1
|
Wu Z, Ou J, Liu N, Wang Z, Chen J, Cai Z, Liu X, Yu X, Dai M, Zhou H. Upregulation of Tim‐3 is associated with poor prognosis in acute myeloid leukemia. Cancer Med 2022; 12:8956-8969. [PMID: 36545697 PMCID: PMC10134367 DOI: 10.1002/cam4.5549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematopoietic malignancy originated from leukemia stem cells (LSC). Emerging evidence suggests T-cell immunoglobulin mucin-3(Tim3) as surface marker for LSC. However, the clinical significance and biology of Tim-3 in AML remain to be determined, especially those LSCs. In public AML databases as well as our data, we separated AML patients into Tim-3high and Tim-3low subsets using the X-tile software and evaluated the associations between Tim-3 and overall survival (OS) and disease-free survival (DFS). The Cancer Genome Atlas (TCGA) cohort revealed that high Tim-3 expression in leukemic cells was linked with poor prognosis (DFS: p = 0.018; OS: p = 0.041). Furthermore, multiple regression analysis shows that Tim-3 was an independent factor for the prognosis (HR = 2.26, 95% CI = 1.15-4.44, p = 0.017). Validation cohort of public gene expression omnibus (GEO) confirmed that Tim-3 was a prognostic candidate in AML. Besides, in our internal cohort, we also confirmed that over expression of Tim-3 protein in LSC/LPC made poor prognosis in AML. Additionally, we revealed that the LSC markers AKR1C3, CD34, and MMRN1 were upregulated in the Tim-3high group of TCGA. We found that the upregulated genes in the Tim-3high group were mainly enriched in immune response, cytokine binding and cell adhesion molecules, and JAK-STAT signaling pathway, by gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Collectively, we revealed that, for the first time, upregulation of Tim-3 in LSCs at the level of gene and protein expression is associated with poor prognosis and the important biological feature of Tim-3 of LSC in AML.
Collapse
Affiliation(s)
- Zhengwei Wu
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Jiawang Ou
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Nannan Liu
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Junjie Chen
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Zihong Cai
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Xiaoli Liu
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Xiao Yu
- Department of Immunology, School of Basic Medical Sciences Southern Medical University Guangzhou China
| | - Min Dai
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital Southern Medical University Guangzhou China
| |
Collapse
|
2
|
Zhou Y, Dai X, Lyu J, Li Y, Bao X, Deng F, Liu K, Cui L, Cheng L. Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs. Medicine (Baltimore) 2022; 101:e31075. [PMID: 36281116 PMCID: PMC9592387 DOI: 10.1097/md.0000000000031075] [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] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND To construct and verify a novel prognostic model for thyroid cancer (THCA) based on N7-methylguanosine modification-related lncRNAs (m7G-lncRNAs) and their association with immune cell infiltration. METHODS In this study, we identified m7G-lncRNAs using co-expression analysis and performed differential expression analysis of m7G-lncRNAs between groups. We then constructed a THCA prognostic model, performed survival analysis and risk assessment for the THCA prognostic model, and performed independent prognostic analysis and receiver operating characteristic curve analyses to evaluate and validate the prognostic value of the model. Furthermore, analysis of the regulatory relationship between prognostic differentially expressed m7G-related lncRNAs (PDEm7G-lncRNAs) and mRNAs and correlation analysis of immune cells and risk scores in THCA patients were carried out. RESULTS We identified 29 N7-methylguanosine modification-related mRNAs and 116 differentially expressed m7G-related lncRNAs, including 87 downregulated and 29 upregulated lncRNAs. Next, we obtained 8 PDEm7G-lncRNAs. A final optimized model was constructed consisting of 5 PDEm7G-lncRNAs (DOCK9-DT, DPP4-DT, TMEM105, SMG7-AS1 and HMGA2-AS1). Six PDEm7G-lncRNAs (DOCK9-DT, DPP4-DT, HMGA2-AS1, LINC01976, MID1IP1-AS1, and SMG7-AS1) had positive regulatory relationships with 10 PDEm7G-mRNAs, while 2 PDEm7G-lncRNAs (LINC02026 and TMEM105) had negative regulatory relationships with 2 PDEm7G-mRNAs. Survival curves and risk assessment predicted the prognostic risk in both groups of patients with THCA. Forest maps and receiver operating characteristic curves were used to evaluate and validate the prognostic value of the model. Finally, we demonstrated a correlation between different immune cells and risk scores. CONCLUSION Our results will help identify high-risk or low-risk patients with THCA and facilitate early prediction and clinical intervention in patients with high risk and poor prognosis.
Collapse
Affiliation(s)
- Yang Zhou
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xuezhong Dai
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jianhong Lyu
- Department of Anesthesiology, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yingyue Li
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xueyu Bao
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Fang Deng
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Kun Liu
- Department of Otorhinolaryngology, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Liming Cui
- Department of Otolaryngology Head and Neck Surgery, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Li Cheng
- Department of Endocrinology, The Third People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- * Correspondence: Li Cheng, The Third People’s Hospital of Yunnan Province, 292 Beijing Road, Guandu District, Kunming City, Yunnan Province 650011, China (e-mail: )
| |
Collapse
|
3
|
Pan J, Jiang Y, Li C, Jin T, Yu K, Jin Z. Characteristics of Pyroptosis-Related Subtypes and Novel Scoring Tool for the Prognosis and Chemotherapy Response in Acute Myeloid Leukemia. Front Oncol 2022; 12:898236. [PMID: 35756629 PMCID: PMC9229173 DOI: 10.3389/fonc.2022.898236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/04/2022] [Indexed: 12/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is usually associated with poor prognosis and low complete remission (CR) rate due to individual biological heterogeneity. Pyroptosis is a special form of inflammatory programmed cell death related to the progression, treatment response, and prognosis of multiple tumors. However, the potential connection of pyroptosis-related genes (PRGs) and AML still remains unclear. We described the genetic and transcriptional alterations of PRGs in 151 AML samples and presented a consensus clustering of these patients into two subtypes with distinct immunological and prognostic characteristics. Cluster A, associated with better prognosis, was characterized by relatively lower PRG expression, activated immune cells, higher immune scores in the tumor microenvironment (TME), and downregulation of immunotherapy checkpoints. Subsequently, a PRG score was constructed to predict overall survival (OS) of AML patients by using univariate and multivariate Cox regression analysis, and its immunological characteristics and predictive capability were further validated by 1,054 AML samples in external datasets. Besides an immune-activated status, low-PRG score cohorts exhibited higher chemotherapeutic drug sensitivity and significant positive correlation with the cancer stem cell (CSC) index. Combined with age, clinical French-American-British (FAB) subtypes, and PRG score, we successfully constructed a nomogram to effectively predict the 1-/3-/5-year survival rate of AML patients, and the predictive capability was further validated in multiple external datasets with a high area under the curve (AUC) value. The various transcriptomic analysis helps us screen significant pyroptosis-related signatures of AML and provide a new clinical application of PRG scores in predicting the prognosis and benefits of treatment for AML patients.
Collapse
Affiliation(s)
- Jingjing Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yinyan Jiang
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Changhong Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ting Jin
- Department of Operating Room, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kang Yu
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhenlin Jin
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
4
|
A Six-Gene Risk Model Based on the Immune Score Reveals Prognosis in Intermediate-Risk Acute Myeloid Leukemia. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4010786. [PMID: 35528167 PMCID: PMC9076319 DOI: 10.1155/2022/4010786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022]
Abstract
Tumor microenvironment (TME) has been revealed as an important determinant of diagnosis and treatment response in AML patients. The scores of immune and stromal cell scores of AML in the intermediate-risk group from The Cancer Genome Atlas (TCGA) database were calculated using the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data algorithm. Differentially expressed genes were identified between high and low scores. Gene set enrichment and pathway analyses were performed. A risk score model based on TME for six immune-related genes was established and validated. Patients with a lower immune score had a longer overall survival than those with a higher score (P = 0.044). A total of 805 intersected genes as differentially expressed genes were identified and selected according to the comparison of both immune and stromal scores. The functional enrichment analysis shows that these genes are mainly associated with the immune/inflammatory response. The risk score model based on TME for six immune-related genes (including MEF2C, ENPP2, FAM107A, CD37, TNFAIP8L2, and CASS4) was established and validated in the TCGA database and well validated in the TARGET database (P = 0.005). A key microenvironment-related gene signature was identified that affects the outcomes of AML patients in the intermediate-risk group and might serve as therapeutic targets.
Collapse
|
5
|
Schmucker AM, Leiby BE, Wilde L. Validation of AML-score in Older Adults Receiving CPX-351 Intensive Induction Chemotherapy for Treatment of Secondary Acute Myeloid Leukemia. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2022; 22:e206-e212. [PMID: 34686446 DOI: 10.1016/j.clml.2021.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION/BACKGROUND The AML-Score has been validated in patients receiving traditional induction chemotherapies but not CPX-351. We conducted a retrospective analysis to evaluate, among patients with secondary acute myeloid leukemia who received intensive induction with CPX-351, if the AML-Score associates with (1) complete remission (CR) and (2) early mortality (EM) within 60 days of induction. MATERIALS AND METHODS We abstracted demographic and clinical data from consecutive patients receiving CPX-351 at Sidney Kimmel Cancer Center at Thomas Jefferson University Hospital between September 2017 and November 2020. We used descriptive statistics and receiver operating curves to evaluate the relationship between AML-Score and rates of CR and EM. RESULTS In total, 40 patients were included. 27 (67.5%) were male, 27 (67.5%) were white, 36 (90.0%) were not Hispanic or Latino, and 29 (72.5%) were aged ≥60 years. Twenty-seven patients (67.5%) had a CR, and 4 (10%) experienced EM. Observed rates of CR and EM generally increased with increasing predicted risk. The area under the curve was 0.75 (95% CI 0.60-0.90) for CR and 0.82 (95% CI 0.68-0.96) for EM. CONCLUSION The AML-Score tool trends in the correct direction for predicting CR and EM, and thus may facilitate oncologist prognostication and treatment planning for patients receiving CPX-351. However, its clinical utility is limited by its underestimation of the risk of CR and overestimation of the risk of EM. Further validation in a larger cohort is needed to calculate accurate point estimates of CR and EM risk in this population.
Collapse
Affiliation(s)
- Abigail M Schmucker
- Department of Internal Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Benjamin E Leiby
- Division of Biostatistics, Department of Pharmacology and Experimental Therapeutics, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Lindsay Wilde
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA.
| |
Collapse
|
6
|
Dong C, Zhang N, Zhang L. The Multi-Omic Prognostic Model of Oxidative Stress-Related Genes in Acute Myeloid Leukemia. Front Genet 2021; 12:722064. [PMID: 34659343 PMCID: PMC8514868 DOI: 10.3389/fgene.2021.722064] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Acute myeloid leukemia (AML) is one of the most common cancers in the world, and oxidative stress is closely related to leukemia. A lot of effort has been made to improve the prognosis of AML. However, the situation remains serious. Hence, we focused on the study of prognostic genes in AML. Materials and Methods: Prognostic oxidative stress genes were screened out. The gene expression profile of AML patients was downloaded from the The Cancer Genome Atlas (TCGA) database. The oxidative stress-related model was constructed, by which the prognosis of AML patients was predicted using the two GEO GSE23143 datasets and the stability of the GSE71014 authentication model. Results: The prognostic oxidative stress genes were screened out in AML, and the prognostic genes were significantly enriched in a large number of pathways based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. There was a complex interaction between prognostic genes and transcription factors. After constructing the prediction model, the clinical predictive value of the model was discussed in a multi-omic study. We investigated the sensitivity of risk score to common chemotherapeutic agents, the influence of signaling pathways on the prognosis of AML patients, and the correlation of multiple genes with immune score and immune dysfunction. Conclusions: A highly effective prognostic risk model for AML patients was established and validated. The association of prognostic oxidative stress genes with drug sensitivity, signaling pathways, and immune infiltration was explored. The results suggested that oxidative stress genes promised to be potential prognostic biomarkers for AML, which may provide a new basis for disease management.
Collapse
Affiliation(s)
- Chao Dong
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Naijin Zhang
- Department of Cardiology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Lijun Zhang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, China
| |
Collapse
|
7
|
Li S, Zhao Z, Yang H, Wang D, Sun W, Li S, Zhang Z, Fu W. Construction and Validation of a Nomogram for the Preoperative Prediction of Lymph Node Metastasis in Gastric Cancer. Cancer Control 2021; 28:10732748211027160. [PMID: 34155937 PMCID: PMC8226383 DOI: 10.1177/10732748211027160] [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] [Indexed: 01/09/2023] Open
Abstract
Background: Increasing evidence indicated that the tumor microenvironment (TME) plays a
critical role in tumor progression. This study aimed to identify and
evaluate mRNA signature involved in lymph node metastasis (LNM) in TME for
gastric cancer (GC). Methods: Gene expression and clinical data were downloaded from The Cancer Genome
Atlas (TCGA). The ESTIMATE algorithm was used to evaluate the TME of GC. The
heatmap and Venn plots were applied for visualizing and screening out
intersect differentially expressed genes (DEGs) involved in LNM in TME.
Functional enrichment analysis, gene set enrichment analysis (GSEA) and
protein-protein interaction (PPI) network were also conducted. Furthermore,
binary logistic regression analysis were employed to develop a 4-mRNAs
signature for the LNM prediction. ROC curves were applied to validate the
LNM predictive ability of the riskscore. Nomogram was constructed and
calibration curve was plotted to verify the predictive power of
nomogram. Results: A total of 88 LNM related DEGs were identified. Functional enrichment
analysis and GSEA implied that those genes were associated with some
biological processes, such as ion transportation, lipid metabolism and
thiolester hydrolase activity. After univariate and multivariate logistic
regression analysis, 4 mRNAs (RASSF2, MS4A2, ANKRD33B and ADH1B) were
eventually screened out to develop a predictive model. ROC curves manifested
the good performance of the 4-mRNAs signature. The proportion of patients
with LNM in high-risk group was significantly higher than that in low-risk
group. The C-index of nomogram from training and test cohorts were 0.865 and
0.765, and the nomogram was well calibrated. Conclusions: In general, we identified a 4-mRNAs signature that effectively predicted LNM
in GC patients. Moreover, the 4-mRNAs signature and nomogram provide a
guidance for the preoperative evaluation and postoperative treatment of GC
patients.
Collapse
Affiliation(s)
- Shilong Li
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Zongxian Zhao
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Huaxiang Yang
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Daohan Wang
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Weilin Sun
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Shuliang Li
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Department of Gastrointestinal Surgery, The Second People's Hospital of Liaocheng, Shandong, China
| | - Zhaoxiong Zhang
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| | - Weihua Fu
- Department of General Surgery, 117865Tianjin Medical University General Hospital, Tianjin, China.,Tianjin General Surgery Institute, Tianjin, China
| |
Collapse
|
8
|
Li C, Liu T, Liu Y, Zhang J, Zuo D. Prognostic value of tumour microenvironment-related genes by TCGA database in rectal cancer. J Cell Mol Med 2021; 25:5811-5822. [PMID: 33949771 PMCID: PMC8184694 DOI: 10.1111/jcmm.16547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Rectal cancer is a common malignant tumour and the progression is highly affected by the tumour microenvironment (TME). This study intended to assess the relationship between TME and prognosis, and explore prognostic genes of rectal cancer. The gene expression profile of rectal cancer was obtained from TCGA and immune/stromal scores were calculated by Estimation of Stromal and Immune cells in Malignant Tumors using Expression data (ESTIMATE) algorithm. The correlation between immune/stromal scores and survival time as well as clinical characteristics were evaluated. Differentially expressed genes (DEGs) were identified according to the stromal/immune scores, and the functional enrichment analyses were conducted to explore functions and pathways of DEGs. The survival analyses were conducted to clarify the DEGs with prognostic value, and the protein‐protein interaction (PPI) network was performed to explore the interrelation of prognostic DEGs. Finally, we validated prognostic DEGs using data from the Gene Expression Omnibus (GEO) database by PrognoScan, and we verified these genes at the protein levels using the Human Protein Atlas (HPA) databases. We downloaded gene expression profiles of 83 rectal cancer patients from The Cancer Genome Atlas (TCGA) database. The Kaplan‐Meier plot demonstrated that low‐immune score was associated with worse clinical outcome (P = .034), metastasis (M1 vs. M0, P = .031) and lymphatic invasion (+ vs. ‐, P < .001). A total of 540 genes were screened as DEGs with 539 up‐regulated genes and 1 down‐regulated gene. In addition, 60 DEGs were identified associated with overall survival. Functional enrichment analyses and PPI networks showed that the DEGs are mainly participated in immune process, and cytokine‐cytokine receptor interaction. Finally, 19 prognostic genes were verified by GSE17536 and GSE17537 from GEO, and five genes (ADAM23, ARHGAP20, ICOS, IRF4,MMRN1) were significantly different in tumour tissues compared with normal tissues at the protein level. In summary, our study demonstrated the associations between TME and prognosis as well as clinical characteristics of rectal cancer. Moreover, we explored and verified microenvironment‐related genes, which may be the potential key prognostic genes of rectal cancer. Further clinical samples and functional studies are needed to validate this finding.
Collapse
Affiliation(s)
- Chao Li
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yi Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jiantao Zhang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Didi Zuo
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
9
|
Li S, Yang H, Li S, Zhao Z, Wang D, Fu W. High expression of regulator of G-protein signalling 1 is associated with the poor differentiation and prognosis of gastric cancer. Oncol Lett 2021; 21:322. [PMID: 33692854 PMCID: PMC7933750 DOI: 10.3892/ol.2021.12584] [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: 10/23/2020] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence has highlighted that immune and stromal cells form the majority of the tumour microenvironment (TME), which plays important roles in tumour progression. The present study aimed to screen vital prognostic genes associated with the TME in gastric cancer (GC). The ESTIMATE algorithm was applied to calculate TME-related scores, and the relationship between clinicopathological variables and these scores was analysed. Heatmaps and Venn plots were then used to visualize and screen differentially expressed genes. Furthermore, functional enrichment analysis was performed, and a protein-protein interaction network was constructed. Kaplan-Meier curves were generated to evaluate survival differences for each hub gene. Reverse transcription quantitative PCR was employed to evaluate the expression of the three hub genes in the validation cohort. The association between gene expression, clinicopathological variables and survival was also evaluated. Higher stromal scores were associated with worse outcomes in patients with GC. In addition, higher scores were significantly associated with a higher tumour grade, American Joint Committee on Cancer stage and T stage with regard to immune scores, stromal scores and ESTIMATE scores, respectively. In total, 644 upregulated intersecting genes and 126 downregulated genes were identified. Moreover, 71 TME-associated hub genes were identified. Batch survival analysis revealed that higher expression of CXCR4, PTGFR and RGS1 was significantly associated with worse outcome. Subsequently, the relationship between high expression of RGS1 and poor prognosis was verified, and high expression of RGS1 was associated with poor differentiation. In conclusion, it was found that compared with immune cells, stromal cells may play a more important role in the prognosis of patients with GC. In addition, the influence of RGS1 expression on survival in GC patients was identified and verified, and high expression of RGS1 was found to be associated with a low differentiation degree of GC.
Collapse
Affiliation(s)
- Shilong Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China.,Tianjin General Surgery Institute, Tianjin 300052, P.R. China
| | - Huaxiang Yang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China.,Tianjin General Surgery Institute, Tianjin 300052, P.R. China
| | - Shuliang Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China.,Department of Gastrointestinal Surgery, The Second People's Hospital of Liaocheng, Liaocheng, Shandong 252600, P.R. China
| | - Zongxian Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China.,Tianjin General Surgery Institute, Tianjin 300052, P.R. China
| | - Daohan Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China.,Tianjin General Surgery Institute, Tianjin 300052, P.R. China
| | - Weihua Fu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China.,Tianjin General Surgery Institute, Tianjin 300052, P.R. China
| |
Collapse
|
10
|
Zhao H, Zhang X, Shi Z, Guo B, Zhang W, He K, Hu X, Shi S. Identification of a Prognostic Signature Model with Tumor Microenvironment for predicting Disease-free Survival after Radical Prostatectomy. J Cancer 2021; 12:2371-2384. [PMID: 33758613 PMCID: PMC7974886 DOI: 10.7150/jca.51173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/18/2021] [Indexed: 12/24/2022] Open
Abstract
Background: The tumor microenvironment (TME) and immune checkpoint inhibitors have been shown to promote active immune responses through different mechanisms. We attempted to identify the important prognostic genes and prognostic characteristics related to TME in prostate cancer (PCa). Methods: The gene transcriptome profiles and clinical information of PCa patients were obtained from The Cancer Genome Atlas (TCGA) database, and the immune and stromal scores were calculated by the ESTIMATE algorithm. We evaluated the prognostic value of the risk score (RS) model based on univariate Cox analysis and least absolute shrinkage and selection operation (LASSO) Cox regression analysis and established a nomogram to predict disease-free survival (DFS) in PCa patients. The GSE70768 dataset was utilized for external validation. Twenty-two subsets of tumor-infiltrating immune cells were analyzed using the CIBERSORT algorithm. Results: In this study, the patients with higher immune/stromal scores were associated with a worse DFS, higher Gleason score, and higher pathological T stage. Based on the immune and stromal scores, 515 differentially expressed genes (DEGs) were identified. The univariate Cox and LASSO Cox regression models were employed to select 18 DEGs from 515 DEGs and construct an RS model. The DFS of the high-RS group was significantly lower than that of the low-RS group (P<0.001). The AUCs for the 1-year, 3-year and 5-year DFS rates in the RS model were 0.890, 0.877 and 0.841, respectively. A nomogram of DFS was established based on the RS and Gleason score, and the AUCs for the 1-year, 3-year and 5-year DFS rates in the nomogram were 0.907, 0.893, and 0.872, respectively. These results were further validated in the GSE70768 dataset. In addition, the proportion of Tregs was determined to be higher in high-RS patients (P<0.05), and the expression levels of five immune checkpoints (CTLA-4, PD-1, LAG-3, TIM-3 and TIGIT) were observed to be higher in high-RS patients (P<0.05). Conclusions: Our study established and validated an 18-gene prognostic signature model associated with TME, which might serve as a prognosis stratification tool to predict DFS in PCa patients after radical prostatectomy.
Collapse
Affiliation(s)
- Hao Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xuening Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Zhan Shi
- Department of Medicine, Zhengzhou First People's Hospital, Zhengzhou 450004, China
| | - Bingxin Guo
- Department of Urology, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou 450002, China
| | - Wenli Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Kun He
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xueqi Hu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songhe Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
11
|
Dai D, Xie L, Shui Y, Li J, Wei Q. Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma. Front Genet 2021; 12:620705. [PMID: 33597971 PMCID: PMC7882740 DOI: 10.3389/fgene.2021.620705] [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] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
Aim Immune cells that infiltrate the tumor microenvironment (TME) are associated with cancer prognosis. The aim of the current study was to identify TME related gene signatures related to the prognosis of sarcoma (SARC) by using the data from The Cancer Genome Atlas (TCGA). Methods Immune and stromal scores were calculated by estimation of stromal and immune cells in malignant tumor tissues using expression data algorithms. The least absolute shrinkage and selection operator (lasso) based cox model was then used to select hub survival genes. A risk score model and nomogram were used to predict the overall survival of patients with SARC. Results We selected 255 patients with SARC for our analysis. The Kaplan–Meier method found that higher immune (p = 0.0018) or stromal scores (p = 0.0022) were associated with better prognosis of SARC. The estimated levels of CD4+ (p = 0.0012) and CD8+ T cells (p = 0.017) via the tumor immune estimation resource were higher in patients with SARC with better overall survival. We identified 393 upregulated genes and 108 downregulated genes (p < 0.05, fold change >4) intersecting between the immune and stromal scores based on differentially expressed gene (DEG) analysis. The univariate Cox analysis of each intersecting DEG and subsequent lasso-based Cox model identified 11 hub survival genes (MYOC, NNAT, MEDAG, TNFSF14, MYH11, NRXN1, P2RY13, CXCR3, IGLV3-25, IGHV1-46, and IGLV2-8). Then, a hub survival gene-based risk score gene signature was constructed; higher risk scores predicted worse SARC prognosis (p < 0.0001). A nomogram including the risk scores, immune/stromal scores and clinical factors showed a good prediction value for SARC overall survival (C-index = 0.716). Finally, connectivity mapping analysis identified that the histone deacetylase inhibitors trichostatin A and vorinostat might have the potential to reverse the harmful TME for patients with SARC. Conclusion The current study provided new indications for the association between the TME and SARC. Lists of TME related survival genes and potential therapeutic drugs were identified for SARC.
Collapse
Affiliation(s)
- Dongjun Dai
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanyu Xie
- Department of Clinical Medicine, Fuzhou Medical College of Nanchang University, Jiangxi, China
| | - Yongjie Shui
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
12
|
Xu C, Li R, Wu J. Effects of Yuanhu- Zhitong tablets on alcohol-induced conditioned place preference in mice. Biomed Pharmacother 2021; 133:110962. [PMID: 33166765 DOI: 10.1016/j.biopha.2020.110962] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/21/2020] [Accepted: 11/01/2020] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES This study aimed at determining the synergistic effects of Yuanhu Zhitong tablets (YHZTP) on alcohol-induced conditioned place preference (CPP) in mice, in addition, the intervention mechanism was preliminarily explored based on traditional Chinese Medicine (TCM) network pharmacology on alcohol addiction. METHODS Alcohol-induced CPP mice were used to evaluate the effects of either YHZTP or levo-tetrahydropalmatine (l-THP) plus imperatorin (IMP) administration on animal behavior. The network pharmacological strategy was used to establish the "compound-target" and "disease-drug-target" network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on the shared targets between the compound and the disease. Twelve algorithms on CytoHubba were used to find the hub genes that were verified by qPCR. RESULTS Systemic administration (2 g/kg, i.p.) of ethanol (EtOH) to mice was used to induce CPP. YHZTP On its own did not induce CPP or conditioned place aversion (CPA) at the doses of 0.3 g/kg or 0.6 g/kg (i.g.), but attenuated the acquisition and expression of EtOH-induce CPP in mice. In addition, YHZTP (0.3 or 0.6 g/kg) did not exhibit any effect on the motor activity of mice. Acquisition of alcohol-induced CPP was blocked by a combination of l-THP (5 mg/kg, i.g.) + IMP (2.5 mg/kg, i.g.) or l-THP (10 mg/kg, i.g.) + IMP (5 mg/kg, i.g.). However, the combination of l-THP (2.5 mg/kg, i.g.) + IMP (1.25 mg/kg, i.g.) or mono-administration of l-THP and IMP did not exhibit any effect on alcohol-induced CPP. YHZTP was also shown to reverse the up-regulation of Gabra1, Ptgs2, Mapk1, Mapk8, Mapk14, Nr3c, Prkca and Sirt1 genes and the down-regulation of Hhtr2a and Drd2 genes in the prefrontal cortex of EtOH induced CPP mice. These genes were associated with neuroactive ligand-receptor interactions, activation of the sphingolipid, calcium, cAMP, ErbB, NF-kappa B and MAPK signaling pathways. CONCLUSION YHZTP inhibits EtOH-induced CPP behavior in mice while a combination of l-THP and IMP exerts a synergistic effect on the reduction of EtOH-induced CPP. Possible pharmacological mechanisms include inhibition of the expression of inflammatory factors and regulation of neurotransmitter receptor levels. Therefore, YHZTP is a novel candidate for the treatment of alcohol addiction.
Collapse
Affiliation(s)
- Changqiong Xu
- Brain Function and Disease Laboratory, Shantou University Medical College, No. 22 Xinling Road, Shantou, 515041, Guangdong Province, PR China
| | - Ran Li
- Brain Function and Disease Laboratory, Shantou University Medical College, No. 22 Xinling Road, Shantou, 515041, Guangdong Province, PR China.
| | - Jie Wu
- Brain Function and Disease Laboratory, Shantou University Medical College, No. 22 Xinling Road, Shantou, 515041, Guangdong Province, PR China.
| |
Collapse
|
13
|
Characterization of somatic mutation-associated microenvironment signatures in acute myeloid leukemia patients based on TCGA analysis. Sci Rep 2020; 10:19037. [PMID: 33149230 PMCID: PMC7643165 DOI: 10.1038/s41598-020-76048-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Recurrent genetic mutations occur in acute myeloid leukemia (AML) and have been incorporated into risk stratification to predict the prognoses of AML patients. The bone marrow microenvironment plays a critical role in the development and progression of AML. However, the characteristics of the genetic mutation-associated microenvironment have not been comprehensively identified to date. In this study, we obtained the gene expression profiles of 173 AML patients from The Cancer Genome Atlas (TCGA) database and calculated their immune and stromal scores by applying the ESTIMATE algorithm. Immune scores were significantly associated with OS and cytogenetic risk. Next, we categorized the intermediate and poor cytogenetic risk patients into individual-mutation and wild-type groups according to RUNX1, ASXL1, TP53, FLT3-ITD, NPM1 and biallelic CEBPA mutation status. The relationships between the immune microenvironment and each genetic mutation were investigated by identifying differentially expressed genes (DEGs) and conducting functional enrichment analyses of them. Significant immune- and stromal-relevant DEGs associated with each mutation were identified, and most of the DEGs (from the FLT3-ITD, NPM1 and biallelic CEBPA mutation groups) were validated in the GSE14468 cohort downloaded from the Gene Expression Omnibus (GEO) database. In summary, we identified key immune- and stromal-relevant gene signatures associated with genetic mutations in AML, which may provide new biomarkers for risk stratification and personalized immunotherapy.
Collapse
|
14
|
Wang S, Yang L, Liu Y, Xu Y, Zhang D, Jiang Z, Wang C, Liu Y. A Novel Immune-Related Competing Endogenous RNA Network Predicts Prognosis of Acute Myeloid Leukemia. Front Oncol 2020; 10:1579. [PMID: 32850463 PMCID: PMC7432272 DOI: 10.3389/fonc.2020.01579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a genetically, biologically and clinically heterogeneous hematopoietic malignancy that is highly dependent on the bone marrow (BM) microenvironment. Infiltrated immune cells and stromal cells are an important part of the BM microenvironment and significantly affect the progression of AML. Recently, the competing endogenous RNA hypothesis has gained great interests in the study of molecular and biological mechanisms of tumor occurrence and progression. However, research on how competing endogenous RNA relates to leukemia tumor microenvironment remains uninvestigated. Methods In this study, mRNA, miRNA and lncRNA data and clinical information of the AML cohort were obtained from The Cancer Genome Atlas (TCGA) database, and the immune and stromal scores were calculated using the ESTIMATE algorithm. Results We found that immune scores were significantly correlated with cytogenetic risk and overall survival, and also identified microenvironment-related mRNAs, miRNAs, and lncRNAs based on the immune and stromal scores. Differentially expressed mRNAs and lncRNAs were applied to weighted correlation network analysis (WGCNA) to identify the modules most relevant to the immune microenvironment of AML. Using miRNA database to predict miRNA-targeted genes, we established the immune-related competing endogenous RNA network consisting of 33 lncRNAs, 21 miRNAs and 135 mRNAs. Prognostic analysis was performed on the genes in the immune-related competing endogenous RNA network to screen out 15 lncRNAs, 2 miRNAs and 31 mRNAs with prognostic values. Conclusion In summary, we identified a novel immune-related mRNA-miRNA-lncRNA competing endogenous RNA network associated with the prognosis of AML, which may contribute to better understanding of the development and progression of AML and to serve as novel therapeutic targets.
Collapse
Affiliation(s)
- Shujuan Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lu Yang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yajun Liu
- Department of Orthopaedics, Rhode Island Hospital, Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Yan Xu
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Danfeng Zhang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhongxing Jiang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanfang Liu
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
15
|
Li T, Liu Q, Zhang R, Liao Q, Zhao Y. Identification of prognosis-related genes and construction of multi-regulatory networks in pancreatic cancer microenvironment by bioinformatics analysis. Cancer Cell Int 2020; 20:341. [PMID: 32724299 PMCID: PMC7382032 DOI: 10.1186/s12935-020-01426-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Background As one of the most lethal cancers, pancreatic cancer has been characterized by abundant supportive tumor-stromal cell microenvironment. Although the advent of tumor-targeted immune checkpoint blockers has brought light to patients with other cancers, its clinical efficacy in pancreatic cancer has been greatly limited due to the protective stroma. Thus, it is urgent to find potential new targets and establish multi-regulatory networks to predict patient prognosis and improve treatment. Methods We followed a strategy based on mining the Cancer Genome Atlas (TCGA) database and ESTIMATE algorithm to obtain the immune scores and stromal scores. Differentially expressed genes (DEGs) associated with poor overall survival of pancreatic cancer were screened from a TCGA cohort. By comparing global gene expression with high vs. low immune scores and subsequent Kaplan–Meier analysis, DEGs that significantly correlate with poor overall survival of pancreatic cancer in TCGA cohort were extracted. After constructing the protein–protein interaction network using STRING and limiting the genes within the above DEGs, we utilized RAID 2.0, TRRUST v2 database and degree and betweenness analysis to obtain non-coding RNA (ncRNA)-pivotal nodes and TF-pivotal nodes. Finally, multi-regulatory networks have been constructed and pivotal drugs with potential benefit for pancreatic cancer patients were obtained by screening in the DrugBank. Results In this study, we obtained 246 DEGs that significantly correlate with poor overall survival of pancreatic cancer in the TCGA cohort. With the advent of 38 ncRNA-pivotal nodes and 7 TF-pivotal nodes, the multi-factor regulatory networks were constructed based on the above pivotal nodes. Prognosis-related genes and factors such as HCAR3, PPY, RFWD2, WSPAR and Amcinonide were screened and investigated. Conclusion The multi-regulatory networks constructed in this study are not only beneficial to improve treatment and evaluate patient prognosis with pancreatic cancer, but also favorable for implementing early diagnosis and personalized treatment. It is suggested that these factors may play an essential role in the progression of pancreatic cancer.
Collapse
Affiliation(s)
- Tong Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| | - Qiaofei Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| | - Ronghua Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| | - Quan Liao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| |
Collapse
|
16
|
Database Mining of Genes of Prognostic Value for the Prostate Adenocarcinoma Microenvironment Using the Cancer Gene Atlas. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5019793. [PMID: 32509861 PMCID: PMC7251429 DOI: 10.1155/2020/5019793] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/26/2020] [Accepted: 04/10/2020] [Indexed: 12/17/2022]
Abstract
Background Prostate adenocarcinoma (PRAD) is a common malignant tumor in elderly men. Our research uses The Cancer Gene Atlas (TCGA) database to find potential related genes for predicting the prognosis of patients with PRAD. Methods We downloaded gene expression profiles and clinical sample information from TCGA for 490 patients with PRAD (patient age: 41-78 years). We calculated stromal and immune scores using the ESTIMATE algorithm to predict the level of stromal and immune cell infiltration. We categorized patients with PRAD in TCGA into high and low score arrays according to their median immune/stromal scores and identified differentially expressed genes (DEGs) that were significantly correlated with the prognosis of PRAD. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. The association between DEGs and overall survival was investigated by weighted Kaplan–Meier survival analysis and multivariate analysis. Furthermore, the protein-protein interaction network (PPI) of DEGs was constructed using the STRING tool. Finally, the hub genes were identified by analyzing the degree of association of PPI networks. Results We found that 8 individual DEGs, C6, S100A12, MLC1, PAX5, C7, FAM162B, CAMK1G, and TCEAL5, were significantly predictive of favorable overall survival and one DEG, EPYC, was associated with poor overall survival. GO and KEGG pathway analyses revealed that the DEGs were associated with immune responses. Moreover, 30 hub genes were obtained using the PPI network of DEGs: ITGAM, CD4, CD3E, IL-10, LCP2, ITGB2, ZAP-70, C3, CCL19, CXCL13, CXCL9, BTK, CCL21, CD247, CD28, CD3D, FCER1G, PTPRC, TYROBP, CCR5, ITK, CCL13, CCR1, CCR2, CD79B, CYBB, IL2RG, JAK3, PLCG2, and CD19. These prominent nodes had the most associations with other genes, indicating that they might play crucial roles in the prognosis of PRAD. Conclusions We extracted a list of genes associated with the prostate adenocarcinoma microenvironment, which might contribute to the prediction and interpretation of PRAD prognosis.
Collapse
|