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Zhong R, Zhan J, Zhang S. Integrative Analysis Reveals STC2 as a Prognostic Biomarker of Laryngeal Squamous Cell Carcinoma. Appl Biochem Biotechnol 2024; 196:3891-3913. [PMID: 37792175 DOI: 10.1007/s12010-023-04727-z] [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] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
Stanniocalcin 2 (STC2) is involved in many tumour types, but it remains unclear what its biological function is in laryngeal squamous cell carcinoma (LSCC). Therefore, we investigated STC2's expression, potential function, and prognostic significance of in LSCC. The expression and prognosis of STC2 in LSCC were described using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. In the TCGA database, the relationship between STC2 and immune infiltration, expression of immune cell chemokine and receptor genes, immune cell molecular marker genes, and epithelial‒mesenchymal transition (EMT) marker genes were analysed. The biological processes involved in STC2 and its expression-related genes were analysed comprehensively using bioinformatics. The single-gene ceRNA network of STC2 was constructed in the TCGA database. Finally, LSCC patients' tumour tissue STC2 expression was verified. STC2 silencing with the RNAi technique was used for the determination of cellular functions in a laryngeal cancer cell line. STC2 expression was higher in most tumours, including LSCC, than in normal tissues and was associated with poor prognosis. The relative proportions of naïve B, plasma, follicular helper T, and macrophage M0 cells in LSCC and normal samples differed significantly. STC2 expression correlated significantly positively with that of TGFB1 (biomarker of Tregs) and significantly negatively with that of D79A and CD19 (biomarkers of B cells). Furthermore, STC2 affected chemokine and receptor gene expression in immune cells. STC2 expression correlated with EMT marker gene expression in LSCC. STC2 was enriched in the PI3K/AKT signalling pathway, extracellular matrix (ECM) organisation, ECM-receptor interaction, and other tumour-related signalling pathways. STC2 was highly expressed in our clinical samples. N-cadherin and vimentin expression were decreased in the TU686 cell line after successful silencing of STC2, indicating that high STC2 expression may prompt LSCC cells to adopt a mesenchymal cell phenotype. STC2 silencing substantially reduced proliferation and migration in the TU686 cell line. STC2 may be a promising predictive biomarker for tumours, providing new approaches for LSCC diagnosis and treatment monitoring.
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Affiliation(s)
- Rong Zhong
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiandong Zhan
- Department of Otorhinolaryngology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Siyi Zhang
- School of Medicine, South China University of Technology, Guangzhou, China.
- Department of Otorhinolaryngology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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Yao HF, He M, Zhu YH, Zhang B, Chen PC, Huo YM, Zhang JF, Yang C. Prediction of immune infiltration and prognosis for patients with cholangiocarcinoma based on a cuproptosis-related lncRNA signature. Heliyon 2024; 10:e22774. [PMID: 38226253 PMCID: PMC10788410 DOI: 10.1016/j.heliyon.2023.e22774] [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: 11/18/2022] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 01/17/2024] Open
Abstract
Objective Cholangiocarcinoma (CHOL) is a malignant disease that affects the digestive tract, and it is characterized by a poor prognosis. This research sought to explore the involvement of cuproptosis-related lncRNAs (CRLs) in the prognostic prediction and immune infiltration of cholangiocarcinoma. Methods The expression profiles and clinical data of CHOL patients were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and CRLs were defined via co-expression analysis. Two molecular clusters distinguished by cuproptosis-related genes (CRGs) were produced. Then a risk signature consisted by four CRLs was formed, and all samples were separated into low- and high-risk groups using a risk score. Kaplan-Meier survival analysis, principal component analysis, differentially expressed analysis, immune cell infiltration analysis, and sensitivities analysis of chemotherapy drugs were conducted between the two groups. Simultaneously, the expression values of four lncRNAs confirmed by real-time PCR in our own 20 CHOL samples were brought into the risk model. Results The CHOL samples could be differentiated into two molecular clusters, which displayed contrasting survival times. Additionally, patients with higher risk scores had significantly worse prognosis compared to those in the low-risk group. Furthermore, both immune infiltration and enrichment analysis revealed significant discrepancies in the tumor immune microenvironment (TIME) between different risk groups. Moreover, the predictive power and the correlation with CA19-9 and CEA of risk signature were validated in our own samples. Conclusion We developed a risk signature which could serve as an independent prognostic factor and offer a promising prediction for not only prognosis but also TIME in CHOL patients.
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Affiliation(s)
- Hong-Fei Yao
- Jiading Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min He
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Heng Zhu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Zhang
- Jiading Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng-Cheng Chen
- Jiading Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan-Miao Huo
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun-Feng Zhang
- Jiading Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Yang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Liu DX, Wu KH, Zang XY, Lu JY, Liu MY, Li CM, Gao L. Dickkopf-related protein 1 as a biomarker of local immune status and worse prognosis of Oral squamous cell carcinoma. Technol Health Care 2024; 32:1473-1488. [PMID: 38073341 DOI: 10.3233/thc-230527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is an infiltrative malignancy characterized by a significantly elevated recurrence rate. Dickkopf-related protein 1 (DKK1), which plays an oncogene role in many cancers, acts as an inhibitor of the Wingless protein (Wnt) signaling pathway. Currently, there is a lack of consensus regarding the role of DKK1 in OSCC or its clinical significance. OBJECTIVE To examine the role and effect of DKK1 in OSCC. METHODS The identification of differentially expressed genes (DEGs) in OSCC was conducted by utilizing databases such as The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A comprehensive analysis of gene expression profile interactions (GEPIA) and Kaplan-Meier curve were conducted to investigate the associations among DEGs, patient survival and prognosis in individuals with OSCC. The biological function of DKK1 in OSCC was investigated by using molecular biology approaches. RESULTS The expression of DKK1 was found to be upregulated in OSCC tissues at various stages. High levels of DKK1 expression exhibited a positive correlation with the overall survival (OS) and progression-free survival (PFS) rates among OSCC patients. DKK1 knockdown suppressed the proliferation and induced apoptotic response in OSCC cells. Moreover, DKK1 exerted a positive regulatory effect on HMGA2 expression, thereby modulating cell growth and apoptosis in OSCC. The expression of DKK1 was found to be positively correlated with the infiltration of immune cells in patients with OSCC. Additionally, higher levels of CD4 + T cells were associated with improved 5-year survival rates. CONCLUSION DKK1 is a prognostic biomarker for patients with OSCC.
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Tang M, Wu H, Zhang H, Xu X, Jiang B, Chen Q, Wei Y, Qian H, Han L. Actin filament-associated protein 1-antisense RNA1 promotes the development and invasion of tongue squamous cell carcinoma via the AFAP1-AS1/miR-133a-5p/ZIC2 axis. J Gene Med 2024; 26:e3654. [PMID: 38282153 DOI: 10.1002/jgm.3654] [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: 08/14/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND The present study aimed to explore the biological role and underlying mechanism of the long non-coding RNA actin filament-associated protein 1-antisense RNA1 (lncRNA AFAP1-AS1) in the progression of tongue squamous cell carcinoma (TSCC). METHODS A quantitative reverse transcriptase-PCR (RT-qPCR) was conducted to assess relative levels of the miR-133a-5p, lncRNAs AFAP1-AS1 and zinc finger family member 2 (ZIC2) in TSCC cell lines and specimens, whereas ZIC2 protein levels were measured using western blotting. After modifying the levels of expression of lncRNA AFP1-AS1, miR-133a-5p and ZIC2 using lentivirus or plasmid transfection, we examined AKT/epithelial-mesenchymal transition signaling pathway alterations, in vivo carcinogenesis of TSCC in nude mice and in vitro malignant phenotypes. A dual-luciferase reporter assay was conducted to confirm the targeting relationship between ZIC2 and miR-133a-5p, as well as between miR-133a-5p and lncRNA AFAP1-AS1. Based on The Cancer Genome Atlas (TCGA) database, we additionally validated AFP1-AS1. The potential biological pathway for AFP1-AS1 was investigated using gene set enrichment analysis (GSEA). We also evaluated the clinical diagnostic capacities of AFP1-AS1 and clustered the most potential biomarkers with the Mfuzz expression pattern. Finally, we also made relevant drug predictions for AFP1-AS1. RESULTS In TSCC cell lines and specimens, lncRNA AFAP1-AS1 was upregulated. ZIC2 was upregulated in TSCC cells as a result of lncRNA AFAP1-AS1 overexpression, which also promoted TSCC cell migration, invasion, viability, and proliferation. Via the microRNA sponge effect, it was found that lncRNA AFAP1-AS1 could upregulate ZIC2 by competitively inhibiting miR-133a-5p. Interestingly, knockdown of ZIC2 reversed the biological roles of lncRNA AFAP1-AS1 with respect to inducing malignant phenotypes in TSCC cells. In addition, in vivo overexpression of lncRNA AFAP1-AS1 triggered subcutaneous tumor growth in nude mice implanted with TSCC cells and upregulated ZIC2 in the tumors. The TCGA database findings revealed that AFAP1-AS1 was significantly upregulated in TSCC specimens and had good clinical diagnostic value. The results of GSEA showed that peroxisome proliferator-activated receptor signaling pathway was significantly correlated with low expression of AFP1-AS1. Finally, the results of drug prediction indicated that the group with high AFAP1-AS1 expression was more sensitive to docetaxel, AZD4547, AZD7762 and nilotinib. CONCLUSIONS The upregulation of lncRNA AFAP1-AS1, which increases TSCC cell viability, migration, proliferation and invasion via the AFAP1-AS1/miR-133a-5p/ZIC2 axis, aids in the progression of TSCC.
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Affiliation(s)
- Mingming Tang
- Department of Head and Neck Surgery, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Hao Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Huaiqin Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Rugao People's Hospital, Rugao, Jiangsu, China
| | - Xinjiang Xu
- Department of Head and Neck Surgery, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Bin Jiang
- Department of Head and Neck Surgery, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Qingwen Chen
- Department of Head and Neck Surgery, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Yingze Wei
- Department of Clinical Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Hongyan Qian
- Central Laboratory of Cancer Research Institute, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Liang Han
- Department of Head and Neck Surgery, Affiliated Tumor Hospital of Nantong University/Nantong Tumor Hospital, Nantong, Jiangsu, China
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Xiang J, He Y, Li Y, Wu K, Cheng M, Wang Y, Chen R. A hypoxia-related lncRNA model for prediction of head and neck squamous cell carcinoma prognosis. Cancer Med 2022; 12:3773-3785. [PMID: 35920349 PMCID: PMC9939198 DOI: 10.1002/cam4.5102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 07/19/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is one of the most common and highly heterogeneous malignancies worldwide. Increasing studies have proven that hypoxia and related long non-coding RNA (lncRNA) are involved in the occurrence and prognosis of HNSCC. The goal of this work is to construct a risk assessment model using hypoxia-related lncRNAs (hrlncRNAs) for HNSCC prognosis prediction and personalized treatment. METHODS Transcriptome expression matrix, clinical follow-up data, and somatic mutation data of HNSCC patients were obtained from The Cancer Genome Atlas (TCGA). We used co-expression analysis to identify hrlncRNAs, then screened for differentially expressed lncRNAs (DEhrlncRNAs), and paired these DEhrlncRNAs. The risk model was established through univariate, least absolute shrinkage and selection operator (LASSO), and stepwise multivariate Cox regression. Finally, we assessed the model from multiple perspectives of tumor mutation burden (TMB), tumor immune infiltration, chemotherapeutic sensitivity, immune checkpoint inhibitor (ICI), and functional enrichment. RESULTS The risk assessment model included 14 hrlncRNA pairs. The risk score was observed to be a reliable prognostic factor. The high-risk patients had an unfavorable prognosis and significant differences from the low-risk group in TMB and tumor immune infiltration. In the high-risk patients, the common immune checkpoints were down-regulated, including CTLA4 and PDCD1, and the sensibility to paclitaxel and docetaxel was higher. The functional enrichment analysis suggested that the low-risk group was accompanied by activated immune function. CONCLUSIONS The risk assessment model of 14-hrlncRNA-pairs demonstrated a promising prognostic prediction for HNSCC patients and can guide personalized clinical treatment.
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Affiliation(s)
- Junwei Xiang
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
| | - Yaodong He
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
| | - Yunshan Li
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
| | - Kexuan Wu
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
| | - Mengxiang Cheng
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
| | - Yuanyin Wang
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
| | - Ran Chen
- Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui ProvinceCollege & Hospital of StomatologyHefeiChina
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Chen F, Sun F, Liu X, Shao J, Zhang B. Glaucocalyxin A Inhibits the Malignant Progression of Epithelial Ovarian Cancer by Affecting the MicroRNA-374b-5p/HMGB3/Wnt-β-Catenin Pathway Axis. Front Oncol 2022; 12:955830. [PMID: 35912216 PMCID: PMC9329791 DOI: 10.3389/fonc.2022.955830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022] Open
Abstract
Objective Glaucocalyxin A (GLA) is an ent-kaurene diterpenoid from Rabdosia japonica var possessing anti-tumor activity. This study aimed to investigate effects of GLA on epithelial ovarian cancer (EOC) and elucidate underlying mechanisms. Methods The expression of HMGB3 in EOC tissues was analyzed by GEPIA and immunohistochemistry. Cell proliferation was determined using CCK-8 and colony formation assays. Cell invasion, migration, and apoptosis were detected using Transwell, wound healing, and flow cytometry assays, respectively. Interactions between HMGB3 and miRNAs were predicted using ENCORI and validated using a dual-luciferase assay. mRNA expression levels of HMGB3 and miRNAs were measured using qPCR. Protein expression levels of HMGB3, E-cadherin, N-cadherin, Wnt3a,β-catenin, Bcl-2, and Bax were measured by western blotting. A tumor xenograft model was established to validate the efficacy and mechanism of GLA in vivo. Results HMGB3 was upregulated in EOC tissues and cells. GLA dose-dependently inhibited EOC cell proliferation and epithelial-mesenchymal transition (EMT). HMGB3 overexpression promoted proliferation, invasion, migration, and EMT, and suppressed the apoptosis of EOC cells. In addition, miR-374b-5p was targeted by HMGB3, and its overexpression hindered malignant characteristics of EOC cells. HMGB3 overexpression weakened antitumor effects of GLA and miR-374b-5p in EOC cells. Moreover, the Wnt-β-catenin pathway was inhibited by the GLA-mediated miR-374b-5p/HMGB3 axis. In vivo experiments showed that GLA inhibited EOC tumor growth, meanwhile, upregulated the miR-374b-5p level and downregulated the expression of HMGB3, Wnt3a, and β-catenin in tumor tissues. Conclusions GLA suppressed the malignant progression of EOC by regulating the miR-374b-5p/HMGB3/Wnt-β-catenin pathway axis.
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Affiliation(s)
- Feng Chen
- Department of Gynecology and Obstetrics, Xuzhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Xuzhou, China
- Department of Gynecology and Obstetrics, Xuzhou Central Hospital, Xuzhou, China
| | - Fang Sun
- Department of Gynecology and Obstetrics, Xuzhou Central Hospital, Xuzhou, China
| | - Xia Liu
- Department of Pathology, Xuzhou Central Hospital, Xuzhou, China
| | - Jing Shao
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou, China
| | - Bei Zhang
- Department of Gynecology and Obstetrics, Xuzhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Xuzhou, China
- Department of Gynecology and Obstetrics, Xuzhou Central Hospital, Xuzhou, China
- *Correspondence: Bei Zhang,
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Interdependent Transcription of a Natural Sense/Antisense Transcripts Pair (SLC34A1/PFN3). Noncoding RNA 2022; 8:ncrna8010019. [PMID: 35202092 PMCID: PMC8877773 DOI: 10.3390/ncrna8010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Natural antisense transcripts (NATs) constitute a significant group of regulatory, long noncoding RNAs. They are prominently expressed in testis but are also detectable in other organs. NATs are transcribed at low levels and co-expressed with related protein coding sense transcripts. Nowadays NATs are generally considered as regulatory, long noncoding RNAs without closer focus on the inevitable interference between sense and antisense expression. This work describes a cellular system where sense and antisense transcription of a specific locus (SLC34A1/PFN3) is induced using epigenetic modifiers and CRISPR-Cas9. The renal cell lines HEK293 and HKC-8 do not express SLC34A1/PFN3 under normal culture conditions. Five-day exposure to dexamethasone significantly stimulates sense transcript (SLC34A1) levels and antisense (PFN3) minimally; the effect is only seen in HEK293 cells. Enhanced expression is paralleled by reduced sense promoter methylation and an increase in activating histone marks. Expression is further modulated by cassettes that stimulate the expression of sense or antisense transcript but disrupt protein coding potential. Constitutive expression of a 5′-truncated SLC34A1 transcript increases sense expression independent of dexamethasone induction but also stimulates antisense expression. Concordant expression is confirmed with the antisense knock-in that also enhances sense expression. The antisense effect acts on transcription in cis since transient transfection with sense or antisense constructs fails to stimulate the expression of the opposite transcript. These results suggest that bi-directional transcription of the SLC34A1/PFN3 locus has a stimulatory influence on the expression of the opposite transcript involving epigenetic changes of the promoters. In perspective of extensive, previous research into bi-directionally transcribed SLC34A loci, the findings underpin a hypothesis where NATs display different biological roles in soma and germ cells. Accordingly, we propose that in somatic cells, NATs act like lncRNAs–with the benefit of close proximity to a potential target gene. In germ cells, however, recent evidence suggests different biological roles for NATs that require RNA complementarity and double-stranded RNA formation.
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