1
|
Chen B, Lu X, Zhou Q, Chen Q, Zhu S, Li G, Liu H. PAXIP1-AS1 is associated with immune infiltration and predicts poor prognosis in ovarian cancer. PLoS One 2023; 18:e0290031. [PMID: 37582104 PMCID: PMC10426951 DOI: 10.1371/journal.pone.0290031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023] Open
Abstract
The long non-coding RNA (LncRNA) PAXIP1 antisense RNA 1 (PAXIP1-AS1) was found to promote proliferation, migration, EMT, and apoptosis of ovarian cancer (OC) cells in OC cell lines, but the relationship between PAXIP1-AS1 expression and clinical characteristics, prognosis, and immune infiltration of OC patients and its regulatory network are unclear. 379 OC tissues were collected from The Cancer Genome Atlas (TCGA) database. 427 OC tissues and 88 normal ovarian tissues were collected from GTEx combined TCGA database. 130 OC samples were collected from GSE138866. Kruskal-Wallis test, Wilcoxon sign-rank test, logistic regression, Kaplan-Meier method, Cox regression analysis, Gene set enrichment analysis (GSEA), and immuno-infiltration analysis were used to evaluate the relationship between clinical characteristics and PAXIP1-AS1 expression, prognostic factors, and determine the significant involvement of PAXIP1-AS1 in function. QRT-PCR was used to validate the expression of PAXIP1-AS1 in OC cell lines. Low PAXIP1-AS1 expression in OC was associated with age (P = 0.045), histological grade (P = 0.011), and lymphatic invasion (P = 0.004). Low PAXIP1-AS1 expression predicted a poorer overall survival (OS) (HR: 0.71; 95% CI: 0.55-0.92; P = 0.009), progression free interval (PFS) (HR: 1.776; 95% CI: 1.067-2.955; P = 0.001) and disease specific survival (DSS) (HR: 0.67; 95% CI: 0.51-0.89; P = 0.006). PAXIP1-AS1 expression (HR: 0.711; 95% CI: 0.542-0.934; P = 0.014) was independently correlated with PFS in OC patients. GSEA demonstrated that neutrophil degranulation, signaling by Interleukins, GPCR-ligand binding, G alpha I signaling events, VEGFAVEGFR-2 signaling pathway, naba secreted factors, Class A 1 Rhodopsin-Like Receptors, PI3K-Akt signaling pathway, and Focal Adhesion-PI3K-Akt-mTOR-signaling pathway were differentially enriched in PAXIP1-AS1 high expression phenotype. PAXIP1-AS1 was significantly downregulated in OC cell lines compared with IOSE29 cell line. The expression of PAXIP1-AS1 was associated with immune infiltration. low expression of PAXIP1-AS1 was correlated with poor OS (HR: 0.52; 95% CI: 0.34-0.80; P = 0.003) from GSE138866. There were some genomic variations between the PAXIP1-AS1 high and low expression groups. Low expression of PAXIP1-AS1 was significantly associated with poor survival and immune infiltration in OC. PAXIP1-AS1 could be a promising prognosis biomarker and response to immunotherapy for OC.
Collapse
Affiliation(s)
- Buze Chen
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Xuzhou Medical University, Xuzhou, China
| | - Xiaoyuan Lu
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Xuzhou Medical University, Xuzhou, China
| | - Qingmei Zhou
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Qing Chen
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Siyan Zhu
- Department of Gynecology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Guilin Li
- Department of Gynecology, Maternal and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Hui Liu
- Department of Pathology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| |
Collapse
|
2
|
Ma Q, Chang L, Wang W, Che L, Song X, Li G, Zhang Y, Chen Y, Gu Z, Ge X. Leucyl and Cystinyl Aminopeptidase as a Prognostic-Related Biomarker in OV Correlating with Immune Infiltrates. Pharmgenomics Pers Med 2023; 16:551-568. [PMID: 37293607 PMCID: PMC10244028 DOI: 10.2147/pgpm.s400145] [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: 12/03/2022] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Background It was indicated that tumor intrinsic heterogeneity and the tumor microenvironment (TME) of ovarian cancer (OV) influence immunotherapy efficacy and patient outcomes. Leucyl and cystinyl aminopeptidase (LNPEP) encodes a zinc-dependent aminopeptidase, which has been proved to participant in the vesicle-mediated transport and class I MHC mediated antigen processing and presentation. However, the function of LNPEP in TME of OV and its potential molecular mechanisms have not been determined. Therefore, we aimed to investigate a prognostic biomarker which may be helpful in identifying TME heterogeneity of ovarian cancer. Methods In this study, bioinformatics databases were used to explore the expression profile and immune infiltration of LNPEP. Bioinformatics analyses of survival data and interactors of LNPEP were conducted to predict the prognostic value of LNPEP in OV. The protein levels of LNPEP were validated by Western blot and immunohistochemistry. Results Based on the TCGA data, our data displayed that the mRNA expression of LNPEP was markedly down-regulated in ovarian cancer than that in para-cancer tissues, contrary to the protein level. Importantly, high LNPEP expression was associated with poor prognosis in patients with OV. Furthermore, Cox regression analysis showed that LNPEP was an independent prognostic factor in OV. GO and KEGG pathway analyses indicated the co-expressed genes of LNPEP were mainly related to a variety of immune-related pathways, including Th1 and Th2 cell differentiation, Th17 cell differentiation, and immunoregulatory interaction. Our data also demonstrated that the expression of LNPEP was strongly correlated with immune infiltration levels, immunomodulators, chemokines and chemokine receptors. Conclusion In our study, we identified and established a prognostic signature of immune-related LNPEP in OV, which will be of great value in predicting the prognosis of clinical trials and may become a new therapeutic target for immunological research and potential prognostic biomarker in OV.
Collapse
Affiliation(s)
- Qian Ma
- Genetics and Prenatal Diagnosis Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Lei Chang
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Wenwen Wang
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Lingyi Che
- Genetics and Prenatal Diagnosis Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Xiaoqin Song
- Physical Examination Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Gailing Li
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Ying Zhang
- Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Yibing Chen
- Genetics and Prenatal Diagnosis Center, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| | - Xin Ge
- Department of Breast Surgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, People’s Republic of China
| |
Collapse
|
3
|
Molecular Analysis of Prognosis and Immune Infiltration of Ovarian Cancer Based on Homeobox D Genes. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3268386. [PMID: 36213580 PMCID: PMC9537619 DOI: 10.1155/2022/3268386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022]
Abstract
Background Homeobox D (HOXD) genes were associated with cancer pathogenesis. However, the role of HOXD genes in ovarian cancer (OC) and the possible mechanisms involved are unclear. In this study, we analyzed the function and regulatory mechanisms and functions of HOXD genes in OC based on comprehensive bioinformatics analysis. Methods Expression of HOXD1/3/4/8/9/10/11/12/13 mRNA was analyzed between OC tissue and normal tissue using ONCOMINE, GEO, and TCGA databases. The relationship between HOXD expression and clinical stage was studied by GEPIA. The Kaplan-Meier plotter was used to analyze prognosis. cBioPortal was used to analyze the mutation and coexpression of HOXDs. GO and KEGG analyses were performed by the DAVID software to predict the function of HOXD coexpression genes. Immune infiltration analysis was used to evaluate the relationship between the expression of HOXD genes and 24 immune infiltrating cells. Results The expression of HOXD3/4/8/9/10/11 was significantly lower in OC tissues than in normal ovarian tissues, while the expression of HOXD1/12/13 was significantly higher in OC tissues. The expression of HOXD genes was associated with FIGO stage, primary therapy outcome, tumor status, anatomic neoplasm subdivision, and age. The expression levels of HOXD1/3/4/8/9/10 correlated with tumor stage. HOXD1/8/9 could be served as ideal biomarkers to distinguish OC from normal tissue. Low HOXD9 expression was associated with shorter overall survival (OS) (HR: 0.75; 95% CI: 0.58–0.98; P = 0.034) and progression-free survival (PFS) (HR: 0.69; 95% CI: 0.54–0.87; P = 0.002). The HOXD coexpression genes were associated with pathways including cell cycle, TGF-beta signaling pathway, cellular senescence, and Hippo signaling pathway. HOXD genes were significantly associated with immune infiltration. Conclusion The expression of HOXD genes is associated with clinical characteristics. HOXD9 is a new biomarker of prognosis in OC, and HOXD1/4/8/9/10 may be potential therapeutic targets. The members of the HOXD genes may be the response to immunotherapy for OC.
Collapse
|
4
|
Zhu W, Xu Z, Huang M, Wang X, Ren X, Cai Y, Peng B, Liang Q, Chen X, Yan Y. Downregulated ADARB1 Facilitates Cell Proliferation, Invasion and has Effect on the Immune Regulation in Ovarian Cancer. Front Bioeng Biotechnol 2022; 9:792911. [PMID: 35004651 PMCID: PMC8733684 DOI: 10.3389/fbioe.2021.792911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer (OC) is typically diagnosed at an advanced stage and poses a significant challenge to treatment and recovery. Rencently, Adenosine deaminase RNA-specific B1 (ADARB1), an adenosine-to-inosine (A-to-I) RNA-editing enzyme, has been found to play an essential role in the development of cancer. However, the specific function of ADARB1 in ovarian cancer is still not fully understood. Here, we investigated the effects of ADARB1 on OC biology. By conducting bioinformatics analyses of several public databases, we found significantly decreased ADARB1 expression in OC cells and tissues. Moreover, RT-PCR and western blot showed lower ADARB1 expression in OVCAR3, HO8910pm and A2780 OC cells compared to human normal ovarian epithelial cell IOSE. Cell proliferation assay and clone formation assay showed that overexpression of ADARB1 (ADARB1-OE) inhibited the proliferation of tumor cells. Wound healing and transwell assay indicated that ADARB1-OE could suppress OC cell invasion and metastasis. Kaplan-Meier methods revealed that the patients with low level of ADARB1 displayed poor prognosis. TISIDB databases were further used to analyze the roles of ADARB1 in tumor-immune system interactions in OC patients. Furthermore, ADARB1-OE down-regulated the expression of phosphorylated AKT. Combination of ADARB1-OE and AKT inhibitor MK2206 exerted stronger cell growth inhibition. Thus, our investigation demonstrated that low levels of ADARB1 might be a potential target in the tumorigenesis and prognostic evaluation of OC patients.
Collapse
Affiliation(s)
- Wei Zhu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Meiyuan Huang
- Department of Pathology, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
5
|
Ren X, Wang X, Peng B, Liang Q, Cai Y, Gao K, Hu Y, Xu Z, Yan Y. Significance of TEAD Family in Diagnosis, Prognosis and Immune Response for Ovarian Serous Carcinoma. Int J Gen Med 2021; 14:7133-7143. [PMID: 34737608 PMCID: PMC8558638 DOI: 10.2147/ijgm.s336602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/19/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose To explore the molecular profiles of transcriptional enhanced associate domain (TEAD) family in ovarian serous carcinoma (OSC). Methods In this study, we use bioinformatics methods including GEPIA, GE-mini, Oncomine 3.0, Kaplan–Meier plotter, cBioPortal, WebGestalt, TIMER2.0 and DiseaseMeth2.0, and in vitro experimental RT-PCR to assess the expression profiles and prognostic significance of TEAD family in OSC. Results According to the bioinformatics analysis, TEAD family was abnormally expressed in OSC. In terms of prognosis, Kaplan–Meier plotter indicated that OSC patients with high level of TEAD4 showed poor overall survival (OS), progression-free survival (PFS) and post progression survival (PPS). TEAD family also had significantly diagnostic values for OSC patients. Tumor Immune Estimation Resource (TIMER) algorithm indicated that TEAD family was significantly associated with different types of infiltrating immune cells, including B cells, macrophages, dendritic cells, neutrophils, CD8+ T cells and CD4+ T cells. Gene set enrichment analysis of TEAD family-associated coexpression genes was further explored. In in vitro experiments, the RT-PCR results showed the upregulated TEAD2/4 in OSC tissues and cells (A2780 and TOV112D). Moreover, decreased expression of TEAD2 could induce the ferroptosis through increasing the ROS accumulation. Conclusion Thus, TEAD family correlated with the diagnosis, prognosis and immune infiltration in OSC. These results could provide comprehensive understanding of TEAD family in the diagnosis and prognosis of OSC patients.
Collapse
Affiliation(s)
- Xinxin Ren
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Kewa Gao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Yongbin Hu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| |
Collapse
|