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Jokelainen O, Rintala TJ, Fortino V, Pasonen-Seppänen S, Sironen R, Nykopp TK. Differential expression analysis identifies a prognostically significant extracellular matrix-enriched gene signature in hyaluronan-positive clear cell renal cell carcinoma. Sci Rep 2024; 14:10626. [PMID: 38724670 PMCID: PMC11082176 DOI: 10.1038/s41598-024-61426-3] [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: 10/28/2023] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Hyaluronan (HA) accumulation in clear cell renal cell carcinoma (ccRCC) is associated with poor prognosis; however, its biology and role in tumorigenesis are unknown. RNA sequencing of 48 HA-positive and 48 HA-negative formalin-fixed paraffin-embedded (FFPE) samples was performed to identify differentially expressed genes (DEG). The DEGs were subjected to pathway and gene enrichment analyses. The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) data and DEGs were used for the cluster analysis. In total, 129 DEGs were identified. HA-positive tumors exhibited enhanced expression of genes related to extracellular matrix (ECM) organization and ECM receptor interaction pathways. Gene set enrichment analysis showed that epithelial-mesenchymal transition-associated genes were highly enriched in the HA-positive phenotype. A protein-protein interaction network was constructed, and 17 hub genes were discovered. Heatmap analysis of TCGA-KIRC data identified two prognostic clusters corresponding to HA-positive and HA-negative phenotypes. These clusters were used to verify the expression levels and conduct survival analysis of the hub genes, 11 of which were linked to poor prognosis. These findings enhance our understanding of hyaluronan in ccRCC.
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Affiliation(s)
- Otto Jokelainen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, 70211, Kuopio, Finland.
- Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Teemu J Rintala
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | - Reijo Sironen
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio Campus, P.O. Box 1627, 70211, Kuopio, Finland
- Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Timo K Nykopp
- Department of Surgery, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Surgery, University of Eastern Finland, Kuopio, Finland
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Huang R, Wu D, Zhang K, Hu G, Liu Y, Jiang Y, Wang C, Zheng Y. ARID1A loss induces P4HB to activate fibroblasts to support lung cancer cell growth, invasion, and chemoresistance. Cancer Sci 2024; 115:439-451. [PMID: 38100120 PMCID: PMC10859615 DOI: 10.1111/cas.16052] [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: 07/18/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 02/13/2024] Open
Abstract
Loss of AT-interacting domain-rich protein 1A (ARID1A) frequently occurs in human malignancies including lung cancer. The biological consequence of ARID1A mutation in lung cancer is not fully understood. This study was designed to determine the effect of ARID1A-depleted lung cancer cells on fibroblast activation. Conditioned media was collected from ARID1A-depleted lung cancer cells and employed to treat lung fibroblasts. The proliferation and migration of lung fibroblasts were investigated. The secretory genes were profiled in lung cancer cells upon ARID1A knockdown. Antibody-based neutralization was utilized to confirm their role in mediating the cross-talk between lung cancer cells and fibroblasts. NOD-SCID-IL2RgammaC-null (NSG) mice received tumor tissues from patients with ARID1A-mutated lung cancer to establish patient-derived xenograft (PDX) models. Notably, ARID1A-depleted lung cancer cells promoted the proliferation and migration of lung fibroblasts. Mechanistically, ARID1A depletion augmented the expression and secretion of prolyl 4-hydroxylase beta (P4HB) in lung cancer cells, which induced the activation of lung fibroblasts through the β-catenin signaling pathway. P4HB-activated lung fibroblasts promoted the proliferation, invasion, and chemoresistance in lung cancer cells. Neutralizing P4HB hampered the tumor growth and increased cisplatin cytotoxic efficacy in two PDX models. Serum P4HB levels were higher in ARID1A-mutated lung cancer patients than in healthy controls. Moreover, increased serum levels of P4HB were significantly associated with lung cancer metastasis. Together, our work indicates a pivotal role for P4HB in orchestrating the cross-talk between ARID1A-mutated cancer cells and cancer-associated fibroblasts during lung cancer progression. P4HB may represent a promising target for improving lung cancer treatment.
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Affiliation(s)
- Risheng Huang
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Danni Wu
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Kangliang Zhang
- Department of Central LabThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Guanqiong Hu
- Department of NursingThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Yu Liu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Yi Jiang
- Department of PathologyThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Chichao Wang
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Yuanliang Zheng
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
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Gao Y, Wang X, Luo H, Chen C, Li J, Sun R, Li D, Sun Z. Exosomal Long Non-Coding Ribonucleic Acid Ribonuclease Component of Mitochondrial Ribonucleic Acid Processing Endoribonuclease Is Defined as a Potential Non-Invasive Diagnostic Biomarker for Bladder Cancer and Facilitates Tumorigenesis via the miR-206/G6PD Axis. Cancers (Basel) 2023; 15:5305. [PMID: 37958478 PMCID: PMC10649581 DOI: 10.3390/cancers15215305] [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: 09/15/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Bladder cancer (BLCA) is one of the cancers that is highly sensitive to specific non-invasive tumor biomarkers that facilitate early diagnosis. Exosome-derived long non-coding RNAs (lncRNAs) hold promise as diagnostic biomarkers for BLCA. In this study, we employed RNA-sequencing to compare the expression patterns of lncRNAs in urine exosomes from three BLCA patients and three healthy individuals. RMRP displayed the most significant differential expression. Elevated RMRP expression levels were observed in urinary and plasma exosomes from BLCA patients compared with those from healthy individuals. RMRP exhibited significant associations with certain BLCA patient clinicopathological features, including tumor stage, poor prognosis, and tumor grade. Combined diagnosis using RMRP in urine and plasma exosomes demonstrated a superior diagnostic performance with receiver operating characteristic curve analysis. RMRP was found to be related to BLCA tumor progression and the cell migration and invasion processes via the miR-206/G6PD axis both in vitro and in vivo. Mechanistically, RMRP serves as an miR-206 sponge, as suggested by dual-luciferase reporter assays and RNA immunoprecipitation. Our study suggests that the combined diagnosis of RMRP in urinary and plasma exosomes can serve as an excellent non-invasive diagnostic biomarker for BLCA patients. Additionally, targeting the RMRP/miR-206/G6PD axis holds promise as a therapeutic strategy for BLCA.
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Affiliation(s)
- Yuting Gao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Xuan Wang
- Department of Pharmacy, Putuo People’s Hospital, School of Medicine, Tongji University, Shanghai 200060, China;
| | - Huarong Luo
- Department of Urology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China;
| | - Chen Chen
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Jing Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Ruixin Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Dong Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
| | - Zujun Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China; (Y.G.); (C.C.); (R.S.)
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Zou Z, Li Z, Sun W, Gao W, Liu B, Liu J, Guo Y. Establishment of prognostic model of bladder cancer based on apoptosis-related genes, in which P4HB promotes BLCA progression. BMC Urol 2023; 23:167. [PMID: 37845668 PMCID: PMC10577908 DOI: 10.1186/s12894-023-01331-5] [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: 09/24/2022] [Accepted: 09/27/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND A variety of apoptosis genes have been confirmed to be related to the occurrence and development of bladder cancer patients, but few studies have paid attention to their significance in the prognosis of bladder cancer. Therefore, this study explored the value of apoptosis-related genes in the prognosis of BLCA by using the data in TCGA database. METHODS We downloaded the mRNA expression profiles and corresponding clinical data of bladder cancer patients from TCGA database, and obtained 2411 apoptosis-related genes from Deathbase database. Screening out differentially expressed apoptosis-related genes. Cox regression was used to determine the prognostic value of apoptosis-related genes, and then a prognostic risk model was developed. A nomogram based on risk model was constructed to predict the prognosis of bladder cancer patients. At the same time, immune infiltration correlation analysis of genes in the prognosis model. RESULTS A prognostic model composed of 12 apoptosis-related genes was constructed. According to the risk score calculated by the model, patients were divided into high-risk group and low-risk group. There are significant differences in the expression of immune cells, immune function and immune checkpoint molecules between high-risk group and low-risk group. P4HB may promote bladder cancer progression. CONCLUSION Based on the differential expression of apoptosis-related genes, we established a risk model to predict the prognosis of bladder cancer patients, in which P4HB promotes BLCA progression.
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Affiliation(s)
- Zhenhai Zou
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China
| | - Zhong Li
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China
| | - Wei Sun
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China
| | - Wuyue Gao
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China
| | - Beibei Liu
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China
| | - Jianmin Liu
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China
| | - Yuanyuan Guo
- Department of Urology, the First Affiliated Hospital of Bengbu Medical College, No.287, Changhuai Road, Longzihu, Bengbu, 233040, Anhui, China.
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Javaid H, Barberis A, Chervova O, Nassiri I, Voloshin V, Sato Y, Ogawa S, Fairfax B, Buffa F, Humphrey TC. A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation. BMC Cancer 2023; 23:721. [PMID: 37528416 PMCID: PMC10394884 DOI: 10.1186/s12885-023-11162-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
SETD2-dependent H3 Lysine-36 trimethylation (H3K36me3) has been recently linked to the deposition of de-novo DNA methylation. SETD2 is frequently mutated in cancer, however, the functional impact of SETD2 loss and depletion on DNA methylation across cancer types and tumorigenesis is currently unknown. Here, we perform a pan-cancer analysis and show that both SETD2 mutation and reduced expression are associated with DNA methylation dysregulation across 21 out of the 24 cancer types tested. In renal cancer, these DNA methylation changes are associated with altered gene expression of oncogenes, tumour suppressors, and genes involved in neoplasm invasiveness, including TP53, FOXO1, and CDK4. This suggests a new role for SETD2 loss in tumorigenesis and cancer aggressiveness through DNA methylation dysregulation. Moreover, using a robust machine learning methodology, we develop and validate a 3-CpG methylation signature which is sufficient to predict SETD2 mutation status with high accuracy and correlates with patient prognosis.
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Affiliation(s)
- Hira Javaid
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alessandro Barberis
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Olga Chervova
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Isar Nassiri
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Vitaly Voloshin
- Royal Botanic Gardens Kew, Kew Green, Richmond, TW9 3AE, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Benjamin Fairfax
- The MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital/Headley Way, OX3 9DS, Oxford, UK
| | - Francesca Buffa
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Timothy C Humphrey
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, BN1 9RQ, Brighton, UK.
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Wang F, Yu Z, Liu X, Hu F, Liu X, Fu X, Liu Y, Zou Z. A meta-analysis and bioinformatics analysis of P4HB expression levels in the prognosis of cancer patients. Pathol Res Pract 2023; 245:154474. [PMID: 37119730 DOI: 10.1016/j.prp.2023.154474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND P4HB (prolyl 4-hydroxylase, beta polypeptide) is a human chromosomal gene that encodes an endoplasmic reticulum (ER) molecular chaperone protein with oxidoreductase, chaperone and isomerase activities. Recent studies indicated that P4HB may have clinical significance, with elevated P4HB expression reported in cancer patients, but its impact on tumor prognosis is not yet clear. To our knowledge, this is the first meta-analysis to show an association between P4HB expression and the prognosis of various cancers. METHODS We conducted a systematic literature search in the PubMed, PubMed Central, Web of Science, Embase, CNKI, Wanfang and Weipu databases, followed by a quantitative meta-analysis using Stata SE14.0 and R statistics software 4.2.1. The hazard ratio (HR) and relative risk (RR) were analyzed to evaluate the relationships of P4HB expression levels with overall survival (OS), disease-free survival (DFS), and clinicopathological parameters of cancer patients. Subsequently, P4HB expression in various cancer types was validated using the Gene Expression Profiling Interactive Analysis (GEPIA) online database. RESULTS Ten articles containing the data of 4121 cancer patients were included in the analysis, and a significant correlation of high P4HB expression with apparently shorter OS was found (HR, 1.90; 95% CI, 1.50-2.40; P < 0.01), while there was no significant correlation with gender (RR, 1.06; 95% CI, 0.91-1.22; P = 0.084), or age. Additionally, GEPIA online analysis revealed significant upregulation of P4HB in 13 types of cancer. Among them, P4HB overexpression was associated with shorter OS in 9 and worse DFS in 11 cancer types. CONCLUSIONS Upregulation of P4HB is correlated with worse prognosis in various cancers, which could provide new ideas for the development of P4HB-related diagnostic biomarkers and new therapeutic targets.
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Affiliation(s)
- Feiyang Wang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The First School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Zhixiang Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China
| | - Xiaohan Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The Second School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Feng Hu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The First School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Xiangjun Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China
| | - Xinyi Fu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The First School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Yan Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China; The Second School of Clinical Medicine of Nanchang University, Jiangxi Medical College of Nanchang University, No.461 Bayi Avenue, Nanchang 330000, Jiangxi, People's Republic of China
| | - Zhenhong Zou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, 1 Minde Road, Nanchang 330006, Jiangxi, People's Republic of China.
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Zhang W, Liu W, Yang Y, Xiao C, Xiao Y, Tan X, Pang Q, Wu H, Hua M, Shi X. Integrative analysis of transcriptomic landscape and urinary signature reveals prognostic biomarkers for clear cell renal cell carcinoma. Front Oncol 2023; 13:1102623. [PMID: 37035174 PMCID: PMC10079990 DOI: 10.3389/fonc.2023.1102623] [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: 11/19/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) patients with venous tumor thrombus (VTT) have poor prognosis. We aimed to reveal features of ccRCC with VTT and develop a urine-based prognostic classifier to predict ccRCC prognosis through integrative analyses of transcriptomic landscape and urinary signature. Methods RNA sequencing was performed in five patients with ccRCC thrombus-tumor-normal tissue triples, while mass spectrometry was performed for urine samples from 12 ccRCC and 11 healthy controls. A urine-based classifier consisting of three proteins was developed to predict patients' survival and validated in an independent cohort. Results Transcriptomic analysis identified 856 invasion-associated differentially expressed genes (DEGs). Furthermore, proteomic analysis showed 133 differentially expressed proteins (DEPs). Integration of transcriptomic landscape and urinary signature reveals 6 urinary detectable proteins (VSIG4, C3, GAL3ST1, TGFBI, AKR1C3, P4HB) displaying abundance changes consistent with corresponding genes in transcriptomic profiling. According to TCGA database, VSIG4, TGFBI, and P4HB were significantly overexpressed in patients with shorter survival and might be independent prognostic factors for ccRCC (all p<0.05). A prognostic classifier consisting of the three DEPs highly associated with survival performed satisfactorily in predicting overall survival (HR=2.0, p<0.01) and disease-free survival (HR=1.6, p<0.001) of ccRCC patients. The ELISA analysis of urine samples from an independent cohort confirmed the satisfied predictive power of the classifier for pathological grade (AUC=0.795, p<0.001) and stage (AUC=0.894, p<0.001). Conclusion Based on integrative analyses of transcriptomic landscape and urinary signature, the urine-based prognostic classifier consisting of VSIG4, TGFBI, and P4HB has satisfied predictive power of ccRCC prognosis and may facilitate ccRCC molecular subtyping and treatment.
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Affiliation(s)
- Wei Zhang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wenqiang Liu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yiren Yang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Chengwu Xiao
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yutian Xiao
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaojie Tan
- Department of Epidemiology, Naval Medical University, Shanghai, China
| | - Qingyang Pang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Han Wu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Meimian Hua
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Xiaolei Shi, ; Meimian Hua,
| | - Xiaolei Shi
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Xiaolei Shi, ; Meimian Hua,
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miR-18a-5p Is Involved in the Developmental Origin of Prostate Cancer in Maternally Malnourished Offspring Rats: A DOHaD Approach. Int J Mol Sci 2022; 23:ijms232314855. [PMID: 36499183 PMCID: PMC9739077 DOI: 10.3390/ijms232314855] [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: 09/09/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022] Open
Abstract
The Developmental Origins of Health and Disease (DOHaD) concept correlates early life exposure to stressor conditions with the increased incidence of non-communicable chronic diseases, including prostate cancer (PCa), throughout the life span. However, the molecular mechanisms involved in this process remain poorly understood. In this study, the deregulation of two miRNAs (rno-miR-18a-5p and rno-miR-345-3p) was described in the ventral prostate VP of old rats born to dams fed with a low protein diet (LPD) (6% protein in the diet) during gestational and lactational periods. Integrative analysis of the (VP) transcriptomic and proteomic data revealed changes in the expression profile of 14 identified predicted targets of these two DE miRNAs, which enriched terms related to post-translational protein modification, metabolism of proteins, protein processing in endoplasmic reticulum, phosphonate and phosphinate metabolism, the calnexin/calreticulin cycle, metabolic pathways, N-glycan trimming in the ER and the calnexin/calreticulin cycle, hedgehog ligand biogenesis, the ER-phagosome pathway, detoxification of reactive oxygen species, antigenprocessing-cross presentation, RAB geranylgeranylation, collagen formation, glutathione metabolism, the metabolism of xenobiotics by cytochrome P450, and platinum drug resistance. RT-qPCR validated the deregulation of the miR-18a-5p/P4HB (prolyl 4-hydroxylase subunit beta) network in the VP of older offspring as well as in the PNT-2 cells transfected with mimic miR-18a-5p. Functional in vitro studies revealed a potential modulation of estrogen receptor α (ESR1) by miR-18a-5p in PNT-2 cells, which was also confirmed in the VP of older offspring. An imbalance of the testosterone/estrogen ratio was also observed in the offspring rats born to dams fed with an LPD. In conclusion, deregulation of the miR-18a-5p/P4HB network can contribute to the developmental origins of prostate cancer in maternally malnourished offspring, highlighting the need for improving maternal healthcare during critical windows of vulnerability early in life.
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Sun M, Qi S, Wu M, Xia W, Xiong H. Calreticulin as a prognostic biomarker and correlated with immune infiltrate in kidney renal clear cell carcinoma. Front Genet 2022; 13:909556. [PMID: 36338983 PMCID: PMC9633671 DOI: 10.3389/fgene.2022.909556] [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: 03/31/2022] [Accepted: 10/05/2022] [Indexed: 01/29/2024] Open
Abstract
Background: Calreticulin (CALR) has been investigated in several malignant diseases and is associated with immune-cell infiltration. However, the prognostic value of CALR in kidney renal clear cell carcinoma (KIRC) is still unknown. Methods: Based on the computational analysis, data from 530 KIRC cases and 72 normal kidney samples from The Cancer Genome Atlas (TGCA-KIRC) database were analyzed in this study. The expression of CALR mRNA in pan-cancer and immune infiltrates was analyzed using the Tumor Immune Estimation Resource (TIMER) database. The CALR protein expression was obtained from the UALCAN and Human Protein Atlas (HPA) databases. Survival, functional, and statistical analyses were conducted using R software. Results: The CALR expression was higher in KIRC cases than in normal kidneys. A high CALR expression was correlated with TNM stage, pathological stage, and histological grade. Kaplan-Meier survival analysis showed that a high CALR expression was associated with poor overall survival, disease-specific survival, and progression-free interval. Gene set enrichment analysis (GSEA) indicated that CALR was enriched in IL-6 and IL-2 signaling, interferon signaling, TNF signaling, inflammatory response, apoptosis, and the p53 pathway. CALR is correlated with immune-infiltrating cells. A significant correlation was observed between CALR expression and immunomodulators. Conclusion: We identified CALR as a prognostic biomarker of KIRC. Meanwhile, the CALR expression associated with immune infiltration indicated that CALR might be a potential immunotherapy target for patients with KIRC.
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Affiliation(s)
| | | | | | | | - Hao Xiong
- Department of Hematology and Oncology, Wuhan Children’s Hospital, Tongji Medical College, HUST, Wuhan, China
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10
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Bai F, Yu K, Yang Y, Zhang Y, Ding L, An X, Feng F, Sun N, Fan J, Liu L, Yang H, Yang X. Identification and validation of P4HB as a novel autophagy-related biomarker in diabetic nephropathy. Front Genet 2022; 13:965816. [PMID: 36226178 PMCID: PMC9548632 DOI: 10.3389/fgene.2022.965816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Diabetic nephropathy (DN), a frequent microvascular complication of diabetes, has been recognized as a primary cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD). Previous studies found that autophagy of renal tubular epithelial cells plays an important role in DN pathogenesis. Our research aimed to investigate the differentially expressed autophagy-related genes (DEARGs) between DN and healthy renal tubule samples and identify a novel autophagy-related biomarker associated with tubulointerstitial injury in DN. In this study, gene expression profiles of renal tubules from 10 DN patients and 24 healthy controls in the GSE30122 dataset were analyzed, and 43 DEARGs were identified by bioinformatics analysis. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and correlation analysis were performed on DEARGs, and the hub gene prolyl 4-hydroxylase subunit beta (P4HB) was screened by protein–protein interaction and verified by utilizing other datasets and stimulating HK-2 cells under high glucose concentration. We found that the expression of P4HB in renal tubules was correlated with renal function. In summary, our research provided novel insights for comprehension of DN molecular mechanisms and identified P4HB as a novel autophagy-related biomarker of DN.
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Affiliation(s)
- Fang Bai
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Laboratory of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Kuipeng Yu
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yanjiang Yang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yimeng Zhang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Lin Ding
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xin An
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Feng Feng
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Nan Sun
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Jiahui Fan
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Lei Liu
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Huimin Yang
- Department of General Practice, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiangdong Yang
- Department of Nephrology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- *Correspondence: Xiangdong Yang,
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11
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Zhou J, Simon JM, Liao C, Zhang C, Hu L, Zurlo G, Liu X, Fan C, Hepperla A, Jia L, Tcheuyap VT, Zhong H, Elias R, Ye J, Henne WM, Kapur P, Nijhawan D, Brugarolas J, Zhang Q. An oncogenic JMJD6-DGAT1 axis tunes the epigenetic regulation of lipid droplet formation in clear cell renal cell carcinoma. Mol Cell 2022; 82:3030-3044.e8. [PMID: 35764091 PMCID: PMC9391320 DOI: 10.1016/j.molcel.2022.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/15/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022]
Abstract
Characterized by intracellular lipid droplet accumulation, clear cell renal cell carcinoma (ccRCC) is resistant to cytotoxic chemotherapy and is a lethal disease. Through an unbiased siRNA screen of 2-oxoglutarate (2-OG)-dependent enzymes, which play a critical role in tumorigenesis, we identified Jumonji domain-containing 6 (JMJD6) as an essential gene for ccRCC tumor development. The downregulation of JMJD6 abolished ccRCC colony formation in vitro and inhibited orthotopic tumor growth in vivo. Integrated ChIP-seq and RNA-seq analyses uncovered diacylglycerol O-acyltransferase 1 (DGAT1) as a critical JMJD6 effector. Mechanistically, JMJD6 interacted with RBM39 and co-occupied DGAT1 gene promoter with H3K4me3 to induce DGAT1 expression. JMJD6 silencing reduced DGAT1, leading to decreased lipid droplet formation and tumorigenesis. The pharmacological inhibition (or depletion) of DGAT1 inhibited lipid droplet formation in vitro and ccRCC tumorigenesis in vivo. Thus, the JMJD6-DGAT1 axis represents a potential new therapeutic target for ccRCC.
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Affiliation(s)
- Jin Zhou
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lianxin Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giada Zurlo
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Austin Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Liwei Jia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vanina Toffessi Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hua Zhong
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Roy Elias
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Ye
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deepak Nijhawan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Zhong T, Jiang Z, Wang X, Wang H, Song M, Chen W, Yang S. Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma. PeerJ 2022; 10:e12493. [PMID: 35036081 PMCID: PMC8740509 DOI: 10.7717/peerj.12493] [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: 07/06/2021] [Accepted: 10/25/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a tumor that frequently shows the hematogenous pathway and tends to be resistant to radiotherapy and chemotherapy. However, the exact mechanism of ccRCC metastasis remains unknown. METHODS Differentially expressed genes (DEGs) of three gene expression profiles (GSE85258, GSE105288 and GSE22541) downloaded from the Gene Expression Omnibus (GEO) database were analyzed by GEO2R analysis, and co-expressed DEGs among the datasets were identified using a Venn drawing tool. The co-expressed DEGs were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and hub genes were determined based on the protein-protein interaction network established by STRING. After survival analysis performed on UALCAN website, possible key genes were selected and verified in ccRCC cell lines and ccRCC tissues (n = 44). Statistical analysis was conducted using GraphPad Prism (Version 8.1.1). RESULTS A total of 104 co-expressed DEGs were identified in the three datasets. Pathway analysis revealed that these genes were enriched in the extracellular matrix (ECM)-receptor interaction, protein digestion and absorption and focal adhesion. Survival analysis on 17 hub genes revealed that four key genes with a significant impact on survival: procollagen C-endopeptidase enhancer (PCOLCE), prolyl 4-hydroxylase subunit beta (P4HB), collagen type VI alpha 2 (COL6A2) and collagen type VI alpha 3 (COL6A3). Patients with higher expression of these key genes had worse survival than those with lower expression. In vitro experiments revealed that the mRNA expression levels of PCOLCE, P4HB and COL6A2 were three times higher and that of COL6A3 mRNA was 16 times higher in the metastatic ccRCC cell line Caki-1 than the corresponding primary cell line Caki-2. Immunohistochemistry revealed higher expression of the proteins encoded by these four genes in metastatic ccRCC compared with tumors from the corresponding primary sites, with statistical significance. CONCLUSION PCOLCE, P4HB, COL6A2 and COL6A3 are upregulated in metastatic ccRCC and might be related to poor prognosis and distant metastases.
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Affiliation(s)
- Tingting Zhong
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zeying Jiang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiangdong Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Honglei Wang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Meiyi Song
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Wenfang Chen
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shicong Yang
- Department of Pathology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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13
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Abd Allah M, Soliman A. Evaluation of prolyl-4-hydroxylase subunit beta and special AT-rich region-binding protein-1 immunoexpression in bladder transitional-cell carcinoma. EGYPTIAN JOURNAL OF PATHOLOGY 2022; 42:28. [DOI: 10.4103/egjp.egjp_7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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14
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Wu P, Xiang T, Wang J, Lv R, Ma S, Yuan L, Wu G, Che X. Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis. BMC Med Genomics 2021; 14:241. [PMID: 34620162 PMCID: PMC8499437 DOI: 10.1186/s12920-021-01092-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack of a clear understanding of the molecular mechanism. Hence, exploring the underlying mechanisms and seeking novel biomarkers for pursuing a precise prognostic biomarker and appropriate therapies are critical. Material and methods In our research, the differentially expressed genes (DEGs) were screened from the TCGA and GEO databases, and a total of 149 upregulated and 285 downregulated genes were sorted. This was followed by construction of functional enrichment and protein–protein interaction (PPI) network, and then the top 15 DEGs were selected for further analysis. The P4HB gene was chosen as our target gene by repetitively validating multiple datasets, and higher levels of P4HB expression predicted lower overall survival (OS) in patients with pRCC. Results We found that P4HB not only connects with immune cell infiltration and co-expression with PD-1, PD-L2, and CTLA-4, but also has a strong connection with the newly discovered hot gene, TOX. Conclusion We speculate that P4HB is a novel gene involved in the progression of pRCC through immunomodulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01092-w.
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Affiliation(s)
- Ping Wu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China
| | - Tingting Xiang
- Department of Rehabilitation, Liguang Rehabilitation Hospital of Dalian Development Zone, Dalian, 116600, China
| | - Jing Wang
- Department of Neurobiology, Harbin Medical University, Harbin, 150086, China
| | - Run Lv
- Department of Anesthesiology, Dalian Medical University, Dalian, 116044, China
| | - Shaoxin Ma
- Department of Anesthesiology, Dalian Medical University, Dalian, 116044, China
| | - Limei Yuan
- Department of Anesthesiology, Dalian Medical University, Dalian, 116044, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China.
| | - Xiangyu Che
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China.
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15
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Wu Y, Peng Y, Guan B, He A, Yang K, He S, Gong Y, Li X, Zhou L. P4HB: A novel diagnostic and prognostic biomarker for bladder carcinoma. Oncol Lett 2020; 21:95. [PMID: 33376528 PMCID: PMC7751343 DOI: 10.3892/ol.2020.12356] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/23/2020] [Indexed: 12/15/2022] Open
Abstract
Prolyl 4-hydroxylase, beta polypeptide (P4HB) protein is an endoplasmic reticulum (ER) molecular chaperone protein and has been reported to be overexpressed in multiple tumor types. However, the role of P4HB in bladder cancer (BLCA) has not yet been elucidated. The aim of the present study was to investigate the prognostic value of P4HB and the association between clinicopathological characteristics and P4HB in BLCA. P4HB expression levels were assessed through The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and validated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis in BLCA tissues and cells. A total of 69 pairs of tumor and normal samples were used to analyze the expression of P4HB via immunohistochemical staining. A co-expression network and functional enrichment analyses were conducted to investigate the biological function of P4HB in BLCA. The protein-protein interaction (PPI) network was constructed by Search Tool for the Retrieval of Interacting Genes. The results showed that P4HB was highly expressed in BLCA cells and tissues. The area under the curve value for P4HB expression to discriminate between tumor and normal tissues was up to 0.888 (95% CI: 0.801–0.975; P<0.001) and 0.881 (95% CI: 0.825–0.937; P<0.001) in TCGA database and our database, respectively. Furthermore, the expression level of P4HB was an independent risk factor for overall survival (OS) and recurrence-free survival (RFS) by univariate and multivariate analyses. Kaplan-Meier survival analysis demonstrated that high P4HB expression was associated with low OS and RFS. Pathway enrichment analysis suggested that P4HB was involved in protein processing in the endoplasmic reticulum (ER), including N-glycan modification and protein metabolic processes responding to ER stress. PPI analysis revealed that the potential targets of P4HB were mainly involved in posttranslational protein modification and response to ER stress. In conclusion, the expression level of P4HB aid in identifying patients with early-stage BLCA and predicting the prognosis of BLCA. Therefore, P4HB may be a novel diagnostic and prognostic biomarker for BLCA.
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Affiliation(s)
- Yucai Wu
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Yiji Peng
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Anbang He
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Kunlin Yang
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Xicheng, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Xicheng, Beijing 100034, P.R. China.,National Urological Cancer Center, Peking University, Xicheng, Beijing 100034, P.R. China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Xicheng, Beijing 100034, P.R. China
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16
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Wei X, Wang W, Wang H, Wang Y, Wang Y, Li G, Ji C, Ren X, Song N, Qin C. Identification of an independent autophagy-gene prognostic index for papillary renal cell carcinoma. Transl Androl Urol 2020; 9:1945-1956. [PMID: 33209659 PMCID: PMC7658136 DOI: 10.21037/tau-20-906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Autophagy was a significant catabolic process which played a critical role in the maintenance of cellular homeostasis and viability in a stressed state. The dysregulation of autophagy was correlated with various diseases. The aim of our study was to develop a prognostic signature for papillary renal cell carcinoma (RCC). Methods First, 40 differently expressed genes related with autophagy (ARGs) were examined via high-throughput sequencing and large-scale databases. Then, functional enrichment analysis was performed to explore the biological attributes of these ARGs. The Cox proportional hazard regression hinted that four ARGs (P4HB, BIRC5, NGR1 and PRKN) were significantly correlated with overall survival (OS). Thus, we got genes with prognostic value. Finally, a prognostic index (PI) was constructed. Results After identifying the 4 ARGs, we profiled our risk signature. Based on the PI we developed, papillary RCC patients were stratified into high-risk and low-risk groups. High-risk patients had significant shorter OS than low-risk patients (P<0.001) and the mortality of high scoring patients was higher than low scoring patients. Additionally, we explored the relationship between the 4 ARGs and clinical parameters and found that the expression of P4HB, BIRC5 and NGR1 was correlated with clinicopathological features. Conclusions Our study suggested that the four-gene signature was an independent prognostic factor which could act as a novel indicator for the prognosis of papillary RCC.
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Affiliation(s)
- Xiyi Wei
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Wang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongye Wang
- First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yamin Wang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yichun Wang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guangyao Li
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chengjian Ji
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaohan Ren
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ninghong Song
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The Affiliated Kezhou People's Hospital of Nanjing Medical University, Kezhou, China
| | - Chao Qin
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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17
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Zhu Z, Xu C, Lin L, Lv T, Cai T, Lin J. Prognostic Value and Potential Biological Functions of CLDN8 in Patients with Clear Cell Renal Cell Carcinoma. Onco Targets Ther 2020; 13:9135-9145. [PMID: 32982302 PMCID: PMC7501992 DOI: 10.2147/ott.s266846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/12/2020] [Indexed: 01/21/2023] Open
Abstract
Purpose Clear cell renal cell carcinoma (ccRCC) is among the most common malignant tumors worldwide, with a high incidence rate and poor prognosis. Currently, there are no biomarkers that can accurately guide prognostic evaluation and therapeutic strategy for ccRCC. The prognostic value and potential biological function of claudin-8 (CLDN8), a critical component of tight junctions in ccRCC, remain unclear. Methods Sequencing data were obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, and Gene Expression Omnibus databases. R packages were used to explore CLDN8 mRNA expression levels and analyze differentially expressed genes. Results were validated in clinical specimens and cell lines, and bioinformatics analyses were conducted to explore the potential biological functions of CLDN8. Finally, functional analyses were carried out using 786–O ccRCC cell line. Results Both CLDN8 mRNA and protein expression levels were significantly lower in ccRCC compared with the normal control tissues. Kaplan–Meier analyses showed that low CLDN8 expression levels were associated with the poor overall survival, while univariate and multivariate Cox regression indicated that CLDN8 could serve as an independent prognostic factor in patient with ccRCC. Bioinformatic and Western blot analyses showed that CLDN8 suppressed proliferation, migration, and invasion of 786–O ccRCC cells through the epithelial–mesenchymal transition and AKT pathways. Conclusion CLDN8 could serve as an independent prognostic factor in ccRCC, in which it suppresses 786–O proliferation, migration, and invasion through EMT and AKT pathways.
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Affiliation(s)
- Zhenpeng Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, People's Republic of China.,Institute of Urology, Peking University, Beijing 100034, People's Republic of China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, People's Republic of China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, People's Republic of China.,Institute of Urology, Peking University, Beijing 100034, People's Republic of China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, People's Republic of China
| | - Lanruo Lin
- College of Basic Medical Science, Capital Medical University, Beijing 100069, People's Republic of China
| | - Tongde Lv
- Department of Urology, Peking University First Hospital, Beijing 100034, People's Republic of China.,Institute of Urology, Peking University, Beijing 100034, People's Republic of China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, People's Republic of China
| | - Tianyu Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, People's Republic of China.,Institute of Urology, Peking University, Beijing 100034, People's Republic of China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, People's Republic of China
| | - Jian Lin
- Department of Urology, Peking University First Hospital, Beijing 100034, People's Republic of China.,Institute of Urology, Peking University, Beijing 100034, People's Republic of China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, People's Republic of China
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18
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Wang X, Bai Y, Zhang F, Yang Y, Feng D, Li A, Yang Z, Li D, Tang Y, Wei X, Wei W, Han P. Targeted Inhibition of P4HB Promotes Cell Sensitivity to Gemcitabine in Urothelial Carcinoma of the Bladder. Onco Targets Ther 2020; 13:9543-9558. [PMID: 33061438 PMCID: PMC7532080 DOI: 10.2147/ott.s267734] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/15/2020] [Indexed: 02/05/2023] Open
Abstract
Background Bladder cancer (BC) is a common malignancy worldwide that accounts for 3% of global cancer diagnoses. Chemotherapy resistance limits the therapeutic effect of chemotherapeutic agents in patients with BC. Prolyl 4-hydroxylase, beta polypeptide (P4HB) is an endoplasmic reticulum (ER) chaperone that is upregulated in bladder cancer tissues (The Cancer Genome Atlas, TCGA datasets). Knockdown or suppression of P4HB exerts anticancer activity and sensitizes cells to chemotherapy in various types of cancer. Purpose We aimed to investigate whether the inhibition of P4HB enhances the anticancer efficacy of gemcitabine (GEM) in BC cells and to study the underlying molecular mechanisms. Patients and Methods The P4HB mRNA expression levels of 411 BC patients from the TCGA database and P4HB expression level of eighty BC paraffin-embedded samples detected by immunohistochemistry (IHC) staining were used for clinical feature and prognostic analyses. Bioinformatics analysis was utilized for the mechanistic investigation. Highly P4HB-expressed BC cell lines (T24 and 5637) treated with P4HB inhibitor (Bacitracin, BAC) were used to study the effects of BAC on the sensitivity of BC cells to GEM and the potential mechanism. P4HB inhibition experiments were performed in highly P4HB-expressed BC cells, and cell viability, colony formation, cell cycle, reactive oxygen species (ROS), apoptosis and pathway proteins were assessed in T24 and 5637 cells. Results Western blot analysis showed that P4HB expression was significantly higher in BC tissues than in paired normal tissues. IHC showed that patients with high P4HB expression had a poorer overall survival (OS) rate than those with low P4HB expression. Furthermore, increased P4HB expression was demonstrated to be an independent prognostic marker for BC. Functionally, P4HB inhibition by BAC decreased the cell proliferation ability in vitro. Moreover, BAC treatment sensitized BC cells to GEM. Molecular mechanism analysis indicated that inhibition of P4HB by BAC treatment enhanced the anticancer effects of GEM through increasing cellular ROS content and promoting cell apoptosis and PERK/eIF2α/ATF4/CHOP signaling. Conclusion High P4HB expression was significantly correlated with poor prognosis in BC patients. Inhibition of P4HB by BAC decreased the cell proliferation ability and sensitized BC cells to GEM by activating apoptosis and the PERK/eIF2α/ATF4/CHOP pathways.
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Affiliation(s)
- Xiaoming Wang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Yunjin Bai
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Facai Zhang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Yubo Yang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Dechao Feng
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Ao Li
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Zhiqiang Yang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Dengxiong Li
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Yin Tang
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Xin Wei
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Wuran Wei
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
| | - Ping Han
- Department of Urology/Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, People's Republic of China
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Zhu Z, He A, Lin L, Xu C, Cai T, Lin J. Biological functions and prognostic value of RNA Binding Proteins in clear cell Renal Cell Carcinoma. J Cancer 2020; 11:6591-6600. [PMID: 33046980 PMCID: PMC7545679 DOI: 10.7150/jca.49175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/11/2020] [Indexed: 12/22/2022] Open
Abstract
Early detection and accurate evaluation were both critical to improving the prognosis of clear cell Renal Cell Carcinoma (ccRCC) patients. More importantly, RNA Binding Proteins (RBPs) play a vital role in the tumorigenesis and progression of numerous cancers. However, the relationship between RBPs and ccRCC is still unclear. Exploring the potential biological functions of RBPs in ccRCC and establishing a prognostic signature to predict the survival probability remains meaningful. In this study, transcriptome profiling and the corresponding clinical information were obtained from the TCGA database, GEO database, and ICGC database. By using the "edgeR" R package, 200 DERBPs were found, including 128 up-regulated and 72 down-regulated RBPs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DERBPs were mainly involved in regulating transcriptional processes and metabolism. Furthermore, there were 4 hub genes (RPS2, RPS14, RPS20, and RPLP0) were found in the PPI network, which may play vital biological roles among those DERBPs. Then we used LASSO regression to construct a prognostic signature and validated the signature in the GEO and ICGC cohort. The time-dependent receiver operating characteristic (ROC) curve showed that the signature could accurately predict the prognosis of ccRCC patients. Then we established a nomogram, and the calibration curve and ROC curve showed that the nomogram could accurately predict 1-year, 3-year, and 5-year overall survival (OS) of ccRCC patients (The AUC value: 0.871, 0.829, and 0.816). In conclusion, we constructed a 10-RBPs-based prognostic signature integrating clinical parameters to predict the prognosis of ccRCC patients. The prognostic signature based on the differentially expressed RBPs (DERBPs) might serve as promising diagnostic and prognostic biomarkers in ccRCC.
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Affiliation(s)
- Zhenpeng Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Anbang He
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Lanruo Lin
- Capital Medical University, Beijing 100069, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Tianyu Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
| | - Jian Lin
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institute of Urology, Peking University, Beijing 100034, China
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20
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Zhu ZP, Lin LR, Lv TD, Xu CR, Cai TY, Lin J. High expression levels of DEF6 predicts a poor prognosis for patients with clear cell renal cell carcinoma. Oncol Rep 2020; 44:2056-2066. [PMID: 33000227 PMCID: PMC7551049 DOI: 10.3892/or.2020.7736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant tumors and early detection contributes to a better prognosis. Finding new biomarkers for the diagnosis or treatment remains meaningful. DEF6 guanine nucleotide exchange factor (DEF6) is upregulated in ccRCC compared to normal controls, but the relationship between DEF6 expression and prognosis in ccRCC is unclear. Moreover, the potential biological functions of DEF6 in ccRCC remains unclear. In the present study, the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), TISIDB and the clinical database of the Peking University First Hospital were used to analyze DEF6 expression in ccRCC. Immunohistochemistry (IHC), western blotting and reverse transcription-quantitative PCR were used to examine the DEF6 protein and mRNA expression levels in cell lines and clinical samples. Subsequently, the Kaplan-Meier method and Cox regression analyses were used to determine the impact of DEF6 expression on the overall survival of patients alongside other clinical variables in both the TCGA database and the present clinical database. The results showed that both DEF6 mRNA and protein expression levels were upregulated in ccRCC compared to normal controls. The Kaplan-Meier survival analysis showed that patients with high DEF6 expression had poor prognoses from both the TCGA database and the present clinical database. Univariate survival analysis and multivariate survival analysis revealed that DEF6 could be an independent prognostic factor for ccRCC. Additionally, bioinformatics analysis indicated that differentially expressed genes related to DEF6 expression influenced ccRCC by regulating the tumor immune microenvironment. In conclusion, overexpression of DEF6 is significantly correlated with a poor prognosis for patients with ccRCC and DEF6 may influence the biological processes involved with ccRCC by regulating the immune microenvironment.
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Affiliation(s)
- Zhen-Peng Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China
| | - Lan-Ruo Lin
- College of Basic Medicine, Capital Medical University, Beijing 100069, P.R. China
| | - Tong-De Lv
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China
| | - Chun-Ru Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China
| | - Tian-Yu Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China
| | - Jian Lin
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China
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21
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Dai J, Jiang L, Qiu L, Shao Y, Shi P, Li J. WHSC1 Promotes Cell Proliferation, Migration, and Invasion in Hepatocellular Carcinoma by Activating mTORC1 Signaling. Onco Targets Ther 2020; 13:7033-7044. [PMID: 32801739 PMCID: PMC7398890 DOI: 10.2147/ott.s248570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
Abstract
Background Wolf-Hirschhorn syndrome candidate gene-1 (WHSC1) plays key regulatory roles in cancer development and progression. However, its specific functions and potential mechanisms of action remain to be described in hepatocellular carcinoma (HCC). Materials and Methods WHSC1 expression in HCC was evaluated using The Cancer Genome Atlas and verified in HCC tissues and cell lines using qRT-PCR, Western blotting, and immunohistochemistry. Functional assays were performed to explore the role of WHSC1 in HCC progression. Immunoprecipitation-mass spectrometry, co-immunoprecipitation, immunofluorescence, and immunohistochemistry were conducted to evaluate the interaction between WHSC1 and prolyl 4-hydroxylase subunit beta (P4HB). Pathway enrichment was performed using gene set enrichment analysis. Results WHSC1 was markedly overexpressed in HCC tissues and cell lines. The level of expression was strongly associated with adverse clinicopathological characteristics. Survival analyses revealed that WHSC1 upregulation predicted poor overall survival and higher recurrence rates in patients with HCC. Functional studies revealed that WHSC1 significantly stimulated HCC proliferation, migration, and invasion in vitro and in vivo. WHSC1 was shown to interact with P4HB to stimulate P4HB expression and subsequently activate mTOR1 signaling. Conclusion We determined the oncogenic role of WHSC1 in HCC, via P4HB interaction, which activates mTOR1 signaling, and identified WHSC1 as a promising therapeutic target for HCC.
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Affiliation(s)
- Jingjing Dai
- Department of Infectious Diseases, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Longfeng Jiang
- Department of Infectious Diseases, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Lei Qiu
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang, Jiangsu, People's Republic of China
| | - Yuyun Shao
- Department of Infectious Diseases, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Ping Shi
- Department of Infectious Diseases, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jun Li
- Department of Infectious Diseases, The First Affiliated Hospital, Nanjing Medical University, Nanjing, People's Republic of China
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