1
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Blanchett R, Lau KH, Pfeifer GP. Homeobox and Polycomb target gene methylation in human solid tumors. Sci Rep 2024; 14:13912. [PMID: 38886487 PMCID: PMC11183203 DOI: 10.1038/s41598-024-64569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
DNA methylation is an epigenetic mark that plays an important role in defining cancer phenotypes, with global hypomethylation and focal hypermethylation at CpG islands observed in tumors. These methylation marks can also be used to define tumor types and provide an avenue for biomarker identification. The homeobox gene class is one that has potential for this use, as well as other genes that are Polycomb Repressive Complex 2 targets. To begin to unravel this relationship, we performed a pan-cancer DNA methylation analysis using sixteen Illumina HM450k array datasets from TCGA, delving into cancer-specific qualities and commonalities between tumor types with a focus on homeobox genes. Our comparisons of tumor to normal samples suggest that homeobox genes commonly harbor significant hypermethylated differentially methylated regions. We identified two homeobox genes, HOXA3 and HOXD10, that are hypermethylated in all 16 cancer types. Furthermore, we identified several potential homeobox gene biomarkers from our analysis that are uniquely methylated in only one tumor type and that could be used as screening tools in the future. Overall, our study demonstrates unique patterns of DNA methylation in multiple tumor types and expands on the interplay between the homeobox gene class and oncogenesis.
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Affiliation(s)
- Reid Blanchett
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
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2
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Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong XB. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Noncoding RNA 2024; 10:28. [PMID: 38668386 PMCID: PMC11053763 DOI: 10.3390/ncrna10020028] [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: 03/08/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
The long non-coding RNA (lncRNA) hepatocyte nuclear factor-1 alpha (HNF1A) antisense RNA 1 (HNF1A-AS1) is an important lncRNA for liver growth, development, cell differentiation, and drug metabolism. Like many lncRNAs, HNF1A-AS1 has multiple annotated alternative transcripts in the human genome. Several fundamental biological questions are still not solved: (1) How many transcripts really exist in biological samples, such as liver samples and liver cell lines? (2) What are the expression patterns of different alternative HNF1A-AS1 transcripts at different conditions, including during cell growth and development, after exposure to xenobiotics (such as drugs), and in disease conditions, such as metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD) cirrhosis, and obesity? (3) Does the siRNA used in previous studies knock down one or multiple transcripts? (4) Do different transcripts have the same or different functions for gene regulation? The presented data confirm the existence of several annotated HNF1A-AS1 transcripts in liver samples and cell lines, but also identify some new transcripts, which are not annotated in the Ensembl genome database. Expression patterns of the identified HNF1A-AS1 transcripts are highly correlated with the cell differentiation of matured hepatocyte-like cells from human embryonic stem cells (hESC), growth and differentiation of HepaRG cells, in response to rifampicin induction, and in various liver disease conditions. The expression levels of the HNF1A-AS1 transcripts are also highly correlated to the expression of cytochrome P450 enzymes, such as CYP3A4, during HepaRG growth, differentiation, and in response to rifampicin induction.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Le Tra Giang Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Andrew Wassef
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
- Center of Excellence for Pharmaceutical Translational Research and Education, Rutgers University, Piscataway, NJ 08901, USA
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Ragui Sadek
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Timothy M. Schmitt
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Ernst Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
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Sosnovski KE, Braun T, Amir A, BenShoshan M, Abbas-Egbariya H, Ben-Yishay R, Anafi L, Avivi C, Barshack I, Denson LA, Haberman Y. Reduced LHFPL3-AS2 lncRNA expression is linked to altered epithelial polarity and proliferation, and to ileal ulceration in Crohn disease. Sci Rep 2023; 13:20513. [PMID: 37993670 PMCID: PMC10665440 DOI: 10.1038/s41598-023-47997-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023] Open
Abstract
Disruption of intestinal epithelial functions is linked to Crohn disease (CD) pathogenesis. We identified a widespread reduction in the expression of long non-coding RNAs (lncRNAs) including LHFPL3-AS2 in the treatment-naïve CD ileum of the RISK pediatric cohort. We validated the reduction of LHFPL3-AS2 in adult CD and noted a further reduction in patients with more severe CD from the RISK cohort. LHFPL3-AS2 knockdown in Caco-2 cells robustly affected epithelial monolayer morphogenesis with markedly reduced confluency and spreading, showing atypical rounding, and clumping. mRNA-seq analysis of LHFPL3-AS2 knockdown cells highlighted the reduction of genes and pathways linked with apical polarity, actin bundles, morphogenesis, and the b-catenin-TCF4 complex. LHFPL3-AS2 knockdown significantly reduced the ability of cells to form an internal lumen within the 3-dimensional (3D) cyst model, with mislocalization of actin and adherent and tight junction proteins, affecting epithelial polarity. LHFPL3-AS2 knockdown also resulted in defective mitotic spindle formation and consequent reduction in epithelial proliferation. Altogether, we show that LHFPL3-AS2 reduction affects epithelial morphogenesis, polarity, mitotic spindle formation, and proliferation, which are key processes in maintaining epithelial homeostasis in CD. Reduced expression of LHFPL3-AS2 in CD patients and its further reduction with ileal ulceration outcome, emphasizes its significance in this context.
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Affiliation(s)
- Katya E Sosnovski
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Marina BenShoshan
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haya Abbas-Egbariya
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rakefet Ben-Yishay
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Liat Anafi
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Camilla Avivi
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, Affiliated with the Tel Aviv University, Tel Aviv, Israel.
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Tesarova T, Koucka K, Vaclavikova R, Seborova K, Hora M, Hes O, Pivovarcikova K, Soucek P, Fiala O. Association of lncRNA and transcriptome intersections with response to targeted therapy in metastatic renal cell carcinoma. Oncol Lett 2023; 26:365. [PMID: 37559591 PMCID: PMC10407709 DOI: 10.3892/ol.2023.13951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/18/2023] [Indexed: 08/11/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) serve an important role in cancer progression and may be used as efficient molecular biomarkers. The present study aimed to identify lncRNAs associated with the response to the receptor tyrosine kinase inhibitor sunitinib and transcriptome profile and clinical features of metastatic renal cell carcinoma (mRCC). The gene expression of 84 cancer-associated lncRNAs in tumor and non-malignant tissue samples of 38 patients with mRCC was evaluated using quantitative PCR. In addition, the coding transcriptome was estimated using RNA sequencing in a subgroup of 20 patients and mRNA-lncRNA intersections were identified. In total, 37 and 13 lncRNAs were down- and upregulated, respectively, in tumor compared with non-malignant adjacent tissue samples. A total of 10 and 4 lncRNAs were up- and downregulated, respectively, in good responders to sunitinib compared with poor responders. High expression of HNF1A-AS1 and IPW lncRNAs was associated with prolonged progression-free survival of patients and a high expression of the TUSC7 lncRNA was associated with poor response and worse survival. Significant associations of dysregulated MEG3 and SNHG16 lncRNAs with expression of protein-coding genes representing various pathways, were identified. Furthermore, a significantly higher expression of CLIP4 gene was observed in good responders. The present study revealed promising candidates for predictive and prognostic biomarkers with further therapeutic potential.
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Affiliation(s)
- Tereza Tesarova
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague 10, Czech Republic
| | - Kamila Koucka
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Radka Vaclavikova
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague 10, Czech Republic
| | - Karolina Seborova
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
| | - Milan Hora
- Department of Urology, Faculty of Medicine in Pilsen and University Hospital, Charles University, 301 00 Pilsen, Czech Republic
| | - Ondrej Hes
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital, Charles University, 301 00 Pilsen, Czech Republic
| | - Kristyna Pivovarcikova
- Department of Pathology, Faculty of Medicine in Pilsen and University Hospital, Charles University, 301 00 Pilsen, Czech Republic
| | - Pavel Soucek
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague 10, Czech Republic
| | - Ondrej Fiala
- Department of Oncology and Radiotherapeutics, Faculty of Medicine in Pilsen and University Hospital, Charles University, 323 00 Pilsen, Czech Republic
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Pilsen, Czech Republic
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5
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Li Y, Li X, Yu Z. Novel methylation-related long non-coding RNA clinical outcome prediction method: the clinical phenotype and immune infiltration research in low-grade gliomas. Front Oncol 2023; 13:1177120. [PMID: 37228500 PMCID: PMC10203515 DOI: 10.3389/fonc.2023.1177120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
Background Recent studies have suggested that long non-coding RNAs (lncRNAs) may play crucial role in low-grade glioma; however, the underlying mechanisms linking them to epigenetic methylation remain unclear. Methods We downloaded expression level data for regulators associated with N1 methyladenosine (m1A), 5-methyladenine (m5C), and N6 methyladenosine (m6A) (M1A/M5C/M6A) methylation from the Cancer Genome Atlas-low-grade glioma (TCGA-LGG) database. We identified the expression patterns of lncRNAs, and selected methylation-related lncRNAs using Pearson correlation coefficient>0.4. Non-negative matrix dimensionality reduction was then used to determine the expression patterns of the methylation-associated lncRNAs. We constructed a weighted gene co-expression network analysis (WGCNA) network to explore the co-expression networks between the two expression patterns. Functional enrichment of the co-expression network was performed to identify biological differences between the expression patterns of different lncRNAs. We also constructed prognostic networks based on the methylation presence in lncRNAs in low-grade gliomas. Results We identified 44 regulators by literature review. Using a correlation coefficient greater than 0.4, we identified 2330 lncRNAs, among which 108 lncRNAs with independent prognostic values were further screened using univariate Cox regression at P< 0.05. Functional enrichment of the co-expression networks revealed that regulation of trans-synaptic signaling, modulation of chemical synaptic transmission, calmodulin binding, and SNARE binding were mostly enriched in the blue module. The calcium and CA2 signaling pathways were associated with different methylation-related long non-coding chains. Using the Least Absolute Shrinkage Selector Operator (LASSO) regression analysis, we analyzed a prognostic model containing four lncRNAs. The model's risk score was 1.12 *AC012063 + 0.74 * AC022382 + 0.32 * AL049712 + 0.16 * GSEC. Gene set variation analysis (GSVA) revealed significant differences in mismatch repair, cell cycle, WNT signaling pathway, NOTCH signaling pathway, Complement and Cascades, and cancer pathways at different GSEC expression levels. Thus, these results suggest that GSEC may be involved in the proliferation and invasion of low-grade glioma, making it a prognostic risk factor for low-grade glioma. Conclusion Our analysis identified methylation-related lncRNAs in low-grade gliomas, providing a foundation for further research on lncRNA methylation. We found that GSEC could serve as a candidate methylation marker and a prognostic risk factor for overall survival in low-grade glioma patients. These findings shed light on the underlying mechanisms of low-grade glioma development and may facilitate the development of new treatment strategies.
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Lu B, Li X, Miao W, Liu Q, Li R, Cui C, Gao Q, Lian R. LncRNA ZFAS1 promotes laryngeal cancer progression through RBFOX2-mediated MENA alternative splicing. ENVIRONMENTAL TOXICOLOGY 2023; 38:522-533. [PMID: 36336961 DOI: 10.1002/tox.23695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/22/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Laryngeal cancer (LC) is the most common aggressive malignancy of the head and neck. LncRNA ZNFX1 antisense RNA 1 (ZFAS1) displays oncogenic properties in head and neck squamous cell carcinoma, but its regulatory role in laryngeal cancer progression remains obscure. Here, we found that ZFAS1 expression in laryngeal cancer tissues and cells was higher than that in adjacent normal tissues and normal nasopharyngeal epithelial cells. Highly expressed ZFAS1 was associated with advanced lymph node metastasis stages and clinical stages. ZFAS1 overexpression promoted LC cell proliferation, invasion, and N-cadherin and Vimentin expression, and suppressed E-cadherin expression. While ZFAS1 knockdown played an opposite role. Mechanistically, ZFAS1 stabilized RNA binding fox-1 homolog 2 (RBFOX2) protein expression by binding to RBFOX2, and RBFOX2 overexpression reversed the effect of ZFAS1 silence on cell functions. Moreover, highly expressed RBFOX2 led to skipping of MENA exon 11a and generating a pro-invasive isoform (MENAINV ). MENAINV overexpression effectively abolished the inhibitory effect of RBFOX2 knockdown on cell malignant progression. Furthermore, Hep2 cells infected with lentivirus-mediated ZFAS1 shRNA or negative control shRNA were subcutaneously injected into mice to assess the role of ZFAS1 in tumor growth. And the data showed that silencing ZFAS1 in vivo hindered xenograft tumor growth. In conclusion, silencing ZFAS1 alleviated malignant progression of laryngeal cancer cells and mouse xenograft tumor growth by regulating RBFOX2-mediated alternative splicing of MENA.
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Affiliation(s)
- Baocai Lu
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Xiao Li
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenjie Miao
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Qi Liu
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Ruixue Li
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Can Cui
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Qingzu Gao
- Department of Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Rong Lian
- Department of Otolaryngology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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Zhang Y, Shi J, Luo J, Liu C, Zhu L. Regulatory mechanisms and potential medical applications of HNF1A-AS1 in cancers. Am J Transl Res 2022; 14:4154-4168. [PMID: 35836869 PMCID: PMC9274608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) are defined as a class of non-protein-coding RNAs that are longer than 200 nucleotides. Previous studies have shown that lncRNAs play a vital role in the progression of multiple diseases, which highlights their potential for medical applications. The lncRNA hepatocyte nuclear factor 1 homeobox A (HNF1A) antisense RNA 1 (HNF1A-AS1) is known to be abnormally expressed in multiple cancers. HNF1A-AS1 exerts its oncogenic roles through a variety of molecular mechanisms. Moreover, aberrant HNF1A-AS1 expression is associated with diverse clinical features in cancer patients. Therefore, HNF1A-AS1 is a promising biomarker for tumor diagnosis and prognosis and thus a potential candidate for tumor therapy. This review summarizes current studies on the role and the underlying mechanisms of HNF1A-AS1 various cancer types, including gastric cancer, liver cancer, glioma, lung cancer, colorectal cancer, breast cancer, bladder cancer, osteosarcoma, esophageal adenocarcinoma, hemangioma, oral squamous cell carcinoma, laryngeal squamous cell carcinoma, cervical cancer, as well as gastroenteropancreatic neuroendocrine neoplasms. We also describe the diagnostic, prognostic, and therapeutic value of HNF1A-AS1 for multiple cancer patients.
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Affiliation(s)
- Yang Zhang
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Jiang Shi
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Junfang Luo
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Cong Liu
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Lixu Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
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9
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Liu Y, Zhao F, Tan F, Tang L, Du Z, Mou J, Zhou G, Yuan C. HNF1A-AS1:A tumor-associated long non-coding RNA. Curr Pharm Des 2022; 28:1720-1729. [PMID: 35619319 DOI: 10.2174/1381612828666220520113846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/31/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatocyte nuclear factor 1 homeobox A antisense RNA 1 (HNF1A-AS1) is a Long non-coding RNA(LncRNA)that participates in the occurrence development of lots of tumors and is supposed to be a new biomarker. The text aims to illustrate the biological effect, specific mechanism and clinical significance of HNF1A-AS1 in various tumors. METHODS Via consulting the literature, analyze and summarize the relationship between HNF1A-AS1 and all kinds of tumors and the specific mechanism. RESULTS This is a review paper about the tumor-associated long non-coding RNA HNF1A-AS1. Many Researches show that LncRNA HNF1A-AS1 is related to the development of tumorous tumors. Its expression is up-regulated in numerous tumors, such as oral squamous cell carcinoma, hepatocellular carcinoma, breast cancer, osteosarcoma, lung cancer, cervical cancer, bladder cancer, colon cancer, colorectal cancer, oesophageal adenocarcinoma and laryngeal squamous cell carcinoma. However, HNF1A-AS1 is down-regulated in gastroenteropancreatic, neuroendocrine neoplasms, oral squamous cell carcinoma. Furthermore, HNF1A-AS1 can affect tumor proliferation, invasion, migration and apoptosis by targeting some microRNAs-miR-661 and miR-124. Or HNF1A-AS1 can also influence the development of tumors by regulating EMT. CONCLUSION These studies show that LncRNA-HNF1A-AS1 is closely related to the occurrence development of numerous cancers. Through various molecular mechanisms to regulate tumor growth, HNF1A-AS1 can possibly become the new biological biomarker and therapeutic target for many kinds of tumors.
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Affiliation(s)
- Yuling Liu
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Fangnan Zhao
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Fangshun Tan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Lu Tang
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Zhuoying Du
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Jie Mou
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Gang Zhou
- College of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China.,Hubei Clinical Research Center for Functional Digestive Diseases of Traditional Chinese Medicine, Yichang Hospital of Traditional Chinese Medicine, Yichang, 443002, China
| | - Chengfu Yuan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine,State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China.,Hubei Clinical Research Center for Functional Digestive Diseases of Traditional Chinese Medicine, Yichang Hospital of Traditional Chinese Medicine, Yichang, 443002, China
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10
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Wang S, Wang R, Gao F, Huang J, Zhao X, Li D. Pan-cancer analysis of the DNA methylation patterns of long non-coding RNA. Genomics 2022; 114:110377. [PMID: 35513292 DOI: 10.1016/j.ygeno.2022.110377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 11/04/2022]
Abstract
Long non-coding RNA (lncRNA) regulated by abnormal DNA methylation (ADM-lncRNA) emerges as a biomarker for cancer diagnosis and treatment. This study comprehensively described the methylation patterns of lncRNA in pan-cancer using the cancer data set in The Cancer Genome Atlas (TCGA). Based on the cancer heterogeneity of ADM-lncRNA in pan-cancer, we constructed a co-expression network of pan-cancer ADM-lncRNA (pADM-lncRNA) in 10 cancers, highlighting the combined action mode of abnormal DNA methylation, and indicating the internal connection among different cancers. Functional analysis revealed the pan-carcinogenic pathway of pADM-lncRNA and suggested potential factors for cancer heterogeneity and tumor immune microenvironment changes. Survival analysis showed the potential of pADM-lncRNA-mRNA co-expression pair as cancer biomarkers. Revealing the action mode of lncRNA and DNA methylation in cancer may help understand the key molecular mechanisms of cell carcinogenesis.
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Affiliation(s)
- Shijia Wang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Rendong Wang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Fang Gao
- Health Management Center, Binzhou People's Hospital, Shandong Province, China
| | - Jun Huang
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Xiaoxiao Zhao
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China
| | - Dongguo Li
- School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical, Capital Medical University, Beijing 100069, China.
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11
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Zhou X, Zhao X, Wu Z, Ma Y, Li H. LncRNA FLVCR1-AS1 mediates miR-23a-5p/SLC7A11 axis to promote malignant behavior of cervical cancer cells. Bioengineered 2022; 13:10454-10466. [PMID: 35465835 PMCID: PMC9161883 DOI: 10.1080/21655979.2022.2059958] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Cervical cancer (CC) is the most common gynecological malignant tumor in the world. Long non-coding RNA (lncRNAs) plays an important role in cell activities of various cancers including CC. This study aims to reveal the biological function of FLVCR1-AS1 in CC and clarify its possible mechanism of action. The findings suggest that the expression of FLVCR1-AS1 was elevated in CC tissues and cell lines, and that high expression of FLVCR1-AS1 was associated with poor prognosis of CC patients. In addition, knockdown of FLVCR1-AS1 could inhibit the proliferation and migration, invasion and epithelial–mesenchymal transformation (EMT) of CC cells, as well as accelerating apoptosis, to inhibit the development of CC. In addition, via the dual-luciferase reporting assay and RIP assay were confirmed that FLVCR1-AS1 acted as a competitive endogenous RNA to inhibit the expression of microRNA (miR)-23a-5p, and miR-23a-5p targeted the 3’-untranslated region site of Solute carrier family 7 member 11 (SLC7A11) and negatively regulated the expression of SLC7A11. Functional rescue experiments showed that miR-23a-5p inhibitors reversed the inhibitory effect of FLVCR1-AS1-silencing on proliferation, EMT, migration and invasion, and the promoting impact of apoptosis of CC cells. In addition, SLC7A11 rescued the effect of miR-23a-5p overexpression on progression of CC cells. In conclusion, FLVCR1-AS1 is involved in the malignant phenotype of CC cells through miR-23a-5p/SLC7A11 axis, which may provide a beneficial direction for the treatment of CC.
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Affiliation(s)
- Xi Zhou
- Department of Gynecology, The First Affiliated Hospital of University of South China Hengyang, Hengyang City, Hunan Province, China
| | - Xia Zhao
- Department of Gynecology, The First Affiliated Hospital of University of South China Hengyang, Hengyang City, Hunan Province, China
| | - ZhouYi Wu
- Medical School, Hunan University of Chinese Medicine, Changsha City, Hunan Province, China
| | - Yan Ma
- Department of Gynecology, The First Affiliated Hospital of University of South China Hengyang, Hengyang City, Hunan Province, China
| | - Heng Li
- Department of Gynecology, Loudi Central Hospital, Loudi City, Hunan Province, China
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12
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Jiang M, Liu F, Yang AG, Wang W, Zhang R. The role of long non-coding RNAs in the pathogenesis of head and neck squamous cell carcinoma. Mol Ther Oncolytics 2022; 24:127-138. [PMID: 35024439 PMCID: PMC8717422 DOI: 10.1016/j.omto.2021.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancers are a heterogeneous collection of malignancies of the upper aerodigestive tract, salivary glands, and thyroid. However, the molecular mechanisms underlying the carcinogenesis of head and neck squamous cell carcinomas (HNSCCs) remain poorly understood. Over the past decades, overwhelming evidence has demonstrated the regulatory roles of long non-coding RNAs (lncRNAs) in tumorigenesis, including HNSCC. Notably, these lncRNAs have vital roles in gene regulation and affect various aspects of cellular homeostasis, including proliferation, survival, and metastasis. They exert regulating functions by interacting with nucleic acids or proteins and affecting cancer cell signaling. LncRNAs represent a burgeoning field of cancer research, and we are only beginning to understand the importance and complicity of lncRNAs in HNSCC. In this review, we summarize the deregulation and function of lncRNAs in human HNSCC. We also review the working mechanism of lncRNAs in HNSCC pathogenesis and discuss the potential application of lncRNAs as diagnostic/prognostic tools and therapeutic targets in human HNSCC.
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Affiliation(s)
- Man Jiang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710032, China.,State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Fang Liu
- Department of Dermatology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - An-Gang Yang
- State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wei Wang
- State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China.,State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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13
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Khashefizadeh A. Hepatocyte nuclear factor 1A-antisense: Review of its role in the carcinogenesis. Pathol Res Pract 2021; 227:153623. [PMID: 34563755 DOI: 10.1016/j.prp.2021.153623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Hepatocyte nuclear factor 1A-antisense (HNF1A-AS) is an RNA gene classified as a long non-coding RNA (lncRNA). This gene is located on 12q24.31 and produces at least seven transcripts. This lncRNA contributes in the pathogenesis of cancer via HNF1A-dependent and -independent routes. Moreover, the role of this lncRNA in this process is context-dependent. The bulk of evidence from cell line, in vivo and clinical studies propose HNF1A-AS as an oncogenic lncRNA. However, in hepatic cancer, gastric cancer and laryngeal cancer, opposite results have been reported. In the current review, we explain the impact of HNF1A-AS in the pathoetiology of cancers. In order to appraise the importance of available evidence on this topic, we have classified evidence to preclinical models (cell liens and animal models) and investigations in tissues obtained from human subjects.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Alireza Khashefizadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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14
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TCF-3-mediated transcription of lncRNA HNF1A-AS1 targeting oncostatin M expression inhibits epithelial-mesenchymal transition via TGFβ signaling in gastroenteropancreatic neuroendocrine neoplasms. Aging (Albany NY) 2021; 13:14065-14077. [PMID: 34037532 PMCID: PMC8202880 DOI: 10.18632/aging.203024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs play key roles in several cancers, but their potential functions in gastroenteropancreatic neuroendocrine neoplasms remain to be investigated. We performed GeneChip assay to explore differentiated lncRNAs in gastric NENs and peri-cancerous tissues. The regulation of HNF1A-AS1 on biological behavior of GEP-NENs cells and in vivo xenograft model was confirmed by CCK8, colony formation assay, transwell, western blot and qRT-PCR. We next detected the potential transcription factors and the binding sites between them with bioinformatic analysis. qRT-PCR was performed to analyze the exact relationship between them. HNF1A-AS1 expression was decreased in gastric NENs tissues (p < 0.01). Over-expression of HNF1A-AS1 suppressed cellular proliferation, migration and invasion. Knockdown of transcription factor 3 inhibited the expression of HNF1A-AS1 and promoted cellular migration and invasion. Oncostatin M was identified as the downstream target of HNF1A-AS1. Inhibition of transforming growth factor-β activity inhibited HNF1A-AS1/Oncostatin M-mediated epithelial-mesenchymal transition. Our data suggest that transcription factor 3/HNF1A-AS1/Oncostatin M axis inhibits the tumorigenesis and metastasis of gastroenteropancreatic neuroendocrine neoplasms via transforming growth factor-β signaling.
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