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Cui Z, Fu Y, Zhou M, Feng H, Zhang L, Ma S, Chen C. Pan-cancer investigation of RFX family and associated genes identifies RFX8 as a therapeutic target in leukemia. Heliyon 2024; 10:e35368. [PMID: 39170430 PMCID: PMC11336603 DOI: 10.1016/j.heliyon.2024.e35368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024] Open
Abstract
Background Several transcription factors and co-factors are encoded by the RFX (Regulatory Factor X) family (RFX1-8) and associated genes (RFXAP and RFXANK). Increasing evidence suggests that the RFX family and associated genes are involved in the development and progression of cancer. However, no prior research has focused on a multi-omic analysis of these genes to evaluate their role in tumor progression. Methods Using combined TCGA and GTEx pan-cancer data, we investigated the expression patterns and survival profiles of these ten genes. We then focused on RFX8 to analyze its clinicopathological and therapeutic features. Finally, we conducted experimental validation of RFX8 function in acute myeloid leukemia (AML). Results RFX5 and RFXANK showed higher expression levels, while RFX6 showed lower expression levels in most types of cancer, with RFX8 being the most upregulated in LAML. RFX2 and RFXAP demonstrated prognostic significance in eight types of cancer, and RFX8 showed significance in six types of cancer. The expression of these ten genes exhibited specific characteristics in immune subtypes, tumor microenvironment, and stemness. The expression of RFX8 was correlated with various tumor stages, microsatellite instability (MSI), tumor mutation burden (TMB), immune cell infiltration, and immune-checkpoint expression. Additionally, RFX8 was found to regulate tumorigenesis and sensitivity to chelerythrine in AML. Conclusions Our work delineated the landscape of the RFX family and associated genes in the pan-cancer context and the specific role of RFX8 in AML. These findings might offer cues for further investigations of these genes in cancer biology.
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Affiliation(s)
- Zelong Cui
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yue Fu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Minran Zhou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Huimin Feng
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lu Zhang
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Sai Ma
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chunyan Chen
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Guan X, Liang J, Xiang Y, Li T, Zhong X. BARX1 repressed FOXF1 expression and activated Wnt/β-catenin signaling pathway to drive lung adenocarcinoma. Int J Biol Macromol 2024; 261:129717. [PMID: 38290639 DOI: 10.1016/j.ijbiomac.2024.129717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/01/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Underlying molecular mechanisms of BARX homeobox 1 (BARX1) in lung adenocarcinoma (LUAD) remain elusive. METHODS Abnormally expressed genes in LUAD tissues were analyzed by RNA-sequencing. CCK-8, colony formation, transwell, and wound healing assays examined proliferation, colony formation, invasion, and migration of LUAD cells, respectively. Electrophoretic mobility shift assay and chromatin immunoprecipitation assay examined the interaction between BARX1 and Forkhead Box F1 (FOXF1). Xenograft mouse model of LUAD was constructed to monitor the growth and metastasis of tumor. RESULTS BARX1 was upregulated, FOXF1 was downregulated in LUAD tissues and cells. There was a negative correlation between BARX1 and FOXF1 expression. BARX1 deficiency limited malignant phenotypes of LUAD cells, including proliferation, invasion, migration and EMT. In vivo, BARX1 knockdown suppressed tumor growth and metastasis in A549-drove xenograft mouse model. BARX1 interacted with FOXF1 promoter and repressed FOXF1 expression. Upregulation of BARX1 promoted the expression of Wnt5a, β-catenin, and phosphorylated-glycogen synthase kinase-3 beta (p-GSK3β), whereas inhibited FOXF1, p-β-catenin, and GSK3β in LUAD cells. BARX1 knockdown caused an opposite result. Rescue assays uncovered that FOXF1 reversed the impact of BARX1 on malignant phenotypes and Wnt/β-catenin of LUAD cells. CONCLUSION BARX1 repressed FOXF1 expression and activated Wnt/β-catenin signaling pathway to drive lung adenocarcinoma.
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Affiliation(s)
- Xiaojiao Guan
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jie Liang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yifan Xiang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an 710032, China.
| | - Xinwen Zhong
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China.
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Wan Z, Wang J, Liu Q, Yang D, Li P, Wang L. Knockdown of DLK4 inhibits non-small cell lung cancer tumor growth by downregulating CKS2. Open Life Sci 2023; 18:20220720. [PMID: 37744456 PMCID: PMC10512446 DOI: 10.1515/biol-2022-0720] [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: 05/17/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) accounts for 85% of all lung cancer cases and is considered as the most common type of cancer. DLX4 was originally identified as a β-globin gene suppressor in red blood cells, which plays critical roles in several types of cancers. However, the role and related mechanism of DLX4 in NSCLC are still unclear. The study aimed to uncover the expression of DLX4 in human NSCLC cells and tissues, reveal its possible role in NSCLC, and investigate the underlying mechanisms. Immunoblot and TCGA database were used to detect the expression of DLX4 in human NSCLC cells and tissues. CCK-8, colony formation, and FCM assays were conducted to detect the effects of DLX4 on the viability and cell cycle of NCI-H2170 and A549 cells. Immunoblot assays were further performed to investigate the possible mechanism underlying DLX4 affecting the growth of NSCLC. We revealed that knockdown of DLX4 inhibited NSCLC cell proliferation. We further revealed that DLX4 knockdown induced the NSCLC cell cycle arrest. Our results further showed that downregulation of DLX4 suppressed YB-1 expression, which further suppressed CKS2 expression, thereby suppressing tumor growth of NSCLC. In conclusion, DLX4 has the potential to serve as a promising drug for NSCLC treatment.
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Affiliation(s)
- Zongren Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huanghe West Road, Huaiyin District, Huai‘an City, Jiangsu Province, 223300, China
| | - Jipeng Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huanghe West Road, Huaiyin District, Huai‘an City, Jiangsu Province, 223300, China
| | - Qing Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huanghe West Road, Huaiyin District, Huai‘an City, Jiangsu Province, 223300, China
| | - Dan Yang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huanghe West Road, Huaiyin District, Huai‘an City, Jiangsu Province, 223300, China
| | - Pengling Li
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huanghe West Road, Huaiyin District, Huai‘an City, Jiangsu Province, 223300, China
| | - Lixin Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huanghe West Road, Huaiyin District, Huai‘an City, Jiangsu Province, 223300, China
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Ge Y, Ma S, Zhang J, Xiong Z, Li B, Ma S, Liu B, Yao X, Wang Z. Integrating bioinformatic analysis and detailed experiments reveal an EMT-related biomarker for clear cell renal cell carcinoma. Cancer Med 2023; 12:19320-19336. [PMID: 37676078 PMCID: PMC10557903 DOI: 10.1002/cam4.6504] [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: 06/23/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) is associated with early recurrence and a poor prognosis in clear cell renal cell carcinoma (ccRCC). Studies have shown that EMT-related genes play an important regulatory role in tumor invasion, metastasis, and drug resistance, but the biological functions of EMT-related genes in ccRCC have not been specifically described. METHODS The mRNA and clinicopathological data of 532 ccRCC and 72 normal samples were downloaded from The Cancer Genome Atlas as a training set. The gene expression matrix and survival data of 91 and 101 ccRCC samples were obtained from the International Cancer Genome Consortium and the ArrayExpress databases as validation sets, respectively. Univariate Cox analysis was used to identify and cluster prognostic genes, and multivariate Cox was performed to construct a prognostic signature. Moreover, CIBERSORT and CellMiner were used to assess immune cell infiltration and prognostic gene-drug sensitivity of the signature, respectively. Most importantly, we performed detailed experiments to verify the oncogenic function of a significant gene, OLFML2B, in vitro and in vivo. RESULTS We constructed a prognostic signature including seven genes and divided patients into high-risk and low-risk groups. The prognosis of the high-risk group was significantly worse than that of the low-risk group through Kaplan-Meier survival analysis. Interestingly, significant differences were observed in clinical characteristics and immune cell infiltration between the two groups. In addition, a significant correlation was found between the expression of prognostic genes and the sensitivity of tumor cells to chemotherapeutics. Most importantly, OLFML2B was proved to contribute to the proliferation and metastasis of ccRCC through detailed functional experiments in vitro and in vivo, and its prognostic efficacy for ccRCC patients was affirmed. CONCLUSION We identified the prognostic signature of seven genes based on EMT-related genes as prognostic biomarkers for ccRCC. Besides, OLFML2B was validated as a potential diagnostic and therapeutic target for ccRCC by our detailed experiments.
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Affiliation(s)
- Yue Ge
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Sheng Ma
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Junbiao Zhang
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Zezhong Xiong
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Beining Li
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Siquan Ma
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiangyang Yao
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Zhang T, Qiu L, Cao J, Li Q, Zhang L, An G, Ni J, Jia H, Li S, Li K. ZFP36 loss-mediated BARX1 stabilization promotes malignant phenotypes by transactivating master oncogenes in NSCLC. Cell Death Dis 2023; 14:527. [PMID: 37587140 PMCID: PMC10432398 DOI: 10.1038/s41419-023-06044-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, with high morbidity and mortality worldwide. Although the dysregulation of BARX1 expression has been shown to be associated with malignant cancers, including NSCLC, the underlying mechanism remains elusive. In this study, we identified BARX1 as a common differentially expressed gene in lung squamous cell carcinoma and adenocarcinoma. Importantly, we uncovered a novel mechanism behind the regulation of BARX1, in which ZFP36 interacted with 3'UTR of BARX1 mRNA to mediate its destabilization. Loss of ZFP36 led to the upregulation of BARX1, which further promoted the proliferation, migration and invasion of NSCLC cells. In addition, the knockdown of BARX1 inhibited tumorigenicity in mouse xenograft. We demonstrated that BARX1 promoted the malignant phenotypes by transactivating a set of master oncogenes involved in the cell cycle, DNA synthesis and metastasis. Overall, our study provides insights into the mechanism of BARX1 actions in NSCLC and aids a better understanding of NSCLC pathogenesis.
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Affiliation(s)
- Tongjia Zhang
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Lizhen Qiu
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Jiashun Cao
- Department of Thoracic Surgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, 102218, Beijing, China
| | - Qiu Li
- Department of Research, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, 102218, Beijing, China
| | - Lifan Zhang
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Guoshun An
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Juhua Ni
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Hongti Jia
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Shuyan Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China.
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China.
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Wang J, Tao L, Liu Y, Liu H, Shen X, Tao L. Identification and validation of DLX4 as a prognostic and diagnostic biomarker for clear cell renal cell carcinoma. Oncol Lett 2023; 25:146. [PMID: 36936018 PMCID: PMC10018244 DOI: 10.3892/ol.2023.13732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/09/2021] [Indexed: 03/04/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a lethal cancer, and biomarkers for exact diagnosis and predicting prognosis are urgently needed. The present study aimed to determine the roles of distal-less homeobox (DLX) family genes in ccRCC. The clinicopathological and mRNA expression data of patients with ccRCC were derived from The Cancer Genome Atlas database. Kaplan-Meier curves, univariate and multivariate Cox hazard analyses, in addition to receiver operator characteristic curves were used to evaluate the prognostic and diagnostic values. A single-sample gene set enrichment analysis was used to quantify the infiltration levels of immune cells. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry were conducted to examine the expression levels of DLX4 in tumor and adjacent tissue; the results demonstrated that DLX4 was highly expressed in ccRCC tissues compared with normal renal tissues. Furthermore, DLX4 expression was associated with tumor stage and grade. High proportions of males, advanced pathological stage, higher tumor grade and T, N and M stage were also observed in the high DLX4 expression group. Patients with the high DLX4 expression levels tended to have lower overall survival and disease-free survival rates compared with those with low DLX4 expression. DLX4 expression also showed favorable diagnostic efficiency in ccRCC patients. Based on functional enrichment analysis, cell cycle related pathways, epithelial-mesenchymal transition, glycolysis and inflammatory response were associated with the expression levels of DLX4. Furthermore, DLX4 expression was revealed to be associated with tumor immunosuppressive microenvironment. Overall, the expression level of DLX4 may be considered a novel prognostic indicator in ccRCC and a specific diagnostic biomarker for patients with ccRCC.
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Affiliation(s)
- Jiawei Wang
- Department of Urology, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, P.R. China
| | - Liangjun Tao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yingqing Liu
- Department of Urology, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, P.R. China
| | - Heqian Liu
- Department of Urology, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, P.R. China
| | - Xudong Shen
- Department of Urology, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, P.R. China
| | - Lingsong Tao
- Department of Urology, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, P.R. China
- Correspondence to: Dr Lingsong Tao, Department of Urology, The Second People's Hospital of Wuhu, 259 JiuHuaShan Avenue, Wuhu, Anhui 241000, P.R. China, E-mail:
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Huang X, Wang Z, Zhang J, Ni X, Bai G, Cao J, Zhang C, Han Z, Liu T. BARX1 promotes osteosarcoma cell proliferation and invasion by regulating HSPA6 expression. J Orthop Surg Res 2023; 18:211. [PMID: 36927457 PMCID: PMC10018937 DOI: 10.1186/s13018-023-03690-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Osteosarcoma (OS) is a bone tumour affecting adolescents. Dysregulation of Barx homeobox 1 (BARX1) expression is involved in various cancers, but its function and mechanism in the process of OS are undefined. This study revealed that BARX1 expression is higher in OS tissue than in adjacent normal tissue. Downregulation of BARX1 in OS cells significantly suppressed their proliferation and migration, whereas enforced expression of exogenous BARX1 exerted the opposite effects on OS cells. Subsequently, heat shock 70-kDa protein 6 (HSPA6) expression was clearly increased after BARX1 overexpression in OS cells, as confirmed by RNA sequencing. The dual-luciferase reporter assay confirmed that HSPA6 expression is directly regulated by BARX1. The in vitro assay indicated that silencing HSPA6 expression attenuated OS proliferation and migration induced by BARX1. A dual immunofluorescence labelling assay provided further evidence that BARX1 was overexpressed and associated with HSPA6 overexpression in OS tumour tissue. In conclusion, BARX1 promotes OS cell proliferation and migration by inducing the expression of HSPA6, which plays an oncogenic role in OS. BARX1 and HSPA6 can potentially act as novel therapeutic targets for OS.
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Affiliation(s)
- Xing Huang
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Zhenhua Wang
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Jing Zhang
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Xiangzhi Ni
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Guangjian Bai
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Jiashi Cao
- Department of Orthopedics, No. 455 Hospital of Chinese People's Liberation Army, The Navy Medical University, No. 338 Huaihai West Road, Shanghai, 200052, China
| | - Chunlei Zhang
- Department of Orthopedics, Nanjing Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.
| | - Zhitao Han
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Tielong Liu
- Department of Orthopaedic Oncology, The Second Affiliated Hospital of Naval Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai, 200003, China.
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Ma S, Ge Y, Xiong Z, Wang Y, Li L, Chao Z, Li B, Zhang J, Ma S, Xiao J, Liu B, Wang Z. A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma. PeerJ 2023; 11:e14784. [PMID: 36785707 PMCID: PMC9921988 DOI: 10.7717/peerj.14784] [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: 10/20/2022] [Accepted: 01/03/2023] [Indexed: 02/10/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is considered to be related to the worse prognosis, which might in part be attributed to the early recurrence and metastasis, compared with other type of kidney cancer. Oxidative stress refers to an imbalance between production of oxidants and antioxidant defense. Accumulative studies have indicated that oxidative stress genes contribute to the tumor invasion, metastasis and drug sensitivity. However, the biological functions of oxidative stress genes in ccRCC remain largely unknown. In this study, we identified 1,399 oxidative stress genes from GeneCards with a relevance score ≥7. Data for analysis were accessed from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database, and were utilized as training set and validation set respectively. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox were employed to construct a prognostic signature in ccRCC. Finally, a prognostic signature including four different oxidative stress genes was constructed from 1,399 genes, and its predictive performance was verified through Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) curve. Interestingly, we found that there was significant correlation between the expression of oxidative stress genes and the immune infiltration and the sensitivity of tumor cells to chemotherapeutics. Moreover, the highest hazard ratio gene urocortin (UCN) was chosen for further study; some necessary vitro experiments proved that the UCN could promote the ability of ccRCC proliferation and migration and contribute to the degree of oxidative stress. In conclusion, it was promising to predict the prognosis of ccRCC through the four oxidative stress genes signature. UCN played oncogenic roles in ccRCC by influencing proliferation and oxidative stress pathway, which was expected to be the novel therapeutic target for ccRCC.
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Affiliation(s)
- Sheng Ma
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yue Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zezhong Xiong
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanan Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Le Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zheng Chao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Beining Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junbiao Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Siquan Ma
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Xiao
- Department of Thyroid and Breast Surgery, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Construction of an Epithelial-Mesenchymal Transition-Related Model for Clear Cell Renal Cell Carcinoma Prognosis Prediction. DISEASE MARKERS 2022; 2022:3780391. [PMID: 35983409 PMCID: PMC9381281 DOI: 10.1155/2022/3780391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022]
Abstract
Background. A rising amount of data demonstrates that the epithelial-mesenchymal transition (EMT) in clear cell renal cell carcinomas (ccRCC) is connected with the advancement of the cancer. In order to understand the role of EMT in ccRCC, it is critical to integrate molecules involved in EMT into prognosis prediction. The objective of this project was to establish a prognosis prediction model using genes associated with EMT in ccRCC. Methods. We acquired the mRNA expression profiles and clinical information about ccRCC from TCGA database. In this study, we measured differentially expressed EMT-related genes (DEEGs) by two comparison groups (tumor versus normal tissues; “stages I-II” versus “stages III-IV” tumor tissues). Based on classification and regression random forest models, we identified the most important DEEGs in predicting prognosis. Afterwards, a risk-score model was created using the identified important DEEGs. The prediction ability of the risk-score model was calculated by the area under the curve (AUC). A nomogram for prognosis prediction was built using the risk-score in combination with clinical factors. Results. Among the 72 DEEGs, the classification and regression random forest models identified six hub genes (DKK1, DLX4, IL6, KCNN4, RPL22L1, and SPDEF), which exhibited the highest importance values in both models. Through the expression of these six hub genes, a novel risk-score was developed for the prognosis prediction of ccRCC. ROC curves showed the risk-score performed well in both the training (0.749) and testing (0.777) datasets. According to the survival analysis, individuals who were separated into high/low-risk groups had statistically different outcomes in terms of prognosis. Besides, the risk-score model also showed outstanding ability in assessing the progression of ccRCC after treatment. In terms of nomogram, the concordance index (C-index) was 0.79. Additionally, we predicted the differences in response to chemotherapy drugs among patients from low- and high-risk groups. Conclusion. Gene signatures related to EMT could be useful in predicting ccRCC prognosis.
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Zhou JD, Zhao YJ, Leng JY, Gu Y, Xu ZJ, Ma JC, Wen XM, Lin J, Zhang TJ, Qian J. DNA methylation-mediated differential expression of DLX4 isoforms has opposing roles in leukemogenesis. Cell Mol Biol Lett 2022; 27:59. [PMID: 35883028 PMCID: PMC9327205 DOI: 10.1186/s11658-022-00358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Background Previously, we reported the expression of DLX4 isoforms (BP1 and DLX7) in myeloid leukemia, but the functional role of DLX4 isoforms remains poorly understood. In the work described herein, we further determined the underlying role of DLX4 isoforms in chronic myeloid leukemia (CML) leukemogenesis. Methods The expression and methylation of DLX4 isoforms were detected by real-time quantitative PCR (RT-qPCR) and real-time quantitative methylation-specific PCR (RT-qMSP) in patients with CML. The functional role of DLX4 isoforms was determined in vitro and in vivo. The molecular mechanism of DLX4 isoforms in leukemogenesis was identified based on chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq)/assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) and RNA sequencing (RNA-Seq). Results BP1 expression was increased in patients with CML with unmethylated promoter, but DLX7 expression was decreased with hypermethylated promoter. Functionally, overexpression of BP1 increased the proliferation rate of K562 cells with S/G2 promotion, whereas DLX7 overexpression reduced the proliferation rate of K562 cells with G1 arrest. Moreover, K562 cells with BP1 overexpression increased the tumorigenicity in NCG mice, whereas K562 cells with DLX7 overexpression decreased the tumorigenicity. Mechanistically, a total of 91 genes including 79 messenger RNAs (mRNAs) and 12 long noncoding RNAs (lncRNAs) were discovered by ChIP-Seq and RNA-Seq as direct downstream targets of BP1. Among the downstream genes, knockdown of RREB1 and SGMS1-AS1 partially revived the proliferation caused by BP1 overexpression in K562 cells. Similarly, using ATAC-Seq and RNA-Seq, a total of 282 genes including 151 mRNA and 131 lncRNAs were identified as direct downstream targets of DLX7. Knockdown of downstream genes PTPRB and NEAT1 partially revived the proliferation caused by DLX7 overexpression in K562 cells. Finally, we also identified and validated a SGMS1-AS1/miR-181d-5p/SRPK2 competing endogenous RNA (ceRNA) network caused by BP1 overexpression in K562 cells. Conclusions The current findings reveal that DNA methylation-mediated differential expression of DLX4 isoforms BP1 and DLX7 plays opposite functions in leukemogenesis. BP1 plays an oncogenic role in leukemia development, whereas DLX7 acts as a tumor suppressor gene. These results suggest DLX4 as a therapeutic target for antileukemia therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00358-0.
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Affiliation(s)
- Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yang-Jing Zhao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Ting-Juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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11
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Jiang A, Wu X, Wang D, Wang A, Dong K, Liu B, Qu L, Luo P, Wang J, Tong Q, Wang L. A New Thinking: Deciphering the Aberrance and Clinical Implication of IGF Axis Regulation Pattern in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:935595. [PMID: 35935986 PMCID: PMC9355597 DOI: 10.3389/fimmu.2022.935595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Rationale The recent research found that IGF regulator genes played a pivotal role in multiple biological processes, which may be developed for cancer treatment. However, the characteristics and implication of IGF regulators in cancers, especially in clear cell renal cell carcinoma (ccRCC), remain elusive. Methods We systematically analyzed the expression, prognostic valuation, genome variation, and functional implication at pan-cancer level from The Cancer Genome Atlas. According to expression levels of IGF regulator genes, ccRCC could be divided into three different subtypes via unsupervised cluster algorithm: IGF pattern cancer type1 (IPCS1), type2 (IPCS2), and type3 (IPCS3). The immune microenvironment, immunotherapy response, metabolic pattern, and tumor progression signature among the three subgroups were investigated. The clinical characteristics, genomic mutations, and potential drug sensitivity were further analyzed. IGF pattern–related risk model was constructed to predict RCC patients’ outcome. Finally, SHC1, a potential IGF axis target, was comprehensively investigated in ccRCC. Results We found that IGF regulator genes were specifically upregulated in various cancer tissues, which were correlated with copy number variations and dysregulated pathways. IPCS1, IPCS2, and IPCS3 exhibited different clinical profiles and biological characteristics in ccRCC. IPCS3 subtype indicated a higher clinical stage and a worse survival. IPSC3 ccRCC displayed activated metabolic signatures to fuel the cancer progression. IPCS3 subgroup holds a higher tumor mutation burden and lower immune activities, which resulted in a low ICI therapy response and tumor immunity dysfunction state. The genome copy numbers of IPCS2/3, including arm gain and arm loss, were significantly higher than IPCS1. Besides, the drug sensitivity profiles were different among the three subgroups. The prognostic risk model based on subtype’s biomarker exerted a promising performance both in training and validation cohorts. Finally, upregulated expression of SHC1 partly induced poorer immunotherapy response and shorter survival of ccRCC patients. Conclusion Targeting IGF regulators may be functioned as a treatment approach among multi-cancers. IGF regulator–related signature could reshape the tumor immune microenvironment via activating multi-step immune programs. The inhibition of SHC1 may enhance the efficacy of immunotherapy, and SHC1 could be a suitable target for ccRCC therapy.
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Affiliation(s)
- Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
| | - Xiaofeng Wu
- Department of Urology, Changhai Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
| | - Desheng Wang
- Department of Urology, The Second People's Hospital of BengBu, Bengbu, China
| | - Anbang Wang
- Department of Urology, Changzheng Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
| | - Kai Dong
- Department of Urology, Changhai Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
| | - Bing Liu
- Department of Urology, The Third Affiliated Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Wang
- Department of Urology, The Second People's Hospital of Nantong, Nantong, China
| | - Qiang Tong
- Department of Urology, No. 905 Hospital of PLA (Chinese People's Liberation Army) Navy, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University, (Second Military Medical University), Shanghai, China
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12
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Vaivads M, Akota I, Pilmane M. Immunohistochemical Evaluation of BARX1, DLX4, FOXE1, HOXB3, and MSX2 in Nonsyndromic Cleft Affected Tissue. Acta Med Litu 2022; 29:271-294. [PMID: 37733420 PMCID: PMC9799009 DOI: 10.15388/amed.2022.29.2.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background Nonsyndromic craniofacial clefts are relatively common congenital malformations which could create a significant negative effect on the health status and life quality of affected individuals within the pediatric population. Multiple cleft candidate genes and their coded proteins have been described with their possible involvement during cleft formation. Some of these proteins like Homeobox Protein BarH-like 1 (BARX1), Distal-Less Homeobox 4 (DLX4), Forkhead Box E1 (FOXE1), Homeobox Protein Hox-B3 (HOXB3), and Muscle Segment Homeobox 2 (MSX2) have been associated with the formation of craniofacial clefts. Understanding the pathogenetic mechanisms of nonsyndromic craniofacial cleft formation could provide a better knowledge in cleft management and could be a possible basis for development and improvement of cleft treatment options. This study investigates the presence of BARX1, DLX4, FOXE1, HOXB3, and MSX2 positive cells by using immunohistochemistry in different types of cleft-affected tissue while determining their possible connection with cleft pathogenesis process. Materials and Methods Craniofacial cleft tissue material was obtained during cleft-correcting surgery from patients with nonsyndromic craniofacial cleft diagnosis. Tissue material was gathered from patients who had unilateral cleft lip (n=36), bilateral cleft lip (n=13), and cleft palate (n=26). Control group (n=7) tissue material was received from individuals without any craniofacial clefts. The number of factor positive cells in the control group and patient group tissue was evaluated by using the semiquantitative counting method. Data was evaluated with the use of nonparametric statistical methods. Results Statistically significant differences were identified between the number of BARX1, FOXE1, HOXB3, and MSX2-containing cells in controls and cleft patient groups but no statistically significant difference was found for DLX4. Statistically significant correlations between the evaluated factors were also notified in cleft patient groups. Conclusions HOXB3 could be more associated with morphopathogenesis of unilateral cleft lip during postnatal course of the disorder. FOXE1 and BARX1 could be involved with both unilateral and bilateral cleft lip morphopathogenesis. The persistence of MSX2 in all evaluated cleft types could indicate its possible interaction within multiple cleft types. DLX4 most likely is not involved with postnatal cleft morphopathogenesis process.
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Affiliation(s)
- Mārtiņš Vaivads
- Institute of Anatomy and Anthropology, Riga Stradins University, Riga, Latvia
| | - Ilze Akota
- Department of Oral and Maxillofacial Surgery, Riga Stradins University, Riga, Latvia
- Cleft Lip and Palate Centre, Institute of Stomatology, Riga Stradins University, Riga, Latvia
| | - Māra Pilmane
- Institute of Anatomy and Anthropology, Riga Stradins University, Riga, Latvia
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13
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Dong K, Gu D, Shi J, Bao Y, Fu Z, Fang Y, Qu L, Zhu W, Jiang A, Wang L. Identification and Verification of m 7G Modification Patterns and Characterization of Tumor Microenvironment Infiltration via Multi-Omics Analysis in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:874792. [PMID: 35592316 PMCID: PMC9113293 DOI: 10.3389/fimmu.2022.874792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
The epigenetic modification of tumorigenesis and progression in neoplasm has been demonstrated in recent studies. Nevertheless, the underlying association of N7-methylguanosine (m7G) regulation with molecular heterogeneity and tumor microenvironment (TME) in clear cell renal cell carcinoma (ccRCC) remains unknown. We explored the expression profiles and genetic variation features of m7G regulators and identified their correlations with patient outcomes in pan-cancer. Three distinct m7G modification patterns, including MGCS1, MGCS2, and MGCS3, were further determined and systematically characterized via multi-omics data in ccRCC. Compared with the other two subtypes, patients in MGCS3 exhibited a lower clinical stage/grade and better prognosis. MGCS1 showed the lowest enrichment of metabolic activities. MGCS2 was characterized by the suppression of immunity. We then established and validated a scoring tool named m7Sig, which could predict the prognosis of ccRCC patients. This study revealed that m7G modification played a vital role in the formation of the tumor microenvironment in ccRCC. Evaluating the m7G modification landscape helps us to raise awareness and strengthen the understanding of ccRCC’s characterization and, furthermore, to guide future clinical decision making.
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Affiliation(s)
- Kai Dong
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Di Gu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jiazi Shi
- Department of Urology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yewei Bao
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zhibin Fu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yu Fang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wentong Zhu
- School of Chinese Medicine, Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
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14
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Šestáková Š, Cerovská E, Šálek C, Kundrát D, Ježíšková I, Folta A, Mayer J, Ráčil Z, Cetkovský P, Remešová H. A validation study of potential prognostic DNA methylation biomarkers in patients with acute myeloid leukemia using a custom DNA methylation sequencing panel. Clin Epigenetics 2022; 14:22. [PMID: 35148810 PMCID: PMC8832751 DOI: 10.1186/s13148-022-01242-6] [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: 09/23/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple studies have reported the prognostic impact of DNA methylation changes in acute myeloid leukemia (AML). However, these epigenetic markers have not been thoroughly validated and therefore are still not considered in clinical practice. Hence, we aimed to independently verify results of selected studies describing the relationship between DNA methylation of specific genes and their prognostic potential in predicting overall survival (OS) and event-free survival (EFS). RESULTS Fourteen studies (published 2011-2019) comprising of 27 genes were subjected to validation by a custom NGS-based sequencing panel in 178 newly diagnosed non-M3 AML patients treated by 3 + 7 induction regimen. The results were considered as successfully validated, if both the log-rank test and multivariate Cox regression analysis had a p-value ≤ 0.05. The predictive role of DNA methylation was confirmed for three studies comprising of four genes: CEBPA (OS: p = 0.02; EFS: p = 0.03), PBX3 (EFS: p = 0.01), LZTS2 (OS: p = 0.05; EFS: p = 0.0003), and NR6A1 (OS: p = 0.004; EFS: p = 0.0003). For all of these genes, higher methylation was an indicator of longer survival. Concurrent higher methylation of both LZTS2 and NR6A1 was highly significant for survival in cytogenetically normal (CN) AML group (OS: p < 0.0001; EFS: p < 0.0001) as well as for the whole AML cohort (OS: p = 0.01; EFS < 0.0001). In contrast, for two studies reporting the poor prognostic effect of higher GPX3 and DLX4 methylation, we found the exact opposite, again linking higher GPX3 (OS: p = 0.006; EFS: p < 0.0001) and DLX4 (OS: p = 0.03; EFS = 0.03) methylation to a favorable treatment outcome. Individual gene significance levels refer to the outcomes of multivariate Cox regression analysis. CONCLUSIONS Out of twenty-seven genes subjected to DNA methylation validation, a prognostic role was observed for six genes. Therefore, independent validation studies are necessary to reveal truly prognostic DNA methylation changes and to enable the introduction of these promising epigenetic markers into clinical practice.
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Affiliation(s)
- Šárka Šestáková
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic.,Institute of Clinical and Experimental Hematology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ela Cerovská
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Cyril Šálek
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic.,Institute of Clinical and Experimental Hematology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Dávid Kundrát
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic
| | - Ivana Ježíšková
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Adam Folta
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Jiří Mayer
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Zdeněk Ráčil
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic
| | - Petr Cetkovský
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic.,Institute of Clinical and Experimental Hematology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hana Remešová
- Department of Genomics, Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20, Prague 2, Czech Republic.
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Li Z, Zou W, Sun J, Zhou S, Zhou Y, Cai X, Zhang J. A comprehensive gene expression profile of allergic rhinitis-derived nasal fibroblasts and the potential mechanism for its phenotype. Hum Exp Toxicol 2022; 41:9603271211069038. [PMID: 35133179 DOI: 10.1177/09603271211069038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Allergic rhinitis (AR) is a common immunoglobulin E-mediated immune response involved various cell types, while the role of nasal fibroblasts (NFs) in the pathogenesis of AR is less understood. PURPOSE The study aimed to uncover the gene expression profile of AR-derived NFs and the potential mechanism for the changed phenotype of AR-NFs. RESEARCH DESIGN The primary NFs were isolated from 3 AR patients (AR-NFs) and 3 controls (Ctrl-NFs), and the proliferation, migration and interleukins production abilities of NFs were detected respectively. RNA-sequence was used to identify differentially expressed genes (DEGs) in AR-NFs. Transcription factor (TF) regulatory network and bioinformatic analyses were both conducted to clarify the biological roles of DEGs including the TFs. The DEG with the highest validated |fold change (FC)| value, detected by qPCR, was selected for further confirmation. RESULTS AR-NFs showed a higher proliferation and migration abilities as well as released higher levels of IL-33 and IL-6, compared to Ctrl-NFs. A total of 729 DEGs were screened out in AR-NFs. TF regulatory network indicated that BARX homeobox 1 (BARX1) and forkhead box L1 were the major node TFs. Bioinformatic analyses showed that a large number of DEGs including several target genes of BARX1 were both enriched cytokine-related GO terms, and immune- or inflammation-related pathways. BARX1 had the highest |FC| value, and silencing BARX1 in AR-NFs resulted in the significant downregulation of proliferation and migration abilities, and the production of interleukins. CONCLUSIONS Our study for the first time provided the gene expression profile of AR-derived NFs, and BARX1 could be developed as a potent target to alleviate the pathogenesis of AR.
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Affiliation(s)
- Zhengwen Li
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Wentao Zou
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Jingwen Sun
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Shuang Zhou
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Yue Zhou
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Xiaojing Cai
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Jiaxiong Zhang
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
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Chen Y, Tang L, Huang W, Zhang Y, Abisola FH, Li L. Identification and validation of a novel cuproptosis-related signature as a prognostic model for lung adenocarcinoma. Front Endocrinol (Lausanne) 2022; 13:963220. [PMID: 36353226 PMCID: PMC9637654 DOI: 10.3389/fendo.2022.963220] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/10/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Cuproptosis is a novel form of copper-induced cell death that targets lipoylated tricarboxylic acid (TCA) cycle proteins. However, its prognostic role in lung adenocarcinoma (LUAD) remains unclear. This study aimed to establish a cuproptosis-related prognostic signature for patients with LUAD. METHODS Transcriptome data of LUAD samples were extracted from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The prognostic value of cuproptosis-related genes (CRGs) was investigated using Cox regression analysis to develop a cuproptosis-related prognostic model. Kyoto Encyclopedia of Genes and Genomes (KEGG), gene ontology (GO) and gene set variation analysis (GSVA) were conducted to characterize different biological activities or pathways between high- or low-CRG groups. The expression pattern and prognostic values of CRGs were validated in 37 paired tumor-normal samples using quantitative PCR. Furthermore, in vitro experiments were performed to investigate the relationship between cuproptosis and CRG expression and to explore the function of target genes in cuproptosis. RESULTS Among the 36 CRGs, 17 genes were upregulated, and 3 genes were downregulated in LUAD. A total of 385 CRGs were identified using Pearson correlation analysis. A cuproptosis-related signature was constructed using least absolute shrinkage and selection operator (LASSO) analysis. The prognostic value of the cuproptosis-related signature was validated in six external validation cohorts and in LUAD specimens from our facility. Patients in the high-risk group based on the CRG signature score had shorter overall survival than those in the low-risk group in both the datasets and clinical specimens. In vitro experiments revealed that the expression of BARX1, GFRA3, and KHDRBS2 was upregulated after cuproptosis was induced by elesclomol-CuCL2, whereas the upregulation was suppressed on pretreatment with tetrathiomolybdate (TTM), a chelator of copper. Further, the cell proliferation assay revealed that the BARX1 and GFRA3 deficiency facilities the cuproptosis induced by elesclomol-CuCL2. CONCLUSION This study established a new CRG signature that can be used to predict the OS of LUAD patients. Moreover, the knockdown of BARX1 and GFRA3 could increase the sensitivity of LUAD cells to the cuproptosis.
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Affiliation(s)
- Yuqiao Chen
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Tang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wentao Huang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Youyu Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fakolade Hannah Abisola
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linfeng Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Linfeng Li,
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