1
|
Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [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: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
Collapse
Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| |
Collapse
|
2
|
Wang S, Wu X, Yang J, Peng Y, Miao F, Li M, Zeng J. Sterigmatocystin declines mouse oocyte quality by inducing ferroptosis and asymmetric division defects. J Ovarian Res 2024; 17:175. [PMID: 39198920 PMCID: PMC11351269 DOI: 10.1186/s13048-024-01499-w] [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: 03/28/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND Sterigmatocystin (STE) is a mycotoxin widely found in contaminated food and foodstuffs, and excessive long-term exposure to STE is associated with several health issues, including infertility. However, there is little information available regarding the effects of STE toxin on the female reproductive system, particularly concerning oocyte maturation. METHODS In the present study, we investigated the toxic effects of STE on mouse oocyte maturation. We also used Western blot, immunofluorescence, and image quantification analyses to assess the impact of STE exposure on the oocyte maturation progression, mitochondrial distribution, oxidative stress, DNA damages, oocyte ferroptosis and asymmetric division defects. RESULTS Our results revealed that STE exposure disrupted mouse oocyte maturation progression. When we examined the cellular changes following 100 µM STE treatment, we found that STE adversely affected polar body extrusion and induced asymmetric division defects in oocytes. RNA-sequencing data showed that STE exposure affects the expression of several pathway-correlated genes during oocyte meiosis in mice, suggesting its toxicity to oocytes. Based on the RNA-seq data, we showed that STE exposure induced oxidative stress and caused DNA damage in oocytes. Besides, ferroptosis and α-tubulin acetylation were also found in STE-exposed oocytes. Moreover, we determined that STE exposure resulted in reduced RAF1 protein expression in mouse oocytes, and inhibition of RAF1 activity also causes defects in asymmetric division of mouse oocytes. CONCLUSIONS Collectively, our research provides novel insights into the molecular mechanisms whereby STE contributes to abnormal meiosis.
Collapse
Affiliation(s)
- Shiwei Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xuan Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juan Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China
| | - Yuwan Peng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China
| | - Fulu Miao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China
| | - Min Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China
| | - Juan Zeng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Heifei, Anhui, 230022, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, China.
| |
Collapse
|
3
|
Liang ZQ, Zhang W, Zeng DT, Chen JH, Luo JY, Shi L, Wei KL, Chen G. Upregulation of hsa-miR-141-3p promotes uterine cervical carcinoma progression via targeting dual-specificity protein phosphatase 1. Funct Integr Genomics 2024; 24:137. [PMID: 39138666 DOI: 10.1007/s10142-024-01413-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024]
Abstract
We aimed to explore the aberrant expression status of hsa-miR-141-3p and dual-specificity protein phosphatase 1 (DUSP1) and their relative mechanisms in uterine cervical carcinoma (UCC).Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was conducted to detect the expression of hsa-miR-141-3p. Immunohistochemical (IHC) staining was performed to examine the expression of DUSP1 in UCC. Gene chips and RNA-seq datasets were also obtained to assess the expression level. Integrated standardized mean difference (SMD) was calculated to evaluate the expression status of hsa-miR-141-3p in UCC tissues comprehensively. DUSP1-overexpression and hsa-miR-141-3p-inhibition HeLa cells were established, and CCK-8, transwell, wound healing, cell cycle, and apoptosis assays were implemented. The targets of hsa-miR-141-3p were obtained with online tools, and the combination of hsa-miR-141-3p and DUSP1 was validated via dual-luciferase reporter assay. Single-cell RNA-seq data were analyzed to explore hsa-miR-141-3p and DUSP1 in different cells. An integrated SMD of 1.41 (95% CI[0.45, 2.38], p = 0.0041) with 558 samples revealed the overexpression of hsa-miR-141-3p in UCC tissues. And the pooled SMD of -1.06 (95% CI[-1.45, -0.66], p < 0.0001) with 1,268 samples indicated the downregulation of DUSP1. Inhibition of hsa-miR-141-3p could upregulate DUSP1 expression and suppress invasiveness and metastasis of HeLa cells. Overexpression of DUSP1 could hamper proliferation, invasion, and migration and boost apoptosis and distribution of G1 phase. The dual-luciferase reporter assay validated the combination of hsa-miR-141-3p and DUSP1. Moreover, the targets of hsa-miR-141-3p were mainly enriched in the MAPK signaling pathway and activated in fibroblasts and endothelial cells. The current study illustrated the upregulation of hsa-miR-141-3p and the downregulation of DUSP1 in UCC tissues. Hsa-miR-141-3p could promote UCC progression by targeting DUSP1.
Collapse
Affiliation(s)
- Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Wei Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Da-Tong Zeng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
- Department of Pathology, Red Cross Hospital of Yulin City, No. 1. Jinwang Rd, Yulin, Guangxi Zhuang Autonomous Region, 537006, P. R. China
| | - Jun-Hong Chen
- Department of Pathology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59. Xiangzhu Road, Nanning, 530003, Guangxi Zhuang Autonomous Region, P. R. China
| | - Jia-Yuan Luo
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China
| | - Lin Shi
- Department of Pathology, The Second Affiliated Hospital of Guangxi Medical University, No. 166. Daxuedong Rd, Nanning, Guangxi Zhuang Autonomous Region, 530005, P. R. China
| | - Kang-Lai Wei
- Department of Pathology, The Second Affiliated Hospital of Guangxi Medical University, No. 166. Daxuedong Rd, Nanning, Guangxi Zhuang Autonomous Region, 530005, P. R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, No. 6. Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, P. R. China.
| |
Collapse
|
4
|
Lin Y, Liu J. Anoikis-related genes as potential prognostic biomarkers in gastric cancer: A multilevel integrative analysis and predictive therapeutic value. IET Syst Biol 2024; 18:41-54. [PMID: 38377622 PMCID: PMC10996445 DOI: 10.1049/syb2.12088] [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: 06/27/2023] [Revised: 11/11/2023] [Accepted: 02/11/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) is a frequent malignancy of the gastrointestinal tract. Exploring the potential anoikis mechanisms and pathways might facilitate GC research. PURPOSE The authors aim to determine the significance of anoikis-related genes (ARGs) in GC prognosis and explore the regulatory mechanisms in epigenetics. METHODS After describing the genetic and transcriptional alterations of ARGs, we searched differentially expressed genes (DEGs) from the cancer genome atlas and gene expression omnibus databases to identify major cancer marker pathways. The non-negative matrix factorisation algorithm, Lasso, and Cox regression analysis were used to construct a risk model, and we validated and assessed the nomogram. Based on multiple levels and online platforms, this research evaluated the regulatory relationship of ARGs with GC. RESULTS Overexpression of ARGs is associated with poor prognosis, which modulates immune signalling and promotes anti-anoikis. The consistency of the DEGs clustering with weighted gene co-expression network analysis results and the nomogram containing 10 variable genes improved the clinical applicability of ARGs. In anti-anoikis mode, cytology, histology, and epigenetics could facilitate the analysis of immunophenotypes, tumour immune microenvironment (TIME), and treatment prognosis. CONCLUSION A novel anoikis-related prognostic model for GC is constructed, and the significance of anoikis-related prognostic genes in the TIME and the metabolic pathways of tumours is initially explored.
Collapse
Affiliation(s)
- Yongjian Lin
- Department of Gastrointestinal and Gland Surgerythe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| | - Jinlu Liu
- Department of Gastrointestinal and Gland Surgerythe First Affiliated Hospital of Guangxi Medical UniversityNanningChina
| |
Collapse
|
5
|
Liu X, Yu J, Li Y, Shi H, Jiao X, Liu X, Guo D, Li Z, Tian Y, Dai F, Niu Z, Zhou Y. Deciphering the tumor immune microenvironment of imatinib-resistance in advanced gastrointestinal stromal tumors at single-cell resolution. Cell Death Dis 2024; 15:190. [PMID: 38443340 PMCID: PMC10914684 DOI: 10.1038/s41419-024-06571-3] [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: 10/30/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
The heterogeneous nature of tumors presents a considerable obstacle in addressing imatinib resistance in advanced cases of gastrointestinal stromal tumors (GIST). To address this issue, we conducted single-cell RNA-sequencing in primary tumors as well as peritoneal and liver metastases from patients diagnosed with locally advanced or advanced GIST. Single-cell transcriptomic signatures of tumor microenvironment (TME) were analyzed. Immunohistochemistry and multiplex immunofluorescence staining were used to further validate it. This analysis revealed unique tumor evolutionary patterns, transcriptome features, dynamic cell-state changes, and different metabolic reprogramming. The findings indicate that in imatinib-resistant TME, tumor cells with activated immune and cytokine-mediated immune responses interacted with a higher proportion of Treg cells via the TIGIT-NECTIN2 axis. Future immunotherapeutic strategies targeting Treg may provide new directions for the treatment of imatinib-resistant patients. In addition, IDO1+ dendritic cells (DC) were highly enriched in imatinib-resistant TME, interacting with various myeloid cells via the BTLA-TNFRSF14 axis, while the interaction was not significant in imatinib-sensitive TME. Our study highlights the transcriptional heterogeneity and distinct immunosuppressive microenvironment of advanced GIST, which provides novel therapeutic strategies and innovative immunotherapeutic agents for imatinib resistance.
Collapse
Affiliation(s)
- Xuechao Liu
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Jing Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Li
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Hailei Shi
- Pathology Department, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Xuelong Jiao
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Xiaodong Liu
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Dong Guo
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Zequn Li
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Yulong Tian
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China
| | - Fan Dai
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Zhaojian Niu
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China.
| | - Yanbing Zhou
- Department of General Surgery, Affiliated Hospital of Qingdao University, 16# Jiangsu Road, Qingdao, Shandong, China.
| |
Collapse
|
6
|
Han G, Sun C, Cui L, Huang Y, Yu L, Liu S, Tao M. Efficacy of the low dose apatinib plus deep hyperthermia as third-line or later treatment in HER-2 negative advanced gastric cancer. Pathol Oncol Res 2023; 29:1611114. [PMID: 37465317 PMCID: PMC10350525 DOI: 10.3389/pore.2023.1611114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023]
Abstract
Aim: To observe the efficacy of the low dose apatinib plus deep hyperthermia as third-line or later treatment for patients with human epidermal growth factor receptor 2 (HER-2) negative advanced gastric cancer. Methods: 80 eligible patients with HER-2 negative advanced gastric cancer admitted to Jingjiang People's Hospital Affiliated with Yangzhou University-from March 2021 to March 2022 were selected, and they were divided into the control group (n = 40, apatinib) and experimental group (n = 40, apatinib plus deep hyperthermia) on the basis of random number table method. The levels of serum carcinoembryonic antigen (CEA), carbohydrate antigen 199 (CA199), and vascular endothelial growth factor (VEGF) were monitored, and the efficacy of the two groups was analyzed by referring to Karnofsky performance status (KPS), overall survival (OS) and disease control rate (DCR) before and after treatment. Results: The levels of CEA, CA199, and VEGF in both groups were lower after treatment than before (p < 0.05), and lower (CEA: 8.85 ± 1.36 vs. 12.87 ± 1.23, CA199: 34.19 ± 4.68 vs. 50.11 ± 5.73, VEGF: 124.8 ± 18.03 vs. 205.9 ± 19.91) in the experimental group than in the control group (p < 0.05). The DCR and KPS of the patients in the experimental group were significantly higher (DCR: 62.50% vs. 40.00%; KPS: 83.25 ± 1.15 vs. 76.25 ± 1.17) than in the control group (p < 0.05). In survival analysis, patients with control group had shorter OS than the experimental group. (median 5.65 vs. 6.50 months; hazard ratio [HR], 1.63 [95% confidence interval (CI) 1.02-2.60], p = 0.0396). Conclusion: The application of low-dose apatinib plus deep hyperthermia for patients with HER-2 negative gastric cancer who failed second-line treatment should be a promising option.
Collapse
Affiliation(s)
- Guohu Han
- Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China
- Department of Oncology, Jingjiang People’s Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Changchun Sun
- Department of Oncology, Jingjiang People’s Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Lihua Cui
- Department of Oncology, Jingjiang People’s Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Yufeng Huang
- Department of Oncology, Jingjiang People’s Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Lijiang Yu
- Department of Oncology, Jingjiang People’s Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Shenzha Liu
- Department of Oncology, Jingjiang People’s Hospital, The Seventh Affiliated Hospital of Yangzhou University, Jingjiang, Jiangsu, China
| | - Min Tao
- Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| |
Collapse
|
7
|
Wang J, Cui X, Weng Y, Wei J, Chen X, Wang P, Wang T, Qin J, Peng M. Application of an angiogenesis-related genes risk model in lung adenocarcinoma prognosis and immunotherapy. Front Genet 2023; 14:1092968. [PMID: 36816016 PMCID: PMC9929558 DOI: 10.3389/fgene.2023.1092968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is an essential pathological subtype of non-small cell lung cancer and offers a severe problem for worldwide public health. There is mounting proof that angiogenesis is a crucial player in LUAD progression. Consequently, the purpose of this research was to construct a novel LUAD risk assessment model based on genetic markers related to angiogenesis. We accessed The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases for LUAD mRNA sequencing data and clinical information. Based on machine algorithms and bioinformatics, angiogenic gene-related risk scores (RS) were calculated. Patients in the high-risk category had a worse prognosis (p < 0.001) in the discovery TCGA cohort, and the results were confirmed by these three cohorts (validation TCGA cohort, total TCGA cohort, and GSE68465 cohort). Moreover, risk scores for genes involved in angiogenesis were independent risk factors for lung cancer in all four cohorts. The low-risk group was associated with better immune status and lower tumor mutational load. In addition, the somatic mutation study revealed that the low-risk group had a lower mutation frequency than the high-risk group. According to an analysis of tumor stem cell infiltration, HLA expression, and TIDE scores, the low-risk group had higher TIDE scores and HLA expression levels than the high-risk group, and the amount of tumor stem cell infiltration correlated with the risk score. In addition, high-risk groups may benefit from immune checkpoint inhibitors and targeted therapies. In conclusion, we developed an angiogenesis-related gene risk model to predict the prognosis of LUAD patients, which may aid in the classification of patients with LUAD and select medications for LUAD patients.
Collapse
Affiliation(s)
- Jinsong Wang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xue Cui
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiming Weng
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiayan Wei
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xinyi Chen
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Peiwei Wang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tong Wang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jian Qin
- Central Laboratory, Renmin Hospital, Wuhan University, Wuhan, China,*Correspondence: Jian Qin, ; Min Peng,
| | - Min Peng
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China,*Correspondence: Jian Qin, ; Min Peng,
| |
Collapse
|
8
|
Sun H, Ren Y, Zhou X, Chen Q, Liu Y, Zhu C, Ruan Y, Ruan H, Tong H, Ying S, Lin P. DUSP1 Signaling Pathway Regulates Cytarabine Sensitivity in Acute Myeloid Leukemia. Technol Cancer Res Treat 2023; 22:15330338231207765. [PMID: 37872685 PMCID: PMC10594969 DOI: 10.1177/15330338231207765] [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: 06/12/2023] [Revised: 07/30/2023] [Accepted: 08/23/2023] [Indexed: 10/25/2023] Open
Abstract
Objectives: Dual specificity phosphatase 1 (DUSP1) is high-expressed in various cancers and plays an important role in the cellular response to agents that damage DNA. We aimed to investigate the expressions and mechanisms of DUSP1 signaling pathway regulating cytarabine (Ara-C) resistance in acute myeloid leukemia (AML). Methods: Immunohistochemistry was performed on bone marrow biopsy specimens from AML and controls to explore the expression of DUSP1. Western blot and Q-PCR were used to detect the protein and mRNA expression levels. MTT assay was used to detect the proliferation of cells. Cell apoptosis was detected by flow cytometry. The immune protein-protein interaction (PPI) network of DUSP1 was analyzed in the platform of Pathway Commons, and immune infiltration analysis was used to study the immune microenvironment of AML. Results: We found that the expression levels of DUSP1 in AML patients exceeded that in controls. Survival analysis in public datasets showed that AML patients with higher levels of DUSP1 had poor clinical outcomes. Further public data analysis indicated that DUSP1 was overexpressed in NRAS mutated AML. DUSP1 knockdown by siRNA could sensitize AML cells to Ara-C treatments. The phosphorylation level of mitogen-activated protein kinase (MAPK) pathway was significantly elevated in DUSP1 down-regulated NRAS G13D mutated AML cells. The PPI analysis showed DUSP1 correlated with immune gene CREB1 and CXCL8 in NRAS mutated AML. We also revealed a correlation between tumor-infiltrating immune cells in RAS mutated AML microenvironment. Conclusion: Our findings suggest that DUSP1 signaling pathways may regulate Ara-C sensitivity in AML.
Collapse
Affiliation(s)
- Huali Sun
- Department of Radiotherapy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Yanling Ren
- Myelodysplastic Syndrome Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xinping Zhou
- Myelodysplastic Syndrome Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qi Chen
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Yanmei Liu
- Department of Radiotherapy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Chumeng Zhu
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Yanyun Ruan
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Hongli Ruan
- Department of Emergency Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Hongyan Tong
- Myelodysplastic Syndrome Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shenpeng Ying
- Department of Radiotherapy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Peipei Lin
- Department of Radiotherapy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| |
Collapse
|
9
|
Cen K, Wu Z, Mai Y, Dai Y, Hong K, Guo Y. Identification of a novel reactive oxygen species (ROS)-related genes model combined with RT-qPCR experiments for prognosis and immunotherapy in gastric cancer. Front Genet 2023; 14:1074900. [PMID: 37124616 PMCID: PMC10141461 DOI: 10.3389/fgene.2023.1074900] [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: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Reactive oxygen species play a crucial role in the prognosis and tumor microenvironment (TME) of malignant tumors. An ROS-related signature was constructed in gastric cancer (GC) samples from TCGA database. ROS-related genes were obtained from the Molecular Signatures Database. Consensus clustering was used to establish distinct ROS-related subtypes related to different survival and immune cell infiltration patterns. Sequentially, prognostic genes were identified in the ROS-related subtypes, which were used to identify a stable ROS-related signature that predicted the prognosis of GC. Correlation analysis revealed the significance of immune cell iniltration, immunotherapy, and drug sensitivity in gastric cancers with different risks. The putative molecular mechanisms of the different gastric cancer risks were revealed by functional enrichment analysis. A robust nomogram was established to predict the outcome of each gastric cancer. Finally, we verified the expression of the genes involved in the model using RT-qPCR. In conclusion, the ROS-related signature in this study is a novel and stable biomarker associated with TME and immunotherapy responses.
Collapse
Affiliation(s)
- Kenan Cen
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Zhixuan Wu
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yifeng Mai
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Ying Dai
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Kai Hong
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
- *Correspondence: Kai Hong, ; Yangyang Guo,
| | - Yangyang Guo
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
- *Correspondence: Kai Hong, ; Yangyang Guo,
| |
Collapse
|
10
|
Xu W, Zhao D, Huang X, Zhang M, Zhu W, Xu C. Significance of monocyte infiltration in patients with gastric cancer: A combined study based on single cell sequencing and TCGA. Front Oncol 2022; 12:1001307. [PMID: 36479092 PMCID: PMC9720400 DOI: 10.3389/fonc.2022.1001307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/28/2022] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Gastric cancer is still one of the most lethal tumor diseases in the world. Despite some improvements, the prognosis of patients with gastric cancer is still not accurately predicted. METHODS Based on single cell sequencing data, we conducted a detailed analysis of gastric cancer patients and normal tissues to determine the role of monocytes in the progression of gastric cancer. WCGA facilitated our search for Grade-related genes in TCGA. Then, according to the marker genes and cell differentiation genes of monocytes, we determined the cancer-promoting genes of monocytes. Based on LASSO regression, we established a prognostic model using TCGA database. The accuracy of the model was verified by PCA, ROC curve, survival analysis and prognostic analysis. Finally, we evaluated the significance of the model in clinical diagnosis and treatment by observing drug sensitivity, immune microenvironment and immune checkpoint expression in patients with different risk groups. RESULTS Monocytes were poorly differentiated in tumor microenvironment. It mainly played a role in promoting cancer in two ways. One was to promote tumor progression indirectly by interacting with other tumor stromal cells. The other was to directly connect with tumor cells through the MIF and TNF pathway to play a tumor-promoting role. The former was more important in these two ways. A total of 292 monocyte tumor-promoting genes were obtained, and 12 genes were finally included in the construction of the prognosis model. A variety of validation methods showed that our model had an accurate prediction ability. Drug sensitivity analysis could provide guidance for clinical medication of patients. The results of immune microenvironment and immune checkpoint also indicated the reasons for poor prognosis of high-risk patients. CONCLUSION In conclusion, we provided a 12-gene risk score formula and nomogram for gastric cancer patients to assist clinical drug therapy and prognosis prediction. This model had good accuracy and clinical significance.
Collapse
Affiliation(s)
- Wei Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dongxu Zhao
- Department of Interventional Radiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaowei Huang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Man Zhang
- Department of Emergency Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Wenxin Zhu
- Department of Gastroenterology, Kunshan Third People’s Hospital, Suzhou, Jiangsu, China
| | - Chunfang Xu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| |
Collapse
|
11
|
Integrating Single-Cell Transcriptome and Network Analysis to Characterize the Therapeutic Response of Chronic Myeloid Leukemia. Int J Mol Sci 2022; 23:ijms232214335. [PMID: 36430822 PMCID: PMC9695508 DOI: 10.3390/ijms232214335] [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: 09/12/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease characterized by a unique BCR-ABL fusion gene. Tyrosine kinase inhibitors (TKIs) were developed to target the BCR-ABL oncoprotein, inhibiting its abnormal kinase activity. TKI treatments have significantly improved CML patient outcomes. However, the patients can develop drug resistance and relapse after therapy discontinues largely due to intratumor heterogeneity. It is critical to understand the differences in therapeutic responses among subpopulations of cells. Single-cell RNA sequencing measures the transcriptome of individual cells, allowing us to differentiate and analyze individual cell populations. Here, we integrated a single-cell RNA sequencing profile of CML stem cells and network analysis to decipher the mechanisms of distinct TKI responses. Compared to normal hematopoietic stem cells, a set of genes that were concordantly differentially expressed in various types of stem cells of CML patients was revealed. Further transcription regulatory network analysis found that most of these genes were directly controlled by one or more transcript factors and the genes have more regulators in the cells of the patients who responded to the treatment. The molecular markers including a known drug-resistance gene and novel gene signatures for treatment response were also identified. Moreover, we combined protein-protein interaction network construction with a cancer drug database and uncovered the drugs that target the marker genes directly or indirectly via the protein interactions. The gene signatures and their interacted proteins identified by this work can be used for treatment response prediction and lead to new strategies for drug resistance monitoring and prevention. Our single-cell-based findings offered novel insights into the mechanisms underlying the therapeutic response of CML.
Collapse
|
12
|
Yin L, Feng S, Sun Y, Jiang Y, Tang C, Sun D. Identification of a five m6A-relevant mRNAs signature and risk score for the prognostication of gastric cancer. J Gastrointest Oncol 2022; 13:2234-2248. [PMID: 36388685 PMCID: PMC9660063 DOI: 10.21037/jgo-22-962] [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: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most abundant form of methylation modification in eukaryotic cell messenger RNA (mRNA). However, the role of m6A in gastric cancer (GC), which is one of the most common gastrointestinal malignancies, is unclear. In this study, m6A-relevant mRNA signatures and risk scores were determined to predict the prognosis of GC. METHODS The expression profiles and clinical information of 367 patients were downloaded from The Cancer Genome Atlas (TCGA). Cluster analysis and univariate Cox analysis were performed to identify the regulatory factors of RNA methylation associated with GC prognosis. A co-expression network was constructed using the WGCNA package in R. The correlations between module eigengenes and clinical traits were then calculated to identify the relevant modules. We used univariate Cox analysis to screen for genes that are significantly associated with prognosis in the module. We identified hub genes by least absolute shrinkage and selection operator (LASSO) and multivariate analysis and developed a Cox prognostic model. Finally, the hub gene expression values weighted by the coefficients from the LASSO regression were applied to generate a risk score for each patient, and receiver operating characteristic (ROC) and Kaplan-Meier curves were used to assess the prognostic capacity of the risk scores. The asporin (ASPN) gene in GC cell lines was verified via quantitative polymerase chain reaction (qPCR) and Western blot. Moreover, 5-ethynyl-2'-deoxyuridine (EdU) and transwell assays were applied to evaluate the effects of the proliferation, migration, and invasion abilities in GC cells after ASPN knockdown. Western blot verified the effects of ASPN on the phosphoinositide 3-kinase (PI3K)/serine/threonine kinase (AKT)/mechanistic target of rapamycin kinase (mTOR) pathway and epithelial-mesenchymal transition (EMT) pathway-related gene expression. RESULTS Our results indicated that AARD, ASPN, SLAMF9, MIR3117 and DUSP1 were hub genes affecting the prognosis of GC patients. Besides, we found that ASPN expression was upregulated in GC cells. The knockdown of ASPN expression suppressed GC cell proliferation, migration, and invasion by deactivating the PI3K/AKT/mTOR and EMT pathways, respectively. CONCLUSIONS Our findings indicated that ASPN participates in the biological process of GC as an oncogene and may be a promising biomarker in GC.
Collapse
Affiliation(s)
- Lei Yin
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Shichun Feng
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Yongqiang Sun
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Yasu Jiang
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Chong Tang
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Dongwei Sun
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People’s Hospital, Yangzhou, China
| |
Collapse
|
13
|
Comparative Transcriptome Analysis Provides Novel Molecular Events for the Differentiation and Maturation of Hepatocytes during the Liver Development of Zebrafish. Biomedicines 2022; 10:biomedicines10092264. [PMID: 36140365 PMCID: PMC9496063 DOI: 10.3390/biomedicines10092264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
The liver plays an essential role in multiple biological functions including metabolism, detoxification, digestion, coagulation, and homeostasis in vertebrates. The specification and differentiation of embryonic hepatoblasts, the proliferation of hepatocytes, and the hepatic tissue architecture are well documented, but molecular events governing the maturation of hepatocytes during liver development remain largely unclear. In this study, we performed a comparative transcriptome analysis of hepatocytes that were sorted by flow cytometry from developing zebrafish embryos at 60, 72, and 96 hpf. We identified 667 up-regulated and 3640 down-regulated genes in hepatocytes between 60 and 72 hpf, 606 up-regulated and 3924 down-regulated genes between 60 and 96 hpf, and 1693 up-regulated genes and 1508 down-regulated genes between 72 and 96 hpf. GO enrichment analysis revealed that key biological processes, cellular components, and molecular functions in hepatocytes between 60 to 72 hpf, such as cell cycle, DNA replication, DNA repair, RNA processing, and transcription regulation, are mainly associated with the proliferation of hepatocytes. In addition to biological processes, cellular components, and molecular functions for cell proliferation, molecular functions for carbohydrate metabolism were enriched in hepatocytes during 72 to 96 hpf. KEGG enrichment analysis identified key signaling pathways, such as cell cycle, RNA degradation, ubiquitin-mediated proteolysis, ErbB and Hedgehog signaling, basal transcription factors, Wnt signaling, and glycan degradation, which are closely associated with cell proliferation or carbohydrate metabolism in hepatocytes between 60 to 72 hpf. Newly enriched signaling pathways in hepatocytes during 72 to 96 hpf include metabolisms of pyrimidine, purine, nicotinate and nicotinamide, caffeine, glycine, serine and threonine, ABC transporters, and p53 signaling that function in metabolisms of lipid, protein and energy, cellular secretion, or detoxification, indicating the functional maturation of hepatocytes between 72 to 96 hpf. These findings provide novel clues for further understanding the functional differentiation and maturation of hepatocytes during liver development.
Collapse
|
14
|
Yuan H, Yu Q, Pang J, Chen Y, Sheng M, Tang W. The Value of the Stemness Index in Ovarian Cancer Prognosis. Genes (Basel) 2022; 13:genes13060993. [PMID: 35741755 PMCID: PMC9222264 DOI: 10.3390/genes13060993] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
Ovarian cancer (OC) is one of the most common gynecological malignancies. It is associated with a difficult diagnosis and poor prognosis. Our study aimed to analyze tumor stemness to determine the prognosis feature of patients with OC. At this job, we selected the gene expression and the clinical profiles of patients with OC in the TCGA database. We calculated the stemness index of each patient using the one-class logistic regression (OCLR) algorithm and performed correlation analysis with immune infiltration. We used consensus clustering methods to classify OC patients into different stemness subtypes and compared the differences in immune infiltration between them. Finally, we established a prognostic signature by Cox and LASSO regression analysis. We found a significant negative correlation between a high stemness index and immune score. Pathway analysis indicated that the differentially expressed genes (DEGs) from the low- and high-mRNAsi groups were enriched in multiple functions and pathways, such as protein digestion and absorption, the PI3K-Akt signaling pathway, and the TGF-β signaling pathway. By consensus cluster analysis, patients with OC were split into two stemness subtypes, with subtype II having a better prognosis and higher immune infiltration. Furthermore, we identified 11 key genes to construct the prognostic signature for patients with OC. Among these genes, the expression levels of nine, including SFRP2, MFAP4, CCDC80, COL16A1, DUSP1, VSTM2L, TGFBI, PXDN, and GAS1, were increased in the high-risk group. The analysis of the KM and ROC curves indicated that this prognostic signature had a great survival prediction ability and could independently predict the prognosis for patients with OC. We established a stemness index-related risk prognostic module for OC, which has prognostic-independent capabilities and is expected to improve the diagnosis and treatment of patients with OC.
Collapse
|
15
|
Efficacy of the Low Dose Apatinib plus Chemotherapy on Advanced Gastric Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:3009494. [PMID: 35401748 PMCID: PMC8986369 DOI: 10.1155/2022/3009494] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/14/2022] [Accepted: 02/10/2022] [Indexed: 12/23/2022]
Abstract
Objective To evaluate the efficacy of low dose apatinib plus chemotherapy on advanced gastric carcinoma. Methods Eligible 50 patients with advanced gastric carcinoma admitted to the hospital from January 2019 to March 2020 were enrolled, and they were assigned into the control group (n = 25, chemotherapy) and observation group (apatinib plus chemotherapy). Changes of CEA, CA72-4, and VEGF levels were measured, and the efficacy of the two groups was evaluated by referring to KPS and RECIST. Results Significant reduction was observed in CEA, CA72-4, and VEGF in both groups, and the treatment in the observation group resulted in a greater reduction (all P < 0.05). The observation group obtained significantly higher KPS scores of compared with the control group (P < 0.05). In addition, the treatment in the observation group led to a better control rate in relative to the control group according to RECIST the score (P < 0.05). Conclusion The combination of low dose apatinib and chemotherapy might be a promising option for advanced gastric cancer and it merits clinical application.
Collapse
|
16
|
Wu X, Pan Z, Liu W, Zha S, Song Y, Zhang Q, Hu K. The Discovery, Validation, and Function of Hypoxia-Related Gene Biomarkers for Obstructive Sleep Apnea. Front Med (Lausanne) 2022; 9:813459. [PMID: 35372438 PMCID: PMC8970318 DOI: 10.3389/fmed.2022.813459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
While there is emerging evidence that hypoxia critically contributes to the pathobiology of obstructive sleep apnea (OSA), the diagnostic value of measuring hypoxia or its surrogates in OSA remains unclear. Here we investigated the diagnostic value of hypoxia-related genes and explored their potential molecular mechanisms of action in OSA. Expression data from OSA and control subjects were downloaded from the Gene Expression Omnibus database. Differentially-expressed genes (DEGs) between OSA and control subjects were identified using the limma R package and their biological functions investigated with the clusterProfiler R package. Hypoxia-related DEGs in OSA were obtained by overlapping DEGs with hypoxia-related genes. The diagnostic value of hypoxia-related DEGs in OSA was evaluated by receiver operating curve (ROC) analysis. Random forest (RF) and lasso machine learning algorithms were used to construct diagnostic models to distinguish OSA from control. Geneset enrichment analysis (GSEA) was performed to explore pathways related to key hypoxia-related genes in OSA. Sixty-three genes associated with hypoxia, transcriptional regulation, and inflammation were identified as differentially expressed between OSA and control samples. By intersecting these with known hypoxia-related genes, 17 hypoxia-related DEGs related to OSA were identified. Protein-protein interaction network analysis showed that 16 hypoxia-related genes interacted, and their diagnostic value was further explored. The 16 hypoxia-related genes accurately predicted OSA with AUCs >0.7. A lasso model constructed using AREG, ATF3, ZFP36, and DUSP1 had a better performance and accuracy in classifying OSA and control samples compared with an RF model as assessed by multiple metrics. Moreover, GSEA revealed that AREG, ATF3, ZFP36, and DUSP1 may regulate OSA via inflammation and contribute to OSA-related cancer risk. Here we constructed a reliable diagnostic model for OSA based on hypoxia-related genes. Furthermore, these transcriptional changes may contribute to the etiology, pathogenesis, and sequelae of OSA.
Collapse
|
17
|
Zandi Z, Kashani B, Alishahi Z, Pourbagheri-Sigaroodi A, Esmaeili F, Ghaffari SH, Bashash D, Momeny M. Dual-specificity phosphatases: therapeutic targets in cancer therapy resistance. J Cancer Res Clin Oncol 2022; 148:57-70. [PMID: 34981193 DOI: 10.1007/s00432-021-03874-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Therapy resistance is the principal obstacle to achieving cures in cancer patients and its successful tackling requires a deep understanding of the resistance mediators. Increasing evidence indicates that tumor phosphatases are novel and druggable targets in translational oncology and their modulation may hinder tumor growth and motility and potentiate therapeutic sensitivity in various neoplasms via regulation of various signal transduction pathways. Dual-specificity phosphatases (DUSPs) are key players of cell growth, survival and death and have essential roles in tumor initiation, malignant progression and therapy resistance through regulation of the MAPK signaling pathway. In this review, different aspects of DUSPs are discussed. METHODS A comprehensive literature review was performed using various websites including PubMed. RESULTS We provide mechanistic insights into the roles of well-known DUSPs in resistance to a wide range of cancer therapeutic approaches including chemotherapy, radiation and molecular targeted therapy in human malignancies. Moreover, we discuss the development of DUSP modulators, with a focus on DUSP1 and 6 inhibitors. Ultimately, the preclinical investigations of small molecule inhibitors of DUSP1 and 6 are outlined. CONCLUSION Emerging evidence indicates that the DUSP family is aberrantly expressed in human malignancies and plays critical roles in determining sensitivity to a wide range of cancer therapeutic strategies through regulation of the MAPK signaling pathways. Consequently, targeting DUSPs and their downstream molecules can pave the way for more effective cancer therapies.
Collapse
Affiliation(s)
- Zahra Zandi
- Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahareh Kashani
- Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zivar Alishahi
- Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Esmaeili
- Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed H Ghaffari
- Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Momeny
- Hematology/Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
18
|
Tan QH, Xie WL, Luo YT, Jiang NF, Ma AH. Ferroptosis-related mRNAs signature predicts prognosis of gastric cancer. Shijie Huaren Xiaohua Zazhi 2021; 29:1410-1420. [DOI: 10.11569/wcjd.v29.i24.1410] [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] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastric cancer is a common gastrointestinal tumor with a poor prognosis. Ferroptosis is a novel form of regulated cell death that plays a critical role in tumorigenesis. Therefore, it is significant to construct a prognosis model of ferroptosis-related genes to predict the prognosis of gastric cancer and related therapeutic targets.
AIM To explore the potential prognostic value of ferroptosis-related mRNAs in gastric cancer.
METHODS Since ferroptosis is a type of cell death driven by lipid iron-dependent peroxidation, a predictive model was constructed based on differentially expressed ferroptosis-related mRNAs in gastric cancer.
RESULTS We identified four differentially expressed mRNAs (DUSP1, MYB, CAV1, and NOX4) associated with gastric cancer prognosis. Kaplan-Meier analysis showed that the high-risk group was associated with a poor prognosis, and risk score was an independent prognostic indicator of survival. The developed prognostic model showed superiority over conventional clinical and pathological features in predicting the prognosis of gastric cancer. In addition, the low-risk and high-risk groups showed significant differences in immune cell infiltration and immune checkpoints.
CONCLUSION A novel ferroptosis-related mRNA signature has been developed, which could precisely predict the prognosis of gastric cancer and serve as therapeutic targets for gastric cancer.
Collapse
Affiliation(s)
- Qi-Huan Tan
- Shaoxing University School of Medicine, Shaoxing 312000, Zhejiang Province, China
| | - Wang-Liang Xie
- Shaoxing University School of Medicine, Shaoxing 312000, Zhejiang Province, China
| | - Yu-Ting Luo
- Shaoxing University School of Medicine, Shaoxing 312000, Zhejiang Province, China
| | - Ning-Fang Jiang
- Department of Gastrointestinal Surgery, Shaoxing People's Hospital, Shaoxing 312000, Zhejiang Province, China
| | - A-Huo Ma
- Department of Gastroenterology, The First Affiliated Hospital of Shaoxing University, Shaoxing 312000, Zhejiang Province, China
| |
Collapse
|
19
|
He C, Sheng L, Pan D, Jiang S, Ding L, Ma X, Liu Y, Jia D. Single-Cell Transcriptomic Analysis Revealed a Critical Role of SPP1/CD44-Mediated Crosstalk Between Macrophages and Cancer Cells in Glioma. Front Cell Dev Biol 2021; 9:779319. [PMID: 34805184 PMCID: PMC8602110 DOI: 10.3389/fcell.2021.779319] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
High-grade glioma is one of the most lethal human cancers characterized by extensive tumor heterogeneity. In order to identify cellular and molecular mechanisms that drive tumor heterogeneity of this lethal disease, we performed single-cell RNA sequencing analysis of one high-grade glioma. Accordingly, we analyzed the individual cellular components in the ecosystem of this tumor. We found that tumor-associated macrophages are predominant in the immune microenvironment. Furthermore, we identified five distinct subpopulations of tumor cells, including one cycling, two OPC/NPC-like and two MES-like cell subpopulations. Moreover, we revealed the evolutionary transition from the cycling to OPC/NPC-like and MES-like cells by trajectory analysis. Importantly, we found that SPP1/CD44 interaction plays a critical role in macrophage-mediated activation of MES-like cells by exploring the cell-cell communication among all cellular components in the tumor ecosystem. Finally, we showed that high expression levels of both SPP1 and CD44 correlate with an increased infiltration of macrophages and poor prognosis of glioma patients. Taken together, this study provided a single-cell atlas of one high-grade glioma and revealed a critical role of macrophage-mediated SPP1/CD44 signaling in glioma progression, indicating that the SPP1/CD44 axis is a potential target for glioma treatment.
Collapse
Affiliation(s)
- Cong He
- Laboratory of Cancer Genomics and Biology, Department of Urology, and Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luoyan Sheng
- Laboratory of Cancer Genomics and Biology, Department of Urology, and Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deshen Pan
- Laboratory of Cancer Genomics and Biology, Department of Urology, and Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuai Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Li Ding
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojun Ma
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaohua Liu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deshui Jia
- Laboratory of Cancer Genomics and Biology, Department of Urology, and Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
20
|
PEI-PEG-Coated Mesoporous Silica Nanoparticles Enhance the Antitumor Activity of Tanshinone IIA and Serve as a Gene Transfer Vector. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6756763. [PMID: 34790248 PMCID: PMC8592735 DOI: 10.1155/2021/6756763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/22/2021] [Accepted: 10/21/2021] [Indexed: 01/20/2023]
Abstract
Tanshinone IIA (TanIIA) and gene therapy both hold promising potentials in hepatocellular carcinoma (HCC) treatment. However, low solubility and poor bioavailability of TanIIA limit its clinical application. Similarly, gene therapy with GPC3-shRNA, a type of short hairpin RNAs (shRNAs) capable of silencing the glypican-3 (GPC3) expression, is seriously limited due to its susceptibility to nuclease degradation and high off-target effects. In the present study, polyethyleneimine (PEI)-polyethylene glycol (PEG)-coated mesoporous silica nanoparticles (MSN-PEG) were used as a drug carrier. By encapsulating TanIIA into MSN-PEG, we synthesized MSN-TanIIA-PEG nanoparticles and observed the involved characteristics. This was followed by exploration of antitumor activity on the HepG2 cell lines in vitro. Meanwhile, in order to construct GPC3-shRNA plasmids, a shRNA sequence targeting GPC3 was synthesized and cloned into the pSLenti-U6 vector. Accordingly, the performance of MSN-PEG as a gene transfer carrier for GPC3-shRNA gene therapy of HCC in vitro was evaluated, including transfection efficiency and DNA binding biological characteristics. The results indicated successful encapsulation of TanIIA in MSN-PEG, which had satisfactory efficacy, favorable dispersity, suitable particle size, and sustained release effect. The in vitro anti-HCC effects of nano-TanIIA were greatly improved, which outperformed free-TanIIA in terms of proliferation and invasion inhibition, as well as apoptosis induction of HCC cells. As expected, MSN-PEG possessed excellent gene delivery capacity with good binding, release, and protection from RNase digestion. Using MSN-PEG as a gene carrier, the plasmids were successfully transfected into HepG2 cells, and both the mRNA and protein expressions of GPC3 were significantly downregulated. It was thus concluded that a sustained release TanIIA delivery system for HCC treatment was synthesized and that MSN-PEG could also serve as a gene transfer carrier for gene therapy. More interestingly, MSN-PEG may be a potential delivery platform that combines TanIIA and GPC3-shRNA together to enhance their synergistic effect.
Collapse
|
21
|
Identification of Novel CircRNA-miRNA-mRNA Regulatory Network and Its Prognostic Prediction in Breast Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:2916398. [PMID: 34745276 PMCID: PMC8570857 DOI: 10.1155/2021/2916398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022]
Abstract
Aim This study aimed to investigate the expression profiles of circRNAs and candidate circRNA-miRNA-mRNA network in BC. Methods Differentially expressed circRNAs, miRNAs, and mRNAs (DEcircRNAs, DEmiRNAs, and DEmRNAs) between BC and normal breast tissue samples were screened by analyzing raw data of the RNA sequencing profile. The expression levels of hub genes in 48 pairs of cancerous and tumor-free breast tissues surgically resected from BC patients were determined by RT-qPCR analysis. Results A total of 145 DEcircRNAs, 140 DEmiRNAs, and 2451 DEmRNAs between BC and normal breast tissue samples were screened out. There were 5 pairs of upcircRNA-downmiRNA-upmRNA network and 20 pairs of downcircRNA-upmiRNA-downmRNA network. EIF4EBP1, DUSP1, EGR2, EZH1, and CBX7 were found to be correlated with overall survival of the patients with BC. The expression level of EIF4EBP1 was increased and the expression levels of DUSP1, EGR2, EZH1, and CBX7 were decreased in cancerous breast tissues compared to tumor-free breast tissues (p < 0.0001). The RT-qPCR results from 48 BC patients were consistent with the bioinformatics results. Conclusion This study provides a novel perspective to study circRNA-miRNA-mRNA network in BC and assists in the identification of new potential biomarkers to be used for diagnostic and prognostic purposes.
Collapse
|
22
|
Du Y, Wang Z, Wan W. High Expression of ERK-related RASGRF2 predicts Poor prognosis in patients with Stomach Adenocarcinoma and correlates with M2 macrophage. J Cancer 2021; 12:7177-7189. [PMID: 34729119 PMCID: PMC8558656 DOI: 10.7150/jca.63029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background: The role of RASGRF2 has been verified in the development of various cancers. However, its roles in stomach adenocarcinoma (STAD) are still under investigation. Methods: RASGRF2 transcript-level data and the associated clinical information from patients with STAD were extracted from The Cancer Genome Atlas (TCGA). Diagnostic and prognostic values of RASGRF2 were analyzed using receiver-operator characteristics (ROC) analysis, correlation analysis, and survival analysis in conjunction with a prognostic model. In addition, gene expression profiles, differentially-expressed genes for co-varying expression, and a differential expressed genes (DEG) protein-protein interaction network for influential nodes were also analyzed. To identify the molecular role of RASGRF2 in STAD, gene ontology (GO) term, Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway, and gene set enrichment analysis (GSEA)-mediated functional module enrichment analyses were conducted. The relationship between RASGRF2 and gene signature-based predicted immune cell infiltration patterns were also investigated. To validate the bioinformatic findings, RASGRF2 protein expression was investigated in vitro using western blot and immunohistochemistry. Furthermore, relationships among RASGRF2 protein expression, clinicopathologic characteristics, and patient survival were analyzed. Results: Bioinformatic analysis revealed a significantly higher RASGRF2 transcript level in STAD tissue, which was positively associated with the T stage, histological type, histological grade, and TP53 status. Moreover, the RASGRF2 transcript level indicated poor overall survival in STAD patients (hazard ratio = 1.47, P = 0.023). Multivariate Cox regression analysis showed that primary therapy outcome, age, and RASGRF2 transcript level were independent prognostic factors for survival, and the C-index of a nomogram was 0.695. Additionally, 159 genes were differentially expressed according to RASGRF2 transcript levels; 15 exhibited co-varying expression, and 13 were identified as influential nodes. The DEG-list was significantly enriched for several GO terms, biological pathways, and functional modules, including MAPK, RAS, ERK, and immunoregulatory pathways. RASGRF2 transcript levels were significantly positively correlated with infiltration levels of Tem, Macrophages, pDCs, and NK cells. Validation analysis showed similar results for the RASGRF2 protein expression level in both in vitro analyses. Conclusion: Bioinformatic predictions combined with in vitro validation suggest that RASGRF2 plays diagnostic and prognostic roles and serves as a negative protective molecular factor in STAD patients.
Collapse
Affiliation(s)
- Yaqi Du
- Department of Gastroenterology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengguang Wang
- Department of Orthopedics, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weina Wan
- Department of Ultrasound, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| |
Collapse
|
23
|
Fan MK, Zhang GC, Chen W, Qi LL, Xie MF, Zhang YY, Wang L, Zhang Q. Siglec-15 Promotes Tumor Progression in Osteosarcoma via DUSP1/MAPK Pathway. Front Oncol 2021; 11:710689. [PMID: 34336699 PMCID: PMC8322944 DOI: 10.3389/fonc.2021.710689] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/01/2021] [Indexed: 12/30/2022] Open
Abstract
Recurrence and metastasis are important features of osteosarcoma (OS) that cause its poor prognosis. Aberrant expression of Sialic acid-binding immunoglobulin-like lectin 15 (Siglec-15) has been reported in various kinds of cancers. However, the expression and function of Siglec-15 in OS remain unclear. In cultured OS cells (143B cells and MNNG/HOS cells) and their xenograft mouse models, we found that downregulation of Siglec-15 could inhibit the proliferation, migration and invasion of by inducing epithelial-mesenchymal transition (EMT) in vitro and in vivo. Conversely, Siglec-15 overexpression promoted the growth, migration and invasion of OS cells in a significant manner. Then, we screened a number of differentially expressed genes (DEGs) between Siglec-15-knockdown group and control group by RNA-Seq assay. Among these DEGs, we found that dual-specificity phosphatase 1 (DUSP1/MKP1) was significantly downregulated after Siglec-15 silencing. We investigated the DUSP1 functions in influencing OS cells’ biology, and found that the proliferation, migration and invasion of OS cells were promoted by overexpressing DUSP1 and crucially, the proliferation, migration and invasion of Siglec-15-knockdown OS cells were rescued by overexpressing DUSP1. Mechanically, we further showed that DUSP1-mediated inhibition of p38/MAPK and JNK/MAPK expression was attenuated when Siglec-15 expression was inhibited, suggesting that Siglec-15 promotes the malignant progression of OS cells by suppressing DUSP1-mediated suppression of the MAPK pathway. Moreover, we showed that both Siglec-15 and DUSP1 were highly expressed in human OS tissues by immunohistochemistry. High Siglec-15 expression was associated with OS lung metastasis, and high DUSP1 expression was associated with the high Enneking stage. Kaplan–Meier analysis indicated that high expression of Siglec-15 could predict poor prognosis of OS patients. Altogether, these results showed that Siglec-15 expression promoted OS development and progression by activating DUSP1 and might be a novel target in OS treatment.
Collapse
Affiliation(s)
- Meng-Ke Fan
- Department of Orthopedic Research Center, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Guo-Chuan Zhang
- Department of Orthopedic Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wei Chen
- Department of Orthopaedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Li-Li Qi
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, China
| | - Ming-Fang Xie
- Department of Orthopedic Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yue-Yao Zhang
- Department of Orthopedic Research Center, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ling Wang
- Department of Orthopedic Research Center, The Third Hospital of Hebei Medical University, Shijiazhuang, China.,Department of Orthopedic Oncology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qi Zhang
- Department of Orthopedic Research Center, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
24
|
Identification and validation of a novel ferroptosis-related gene model for predicting the prognosis of gastric cancer patients. PLoS One 2021; 16:e0254368. [PMID: 34252149 PMCID: PMC8274920 DOI: 10.1371/journal.pone.0254368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ferroptosis is a novel form of regulated cell death that plays a critical role in tumorigenesis. The purpose of this study was to establish a ferroptosis-associated gene (FRG) signature and assess its clinical outcome in gastric cancer (GC). Methods Differentially expressed FRGs were identified using gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses were performed to construct a prognostic signature. The model was validated using an independent GEO dataset, and a genomic-clinicopathologic nomogram integrating risk scores and clinicopathological features was established. Results An 8-FRG signature was constructed to calculate the risk score and classify GC patients into two risk groups (high- and low-risk) according to the median value of the risk score. The signature showed a robust predictive capacity in the stratification analysis. A high-risk score was associated with advanced clinicopathological features and an unfavorable prognosis. The predictive accuracy of the signature was confirmed using an independent GSE84437 dataset. Patients in the two groups showed different enrichment of immune cells and immune-related pathways. Finally, we established a genomic-clinicopathologic nomogram (based on risk score, age, and tumor stage) to predict the overall survival (OS) of GC patients. Conclusions The novel FRG signature may be a reliable tool for assisting clinicians in predicting the OS of GC patients and may facilitate personalized treatment.
Collapse
|
25
|
Wang MFZ, Mantri M, Chou SP, Scuderi GJ, McKellar DW, Butcher JT, Danko CG, De Vlaminck I. Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis. Nat Commun 2021; 12:2158. [PMID: 33846360 PMCID: PMC8042062 DOI: 10.1038/s41467-021-22496-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/17/2021] [Indexed: 11/09/2022] Open
Abstract
Conventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark. Conventional single-cell RNA sequencing analysis rely on genome annotations that may be incomplete or inaccurate especially for understudied organisms. Here the authors present a bioinformatic tool that leverages single-cell data to uncover biologically relevant transcripts beyond the best available genome annotation.
Collapse
Affiliation(s)
- Michael F Z Wang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Shao-Pei Chou
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gaetano J Scuderi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - David W McKellar
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jonathan T Butcher
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
26
|
Zheng S, Zhang Z, Ding N, Sun J, Lin Y, Chen J, Zhong J, Shao L, Lin Z, Xue M. Identification of the angiogenesis related genes for predicting prognosis of patients with gastric cancer. BMC Gastroenterol 2021; 21:146. [PMID: 33794777 PMCID: PMC8017607 DOI: 10.1186/s12876-021-01734-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Angiogenesis is a key factor in promoting tumor growth, invasion and metastasis. In this study we aimed to investigate the prognostic value of angiogenesis-related genes (ARGs) in gastric cancer (GC). METHODS mRNA sequencing data with clinical information of GC were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. The differentially expressed ARGs between normal and tumor tissues were analyzed by limma package, and then prognosis‑associated genes were screened using Cox regression analysis. Nine angiogenesis genes were identified as crucially related to the overall survival (OS) of patients through least absolute shrinkage and selection operator (LASSO) regression. The prognostic model and corresponding nomograms were establish based on 9 ARGs and verified in in both TCGA and GEO GC cohorts respectively. RESULTS Eighty-five differentially expressed ARGs and their enriched pathways were confirmed. Significant enrichment analysis revealed that ARGs-related signaling pathway genes were highly related to tumor angiogenesis development. Kaplan-Meier analysis revealed that patients in the high-risk group had worse OS rates compared with the low-risk group in training cohort and validation cohort. In addition, RS had a good prognostic effect on GC patients with different clinical features, especially those with advanced GC. Besides, the calibration curves verified fine concordance between the nomogram prediction model and actual observation. CONCLUSIONS We developed a nine gene signature related to the angiogenesis that can predict overall survival for GC. It's assumed to be a valuable prognosis model with high efficiency, providing new perspectives in targeted therapy.
Collapse
Affiliation(s)
- Sheng Zheng
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Zizhen Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Ning Ding
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jiawei Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Yifeng Lin
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jingyu Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jing Zhong
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Liming Shao
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China
| | - Zhenghua Lin
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Meng Xue
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, Zhejiang, China. .,Institute of Gastroenterology, Zhejiang University, Hangzhou, China.
| |
Collapse
|
27
|
Liu Z, Gao J, Yang Y, Zhao H, Ma C, Yu T. Potential targets identified in adenoid cystic carcinoma point out new directions for further research. Am J Transl Res 2021; 13:1085-1108. [PMID: 33841642 PMCID: PMC8014416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Adenoid cystic carcinoma (AdCC) of the head and neck originates from salivary glands, with high risks of recurrence and metastasis that account for the poor prognosis of patients. The purpose of this research was to identify key genes related to AdCC for further investigation of their diagnostic and prognostic significance. In our study, the AdCC sample datasets GSE36820, GSE59702 and GSE88804 from the Gene Expression Omnibus (GEO) database were used to explore the abnormal coexpression of genes in AdCC compared with their expression in normal tissue. A total of 115 DEGs were obtained by screening with GEO2R and FunRich software. According to functional annotation analysis using Enrichr, these DEGs were mainly enriched in the SOX2, AR, SMAD and MAPK signaling pathways. A protein-protein network of the DEGs was established by the Search Tool for the Retrieval of Interacting Genes (STRING) and annotated through the WEB-based Gene SeT AnaLysis Toolkit (WebGestalt) and was shown to be enriched with proteins involved in cardiac muscle cell proliferation and extracellular matrix organization. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that ITGA9, LAMB1 and BAMBI were associated with the PI3K-Akt and TGF-β pathways. Furthermore, 36 potential target miRNAs were identified by the OncomiR and miRNA Pathway Dictionary Database (miRPathDB). In conclusion, SLC22A3, FOXP2, Cdc42EP3, COL27A1, DUSP1 and HSPB8 played critical roles according to the enrichment analysis; ITGA9, LAMB1 and BAMBI were involved in significant pathways according to the KEGG analysis; ST3Gal4 is a pivotal component of the PPI network of all the DEGs obtained; SPARC, COL4A2 and PRELP were highly related to multiple malignancies in pan-cancer research; hsa-miR-29-3p, hsa-miR-132-3p and hsa-miR-708-5p were potential regulators in AdCC. The involved pathways, biological processes and miRNAs have been shown to play significant roles in the genesis, growth, invasion and metastasis of AdCC. In this study, these identified DEGs were considered to have a potential influence on AdCC but have not been studied in this disease. The analysis results promote our understanding of the molecular mechanisms and biological processes of AdCC, which might be useful for targeted therapy or diagnosis.
Collapse
Affiliation(s)
- Zhenan Liu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan, China
| | - Jian Gao
- Department of Stomatology, Xintai Hospital of Traditional Chinese MedicineTaian, China
| | - Yihui Yang
- Department of Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan, China
| | - Huaqiang Zhao
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan, China
| | - Chuan Ma
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan, China
| | - Tingting Yu
- Department of Oral and Maxillofacial Surgery, Jinan Stomatological HospitalJinan, China
| |
Collapse
|
28
|
Zhang Z, Yang W, Ma F, Ma Q, Zhang B, Zhang Y, Liu Y, Liu H, Hua Y. Enhancing the chemotherapy effect of Apatinib on gastric cancer by co-treating with salidroside to reprogram the tumor hypoxia micro-environment and induce cell apoptosis. Drug Deliv 2021; 27:691-702. [PMID: 32397840 PMCID: PMC7269049 DOI: 10.1080/10717544.2020.1754528] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hypoxic microenvironment commonly occurred in the solid tumors considerably decreases the chemosensitivity of cancer cells. Salidroside (Sal), the main active ingredient of Rhodiola rosea, was shown to be able of regulating the tumor hypoxia micro-environment and enhancing the chemotherapeutic efficacy of drug-resistant cancer. Therefore, in this study, the Sal was co-loaded with Apatinib (Apa) by the PLGA-based nanoparticles (NPs) to improve the chemosensitivity of gastric cancer cells. Additionally, to improve the drug delivery efficacy, the tumor-homing peptide (iVR1 peptides) was further decorated on the surface of NPs. The tumor targeting ability of the peptides-functionalized nanoparticles (iVR1-NPs-Apa/Sal) was evaluated by in vitro and in vivo experiments. As the obtained results revealed that the iVR1-NPs-Apa/Sal displayed excellent tumor affinity than the unmodified ones (NPs-Apa/Sal), which in turn resulted in more efficient of anti-proliferation of gastric cancer cells and anti-tumor effect in vivo. In addition, compared with the cells or tumor-bearing mice only treaded by monotherapy of Apa, the cells or mice received combinational treatment of Apa and Sal showed obvious lower rate of growth, invasion, and migration or tumor growth and progress. Underlying mechanisms were further investigated and it was revealed that the anti-gastric cancer effect of Apa was signally improved by Sal through down-regulation the proliferation factors and increase the pro-apoptotic genes, as well as reprograming the tumor hypoxia micro-environment. In a word, the study showed that the Sal was able of improving the chemosensitivity of gastric cancer to Apa and the iVR1-NPs-Apa/Sal was capable of realizing highly efficient of tumor-targeting drug delivery.
Collapse
Affiliation(s)
- Zhandong Zhang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Wei Yang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Fei Ma
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Qi Ma
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Bin Zhang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Yonglei Zhang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Yingqiang Liu
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Hongxing Liu
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| | - Yawei Hua
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Henan, Zhengzhou
| |
Collapse
|
29
|
Sun Z, Chen H, Han Z, Huang W, Hu Y, Zhao M, Lin T, Yu J, Liu H, Jiang Y, Li G. Genomics Score Based on Genome-Wide Network Analysis for Prediction of Survival in Gastric Cancer: A Novel Prognostic Signature. Front Genet 2020; 11:835. [PMID: 32849822 PMCID: PMC7423976 DOI: 10.3389/fgene.2020.00835] [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] [Received: 04/25/2020] [Accepted: 07/10/2020] [Indexed: 01/02/2023] Open
Abstract
Purpose Gastric cancer (GC) is a product of multiple genetic abnormalities, including genetic and epigenetic modifications. This study aimed to integrate various biomolecules, such as miRNAs, mRNA, and DNA methylation, into a genome-wide network and develop a nomogram for predicting the overall survival (OS) of GC. Materials and Methods A total of 329 GC cases, as a training cohort with a random of 150 examples included as a validation cohort, were screened from The Cancer Genome Atlas database. A genome-wide network was constructed based on a combination of univariate Cox regression and least absolute shrinkage and selection operator analyses, and a nomogram was established to predict 1-, 3-, and 5-year OS in the training cohort. The nomogram was then assessed in terms of calibration, discrimination, and clinical usefulness in the validation cohort. Afterward, in order to confirm the superiority of the whole gene network model and further reduce the biomarkers for the improvement of clinical usefulness, we also constructed eight other models according to the different combinations of miRNAs, mRNA, and DNA methylation sites and made corresponding comparisons. Finally, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were also performed to describe the function of this genome-wide network. Results A multivariate analysis revealed a novel prognostic factor, a genomics score (GS) comprising seven miRNAs, eight mRNA, and 19 DNA methylation sites. In the validation cohort, comparing to patients with low GS, high-GS patients (HR, 12.886; P < 0.001) were significantly associated with increased all-cause mortality. Furthermore, after stratification of the TNM stage (I, II, III, and IV), there were significant differences revealed in the survival rates between the high-GS and low-GS groups as well (P < 0.001). The 1-, 3-, and 5-year C-index of whole genomics-based nomogram were 0.868, 0.895, and 0.928, respectively. The other models have comparable or relatively poor comprehensive performance, while they had fewer biomarkers. Besides that, DAVID 6.8 further revealed multiple molecules and pathways related to the genome-wide network, such as cytomembranes, cell cycle, and adipocytokine signaling. Conclusion We successfully developed a GS based on genome-wide network, which may represent a novel prognostic factor for GC. A combination of GS and TNM staging provides additional precision in stratifying patients with different OS prognoses, constituting a more comprehensive sub-typing system. This could potentially play an important role in future clinical practice.
Collapse
Affiliation(s)
- Zepang Sun
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Chen
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhen Han
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weicai Huang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanfeng Hu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingli Zhao
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tian Lin
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiang Yu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuming Jiang
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
30
|
Magnelli L, Schiavone N, Staderini F, Biagioni A, Papucci L. MAP Kinases Pathways in Gastric Cancer. Int J Mol Sci 2020; 21:ijms21082893. [PMID: 32326163 PMCID: PMC7215608 DOI: 10.3390/ijms21082893] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is turning out today to be one of the most important welfare issues for both Asian and European countries. Indeed, while the vast majority of the disease burden is located in China and in Pacific and East Asia, GC in European countries still account for about 100,000 deaths per year. With this review article, we aim to focus the attention on one of the most complex cellular pathways involved in GC proliferation, invasion, migration, and metastasis: the MAP kinases. Such large kinases family is to date constantly studied, since their discovery more than 30 years ago, due to the important role that it plays in the regulation of physiological and pathological processes. Interactions with other cellular proteins as well as miRNAs and lncRNAs may modulate their expression influencing the cellular biological features. Here, we summarize the most important and recent studies involving MAPK in GC. At the same time, we need to underly that, differently from cancers arising from other tissues, where MAPK pathways seems to be a gold target for anticancer therapies, GC seems to be unique in any aspect. Our aim is to review the current knowledge in MAPK pathways alterations leading to GC, including H. pylori MAPK-triggering to derail from gastric normal epithelium to GC and to encourage researches involved in MAPK signal transduction, that seems to definitely sustain GC development.
Collapse
Affiliation(s)
- Lucia Magnelli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134 Firenze, Italy; (N.S.); (A.B.); (L.P.)
- Correspondence: ; Tel.: +39-055-2751397
| | - Nicola Schiavone
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134 Firenze, Italy; (N.S.); (A.B.); (L.P.)
| | - Fabio Staderini
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Firenze, Italy;
| | - Alessio Biagioni
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134 Firenze, Italy; (N.S.); (A.B.); (L.P.)
| | - Laura Papucci
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134 Firenze, Italy; (N.S.); (A.B.); (L.P.)
| |
Collapse
|
31
|
Huang P, Tang W, Shen R, Ju X, Shao G, Xu X, Jiang A, Qian X, Chen M, Zhou Z, Ren C. Analysis of candidate biomarkers and related transcription factors involved in the development and restoration of stress-induced gastric ulcer by transcriptomics. Cell Stress Chaperones 2020; 25:265-275. [PMID: 32088906 PMCID: PMC7058781 DOI: 10.1007/s12192-020-01070-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 01/01/2023] Open
Abstract
Stress-induced gastric ulcer is one of the common complications affecting patients after trauma, mainly leading to gastrointestinal bleeding and perforation, and severe cases may be life-threatening. However, the molecular mechanism of stress-induced gastric ulcer remains unclear. In the present study, RNA-sequencing was performed on gastric tissues of normal rats (C), stress-induced gastric ulcer rats (T0), and rats recovered from gastric ulcer for 3 days (T3), and bioinformatics analysis was performed to determine changes in gene expression and biological pathways. The protein-protein interaction (PPI) networks of differentially expressed genes (DEGs) were constructed by STRING and visualized by the Cytoscape software. The associated transcriptional factor (TFs)-gene regulatory network of the hub DEGs was also constructed. Pairwise comparisons obtained 103 (T0_C), 127 (T3_T0), and 13 (T3_C) DEGs, respectively. Gene ontology (GO) enrichment analysis indicated DEGs in T0_C and T3_T0 were significantly enriched in response to oxygen-containing compound, response to organic substance, and response to external stimulus. Pathway analysis suggested that DEGs were enriched in TNF signaling pathway, PPAR signaling pathway, apoptosis, and IL-17 signaling pathway. Seven hub genes (Fos, Jun, Nfkbia, Dusp1, Pim3, Junb, and Fosb) were obtained from the PPI networks of T0_C and T3_T0. Key TFs with close interactions, such as Fos, Jun, Nfkbia, Junb, Egr1, and Fosb, were screened This study used RNA-sequencing and bioinformatics analysis to screen out genes associated with gastric ulcer, which can help reveal the molecular mechanism of gastric ulcer development and restoration, and provide reference for the treatment of human gastric ulcers.
Collapse
Affiliation(s)
- Pan Huang
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Weihong Tang
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Rong Shen
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Xiaoli Ju
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Genbao Shao
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Xiao Xu
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Anqi Jiang
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Xiaobin Qian
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Miao Chen
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Zhengrong Zhou
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Caifang Ren
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| |
Collapse
|
32
|
Liu W, Tian X, Ding X, Zhang L. Expression of Dual-Specificity Phosphatase 2 (DUSP2) in Patients with Serous Ovarian Carcinoma and in SKOV3 and OVCAR3 Cells In Vitro. Med Sci Monit 2019; 25:10180-10189. [PMID: 31889045 PMCID: PMC6953438 DOI: 10.12659/msm.919089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Ovarian cancer commonly presents at a late stage and is associated with poor prognosis. The most common histological subtype is serous ovarian carcinoma. Dual-specificity phosphatase 2 (DUSP2) is a protein phosphatase and substrate for mitogen-activated protein kinases (MAPKs) with increased expression levels in malignancy. This study aimed to evaluate the expression of DUSP2 in tumor tissues from patients with serous ovarian carcinoma and the association with tumor grade, stage, and patient survival and to investigate the effects of DUSP2 expression in SKOV3 and OVCAR3 cells in vitro. MATERIAL AND METHODS Tumor tissue and adjacent normal ovarian tissue from 127 patients with histologically confirmed serous ovarian carcinoma underwent quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry to measure DUSP2 mRNA and protein expression, respectively. Tumor grade, stage, and clinicopathological data underwent correlation analysis with DUSP2 expression, and survival data were assessed with Kaplan-Meier and Cox regression analysis. The effects of DUSP2 expression on the proliferation and migration of SKOV3 and OVCAR3 cells were evaluated. RESULTS Immunohistochemistry showed that DUSP2 was down-regulated in serous ovarian carcinoma tissues compared with adjacent ovarian tissues, and was significantly correlated with tumor stage. Survival analysis showed that DUSP2 expression was an independent risk factor for patient survival. DUSP2 expression in SKOV3 and OVCAR3 cells in vitro suppressed cell proliferation and migration. CONCLUSIONS Down-regulation of DUSP2 expression in serous ovarian carcinoma was an independent risk factor for patient survival, and its expression in SKOV3 and OVCAR3 cells inhibited cell proliferation and migration in vitro.
Collapse
Affiliation(s)
- Wei Liu
- Department of Cardiology, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Xiaomin Tian
- Department of Cardiology, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Xue Ding
- Department of Cardiology, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Leiying Zhang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China (mainland)
| |
Collapse
|
33
|
Guo W, Li W, Yuan L, Mei X, Hu W. MicroRNA-106a-3p Induces Apatinib Resistance and Activates Janus-Activated Kinase 2 (JAK2)/Signal Transducer and Activator of Transcription 3 (STAT3) by Targeting the SOCS System in Gastric Cancer. Med Sci Monit 2019; 25:10122-10128. [PMID: 31884511 PMCID: PMC6948289 DOI: 10.12659/msm.919610] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background MicroRNA (miR)-106a was involved in the tumorigenesis and highly expressed in gastric cancer. Required apatinib resistance greatly limits its efficacy in patients. Thus, the aim of the present study was to investigate the potential role of miR-106a-3p in gastric cancer cells with apatinib-resistance. Material/Methods The expression of miR-106a-3p was quantified by real-time quantitative polymerase chain reaction (RT-qPCR). Cell Counting Kit-8 (CCK-8) assay was performed to analyze the sensitivity of gastric cancer cells to apatinib. The expression of relevant drug-resistant proteins was detected by western blot. We searched Targetscan6.2 to find out the target gene of miR-106a-3p. Luciferase reporter assay was used to analyze whether miR-106a-3p bound to relevant gene of SOCS family. The SOCS2, SOCS4, and SOCS5 were qualified by western blot, and their mRNA levels were detected by RT-qPCR. Further, JAK2, STAT3, and their phosphorylation levels were detected by western blot. Results The results showed that the expression of miR-106a-3p was increased in apatinib-resistant gastric cancer, while miR-106a-3p inhibitor reduced the drug-resistance of SGC-7901-AP cells to apatinib. Dual luciferase reporter gene assay suggested that SOCS2, SOCS4, and SOCS5 were target genes of miR-106a-3p. The relevant SOCS genes silencing reversed the effects of miR-106a-3p inhibitor on decreasing the apatinib resistance of SGC-7901-AP cells, while the phosphorylation level of JAK and STAT reduced by miR-106a-3p inhibitor were increased. Conclusions miR-106a-3p induces apatinib resistance and activates JAK2/STAT3 by targeting SOCS system in gastric cancer. miR-106a-3p/SOCS plays a potent role in gastric cancer cell resistance to apatinib.
Collapse
Affiliation(s)
- Wei Guo
- Department of Gastrointestinal Surgery, Affiliated Heji Hospital of Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Wenyuan Li
- Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Li Yuan
- Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Xianghuang Mei
- Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Wenqing Hu
- Department of Gastrointestinal Surgery, Affiliated Heji Hospital of Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| |
Collapse
|
34
|
Hu C, Xu Z, Chen S, Lv H, Wang Y, Wang X, Mo S, Shi C, Wei S, Hu L, Chen W, Cheng X. Overexpression of B7H5/CD28H is associated with worse survival in human gastric cancer. J Cell Mol Med 2019; 24:1360-1369. [PMID: 31883303 PMCID: PMC6991633 DOI: 10.1111/jcmm.14812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/20/2019] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer (GC) is a common malignancy with low 5‐year overall survival (OS). Recently, immune therapy has been used to treat cancer. B7H5 and CD28H are novel immune checkpoint molecules. However, the prognostic value of B7H5/CD28H expression in patients with GC remains unclear. In this study, seventy‐one patients diagnosed with GC were included in this study. Patients' GC tissues and matched adjacent tissue constructed a tissue microarray. The expression levels of B7H5 and CD28H were examined using immunohistochemistry. Correlations between the expression of B7H5 and CD28H and the clinical data were evaluated. We found that the expression of B7H5 and CD28H (both P = .001) were higher in GC tumour tissues than in adjacent noncancerous tissues. B7H5/CD28H expression acted as an independent predictive factor in the OS of patients with GC. High expression of B7H5 and CD28H predicted poor outcome. Patients in the B7H5+CD28H+ group had a lower 5‐year OS compared with patients in the B7H5−CD28− group (4.5% vs 55.6%, P = .001). A significant difference was found in the 5‐year OS between patients in the B7H5+CD28H− and B7H5+CD28H+ groups (33.5% vs 4.5%, P = .006). However, there was no correlation between B7H5 and CD28H expression (P = .844). Therefore, B7H5 and CD28H expression are up‐regulated in GC and are independent prognostic factors for overall survival in patients with GC. Although there was no correlation between B7H5 and CD28H expression, high expression of B7H5 and CD28H predicts poor prognosis, especially when both are highly expressed.
Collapse
Affiliation(s)
- Can Hu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Zhiyuan Xu
- Department of Abdominal Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Shangqi Chen
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Hang Lv
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Diagnosis and Treatment of Digestive System Tumor, Hangzhou, Zhejiang, China
| | - Yiping Wang
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Diagnosis and Treatment of Digestive System Tumor, Hangzhou, Zhejiang, China
| | - Xiaofeng Wang
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shaowei Mo
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Chengwei Shi
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shenyu Wei
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Liqiang Hu
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Wei Chen
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Key Laboratory of Cancer Prevention and Therapy Combining Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Xiangdong Cheng
- Department of Abdominal Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| |
Collapse
|
35
|
Yin X, Zhang F, Guo Z, Kong W, Wang Y. Integrative analysis of miRNA and mRNA expression profiles reveals a novel mRNA/miRNA signature to improve risk classification for patients with gastric cancer. Oncol Lett 2019; 18:2330-2339. [PMID: 31402938 PMCID: PMC6676680 DOI: 10.3892/ol.2019.10536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 05/25/2019] [Indexed: 02/03/2023] Open
Abstract
Gastric cancer (GC) is one of the most common types of malignant cancer and is associated with poor prognosis. Although the prognosis of patients with GC is associated with grade, stage and lymph node metastases, these traditional clinical features are inadequate to predict the outcome of GC. Therefore, there has been an increased focus on identifying novel molecular biomarkers for early diagnosis and prognosis, in order to improve outcomes in GC. In the present study, an integrative analysis of microRNA (miRNA) expression profiles, mRNA expression profiles and clinical characteristics was performed in a large cohort of patients with GC in order to identify an integrative prognostic model for improving postoperative risk classification. An integrative mRNA/miRNA signature (IMMIS), comprised of three miRNAs and one mRNA, was identified from a large number of differentially expressed miRNAs and mRNAs using univariate and multivariate Cox regression analysis. The prognostic value of the IMMIS was validated in the discovery cohort, testing cohort and The Cancer Genome Atlas (TCGA) cohort. The present results suggested that the identified signature had a reliable predictive performance and could classify the patients into high- and low-risk groups with significantly different overall survival times. In the discovery cohort, the hazard ratio (HR) was 2.805 with a 95% CI=1.722–4.567 (P<0.001). The median overall survival time as 1.49 vs. 3.85 years. In the testing cohort, the HR was 1.625 with a 95% CI=1.004–2.638 (P=0.039) and the median overall survival time was 2.17 vs. 4.62 years. In the TCGA cohort, the HR was 2.139 with a 95% CI=1.519–3.012 (P<0.001) and the median overall survival time was 1.53 vs. 4.62 years. The IMMIS constituted a reliable independent prognostic factor compared with clinical covariates, including age, sex, grade and stage, as indicated by multivariate and stratified analyses. Furthermore, comparative analysis revealed that the predictive value of the IMMIS was superior to the mRNA-based signature alone. The present results suggested the potential value of the IMMIS as a promising novel biomarker for improving the clinical management of patients with GC.
Collapse
Affiliation(s)
- Xiang Yin
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Fumin Zhang
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Zhongwu Guo
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Weiyuan Kong
- Department of Minimally Invasive Tumor Surgery, Daqing Oilfield General Hospital, Daqing, Heilongjiang 163453, P.R. China
| | - Yuanyuan Wang
- Department of Gastroenterology, Daqing Long Nan Hospital, Daqing, Heilongjiang 163453, P.R. China
| |
Collapse
|
36
|
Zhang L, Lu D, Liu M, Zhang M, Peng Q. Identification and interaction analysis of key miRNAs in medullary thyroid carcinoma by bioinformatics analysis. Mol Med Rep 2019; 20:2316-2324. [PMID: 31322209 PMCID: PMC6691269 DOI: 10.3892/mmr.2019.10463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Medullary thyroid carcinoma (MTC) is an endocrine tumor and comprises 5–10% of all primary thyroid malignancies. However, the biomechanical contribution to the development and progression of MTC remains unclear. In this study, To discover the key microRNAs (miRNAs or miRs) and their potential roles in the tumorigenesis of MTC, the microarray datasets GSE97070, GSE40807 and GSE27155 were analyzed. The datasets were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed miRNAs (DEMs) and genes (DEGs) were accessed by R. Targets of DEMs and predicted using starBase, and functional and pathway enrichment analyses were performed using Metascape. A protein-protein interaction (PPI) network and an analysis of modules were constructed using NetworkAnalyst. Finally, a network was constructed to show the regulatory association between transcription factors (TFs), DEMs and downstream genes. A total of 5 DEMs were found both in GSE97070 and GSE40807, including 3 upregulated DEMs and 2 downregulated DEMs. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses from Metascape revealed that the target genes of upregulated DEMs were significantly enriched in adherens junction, kinase and protein binding, while the target genes of downregulated DEMs were mainly involved in non-canonical Wnt signaling pathway and RNA transport. From the PPI network, 13 nodes were screened as hub genes. Pathway enrichment analysis revealed that the top 5 modules were mostly enriched in the neurotrophin signaling pathway, mRNA surveillance pathway and MAPK signaling pathway. In addition, the TF-DEMs-target gene and DEGs regulatory network revealed that 17 TFs regulated 2 miRNAs, including upregulated or downregulated DEMs, CREB1 regulated all upregulated DEMs, and TGFB1 was an activator of hsa-miR-199a-3p and a repressor of hsa-miR-429. Taken together, the present study identified several miRNAs and potential biological mechanisms involved in the tumorigenesis of MTC. This study identified the key DEMs and potential mechanisms underlying the development of MTC, and provided a series of biomarkers and targets for the management of MTC.
Collapse
Affiliation(s)
- Lijie Zhang
- Tumor Diagnosis and Treatment Center, PLA 901 Hospital, Hefei, Anhui 230031, P.R. China
| | - Donghui Lu
- Tumor Diagnosis and Treatment Center, PLA 901 Hospital, Hefei, Anhui 230031, P.R. China
| | - Meiqin Liu
- Tumor Diagnosis and Treatment Center, PLA 901 Hospital, Hefei, Anhui 230031, P.R. China
| | - Mingjin Zhang
- General Surgery Department, PLA 901 Hospital, Hefei, Anhui 230031, P.R. China
| | - Quan Peng
- General Surgery Department, PLA 901 Hospital, Hefei, Anhui 230031, P.R. China
| |
Collapse
|
37
|
Ruckert MT, de Andrade PV, Santos VS, Silveira VS. Protein tyrosine phosphatases: promising targets in pancreatic ductal adenocarcinoma. Cell Mol Life Sci 2019; 76:2571-2592. [PMID: 30982078 PMCID: PMC11105579 DOI: 10.1007/s00018-019-03095-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. It is the fourth leading cause of cancer-related death and is associated with a very poor prognosis. KRAS driver mutations occur in approximately 95% of PDAC cases and cause the activation of several signaling pathways such as mitogen-activated protein kinase (MAPK) pathways. Regulation of these signaling pathways is orchestrated by feedback loops mediated by the balance between protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs), leading to activation or inhibition of its downstream targets. The human PTPome comprises 125 members, and these proteins are classified into three distinct families according to their structure. Since PTP activity description, it has become clear that they have both inhibitory and stimulatory effects on cancer-associated signaling processes and that deregulation of PTP function is closely associated with tumorigenesis. Several PTPs have displayed either tumor suppressor or oncogenic characteristics during the development and progression of PDAC. In this sense, PTPs have been presented as promising candidates for the treatment of human pancreatic cancer, and many PTP inhibitors have been developed since these proteins were first associated with cancer. Nevertheless, some challenges persist regarding the development of effective and safe methods to target these molecules and deliver these drugs. In this review, we discuss the role of PTPs in tumorigenesis as tumor suppressor and oncogenic proteins. We have focused on the differential expression of these proteins in PDAC, as well as their clinical implications and possible targeting for pharmacological inhibition in cancer therapy.
Collapse
Affiliation(s)
- Mariana Tannús Ruckert
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Pamela Viani de Andrade
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Verena Silva Santos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil
| | - Vanessa Silva Silveira
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, São Paulo, Brazil.
| |
Collapse
|
38
|
Glucocorticoid Receptor Modulates EGFR Feedback upon Acquisition of Resistance to Monoclonal Antibodies. J Clin Med 2019; 8:jcm8050600. [PMID: 31052457 PMCID: PMC6572202 DOI: 10.3390/jcm8050600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/20/2022] Open
Abstract
Evidences of a crosstalk between Epidermal Growth Factor Receptor (EGFR) and Glucocorticoid Receptor (GR) has been reported, ranging from the modulation of receptor levels or GR mediated transcriptional repression of EGFR target genes, with modifications of epigenetic markers. The present study focuses on the involvement of EGFR positive and negative feedback genes in the establishment of cetuximab (CTX) resistance in metastatic Colorectal Cancer (CRC) patients. We evaluated the expression profile of the EGFR ligands TGFA and HBEGF, along with the pro-inflammatory cytokines IL-1B and IL-8, which were previously reported to be negatively associated with monoclonal antibody response, both in mice and patient specimens. Among EGFR negative feedback loops, we focused on ERRFI1, DUSP1, LRIG3, and LRIG1. We observed that EGFR positive feedback genes are increased in CTX-resistant cells, whereas negative feedback genes are reduced. Next, we tested the expression of these genes in CTX-resistant cells upon GR modulation. We unveiled that GR activation leads to an increase in ERRFI1, DUSP1, and LRIG1, which were shown to restrict EGFR activity, along with a decrease in the EGFR activators (TGFA and IL-8). Finally, in a cohort of xenopatients, stratified for response to cetuximab, we observed an inverse association between the expression level of LRIG1 and CRC progression upon CTX treatment. Our model implies that combining GR modulation to EGFR inhibition may yield an effective treatment strategy in halting cancer progression.
Collapse
|
39
|
Zhao B, You Y, Wan Z, Ma Y, Huo Y, Liu H, Zhou Y, Quan W, Chen W, Zhang X, Li F, Zhao Y. Weighted correlation network and differential expression analyses identify candidate genes associated with BRAF gene in melanoma. BMC MEDICAL GENETICS 2019; 20:54. [PMID: 30925905 PMCID: PMC6441238 DOI: 10.1186/s12881-019-0791-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 03/22/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Primary cutaneous malignant melanoma is a cancer of the pigment cells of the skin, some of which are accompanied by BRAF mutation. Melanoma incidence and mortality rates have been rising around the world. As the current knowledge about pathogenesis, clinical and genetic features of cutaneous melanoma is not very clear, we aim to use bioinformatics to identify the potential key genes involved in the expression and mutation status of BRAF. METHODS Firstly, we used UCSC public hub datasets of melanoma (Lin et al., Cancer Res 68(3):664, 2008) to perform weighted genes co-expression network analysis (WGCNA) and differentially expressed genes analysis (DEGs), respectively. Secondly, overlapping genes between significant gene modules and DEGs were screened and validated at transcriptional levels and overall survival in TCGA and GTEx datasets. Lastly, the functional enrichment analysis was accomplished to find biological functions on the web-server database. RESULTS We performed weighted correlation network and differential expression analyses, using gene expression data in melanoma samples. We identified 20 genes whose expression was correlated with the mutation status of BRAF. For further validation, three of these genes (CYR61, DUSP1, and RNASE4) were found to have similar expression patterns in skin tumors from TCGA compared with normal skin samples from GTEx. We also found that weak expression of these three genes was associated with worse overall survival in the TCGA data. These three genes were involved in the nucleic acid metabolic process. CONCLUSION In this study, CYR61, DUSP1, and RNASE4 were identified as potential genes of interest for future molecular studies in melanoma, which would improve our understanding of its causes and underlying molecular events. These candidate genes may provide a promising avenue of future research for therapeutic targets in melanoma.
Collapse
Affiliation(s)
- Bin Zhao
- School of Medicine, Xiamen University, Xiamen, Fujian China
- The Department of Oncology and Vascular Interventional Radiology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yanqiu You
- The Department of Clinical Laboratory, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang China
| | - Zheng Wan
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Yunhan Ma
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Yani Huo
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Hongyi Liu
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Yuanyuan Zhou
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Wei Quan
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Weibin Chen
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Xiaohong Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian China
| | - Fujun Li
- The Department of Anesthesiology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang China
| | - Yilin Zhao
- School of Medicine, Xiamen University, Xiamen, Fujian China
- The Department of Oncology and Vascular Interventional Radiology, Zhongshan Hospital, Xiamen University, Xiamen, China
| |
Collapse
|