- Qingfu Su
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Zhenliang Pan
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Heyi Chen
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Jiabi Chen
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Yanmei Zhang
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
| | - Wei Zhuang
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
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2
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Zhao J, Zhang X, Zhang D, Tang Q, Bi Y, Yuan L, Yang B, Li X, Li Z, Deng D, Cao W. Critical genes in human photoaged skin identified using weighted gene co-expression network analysis. Genomics 2023; 115:110682. [PMID: 37454939 DOI: 10.1016/j.ygeno.2023.110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/24/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Photoaging is unique to the skin and is accompanied by an increased risk of tumors. To explore the transcriptomic regulatory mechanism of skin photoaging, the epidermis, and dermis of 16 healthy donors (eight exposed and eight non-exposed) were surgically excised and detected using total RNA-Seq. Weighted gene co-expression network analysis (WGCNA) identified the most relevant modules with exposure. The hub genes were identified using correlation, p-value, and enrichment analysis. The critical genes were identified using Support Vector Machine-Recursive Feature Elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO) regression, then enriched using single-gene GSEA. A competitive endogenous RNA (ceRNA) network was constructed and validated using qRT-PCR. Compared with non-exposed sites, 430 mRNAs, 168 lncRNAs, and 136 miRNAs were differentially expressed in the exposed skin. WGCNA identified the module MEthistle and 12 intersecting genes from the 71 genes in this module. The enriched pathways were related to muscle. The critical genes were KLHL41, MYBPC2, and ERAP2. Single-gene GSEA identified the Hippo signaling pathway, basal cell carcinoma, cell adhesion molecules, and other pathways. Six miRNAs and 18 lncRNAs related to the critical genes constituted the ceRNA network and were verified using qPCR. The differential expression of KLHL41, MYBPC2, and ERAP2 at the protein level was verified using immunohistochemistry. KLHL41, MYBPC2, and ERAP2 genes are related to skin photoaging. The prediction model based on the three critical genes can indicate photoaging. These critical genes may have a role in skin photoaging by regulating cell growth, intercellular adhesion, and substance metabolism pathways.
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Affiliation(s)
- Jie Zhao
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xun Zhang
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Dafu Zhang
- Department of Radiology, Yunnan Cancer Hospital, Kunming, Yunnan, China
| | - Qiao Tang
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China; Department of dermatology, Qionglai City Medical Center Hospital, Qionglai, Sichuan, China
| | - Yunfeng Bi
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Limei Yuan
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Binbin Yang
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xiaolan Li
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zhenhui Li
- Department of Radiology, Yunnan Cancer Hospital, Kunming, Yunnan, China.
| | - Danqi Deng
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
| | - Wenting Cao
- Department of dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
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3
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Liu L, Qiang X. Hsa_circ_0044907 promotes acute myeloid leukemia progression through upregulating oncogene KIT via sequestering miR-186-5p. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:960-970. [PMID: 36004511 DOI: 10.1080/16078454.2022.2113574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND It has been reported that circular RNA hsa_circ_0044907 (circ_0044907) expression is overtly elevated in acute myeloid leukemia (AML) patient-derived BMMCs. However, the effect of circ_0044907 on AML progression remains un-clarified. METHODS Expression of circ_0044907 in BM and AML cells were detected with real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Cell viability, proliferation, apoptosis, and cycle progression were determined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT), 5-ethynyl-2'-deoxyuridine (EDU), and flow cytometry assays. The regulatory mechanism of circ_0044907 was predicted by bioinformatics analysis and validated by dual-luciferase reporter, RNA pull-down, and RNA immunoprecipitation (RIP) assays. In vivo experiments were carried out to verify the function of circ_0044907. RESULTS Circ_0044907 was overexpressed in AML patient-derived BM and AML cells. Furthermore, circ_0044907 could distinguish AML patients from healthy controls, and high circ_0044907 expression in BM had a poor prognosis for AML patients, implying that circ_0044907 served as a diagnostic and prognostic indicator for AML. Functionally, circ_0044907 silencing reduced cell viability, restrained cell proliferation, arrested cell cycle progression, and induced cell apoptosis in AML cells in vitro. Furthermore, circ_0044907 knockdown decreased AML cell growth in xenograft mouse models. Mechanically, circ_0044907 sponged miR-186-5p to block the inhibiting effect of miR-186-5p on KIT. Silenced miR-186-5p expression weakened circ_0044907 knockdown mediated suppression on AML cell viability, proliferation, and cycle progression. Also, forced KIT expression weakened miR-186-5p upregulation mediated inhibition on AML cell viability, proliferation, and cycle progression. CONCLUSION Circ_0044907 absorbed miR-186-5p to block the inhibiting impact of miR-186-5p on KIT, thus promoting AML progression.
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Affiliation(s)
- Ling Liu
- Department of Laboratory, Liangjiang New Area First People's Hospital, Chongqing, People's Republic of China
| | - Xing Qiang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, People's Republic of China
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4
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Chen Y, Wang N, Cao L, Zhang D, Peng H, Xue P. Long non-coding RNA HOXB-AS1 is a prognostic marker and promotes hepatocellular carcinoma cells' proliferation and invasion. Open Life Sci 2022; 17:944-951. [PMID: 36045719 PMCID: PMC9380905 DOI: 10.1515/biol-2022-0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/12/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are broadly transcribed in the genome of human and play critical roles in the progression of multiple diseases. Long non-coding HOXB cluster antisense RNA 1 (HOXB-AS1) is a tumor exciter in various cancers. This study aimed to investigate the involvement of HOXB-AS1 in hepatocellular carcinoma (HCC). In the following study, HOXB-AS1 was unveiled to be highly expressed in HCC tissues as opposed to normal tissues. Silencing of HOXB-AS1 led to the loss of proliferation, migration, and invasiveness of HCC cells, namely Hep3B and Huh7. Moreover, the data showed that expression levels of HOXB-AS1 contribute significantly to the patient's survival rates. Otherwise, HOXB-AS1 levels in the serum of patients proved HOXB-AS1 as a biomarker for analysis and treatment of HCC. In summary, this study highlights HOXB-AS1 as key upregulated lncRNA in HCC which being an oncogene can cause proliferation and metastasis of HCC cells. The results also highlighted HOXB-AS1 as a promising biomarker for early diagnosis and prognosis of patients with HCC.
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Affiliation(s)
- Yubin Chen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Na Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Liangqi Cao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Dawei Zhang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Heping Peng
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
| | - Ping Xue
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, No. 63 Yayun South Road, Guangzhou, 510000, Guangdong Province, China
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5
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Sun J, Guo Y, Chen T, Jin T, Ma L, Ai L, Guo J, Niu Z, Yang R, Wang Q, Yu X, Gao H, Zhang Y, Su W, Song X, Ji W, Zhang Q, Huang M, Fan X, Du Z, Liang H. Systematic analyses identify the anti-fibrotic role of lncRNA TP53TG1 in IPF. Cell Death Dis 2022; 13:525. [PMID: 35661695 PMCID: PMC9166247 DOI: 10.1038/s41419-022-04975-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 01/21/2023]
Abstract
Long non-coding RNA (lncRNA) was reported to be a critical regulator of cellular homeostasis, but poorly understood in idiopathic pulmonary fibrosis (IPF). Here, we systematically identified a crucial lncRNA, p53-induced long non-coding RNA TP53 target 1 (TP53TG1), which was the dysregulated hub gene in IPF regulatory network and one of the top degree genes and down-regulated in IPF-drived fibroblasts. Functional experiments revealed that overexpression of TP53TG1 attenuated the increased expression of fibronectin 1 (Fn1), Collagen 1α1, Collagen 3α1, ACTA2 mRNA, Fn1, and Collagen I protein level, excessive fibroblasts proliferation, migration and differentiation induced by TGF-β1 in MRC-5 as well as PMLFs. In vivo assays identified that forced expression of TP53TG1 by adeno-associated virus 5 (AAV5) not only prevented BLM-induced experimental fibrosis but also reversed established lung fibrosis in the murine model. Mechanistically, TP53TG1 was found to bind to amount of tight junction proteins. Importantly, we found that TP53TG1 binds to the Myosin Heavy Chain 9 (MYH9) to inhibit its protein expression and thus the MYH9-mediated activation of fibroblasts. Collectively, we identified the TP53TG1 as a master suppressor of fibroblast activation and IPF, which could be a potential hub for targeting treatment of the disease.
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Affiliation(s)
- Jian Sun
- grid.258164.c0000 0004 1790 3548Zhuhai People’s Hospital, Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated With Jinan University, Jinan University, Zhuhai, 519000 Guangdong China ,grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Yingying Guo
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Tingting Chen
- grid.410736.70000 0001 2204 9268Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081 China
| | - Tongzhu Jin
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Lu Ma
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Liqiang Ai
- grid.410736.70000 0001 2204 9268Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081 China
| | - Jiayu Guo
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Zhihui Niu
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Ruoxuan Yang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Qianqian Wang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Xiaojiang Yu
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Huiying Gao
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Yuhan Zhang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Wei Su
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Xiaoying Song
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Weihang Ji
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Qing Zhang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Mengqin Huang
- grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China
| | - Xingxing Fan
- grid.259384.10000 0000 8945 4455State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Zhimin Du
- grid.258164.c0000 0004 1790 3548Zhuhai People’s Hospital, Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated With Jinan University, Jinan University, Zhuhai, 519000 Guangdong China ,grid.410736.70000 0001 2204 9268Institute of Clinical Pharmacy, the 2nd Affiliated Hospital, Harbin Medical University, Harbin, 150081 China
| | - Haihai Liang
- grid.258164.c0000 0004 1790 3548Zhuhai People’s Hospital, Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated With Jinan University, Jinan University, Zhuhai, 519000 Guangdong China ,grid.410736.70000 0001 2204 9268Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081 China ,Research Unit of Noninfectious Chronic Diseases in Frigid Zone (2019RU070), Chinese Academy of Medical Sciences, Harbin, 150081 China
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6
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Construction of immune-related LncRNAs classifier to predict prognosis and immunotherapy response in thymic epithelial tumors. Biosci Rep 2022; 42:231178. [PMID: 35438133 PMCID: PMC9109460 DOI: 10.1042/bsr20220317] [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: 02/17/2022] [Revised: 03/23/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
The primary objective of this study was to construct an immune-related long non-coding RNAs (IRLs) classifier to precisely predict the prognosis and immunotherapy response of patients with thymic epithelial tumors (TET).Based on univariable Cox regression analysis and Lasso regression, six prognosis-related IRLs (AC004466.3,AC138207.2, AC148477.2, AL450270.1, HOXB-AS1 and SNHG8) were selected to build an IRL classifier. Importantly, results of qRT-PCR validated that higher expression levels of AC138207.2, AC148477.2, AL450270.1 and SNHG8 as well as lower expression levels of AC004466.3, and HOXB-AS1 in TETs samples compared to normal controls. The IRL classifier could effectively classify patients into the low-risk and high-risk groups based on the different survival parameters. In terms of predictive ability and clinical utility, the IRL classifier was superior to Masaoka staging system. Additionally, IRL classifier is significantly associated with immune cells infiltration (dendritic cells, activated CD4 memory T cells and tumor-infiltrating lymphocyte (TIL), T cell subsets in particular), immune microenvironment (immune score and immune checkpoint inhibitors), and immunogenicity (TMB) in TETs, which hints that IRL classifier is tightly correlated with immune characteristics and might guide more effective immunotherapy strategies for TETs patients. Encouragingly, according to TIDE algorithm, there were more immunotherapy responders in the low-risk IRL subgroup and the IRL score was robustly negatively linked to the immunotherapeutic response. To sum up, the IRL classifier was established, which can be used to predict the prognosis, immune infiltration status, immunotherapy response in TETs patients, and may facilitate personalized counseling for immunotherapy.
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7
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Qian D, Qian C, Ye B, Xu M, Wu D, Li J, Li D, Yu B, Tao Y. Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis. Front Genet 2022; 13:760514. [PMID: 35273635 PMCID: PMC8902307 DOI: 10.3389/fgene.2022.760514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Breast cancer (BC) is a major leading cause of woman deaths worldwide. Increasing evidence has revealed that stemness features are related to the prognosis and progression of tumors. Nevertheless, the roles of stemness-index-related long noncoding RNAs (lncRNAs) in BC remain unclear. Methods: Differentially expressed stemness-index-related lncRNAs between BC and normal samples in The Cancer Genome Atlas database were screened based on weighted gene co-expression network analysis and differential analysis. Univariate Cox and least absolute shrinkage and selection operator regression analyses were performed to identify prognostic lncRNAs and construct a stemness-index-related lncRNA signature. Time-dependent receiver operating characteristic curves were plotted to evaluate the predictive capability of the stemness-index-related lncRNA signature. Moreover, correlation analysis and functional enrichment analyses were conducted to investigate the stemness-index-related lncRNA signature-related biological function. Finally, a quantitative real-time polymerase chain reaction was used to detect the expression levels of lncRNAs. Results: A total of 73 differentially expressed stemness-index-related lncRNAs were identified. Next, FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 were used to construct a stemness-index-related lncRNA signature, and receiver operating characteristic curves indicated that stemness-index-related lncRNA signature could predict the prognosis of BC well. Moreover, functional enrichment analysis suggested that differentially expressed genes between the high-risk group and low-risk group were mainly involved in immune-related biological processes and pathways. Furthermore, functional enrichment analysis of lncRNA-related protein-coding genes revealed that FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 were associated with neuroactive ligand–receptor interaction, AMPK signaling pathway, PPAR signaling pathway, and cGMP-PKG signaling pathway. Finally, quantitative real-time polymerase chain reaction revealed that FAM83H-AS1, HID1-AS1, RP11-1100L3.8, and RP11-696F12.1 might be used as the potential diagnostic biomarkers of BC. Conclusion: The stemness-index-related lncRNA signature based on FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 could be used as an independent predictor for the survival of BC, and FAM83H-AS1, HID1-AS1, RP11-1100L3.8, and RP11-696F12.1 might be used as the diagnostic markers of BC.
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Affiliation(s)
- Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu, China
| | - Cheng Qian
- School of Computer Science and Engineering, Changshu Institute of Technology, Changshu, China
| | - Buyun Ye
- Second Clinical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ming Xu
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu, China
| | - Danping Wu
- Department of Breast Surgery, Changshu Hospital Affiliated to Soochow University, Changshu, China
| | - Jialu Li
- Department of Breast Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, China
| | - Dong Li
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu, China
| | - Bin Yu
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu, China
| | - Yijing Tao
- Department of Cardiology, Changshu Hospital Affiliated to Soochow University, Changshu, China
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8
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Shao W, Ding Q, Guo Y, Xing J, Huo Z, Wang Z, Xu Q, Guo Y. A Pan-Cancer Landscape of HOX-Related lncRNAs and Their Association With Prognosis and Tumor Microenvironment. Front Mol Biosci 2021; 8:767856. [PMID: 34805277 PMCID: PMC8602076 DOI: 10.3389/fmolb.2021.767856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 12/27/2022] Open
Abstract
The highly conserved homology cassette family (HOX) as well as 18 referenced long non-coding antisense transcripts (HOXATs) play vital roles in the development of some cancers. Nevertheless, their expression patterns as well as their association with cancer prognosis and the tumor microenvironment (TME) in pan-cancers are still unclear. Here, based on public databases, the expression levels of HOXATs, their prognostic potentials, and correlation with tumor mutation burden (TMB), immune cell infiltration, immune subtype, immune response-related genes, and stemness scores corresponding to 33 tumor types were analyzed systematically using R language. The results of the analysis indicated that different cancer tissues show different HOXAT expression profiles. Further, HOXAT expression showed association with cancer prognosis and immune and stemness regulation. Gene set enrichment analysis also demonstrated that HOXATs participate in cancer- and immune-related pathways, and based on their expression levels, HOTAIRM1 and HOXB-AS1 showed potential involvement in oncogenesis as well as possible involvement in immune regulation across a variety of cancer types. Further investigation also confirmed a significantly higher expression of HOXB-AS1 in GBM than in lower grade glioma tissues. Importantly, in vitro cell function experiments indicated that HOXB-AS1 supports cancer stem cell and plays a fundamental role in glioma metastasis. In conclusion, our results provide valuable resources that can guide the investigation of the mechanisms related to the role of HOXATs in cancers as well as therapeutic analysis in this regard.
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Affiliation(s)
- Wei Shao
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Juan Xing
- Henan Provincial Nanyang Central Hospital, Nanyang, China
| | - Zheng Huo
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Zhan Wang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Yue Guo
- Henan Provincial Nanyang Central Hospital, Nanyang, China
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9
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Feng Y, Zhang T, Wang Y, Xie M, Ji X, Luo X, Huang W, Xia L. Homeobox Genes in Cancers: From Carcinogenesis to Recent Therapeutic Intervention. Front Oncol 2021; 11:770428. [PMID: 34722321 PMCID: PMC8551923 DOI: 10.3389/fonc.2021.770428] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022] Open
Abstract
The homeobox (HOX) genes encoding an evolutionarily highly conserved family of homeodomain-containing transcriptional factors are essential for embryogenesis and tumorigenesis. HOX genes are involved in cell identity determination during early embryonic development and postnatal processes. The deregulation of HOX genes is closely associated with numerous human malignancies, highlighting the indispensable involvement in mortal cancer development. Since most HOX genes behave as oncogenes or tumor suppressors in human cancer, a better comprehension of their upstream regulators and downstream targets contributes to elucidating the function of HOX genes in cancer development. In addition, targeting HOX genes may imply therapeutic potential. Recently, novel therapies such as monoclonal antibodies targeting tyrosine receptor kinases, small molecular chemical inhibitors, and small interfering RNA strategies, are difficult to implement for targeting transcriptional factors on account of the dual function and pleiotropic nature of HOX genes-related molecular networks. This paper summarizes the current state of knowledge on the roles of HOX genes in human cancer and emphasizes the emerging importance of HOX genes as potential therapeutic targets to overcome the limitations of present cancer therapy.
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Affiliation(s)
- Yangyang Feng
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongyue Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yijun Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Xie
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Ji
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Liu B, Xiang W, Liu J, Tang J, Wang J, Liu B, Long Z, Wang L, Yin G, Liu J. The regulatory role of antisense lncRNAs in cancer. Cancer Cell Int 2021; 21:459. [PMID: 34461912 PMCID: PMC8404292 DOI: 10.1186/s12935-021-02168-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
Antisense long non-coding RNAs (antisense lncRNAs), transcribed from the opposite strand of genes with either protein coding or non-coding function, were reported recently to play a crucial role in the process of tumor onset and development. Functionally, antisense lncRNAs either promote or suppress cancer cell proliferation, migration, invasion, and chemoradiosensitivity. Mechanistically, they exert their regulatory functions through epigenetic, transcriptional, post-transcriptional, and translational modulations. Simultaneously, because of nucleotide sequence complementarity, antisense lncRNAs have a special role on its corresponding sense gene. We highlight the functions and molecular mechanisms of antisense lncRNAs in cancer tumorigenesis and progression. We also discuss the potential of antisense lncRNAs to become cancer diagnostic biomarkers and targets for tumor treatment.
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Affiliation(s)
- Biao Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Wei Xiang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jiahao Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jin Tang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jinrong Wang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Bin Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Zhi Long
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Guangming Yin
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China
| | - Jianye Liu
- Department of Urology, The Third Xiangya Hospital of Central South University, No.138, Tongzipo Road, Changsha, 410013, Hunan, China.
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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