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Sun J, Li Y, Tian H, Chen H, Li J, Li Z. Comprehensive analysis identifies long non-coding RNA RNASEH1-AS1 as a potential prognostic biomarker and oncogenic target in hepatocellular carcinoma. Am J Cancer Res 2024; 14:996-1014. [PMID: 38590422 PMCID: PMC10998738 DOI: 10.62347/jphf4071] [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: 07/13/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
RNASEH1-AS1, a long non-coding RNA (lncRNA) divergently transcribed from the antisense strand of its neighboring protein-coding gene ribonuclease H1 (RNASEH1), has recently been demonstrated to be involved in tumor progression. However, the association between RNASEH1-AS1 and hepatocellular carcinoma (HCC) remains unclear. In the present study, first, the expression of RNASEH1-AS1 in HCC and its correlation with clinicopathological features, prognosis, diagnosis, immune cell infiltration of HCC patients was inspected using relevant R packages based on The Cancer Genome Atlas (TCGA) data. RNASEH1-AS1 was found to be up-regulated in most cancer types, including HCC, and its overexpression was significantly associated with histologic grade and AFP level as well as poor prognosis, and was an independent risk factor affecting overall survival with good diagnostic and prognostic values for HCC. RNASEH1-AS1 was inversely associated with the infiltration of most immune cell types, including plasmacytoid dendritic cells (pDC), B cells and neutrophils. Second, a total of 1109 positively co-expressed genes (PCEGs) of RNASEH1-AS1 were screened out in HCC by correlation analysis in batches (|Spearman's r| >0.4 and adjusted P value <0.01). GO and KEGG enrichment analysis indicated that PCEGs of RNASEH1-AS1 were mainly related to RNA processing, ribosome biogenesis, transcription and histone acetylation. The top 10 hub genes (EIF4A3, WDR43, WDR12, DKC1, NAT10, UTP18, DDX18, BYSL, DDX10, PDCD11) were identified by constructing the protein-protein interaction (PPI) network, and they were all highly expressed in HCC and positively correlated with histological grade. Third, a risk model was constructed based on four RNASEH1-AS1-related hub genes (EIF4A3, WDR12, DKC1, and NAT10) with good prognostic predictive potential via univariate Cox and the least absolute selection operator (LASSO) regression analysis. Fourth, experimental validation revealed that RNASEH1-AS1 was significantly elevated in HCC tissues and several cell lines, and its knockdown could suppress the proliferation, migration, and invasion of HCC cells. Finally, mechanistic studies demonstrated that the stability of RNASEH1-AS1 could be regulated by DKC1 via their direct interaction. Taken together, RNASEH1-AS1 may serve as a potential prognostic and diagnostic biomarker and oncogenic lncRNA for HCC.
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Affiliation(s)
- Jin Sun
- National and Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Hepatic and Splenic Diseases, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Center for Tumor and Immunology, The Precision Medical Institute, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Yingnan Li
- Center for Tumor and Immunology, The Precision Medical Institute, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Hongwei Tian
- National and Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Hepatic and Splenic Diseases, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Center for Tumor and Immunology, The Precision Medical Institute, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Haiyan Chen
- National and Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Core Research Laboratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Jun Li
- National and Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Hepatic and Splenic Diseases, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Center for Tumor and Immunology, The Precision Medical Institute, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
| | - Zongfang Li
- Department of General Surgery, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- National and Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Hepatic and Splenic Diseases, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, Shaanxi, China
- Center for Tumor and Immunology, The Precision Medical Institute, Xi’an Jiaotong UniversityXi’an, Shaanxi, China
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Chen S, Pan X, Zhang L, Cui X, Ye J. FOXK1 upregulation is correlated with tumor progression and tumor associated macrophages infiltration in renal cell carcinoma. Mol Carcinog 2024; 63:136-144. [PMID: 37818826 DOI: 10.1002/mc.23641] [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: 08/11/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
Renal cell carcinoma (RCC) is one of the most common urological cancers in adults. Forkhead box k1 (FOXK1) is a transcription factor involved in the progression of various malignant tumors. In this study, we aimed to investigate the expression and roles of FOXK1 in RCC development. Our findings revealed increased expression of FOXK1 in RCC tumor tissues and cell lines compared with normal controls. Functional assays demonstrated that knockdown of FOXK1 significantly inhibited proliferation, migration, invasion, and promoted apoptosis in RCC cells. Furthermore, FOXK1 knockdown suppressed epithelial-mesenchymal transition and Wnt signaling in RCC cells. Additionally, we observed a correlation between FOXK1 upregulation and tumor associated macrophages infiltration in RCC. These results suggest that FOXK1 acts as an oncogene in RCC and may serve as a potential therapeutic target for RCC treatment.
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Affiliation(s)
- Shaojun Chen
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Zhang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianqing Ye
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Chen X, He YQ, Miao TW, Yin J, Liu J, Zeng HP, Zhu Q. IER5L is a Prognostic Biomarker in Pan-Cancer Analysis and Correlates with Immune Infiltration and Immune Molecules in Non-Small Cell Lung Cancer. Int J Gen Med 2023; 16:5889-5908. [PMID: 38106972 PMCID: PMC10725786 DOI: 10.2147/ijgm.s439190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Purpose Non-small cell lung cancer (NSCLC) accounts for the majority of lung cancer cases. Immediate early response 5 like (IER5L) plays crucial roles in progression and prognosis for several tumors, but its role in NSCLC remains unclear. Patients and Methods Gene expression and mutation profiles, DNA methylation data, and clinical information for cancers were downloaded from multiple databases. Relative expression, prognostic value, and correlation with disease progression of IER5L were analyzed in multiple cancers, including NSCLC. Upstream mechanisms were explored using a transcriptional network. Functional enrichment analysis, protein-protein interaction network, and gene set enrichment analysis were applied to study downstream mechanisms. Correlations of IER5L with immune infiltration, immune molecules, methylation status, and tumor mutation burden (TMB) were analyzed using R language. Finally, quantitative polymerase chain reaction (qPCR) and single-cell RNA sequencing (scRNA seq) analysis were performed to validate IER5L expression in NSCLC. Results Pan-cancer analysis displayed that IER5L expression was upregulated in multiple cancers and was associated with disease prognosis and progression, including NSCLC, which was validated using qPCR. scRNA seq analysis showed that multiple cells had increased IER5L expression. An EGR1-hsa-miR-8075-IER5L network was constructed for NSCLC. A total of 191 DEGs were identified between the two IER5L groups, which were significantly enriched in biological process of action potential, sodium ion transport, and regulation of membrane potential. Increased IER5L expression was primarily enriched in cell cycle, NOTCH signaling pathway, and oxidative phosphorylation pathway, and was correlated with increased regulatory T cells and neutrophils, elevated levels of immune molecules, and higher TMB. Conclusion Our findings show that increased IER5L expression was correlated with progression and prognosis in multiple cancers as well as with immune infiltration and immune molecules in NSCLC. Thus, IER5L is a prognostic biomarker in multiple cancers and may correlate with immunotherapeutic response in NSCLC.
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Affiliation(s)
- Xin Chen
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, People’s Republic of China
| | - Yan-Qiu He
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, People’s Republic of China
| | - Ti-Wei Miao
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, People’s Republic of China
| | - Jie Yin
- School of Automation & Information Engineering, Sichuan University of Science & Engineering, Zigong, People’s Republic of China
| | - Jie Liu
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, People’s Republic of China
| | - Hong-Ping Zeng
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, People’s Republic of China
| | - Qi Zhu
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People’s Hospital, Zigong, People’s Republic of China
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Hashemi M, Khosroshahi EM, Chegini MK, Abedi M, Matinahmadi A, Hosnarody YSD, Rezaei M, Saghari Y, Fattah E, Abdi S, Entezari M, Nabavi N, Rashidi M, Raesi R, Taheriazam A. miRNAs and exosomal miRNAs in lung cancer: New emerging players in tumor progression and therapy response. Pathol Res Pract 2023; 251:154906. [PMID: 37939448 DOI: 10.1016/j.prp.2023.154906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
Non-coding RNAs have shown key roles in cancer and among them, short RNA molecules are known as microRNAs (miRNAs). These molecules have length less than 25 nucleotides and suppress translation and expression. The functional miRNAs are produced in cytoplasm. Lung cancer is a devastating disease that its mortality and morbidity have undergone an increase in recent years. Aggressive behavior leads to undesirable prognosis and tumors demonstrate abnormal proliferation and invasion. In the present review, miRNA functions in lung cancer is described. miRNAs reduce/increase proliferation and metastasis. They modulate cell death and proliferation. Overexpression of oncogenic miRNAs facilitates drug resistance and radio-resistance in lung cancer. Tumor microenvironment components including macrophages and cancer-associated fibroblasts demonstrate interactions with miRNAs in lung cancer. Other factors such as HIF-1α, lncRNAs and circRNAs modulate miRNA expression. miRNAs have also value in the diagnosis of lung cancer. Understanding such interactions can pave the way for developing novel therapeutics in near future for lung cancer patients.
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Affiliation(s)
- Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Elaheh Mohandesi Khosroshahi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehrnaz Kalhor Chegini
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Abedi
- Department of Pathology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Matinahmadi
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun, Poland
| | - Yasaman Sotodeh Dokht Hosnarody
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahdi Rezaei
- Faculty of Medicine, Shahed University, Tehran, Iran
| | - Yalda Saghari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Eisa Fattah
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soheila Abdi
- Department of Physics, Safadasht Branch, Islamic Azad university, Tehran, Iran
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6 Vancouver, BC, Canada
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Rasoul Raesi
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical-Surgical Nursing, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Vitamin A- and D-Deficient Diets Disrupt Intestinal Antimicrobial Peptide Defense Involving Wnt and STAT5 Signaling Pathways in Mice. Nutrients 2023; 15:nu15020376. [PMID: 36678247 PMCID: PMC9863741 DOI: 10.3390/nu15020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/14/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Vitamin A and D deficiencies are associated with immune modulatory effects and intestinal barrier impairment. However, the underlying mechanisms remain unclear. C57BL/6J mice were fed either a diet lacking in vitamin A (VAd), vitamin D (VDd) or a control diet (CD) for 12 weeks. Gut barrier function, antimicrobial peptide (AMP) defense and regulatory pathways were assessed. VAd mice compared to CD mice showed a reduced villus length in the ileum (p < 0.01) and decreased crypt depth in the colon (p < 0.05). In both VAd- and VDd-fed mice, ileal α-defensin 5 (p < 0.05/p < 0.0001 for VAd/VDd) and lysozyme protein levels (p < 0.001/p < 0.0001) were decreased. Moreover, mRNA expression of lysozyme (p < 0.05/p < 0.05) and total cryptdins (p < 0.001/p < 0.01) were reduced compared to controls. Furthermore, matrix metalloproteinase-7 (Mmp7) mRNA (p < 0.0001/p < 0.001) as well as components of the Wnt signaling pathway were decreased. VAd- and VDd-fed mice, compared to control mice, exhibited increased expression of pro-inflammatory markers and β-defensins in the colon. Organoid cell culture confirmed that vitamins A and D regulate AMP expression, likely through the Jak/STAT5 signaling pathway. In conclusion, our data show that vitamin A and D regulate intestinal antimicrobial peptide defense through Wnt and STAT5 signaling pathways.
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Liu M, Liu C, Li X, Li S. RP11-79H23.3 Inhibits the Proliferation and Metastasis of Non-small-cell Lung Cancer Through Promoting miR-29c. Biochem Genet 2022; 61:506-520. [PMID: 35972581 DOI: 10.1007/s10528-022-10263-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
Evidences indicate that long non-coding RNAs (lncRNAs) are closely involved and contributed to tumorigenesis and cancer progression. As a novel lncRNA, RP11-79H23.3 was found to be an anti-oncogene in bladder cancer. However, the essential roles and functions of RP11-79H23.3 in non-small-cell lung cancer (NSCLC) remains to be elucidated. Here, loss of functional assay was applied to gain insights into the functions of RP11-79H23.3 on the proliferation and metastasis capabilities of A549 and H1299 cells. Meantime, Real-time PCR was utilized to measure RP11-79H23.3 and miR-29c expression in NSCLC tissues. Dual-luciferase reporter assay, CCK8, colony formation assay, transwell and Western blot were performed to illustrate the potential molecular basis of RP11-79H23.3 in NSCLC. RP11-79H23.3 downregulation facilitated cell proliferation, migration, and invasion of NSCLC. The result of dual-luciferase reporter assay represented a direct interaction of RP11-79H23.3 with miR-29c, which suppressed miR-29c expression that showed inversely correlation in NSCLC. Moreover, RP11-79H23.3 siRNA facilitated the progression of NSCLC partially via regulating the expression of miR-29c and the activation of Wnt/β-catenin signaling pathway. Our findings highlighted that RP11-79H23.3, served as an anti-oncogene, accelerated NSCLC progression through sequestering miR-29c, providing a promising therapeutic target for NSCLC.
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Affiliation(s)
- Mulin Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning Province, China
| | - Chang Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning Province, China
| | - Xi Li
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, 261000, Shandong Province, China
| | - Shijun Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, No. 222 Zhongshan Road, Dalian, 116011, Liaoning Province, China.
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