1
|
Zhu Z, Jin Y, Zhou J, Chen F, Chen M, Gao Z, Hu L, Xuan J, Li X, Song Z, Guo X. PD1/PD-L1 blockade in clear cell renal cell carcinoma: mechanistic insights, clinical efficacy, and future perspectives. Mol Cancer 2024; 23:146. [PMID: 39014460 PMCID: PMC11251344 DOI: 10.1186/s12943-024-02059-y] [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: 05/31/2024] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
The advent of PD1/PD-L1 inhibitors has significantly transformed the therapeutic landscape for clear cell renal cell carcinoma (ccRCC). This review provides an in-depth analysis of the biological functions and regulatory mechanisms of PD1 and PD-L1 in ccRCC, emphasizing their role in tumor immune evasion. We comprehensively evaluate the clinical efficacy and safety profiles of PD1/PD-L1 inhibitors, such as Nivolumab and Pembrolizumab, through a critical examination of recent clinical trial data. Furthermore, we discuss the challenges posed by resistance mechanisms to these therapies and potential strategies to overcome them. We also explores the synergistic potential of combination therapies, integrating PD1/PD-L1 inhibitors with other immunotherapies, targeted therapies, and conventional modalities such as chemotherapy and radiotherapy. In addition, we examine emerging predictive biomarkers for response to PD1/PD-L1 blockade and biomarkers indicative of resistance, providing a foundation for personalized therapeutic approaches. Finally, we outline future research directions, highlighting the need for novel therapeutic strategies, deeper mechanistic insights, and the development of individualized treatment regimens. Our work summarizes the latest knowledge and progress in this field, aiming to provide a valuable reference for improving clinical efficacy and guiding future research on the application of PD1/PD-L1 inhibitors in ccRCC.
Collapse
Affiliation(s)
- Zhaoyang Zhu
- Jiaxing University Master Degree Cultivation Base, Zhejiang Chinese Medical University, Hangzhou, 310000, Zhejiang, P.R. China
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Yigang Jin
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Jing Zhou
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Fei Chen
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Minjie Chen
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Zhaofeng Gao
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Lingyu Hu
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Jinyan Xuan
- Department of General Practice, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China
| | - Xiaoping Li
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China.
| | - Zhengwei Song
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China.
| | - Xiao Guo
- Department of Urology, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 310000, Zhejiang, P.R. China.
| |
Collapse
|
2
|
Zhang J, Feng S, Chen M, Zhang W, Zhang X, Wang S, Gan X, Zheng Y, Wang G. Identification of potential crucial genes shared in psoriasis and ulcerative colitis by machine learning and integrated bioinformatics. Skin Res Technol 2024; 30:e13574. [PMID: 38303405 PMCID: PMC10835022 DOI: 10.1111/srt.13574] [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: 11/22/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Mounting evidence suggest that there are an association between psoriasis and ulcerative colitis (UC), although the common pathogeneses are not fully understood. Our study aimed to find potential crucial genes in psoriasis and UC through machine learning and integrated bioinformatics. METHODS The overlapping differentially expressed genes (DEGs) of the datasets GSE13355 and GSE87466 were identified. Then the functional enrichment analysis was performed. The overlapping genes in LASSO, SVM-RFE and key module in WGCNA were considered as potential crucial genes. The receiver operator characteristic (ROC) curve was used to estimate their diagnostic confidence. The CIBERSORT was conducted to evaluate immune cell infiltration. Finally, the datasets GSE30999 and GSE107499 were retrieved to validate. RESULTS 112 overlapping DEGs were identified in psoriasis and UC and the functional enrichment analysis revealed they were closely related to the inflammatory and immune response. Eight genes, including S100A9, PI3, KYNU, WNT5A, SERPINB3, CHI3L2, ARNTL2, and SLAMF7, were ultimately identified as potential crucial genes. ROC curves showed they all had high confidence in the test and validation datasets. CIBERSORT analysis indicated there was a correlation between infiltrating immune cells and potential crucial genes. CONCLUSION In our study, we focused on the comprehensive understanding of pathogeneses in psoriasis and UC. The identification of eight potential crucial genes may contribute to not only understanding the common mechanism, but also identifying occult UC in psoriasis patients, even serving as therapeutic targets in the future.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Shuo Feng
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Minfei Chen
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Wen Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Xiu Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Shengbang Wang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Xinyi Gan
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Yan Zheng
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Guorong Wang
- The First Department of General Surgerythe Third Affiliated Hospital and Shaanxi Provincial People's HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| |
Collapse
|
3
|
Singh S, Kaushik AC, Gupta H, Jhinjharia D, Sahi S. Identification of Prognostic Markers and Potential Therapeutic Targets using Gene Expression Profiling and Simulation Studies in Pancreatic Cancer. Curr Comput Aided Drug Des 2024; 20:955-973. [PMID: 37711100 DOI: 10.2174/1573409920666230914100826] [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: 04/28/2023] [Revised: 07/07/2023] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has a 5-year relative survival rate of less than 10% making it one of the most fatal cancers. A lack of early measures of prognosis, challenges in molecular targeted therapy, ineffective adjuvant chemotherapy, and strong resistance to chemotherapy cumulatively make pancreatic cancer challenging to manage. OBJECTIVE The present study aims to enhance understanding of the disease mechanism and its progression by identifying prognostic biomarkers, potential drug targets, and candidate drugs that can be used for therapy in pancreatic cancer. METHODS Gene expression profiles from the GEO database were analyzed to identify reliable prognostic markers and potential drug targets. The disease's molecular mechanism and biological pathways were studied by investigating gene ontologies, KEGG pathways, and survival analysis to understand the strong prognostic power of key DEGs. FDA-approved anti-cancer drugs were screened through cell line databases, and docking studies were performed to identify drugs with high affinity for ARNTL2 and PIK3C2A. Molecular dynamic simulations of drug targets ARNTL2 and PIK3C2A in their native state and complex with nilotinib were carried out for 100 ns to validate their therapeutic potential in PDAC. RESULTS Differentially expressed genes that are crucial regulators, including SUN1, PSMG3, PIK3C2A, SCRN1, and TRIAP1, were identified. Nilotinib as a candidate drug was screened using sensitivity analysis on CCLE and GDSC pancreatic cancer cell lines. Molecular dynamics simulations revealed the underlying mechanism of the binding of nilotinib with ARNTL2 and PIK3C2A and the dynamic perturbations. It validated nilotinib as a promising drug for pancreatic cancer. CONCLUSION This study accounts for prognostic markers, drug targets, and repurposed anti-cancer drugs to highlight their usefulness for translational research on developing novel therapies. Our results revealed potential and prospective clinical applications in drug targets ARNTL2, EGFR, and PI3KC2A for pancreatic cancer therapy.
Collapse
Affiliation(s)
- Samvedna Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | | | - Himanshi Gupta
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Divya Jhinjharia
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Shakti Sahi
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| |
Collapse
|
4
|
Guo W, Wang X, Zhang Y, Liu H, Ma S, Guan F. Construction and validation of a novel prognostic signature for cutaneous melanoma based on ferroptosis-related genes. Heliyon 2023; 9:e15725. [PMID: 37159694 PMCID: PMC10163649 DOI: 10.1016/j.heliyon.2023.e15725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 05/11/2023] Open
Abstract
Ferroptosis, a recently uncovered iron-dependent, non-apoptotic cell death process, has been increasingly linked to cancer development. In this study, our objective was to develop a prognostic model centered on ferroptosis-related genes (FRGs) and assess its efficacy as an overall survival (OS) prediction biomarker. We conducted a systematic analysis of cutaneous melanoma (CM) and devised a novel ferroptosis-related prognostic signature (FRGSig) using the TCGA database. An independent dataset from GSE65904 was employed to corroborate the validity of the FRGSig. Both univariate and multivariate Cox proportional hazard regression analyses were utilized to construct a FRGSig composed of five FRGs. mRNA expression and immunohistochemistry (IHC) analysis demonstrated that the expression of FRGSig genes varied between tumor and normal tissues. According to Kaplan-Meier analysis, patients with elevated FRGsig scores faced a worse prognosis. The predictive accuracy of FRGSig was evaluated using the time-dependent receiver operating characteristic curve (ROC), with the area under the curve (AUC) values for 1, 3, and 5 OS at 0.682, 0.711, 0.735 in the TCGA cohort, and 0.662, 0.695, 0.712 in the validation dataset, respectively. Univariate and multivariate Cox regression analyses demonstrated that FRGSig served as an independent prognostic factor. Further analysis revealed a significant relationship between FRGSig and Tumor Mutational Burden (TMB) as well as immune infiltration levels. Gene set enrichment analysis (GSEA) disclosed functional disparities between high- and low-risk groups, suggesting that immune checkpoint-related pathways could be instrumental in the improved prognosis of the low-risk group. Taken together, the FRGSig has potential guidance for prognosis prediction and clinical treatment of CM.
Collapse
Affiliation(s)
- Wenna Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xue Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yanting Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongtao Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Shanshan Ma
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Corresponding author.
| | - Fangxia Guan
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Corresponding author.
| |
Collapse
|
5
|
Wang T, Wang K, Zhu X, Chen N. ARNTL2 upregulation of ACOT7 promotes NSCLC cell proliferation through inhibition of apoptosis and ferroptosis. BMC Mol Cell Biol 2023; 24:14. [PMID: 37003979 PMCID: PMC10064581 DOI: 10.1186/s12860-022-00450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/05/2022] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Recent studies have reported that the circadian transcription factor aryl hydrocarbon receptor nuclear translocator like 2 (ARNTL2) promotes the metastatic progression of lung adenocarcinoma. However, the molecular mechanisms of ARNTL2 in non-small cell lung cancer (NSCLC) cell growth and proliferation remain to be explored. METHODS The expression of ARNTL2 and acyl-CoA thioesterase 7 (ACOT7) in lung cancer patients was analyzed based on TCGA database. Gain-of-function of ARNTL2 and ACOT7 was conducted by transfecting the cells with plasmids or lentivirus. Knockdown assay was carried out by siRNAs. Western blot and qRT-PCR were performed to check the protein and mRNA expression. Dual luciferase and ChIP-qPCR assay was applied to check the interaction of ARNTL2 on ACOT7's promoter sequence. Triglyceride level, MDA production, the activity of casapase 3 to caspase 7, and lipid ROS were measured by indicated assay kit. Cellular function was detected by CCK8, colony formation and flow cytometry analysis of cell death and cell cycle. RESULTS We demonstrated that ARNTL2 upregulation of ACOT7 was critical for NSCLC cell growth and proliferation. Firstly, overexpression of ARNTL2 conferred the poor prognosis of LUAD patients and supported the proliferation of NSCLC cells. Based on molecular experiments, we showed that ARNTL2 potentiated the transcription activity of ACOT7 gene via direct binding to ACOT7's promoter sequence. ACOT7 high expression was correlated with the worse prognosis of LUAD patients. Gain-of-function and loss-of-function experiments revealed that AOCT7 contributed to NSCLC cell growth and proliferation. ACOT7 regulated the apoptosis and ferroptosis of NSCLC cells, while exhibited no effect on cell cycle progression. ACOT7 overexpression also potentiated fatty acid synthesis and suppressed lipid peroxidation. Lastly, we showed that ARNTL2 knockdown and overexpression inhibited and promoted the cellular triglyceride production and subsequent cell proliferation, which could be reversed by ACOT7 overexpression and knockdown. CONCLUSION Our study illustrated the oncogenic function of ARNTL2/ACOT7 axis in the development of NSCLC. Targeting ARNTL2 or ACOT7 might be promising therapeutic strategies for NSCLC patients with highly expressed ARNTL2.
Collapse
Affiliation(s)
- Tao Wang
- Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Kai Wang
- Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xu Zhu
- Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Nan Chen
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, China.
| |
Collapse
|
6
|
Zhang H, Shan G, Jin X, Yu X, Bi G, Feng M, Wang H, Lin M, Zhan C, Wang Q, Li M. ARNTL2 is an indicator of poor prognosis, promotes epithelial-to-mesenchymal transition and inhibits ferroptosis in lung adenocarcinoma. Transl Oncol 2022; 26:101562. [PMID: 36228410 PMCID: PMC9563212 DOI: 10.1016/j.tranon.2022.101562] [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: 04/15/2022] [Revised: 09/17/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES ARNTL2, as a circadian transcription factor, has been recently proposed to play an important role in a variety of tumors. however, the role of ARNTL2 in lung carcinogenesis and progression remains unclear. The purpose of this study was to investigate the effect of ARNTL2 on the clinical characteristics and prognosis of lung adenocarcinoma and to explore the relationship between ARNTL2 and EMT, ferroptosis in lung adenocarcinoma. METHODS The Cancer Genome Atlas (TCGA) database's multi-omics data were downloaded using the Xena browser. Based on the expression levels of ARNTL2, patients with lung adenocarcinoma from TCGA were divided into two groups: those with high ARNTL2 expression and those with low ARNTL2 expression. ARNTL2 was studied for its effects on lung adenocarcinoma's clinicopathological, genomic, and immunological characteristics. Furthermore, in vivo and in vitro assays were used to confirm the impact of ARNLT2 knockdown on lung adenocarcinoma cells. RESULTS We found ARNTL2 is highly expressed in lung adenocarcinoma and was an independent predictor of a poor prognosis in patients with lung adenocarcinoma. In addition, we demonstrated that knockdown of ARNTL2 promoted ferroptosis, inhibited EMT, cell proliferation, migration and invasion in lung adenocarcinoma. In contrast, overexpressing ARNTL2 yielded the opposite results. CONCLUSIONS ARNTL2 is an independent unfavorable prognostic factor for lung adenocarcinoma. It plays a facilitating role in the development of lung adenocarcinoma, especially in promoting EMT and inhibiting ferroptosis, revealing that ARNTL2 may be a potential biomarker for lung adenocarcinoma.
Collapse
Affiliation(s)
- Huan Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guangyao Shan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xing Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, Peking Union Medical College, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital/Shenzhen Hospital, Chinese Academy of Medical Sciences, Shenzhen, China
| | - GuoShu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mingxiang Feng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
7
|
Wang S, Wang H, Zhu S, Li F. Systematical analysis of ferroptosis regulators and identification of GCLM as a tumor promotor and immunological biomarker in bladder cancer. Front Oncol 2022; 12:1040892. [PMID: 36353567 PMCID: PMC9638099 DOI: 10.3389/fonc.2022.1040892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 11/20/2022] Open
Abstract
Bladder cancer (BCa) is a life-threaten disease with an increasing incidence with age, and immunotherapy has become an important treatment for BCa, while the efficiency of the immune system declines with age. It is vital to reveal the mechanisms of tumor immune microenvironment (TIME) and identify novel immunotherapy targets for BCa. Through analyzing the RNA-seq of TCGA-BLCA cohort, we distinguished two ferroptosis-related BCa clusters, and we discovered that in comparation with cluster 2, the cluster 1 BCa patients showed higher PD-L1 expression, more unfavorable overall survival and higher tumor stage and grade. XCELL analyses showed that higher level of Th2 cell and Myeloid dendritic cell were enriched in cluster 1, while NK T cell was enriched in cluster 2, and TIDE analysis revealed that cluster 2 was more sensitive to immunotherapy than cluster 1. GSEA analysis implied that Toll-like signaling pathway and JAK_STAT signaling pathway were significantly enriched in cluster 1. Subsequently, through performing bioinformatic analysis and cell experiments, we demonstrated that GCLM is overexpressed in BCa and indicates dismal prognosis, and knockdown of GCLM can significantly suppress the colony formation ability of BCa cells. Furthermore, we also found that GCLM might be correlated with immune infiltration in BCa, and can serve as a tumor promotor and immunological biomarker in BCa, our research showed the vital roles of ferroptosis regulators in TIME of BCa, and GCLM is a latent therapeutic target for cancer immunotherapy.
Collapse
Affiliation(s)
- Song Wang
- Department of Urology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - He Wang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shaoxing Zhu
- Department of Urology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Fangyin Li
- Department of Urology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- *Correspondence: Fangyin Li,
| |
Collapse
|
8
|
Huang W, Li J, Zhou S, Li Y, Yuan X. Discovering a Four-Gene Prognostic Model Based on Single-Cell Data and Gene Expression Data of Pancreatic Adenocarcinoma. Front Endocrinol (Lausanne) 2022; 13:883548. [PMID: 35800432 PMCID: PMC9253429 DOI: 10.3389/fendo.2022.883548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Background Pancreatic cancer has a 5-year overall survival lower than 8%. Pancreatic adenocarcinoma (PAAD) is the most common type. This study attempted to explore novel molecular subtypes and a prognostic model through analyzing tumor microenvironment (TME). Materials and Methods Single-cell RNA sequencing (scRNA-seq) data and expression profiles from public databases were downloaded. Three PAAD samples with single-cell data and 566 samples with gene expression data were included. Seurat was used to identify cell subsets. SVA merged and removed batch effects from multichip datasets. CIBERSORT was used to evaluate the components of different cells in transcriptome, ConsensusClusterPlus was used to identify molecular subtypes, and gene set enrichment analysis was used for functional enrichment analysis. LASSO Cox was performed to construct dimensionality reduction and prognosis model. Results Memory B cells (MBCs) were identified to be significantly with PAAD prognosis. Two immune subtypes (IS1 and IS2) with distinct overall survival were constructed. Forty-one DEGs were identified between IS1 and IS2. Four prognostic genes (ANLN, ARNTL2, SERPINB5, and DKK1) were screened to develop a prognostic model. The model was effective in classifying samples into high-risk and low-risk groups with distinct prognosis. Three subgroups of MBCs were identified, where MBC_0 and MBC_1 were differentially distributed between IS1 and IS2, high-risk and low-risk groups. Conclusions MBCs were closely involved in PAAD progression, especially MBC_0 and MBC_1 subgroups. The four-gene prognostic model was predictive of overall survival and could guide immunotherapy for patients with PAAD.
Collapse
Affiliation(s)
- Weizhen Huang
- The Second Department of Medical Oncology, Huizhou First Hospital, Huizhou, China
| | - Jun Li
- The Second Department of Medical Oncology, Huizhou First Hospital, Huizhou, China
| | - Siwei Zhou
- The Second Department of Medical Oncology, Huizhou First Hospital, Huizhou, China
| | - Yi Li
- The Second Department of Medical Oncology, Huizhou First Hospital, Huizhou, China
| | - Xia Yuan
- Cancer Center, Huizhou First Hospital, Huizhou, China
| |
Collapse
|
9
|
Lu F, Gao J, Hou Y, Cao K, Xia Y, Chen Z, Yu H, Chang L, Li W. Construction of a Novel Prognostic Model in Lung Adenocarcinoma Based on 7-Methylguanosine-Related Gene Signatures. Front Oncol 2022; 12:876360. [PMID: 35785179 PMCID: PMC9243265 DOI: 10.3389/fonc.2022.876360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence has implicated the modification of 7-methylguanosine (m7G), a type of RNA modification, in tumor progression. However, no comprehensive analysis to date has summarized the predicted role of m7G-related gene signatures in lung adenocarcinoma (LUAD). Herein, we aimed to develop a novel prognostic model in LUAD based on m7G-related gene signatures. The LUAD transcriptome profiling data and corresponding clinical data were acquired from the Cancer Genome Atlas (TCGA) and two Gene Expression Omnibus datasets. After screening, we first obtained 29 m7G-related genes, most of which were upregulated in tumor tissues and negatively associated with overall survival (OS). According to the expression similarity of m7G-related genes, the combined samples from the TCGA-LUAD and GSE68465 datasets were further classified as two clusters that exhibit distinct OS rates and genetic heterogeneity. Then, we constructed a novel prognostic model involving four genes by using 130 differentially expressed genes among the two clusters. The combined samples were randomly divided into a training cohort and an internal validation cohort in a 1:1 ratio, and the GSE72094 dataset was used as an external validation cohort. The samples were divided into high- and low-risk groups. We demonstrated that a higher risk score was an independent negative prognostic factor and predicted poor OS. A nomogram was further constructed to better predict the survival of LUAD patients. Functional enrichment analyses indicated that cell cycle and DNA replication-related biological processes and pathways were enriched in the high-risk group. More importantly, the low-risk group had greater infiltration and enrichment of most immune cells, as well as higher ESTIMATE, immune, and stromal scores. In addition, the high-risk group had a lower TIDE score and higher expressions of most immune checkpoint-related genes. We finally noticed that patients in the high-risk group were more sensitive to chemotherapeutic agents commonly used in LUAD. In conclusion, we herein summarized for the first time the alterations and prognostic role of m7G-related genes in LUAD and then constructed a prognostic model based on m7G-related gene signatures that could accurately and stably predict survival and guide individualized treatment decision-making in LUAD patients.
Collapse
Affiliation(s)
- Fei Lu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- Department of Oncology and Hematology, Southern Central Hospital of Yunnan Province, The First People’s Hospital of Honghe State, Mengzi, China
| | - Jingyan Gao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yu Hou
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Ke Cao
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Yaoxiong Xia
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Zhengting Chen
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Hui Yu
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Li Chang
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
| | - Wenhui Li
- Department of Radiation Oncology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
- *Correspondence: Wenhui Li, ; Li Chang,
| |
Collapse
|
10
|
Jing J, Sun J, Wu Y, Zhang N, Liu C, Chen S, Li W, Hong C, Xu B, Chen M. AQP9 Is a Prognostic Factor for Kidney Cancer and a Promising Indicator for M2 TAM Polarization and CD8+ T-Cell Recruitment. Front Oncol 2021; 11:770565. [PMID: 34804972 PMCID: PMC8602816 DOI: 10.3389/fonc.2021.770565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background It is undeniable that the tumor microenvironment (TME) plays an indispensable role in the progression of kidney renal clear cell carcinoma (KIRC). However, the precise mechanism of activities in TME is still unclear. Methods and Results Using the CIBERSORT and ESTIMATE calculation methods, the scores of the two main fractions of tumor-infiltrating immune cells (TICs) from The Cancer Genome Atlas (TCGA) database of 537 KIRC patients were calculated. Subsequently, differentially expressed genes (DEGs) were drawn out by performing an overlap between Cox regression analysis and protein–protein interaction (PPI) network. Aquaporin 9 (AQP9) was identified as a latent predictor through the process. Following research revealed that AQP9 expression was positively correlated with the pathological characteristics (TNM stage) and negatively connected with survival time. Then, by performing gene set enrichment analysis (GSEA), it can be inferred that genes with high expression level of AQP9 were mainly enriched in immune-related activities, while low AQP9 group was associated with functions of cellular metabolism. Further studies have shown that regulatory T cells (Tregs), macrophages M2, macrophages M0, CD4+ T cells, and neutrophils were positively correlated with AQP9 expression. While the levels of mast cells, natural killer (NK) cells, and CD8+ T cells are negatively correlated with AQP9. The result of multiple immunohistochemistry (mIHC) suggests a negative relevance between AQP9 and CD8+ T cells and reveals a trend of consistent change on AQP9 and M2 macrophages. Conclusion The expression level of AQP9 may be helpful in predicting the prognosis of patients with KIRC, especially to the TME state transition, the mechanism of which is possibly through lipid metabolism and P53, Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathways that affect M2 polarization. AQP9 was associated with the expression levels of M2, tumor-associated macrophages (TAMs), and the recruitment of CD8+ T cells in tumor environment. The research result indicates that AQP9 may be an obstacle to maintain the immune activity of TME.
Collapse
Affiliation(s)
- Jibo Jing
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Jin Sun
- Department of Urology, People's Hospital of Xuyi County, Nanjing, China
| | - Yuqing Wu
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Nieke Zhang
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Chunhui Liu
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Saisai Chen
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Cheng Hong
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Bin Xu
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Ming Chen
- Institute of Urology, Surgical Research Center, Institute of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Medical School of Southeast University, Nanjing, China.,Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| |
Collapse
|
11
|
Fu S, Gong B, Wang S, Chen Q, Liu Y, Zhuang C, Li Z, Zhang Z, Ma M, Sun T. Prognostic Value of Long Noncoding RNA DLEU2 and Its Relationship with Immune Infiltration in Kidney Renal Clear Cell Carcinoma and Liver Hepatocellular Carcinoma. Int J Gen Med 2021; 14:8047-8064. [PMID: 34795513 PMCID: PMC8593347 DOI: 10.2147/ijgm.s336428] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022] Open
Abstract
Background DLEU2 is a long noncoding RNA considered important in the progression of many cancers. However, correlations between DLEU2 and kidney renal clear cell carcinoma (KIRC) and liver hepatocellular carcinoma (LIHC) have rarely been reported. Methods We first analysed the expression of DLEU2 across cancers and the correlation between DLEU2 and the clinical features of KIRC and LIHC by using the “ggplot2” package in R and searched the Oncomine database and Timer website platform. We verified the expression of DLEU2 in the GEO dataset (GSE105261 and GSE45267). Receiver operating characteristic (ROC) curves were drawn using the “pROC” and “ggplot2” packages in R, and we constructed a DLEU2-based prognostic nomogram for KIRC and LIHC by using the “survival” and “rms” packages in R. Then, we analysed the correlation between DLEU2 expression and prognosis in R as well as the correlation between DLEU2 and immune cell infiltration in the TIMER database. Finally, we explored the causes of DLEU2 upregulation in the UCSC Xena and UALCAN databases. Results We found that DLEU2 was upregulated in many cancers, including KIRC and LIHC. Expression of DLEU2 is associated with tumour stage, grade, lymphatic metastasis, and distant metastasis in KIRC as well as alpha-fetoprotein (AFP), tumour stage, grade, lymphatic metastasis, and distant metastasis in LIHC. DLEU2 is an adverse factor for the prognosis of KIRC and LIHC. In addition, DLEU2 has moderate accuracy in diagnosing KIRC and LIHC and predicting their prognosis. Moreover, we found that expression of DLEU2 correlated positively with immune cell infiltration in KIRC and LIHC, and upregulation of DLEU2 in KIRC and LIHC suggests a poor prognosis based on immune cells analysis. Genetic and epigenetic analyses of DLEU2 indicate that copy number variations (CNVs) and methylation contribute to the upregulation of DLEU2. Conclusion The long noncoding RNA DLEU2 has the potential to predict the prognosis and immune infiltration of KIRC and LIHC.
Collapse
Affiliation(s)
- Shengqiang Fu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Siyuan Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Qiang Chen
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Yifu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Changshui Zhuang
- Department of Urology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, People's Republic of China
| | - Zhilong Li
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Zhicheng Zhang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Ming Ma
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| |
Collapse
|
12
|
Wang X, Li Y, Fu J, Zhou K, Wang T. ARNTL2 is a Prognostic Biomarker and Correlates with Immune Cell Infiltration in Triple-Negative Breast Cancer. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:1425-1440. [PMID: 34785930 PMCID: PMC8591114 DOI: 10.2147/pgpm.s331431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Background Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype and is associated with poor prognosis. The aberrant expression of circadian genes contributes to the origin and progression of breast cancer. The present study was designed to explore the potential function and prognosis value of circadian genes in TNBC. Methods The transcriptome data of circadian genes were downloaded from The Cancer Genomic Atlas (TCGA), GSE25066 and GSE31448 datasets. The differential expressed circadian genes between non-TNBC and TNBC patients were analysed by Wilcoxon test. Univariate and multivariate Cox regression analyses were employed to identify the prognostic circadian genes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) were performed to study the biological functions of ARNTL2. The composition of 22 immune cells in the tumour samples was estimated with CIBERSORT algorithm. The correlations between ARNTL2 expression and tumour-infiltrating immune cells were evaluated by Spearman correlation coefficient. Results A total of 8 circadian genes were found to be differentially expressed between non-TNBC and TNBC, but only ARNTL2 has prognostic value. Multivariate Cox analysis identified that ARNTL2 was an independent prognosis factor for overall survival and relapse-free survival in TNBC patients. Functionally, ARNTL2 was mainly involved in immune response processes such as positive regulation of cytokine production, regulation of innate immune response, and cellular responses to molecules of bacterial origin. High expression of ARNTL2 was positively correlated with activated CD4 memory T cells, activated mast cells, and neutrophil infiltration and the expression of markers of neutrophils (ITGAM), dendritic cells (HLA-DRA, HLA-DPA1, ITGAM), Th1 (IL1B, STAT1), Th2 (IL13), Th17 (STAT3) and mast cells (TPSB2, TPSAB1). Conclusion ARNTL2 may be linked with the functional modulation of the tumour immune microenvironment and serve as a potential biomarker for predicting the prognosis of TNBC patients.
Collapse
Affiliation(s)
- Xiaoyu Wang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Yan Li
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Jianchang Fu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Kewen Zhou
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Tinghuai Wang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| |
Collapse
|
13
|
Zhang Z, Xiong X, Zhang R, Xiong G, Yu C, Xu L. Bioinformatics analysis reveals biomarkers with cancer stem cell characteristics in kidney renal clear cell carcinoma. Transl Androl Urol 2021; 10:3501-3514. [PMID: 34532274 PMCID: PMC8421844 DOI: 10.21037/tau-21-647] [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: 06/28/2021] [Accepted: 08/16/2021] [Indexed: 11/06/2022] Open
Abstract
Background Kidney renal clear cell carcinoma (KIRC) is a renal cortical tumor. KIRC is the most common subtype of kidney cancer, accounting for 70%-80% of kidney cancer. Early identification of the risk of KIRC patients can facilitate more accurate clinical treatment, but there is a lack of effective prognostic markers. We aimed to identify new prognostic biomarkers for KIRC on the basis of the cancer stem cell (CSC) theory. Methods RNA-sequencing (RNA-seq) data and related clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Weighted gene co-expression network analysis (WGCNA) was used to identify significant modules and hub genes, and predictive hub genes were used to construct prognostic characteristics. Results The messenger RNA expression-based stemness index (mRNAsi) in tumor tissues of patients in the TCGA database is higher than that of the corresponding normal tissues. In addition, some clinical features and results are highly correlated with mRNAsi. WGCNA found that the green module is the most prominent module associated with mRNAsi; the genes in the green module are mainly concentration in Notch binding, endothelial cell development, Notch signaling pathway, and Rap 1 signaling pathway. A protein-protein interaction (PPI) network showed that the top 10 central genes were significantly associated with the transcriptional level. Moreover, the 10 hub genes were up-regulated in KIRC. Regarding survival analysis, the nomogram of the prognostic markers of the seven pivotal genes showed a higher predictive value. The classical receiver operating characteristic (ROC) curve analysis showed that risk score biomarkers had the highest accuracy and specificity with an area under the curve (AUC) value of 0.701. Conclusions mRNAsi-related genes may be good prognostic biomarkers for KIRC.
Collapse
Affiliation(s)
- Zan Zhang
- College of Life Sciences and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xueyang Xiong
- College of Life Sciences and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Rufeng Zhang
- College of Life Sciences and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Guoliang Xiong
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Changyuan Yu
- College of Life Sciences and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lida Xu
- College of Life Sciences and Technology, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|