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Jafari-Raddani F, Davoodi-Moghaddam Z, Bashash D. Construction of immune-related gene pairs signature to predict the overall survival of multiple myeloma patients based on whole bone marrow gene expression profiling. Mol Genet Genomics 2024; 299:47. [PMID: 38649532 DOI: 10.1007/s00438-024-02140-7] [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: 03/23/2023] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
Multiple myeloma (MM) is a plasma cell dyscrasia that is characterized by the uncontrolled proliferation of malignant PCs in the bone marrow. Due to immunotherapy, attention has returned to the immune system in MM, and it appears necessary to identify biomarkers in this area. In this study, we created a prognostic model for MM using immune-related gene pairs (IRGPs), with the advantage that it is not affected by technical bias. After retrieving microarray data of MM patients, bioinformatics analyses like COX regression and least absolute shrinkage and selection operator (LASSO) were used to construct the signature. Then its prognostic value is assessed via time-dependent receiver operating characteristic (ROC) and the Kaplan-Meier (KM) analysis. We also used XCELL to examine the status of immune cell infiltration among MM patients. 6-IRGP signatures were developed and proved to predict MM prognosis with a P-value of 0.001 in the KM analysis. Moreover, the risk score was significantly associated with clinicopathological characteristics and was an independent prognostic factor. Of note, the combination of age and β2-microglobulin with risk score could improve the accuracy of determining patients' prognosis with the values of the area under the curve (AUC) of 0.73 in 5 years ROC curves. Our model was also associated with the distribution of immune cells. This novel signature, either alone or in combination with age and β2-microglobulin, showed a good prognostic predictive value and might be used to guide the management of MM patients in clinical practice.
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Affiliation(s)
- Farideh Jafari-Raddani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Davoodi-Moghaddam
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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2
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Tian W, Tan S, Wang J, Shen P, Qin Q, Zi D. Immune-related LncRNAs scores predicts chemotherapeutic responses and prognosis in cervical cancer patients. Discov Oncol 2024; 15:119. [PMID: 38615287 PMCID: PMC11016529 DOI: 10.1007/s12672-024-00979-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/10/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) regulating the immune microenvironment of cancer is a hot spot. But little is known about the influence of the immune-related lncRNA (IRlncRs) on the chemotherapeutic responses and prognosis of cervical cancer (CC) patients. The purpose of the study was to identify an immune-related lncRNAs (IRlncRs)-based model for the prospective prediction of clinical outcomes in CC patients. METHODS CC patients' relevant data was acquired from The Cancer Genome Atlas (TCGA). Correlation analysis and Cox regression analyses were applied. A risk score formula was formulated. Prognostic factors were combined into a nomogram, while sensitivity for chemotherapy drugs was analyzed using the OncoPredict algorithm. RESULTS Eight optimal IRlncRs(ATP2A1-AS1, LINC01943, AL158166.1, LINC00963, AC009065.8, LIPE-AS1, AC105277.1, AC098613.1.) were incorporated in the IRlncRs model. The overall survival (OS) of the high-risk group of the model was inferior to those in the low-risk group. Further analysis demonstrated this eight-IRlncRs model as a useful prognostic marker. The Nomogram had a concordance index of survival prediction of 0.763(95% CI 0.746-0.780) and more robust predictive accuracy. Furthermore, patients in the low-risk group were found to be more sensitive to chemotherapy, including Paclitaxel, Rapamycin, Epirubicin, Vincristine, Docetaxel and Vinorelbine. CONCLUSIONS An eight-IRlncRs-based prediction model was identified that has the potential to be an important tool to predict chemotherapeutic responses and prognosis for CC patients.
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Affiliation(s)
- Weijie Tian
- Department of Gynecology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Songsong Tan
- Department of Gynecology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Jun Wang
- Department of Gynecology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Ping Shen
- Department of Gynecology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Qingfen Qin
- Department of Gynecology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, People's Republic of China.
| | - Dan Zi
- Department of Gynecology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, Guizhou, People's Republic of China.
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Huang S, Liu W, Zhao Q, Chen T, Huang R, Dong L, Nian Z, Yang L. Immunogenic Cell Death-related Signature Evaluates the Tumor Microenvironment and Predicts the Prognosis in Diffuse Large B-Cell Lymphoma. Biochem Genet 2024:10.1007/s10528-024-10697-6. [PMID: 38446321 DOI: 10.1007/s10528-024-10697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/10/2024] [Indexed: 03/07/2024]
Abstract
Current literatures suggest a growing body of evidence highlighting the pivotal role of Immunogenic Cell Death (ICD) in multiple tumor types. Nevertheless, the potential and mechanisms of ICD in diffuse large B-cell lymphoma (DLBCL) remain inadequately studied. To address this gap, our current study aims to examine the impact of ICD on DLBCL and identify a corresponding gene signature in DLBC. Using the expression profiles of ICD-associated genes, the gene expression omnibus (GEO) samples were segregated into ICD-high and ICD-low subtypes utilizing non-negative matrix factorization clustering. Next, univariate and LASSO Cox regression analyses were employed to establish the ICD-related gene signature. Subsequently, the CIBERSORT tool, ssGSEA, and ESTIMATE algorithm were utilized to examine the association between the signature and tumor immune microenvironment of DLBC. Finally, the oncoPredict algorithm was implemented to evaluate the drug sensitivity prediction of DLBCL patients. These findings suggest that the immune microenvironment of the ICD-high group with a poor prognosis was significantly suppressed. An 8-gene ICD-related signature was identified and validated to prognosticate and evaluate the tumor immune microenvironment in DLBCL. Similarly, the high-risk group exhibited a worse prognosis compared to the low-risk group, and the immune function was considerably suppressed. Moreover, the results of oncoPredict algorithm indicated that patients in the high-risk group exhibited higher sensitivity to Cisplatin, Cytarabine, Epirubicin, Oxaliplatin, and Vincristine with low IC50. In conclusion, the present study provides novel insights into the role of ICD in DLBCL by identifying a new biomarker for the disease and may have implications for the development of immune-targeted therapies for the tumor.
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Affiliation(s)
- Shengqiang Huang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Wenbin Liu
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Qiuling Zhao
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Ting Chen
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Ruyi Huang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Liangliang Dong
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Zilin Nian
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China
| | - Lin Yang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, No.420, Fuma Road, Fuzhou, Fujian, China.
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Jiang D, Zhang LY, Wang DH, Liu YR. Identification of an optimized glycolytic-related risk signature for predicting the prognosis in breast cancer using integrated bioinformatic analysis. Medicine (Baltimore) 2023; 102:e34715. [PMID: 37656998 PMCID: PMC10476720 DOI: 10.1097/md.0000000000034715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/21/2023] [Indexed: 09/03/2023] Open
Abstract
Aberrant metabolic disorders and significant glycolytic alterations in tumor tissues and cells are hallmarks of breast cancer (BC) progression. This study aims to elucidate the key biomarkers and pathways mediating abnormal glycolysis in breast cancer using bioinformatics analysis. Differential genes expression analysis, gene ontology analysis, Kyoto encyclopedia of genes and genomes analysis, gene set enrichment analyses, and correlation analysis were performed to explore the expression and prognostic implications of glycolysis-related genes. We effectively integrated 4 genes to construct a prognostic model of shorter survival in the high-risk versus low-risk group. The prognostic model showed promising predictive value and may be an integral part of the prognosis of BC. The survival analysis and receiver operating characteristic curves suggested that the signature showed a good predictive performance in both the The Cancer Genome Atlas training set and 2 gene expression omnibus validation sets. Multivariable analysis demonstrated that the 4-gene signature had an independent prognostic value. Furthermore, all calibration curves exhibited robust validity in prognostic prediction. We established an optimized 4-gene signature to clarify the connection between glycolysis and BC, and offered an attractive platform for risk stratification and prognosis predication of BC patients.
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Affiliation(s)
- Di Jiang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ling-Yu Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, Anhui, China
| | - Dan-Hua Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yan-rong Liu
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
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Qu J, Tao D, Huang W, Lu L, Fan J, Zhang S, Huang F. Assessment of prognostic role of a novel 7-lncRNA signature in HCC patients. Heliyon 2023; 9:e18493. [PMID: 37520979 PMCID: PMC10382640 DOI: 10.1016/j.heliyon.2023.e18493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is characterized by extensive risk factors, high morbidity and mortality. Clinical prognostic evaluation assay assumes a nonspecific quality. Better HCC prognostics are urgently needed. Long noncoding RNAs (lncRNAs) exerts a crucial role in tumorigenesis and development. Excavating specific lncRNAs signature to ameliorate the high-risk survival prediction in HCC patients is worthwhile. Methods Differentially expressed lncRNAs (DElncRNAs) profile was acquired from The Cancer Genome Atlas database (TCGA). Then, the lncRNAs high-risk survival prognostic model was established using the least absolute shrinkage and selection operator (LASSO)-Cox regression algorithm. The lncRNAs were evaluated in clinical specimen by PCR. The receiver operating characteristic curve (ROC) analysis was further conducted to assess the potential prognostic value of the model. Moreover, a visible nomogram containing clinicopathological features and prognostic model was developed for prediction of survival property. Potential molecular mechanism was assessed by GO, KEGG, GSEA enrichment analysis and CIBERSORT immune infiltration analysis. Results A novel 7-lncRNA risk model (AL161937.2, LINC01063, AC145207.5, POLH-AS1, LNCSRLR, MKLN1-AS, AC105345.1) was constructed and validated for HCC prognosis prediction. Kaplan-Meier analysis revealed that patients in the high-risk group suffered a poor prognosis (p = 1.813 × 10-8). These genes were detected by PCR, and the expression trend was in accordance with TCGA database. Interestingly, the risk score served as an independent risk factor for HCC patients (HR: 1.166, 95% CI:1.119-1.214, p < 0.001). The nomogram was established, and the predictive accuracy in the nomogram was prior to the TNM stage according to the ROC curve analysis. Cell proliferation related pathway, decreased CD4+ T cell, CD8+ T cell, NK cell and elevated Neutrophil, Macrophage M0 were observed in high-risk group. Besides, suppression of MKLN1-AS expression inhibited cell proliferation of HCC cells by CCK8 assay in vitro. Conclusion The 7-lncRNA signature may exert a particular prognostic prediction role in HCC and provide new insight in HCC carcinogenesis.
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Affiliation(s)
- Junchi Qu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Gastroenterology, The First People's Hospital of PingJiang, Yueyang 410400, China
| | - Di Tao
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wei Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Liting Lu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Junming Fan
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shineng Zhang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Fengting Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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Ye C, Huang Y, Gao Y, Zhu S, Yuan J. Exploring the glycolytic cross-talk genes between inflammatory bowel disease and colorectal cancer. Funct Integr Genomics 2023; 23:230. [PMID: 37428395 PMCID: PMC10333365 DOI: 10.1007/s10142-023-01170-5] [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: 03/23/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
Patients with inflammatory bowel disease (IBD) have a higher risk of developing colorectal cancer (CRC). Glycolysis is involved in the development of both IBD and CRC. However, the mechanisms and outcomes of glycolysis shared between IBD and CRC remain unclear. This study aimed to explore the glycolytic cross-talk genes between IBD and CRC integrating bioinformatics and machine learning. With WGCNA, LASSO, COX, and SVM-RFE algorithms, P4HA1 and PMM2 were identified as glycolytic cross-talk genes. The independent risk signature of P4HA1 and PMM2 was constructed to predict the overall survival rate of patients with CRC. The risk signature correlated with clinical characteristics, prognosis, tumor microenvironment, immune checkpoint, mutants, cancer stemness, and chemotherapeutic drug sensitivity. CRC patients with high risk have increased microsatellite instability, tumor mutation burden. The nomogram integrating risk score, tumor stage, and age showed high accuracy for predicting overall survival rate. In addition, the diagnostic model for IBD based on P4HA1 and PMM2 showed excellent accuracy. Finally, immunohistochemistry results showed that P4HA1 and PMM2 were significantly upregulated in IBD and CRC. Our study reveals the presence of glycolytic cross-talk genes P4HA1 and PMM2 between IBD and CRC. This may prove to be beneficial in advancing research on the mechanism of development of IBD-associated CRC.
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Affiliation(s)
- Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yabing Huang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yuan Gao
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Sizhe Zhu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, People's Republic of China.
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China.
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Li C, Wirth U, Schardey J, Ehrlich-Treuenstätt VV, Bazhin AV, Werner J, Kühn F. An immune-related gene prognostic index for predicting prognosis in patients with colorectal cancer. Front Immunol 2023; 14:1156488. [PMID: 37483596 PMCID: PMC10358773 DOI: 10.3389/fimmu.2023.1156488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common solid malignant burdens worldwide. Cancer immunology and immunotherapy have become fundamental areas in CRC research and treatment. Currently, the method of generating Immune-Related Gene Prognostic Indices (IRGPIs) has been found to predict patient prognosis as an immune-related prognostic biomarker in a variety of tumors. However, their role in patients with CRC remains mostly unknown. Therefore, we aimed to establish an IRGPI for prognosis evaluation in CRC. Methods RNA-sequencing data and clinical information of CRC patients were retrieved from The Cancer Genome Atlas (TCGA) and The Gene Expression Omnibus (GEO) databases as training and validation sets, respectively. Immune-related gene data was obtained from the ImmPort and InnateDB databases. The weighted gene co-expression network analysis (WGCNA) was used to identify hub immune-related genes. An IRGPI was then constructed using Cox regression methods. Based on the median risk score of IRGPI, patients could be divided into high-risk and low-risk groups. To further investigate the immunologic differences, Gene set variation analysis (GSVA) studies were conducted. In addition, immune cell infiltration and related functional analysis were used to identify the differential immune cell subsets and related functional pathways. Results We identified 49 immune-related genes associated with the prognosis of CRC, 17 of which were selected for an IRGPI. The IRGPI model significantly differentiates the survival rates of CRC patients in the different groups. The IRGPI as an independent prognostic factor significantly correlates with clinico-pathological factors such as age and tumor stage. Furthermore, we developed a nomogram to improve the clinical utility of the IRGPI score. Immuno-correlation analysis in different IRGPI groups revealed distinct immune cell infiltration (CD4+ T cells resting memory) and associated pathways (macrophages, Type I IFNs responses, iDCs.), providing new insights into the tumor microenvironment. At last, drug sensitivity analysis revealed that the high-risk IRGPI group was sensitive to 11 and resistant to 15 drugs. Conclusion Our study established a promising immune-related risk model for predicting survival in CRC patients. This could help to better understand the correlation between immunity and the prognosis of CRC providing a new perspective for personalized treatment of CRC.
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Affiliation(s)
- Chao Li
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Ulrich Wirth
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Josefine Schardey
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | | | - Alexandr V. Bazhin
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Jens Werner
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Florian Kühn
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
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Tian L, Wang Y, Tian J, Song W, Li L, Che G. Prognostic Value and Genome Signature of m6A/m5C Regulated Genes in Early-Stage Lung Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24076520. [PMID: 37047493 PMCID: PMC10095361 DOI: 10.3390/ijms24076520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
RNA modifications implicate pathological and prognosis significance in cancer development and progression, of which, m6A and m5C are representative regulators. These RNA modifications could produce effects on the function of other RNA by regulating gene expression. Thus, in this study, we aimed to explore the correlation between m6A/m5C regulators and early-stage lung adenocarcinoma (LUAD). Only the early-stage LUAD samples were included in this investigation, and the RNA-seq dataset of The Cancer Genome Atlas (TCGA) cohort was utilized to evaluate the expression of 37 m6A/m5C regulated genes. Based on the expression level of these 37 genes, early-stage LUAD patients were divided into 2 clusters, which were performed by consensus clustering, and the m6A/m5C subtypes had significantly different prognostic outcomes (p < 0.001). Cluster1, which has a better prognosis, was characterized by the C3 (inflammatory) immune subtype, low immune infiltration, chemokine expression, major histocompatibility complex (MHC) expression, and immune checkpoint molecule expression. Furthermore, compared with cluster1, cluster2 showed a T cell exhaustion state, characterized by a high expression of immune checkpoint genes, and immune cells, such as T cells, CD8+ T cells, cytotoxic lymphocytes, NK cells, and so on. In addition, patients in cluster2 were with high tumor mutational burden (TMB) and numerous significant mutated oncogene and tumor suppressor genes, such as WNT10B, ERBB4, SMARCA4, TP53, and CDKN2A (p < 0.001). A total of 19 genes were mostly related to the prognosis of LUAD and were upregulated in cluster2 (p < 0.05), showing a positive correlation with the mRNA expression of 37 m6A/m5C regulated genes. The predictive risk model was constructed using Cox and LASSO (least absolute shrinkage and selection operator) regression analysis. Finally, a seven-gene m6A/m5C risk model, comprising of METTL3, NPLOC4, RBM15, YTHDF1, IGF2BP1, NSUN3, and NSUN7, was constructed to stratify the prognosis of early-stage LUAD (p = 0.0049, AUC = 0.791). The high-risk score was associated with a poorer prognosis. This model was also validated using two additional GEO datasets: GSE72094 (p = 0.011, AUC = 0.736) and GSE50081 (p = 0.012, AUC = 0.628). In summary, it was established that the m6A/m5C-regulated genes performed a crosstalk function in the mRNA expression of early-stage LUAD. By interacting with other mRNA genes, m6A/m5C modification disturbs DNA replication and the tumor immune microenvironment (TIME). The seven-gene risk model may be a critical tool for the prognostic assessment of early-stage LUAD.
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Affiliation(s)
- Long Tian
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Wang
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Tian
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenpeng Song
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lu Li
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (L.L.); (G.C.)
| | - Guowei Che
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (L.L.); (G.C.)
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Liu H, Chen C, Liu L, Wang Z. A four-lncRNA risk signature for prognostic prediction of osteosarcoma. Front Genet 2023; 13:1081478. [PMID: 36685868 PMCID: PMC9847501 DOI: 10.3389/fgene.2022.1081478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/23/2022] [Indexed: 01/06/2023] Open
Abstract
Aim: Osteosarcoma is the most common primary malignant tumor of bone. However, our understanding of the prognostic indicators and the genetic mechanisms of the disease progression are still incomplete. The aim of this study was to identify a long noncoding RNA (lncRNA) risk signature for osteosarcoma survival prediction. Methods: RNA sequencing data and relevant clinical information of osteosarcoma patients were downloaded from the database of Therapeutically Applicable Research to Generate Effective Treatments (TARGET). We analyzed the differentially expressed lncRNAs between deceased and living patients by univariate and multivariate Cox regression analysis to identify a risk signature. We calculated a prognostic risk score for each sample according to this prognosis signature, and divided patients into high-risk and low-risk groups according to the median value of the risk score (0.975). Kaplan-Meier analysis and receiver operating characteristic (ROC) curve statistics were used to evaluate the performance of the signature. Next, we analyzed the signature's potential function through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene-set enrichment analysis (GSEA). Lastly, qRT-PCR was used to validate the expression levels of the four lncRNAs in clinical samples. Results: Twenty-six differentially expressed lncRNAs were identified between deceased and living patients. Four of these lncRNAs (CTB-4E7.1, RP11-553A10.1, RP11-24N18.1, and PVRL3-AS1) were identified as independent prognostic factors, and a risk signature of these four lncRNAs for osteosarcoma survival prediction was constructed. Kaplan-Meier analysis showed that the five-year survival time in high-risk and low-risk groups was 33.1% and 82.5%, and the area under the curve (AUC) of the ROC was 0.784, which demonstrated that the prognostic signature was reliable and had the potential to predict the survival of patients with osteosarcoma. The expression level of the four lncRNAs in osteosarcoma tissues and cells was determined by qRT-PCR. Functional enrichment analysis suggested that the signature might be related to osteosarcoma through regulation of the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the extracellular matrix and also provided new insights into the study of osteosarcoma, including the role of papillomavirus infection, olfactory receptor activity, and olfactory transduction in osteosarcoma. Conclusion: We constructed a novel lncRNA risk signature that served as an independent biomarker for predicting the prognosis of osteosarcoma patients.
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Affiliation(s)
- Huanlong Liu
- Hand and Foot Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China,Hand and Foot Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Chao Chen
- Hand and Foot Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Long Liu
- Engineering Research Center of Failure Analysis and Safety Assessment, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Zengtao Wang
- Hand and Foot Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China,Hand and Foot Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,*Correspondence: Zengtao Wang,
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10
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A Five-LLPS Gene Risk Score Prognostic Signature Predicts Survival in Hepatocellular Carcinoma. Int J Genomics 2023; 2023:7299276. [PMID: 36873244 PMCID: PMC9977538 DOI: 10.1155/2023/7299276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Background Primary liver cancer, dominated by hepatocellular carcinoma (HCC), is one of the most common cancer types and the third leading cause of cancer death in 2020. Previous studies have shown that liquid-liquid phase separation (LLPS) plays an important role in the occurrence and development of cancer including HCC, but its influence on the patient prognosis is still unknown. It is necessary to explore the effect of LLPS genes on prognosis to accurately forecast the prognosis of HCC patients and identify relevant targeted therapeutic sites. Methods Using The Cancer Genome Atlas dataset and PhaSepDB dataset, we identified LLPS genes linked to the overall survival (OS) of HCC patients. We applied Least Absolute Shrinkage and Selection Operator (LASSO) Cox penalized regression analysis to choose the best genes for the risk score prognostic signature. We then analysed the validation dataset and evaluated the effectiveness of the risk score prognostic signature. Finally, we performed quantitative real-time PCR experiments to validate the genes in the prognostic signature. Results We identified 43 differentially expressed LLPS genes that were associated with the OS of HCC patients. Five of these genes (BMX, FYN, KPNA2, PFKFB4, and SPP1) were selected to generate a prognostic risk score signature. Patients in the low-risk group were associated with better OS than those in the high-risk group in both the training dataset and the validation dataset. We found that BMX and FYN had lower expression levels in HCC tumour tissues, whereas KPNA2, PFKFB4, and SPP1 had higher expression levels in HCC tumour tissues. The validation demonstrated that the five-LLPS gene risk score signature has the capability of predicting the OS of HCC patients. Conclusion Our study constructed a five-LLPS gene risk score signature that can be applied as an effective and convenient prognostic tool. These five genes might serve as potential targets for therapy and the treatment of HCC.
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Huo X, Guo T, Wang K, Yao B, Li D, Li H, Chen W, Wang L, Wu Z. Methylation-based reclassification and risk stratification of skull-base chordomas. Front Oncol 2022; 12:960005. [PMID: 36439461 PMCID: PMC9691996 DOI: 10.3389/fonc.2022.960005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/11/2022] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Skull-base chordomas are rare malignant bone cancers originating from the remnant of the notochord. Survival is variable, and clinical or molecular factors cannot reliably predict their outcomes. This study therefore identified epigenetic subtypes that defined new chordoma epigenetic profiles and their corresponding characteristics. METHODS Methylation profiles of 46 chordoma-resected neoplasms between 2008 and 2014, along with clinical information, were collected. K-means consensus clustering and principal component analysis were used to identify and validate the clusters. Single-sample gene set enrichment analysis, methylCIBERSORT algorithm, and copy number analysis were used to identify the characteristics of the clusters. RESULTS Unsupervised clustering analysis confirmed two clusters with a progression-free survival difference. Gene set enrichment analysis indicated that the early and late estrogen response pathways and the hypoxia pathway were activated whereas the inflammatory and interferon gamma responses were suppressed. Forty-six potential therapeutic targets corresponding to differentially methylated sites were identified from chordoma patients. Subgroups with a worse outcome were characterized by low immune cell infiltration, higher tumor purity, and higher stemness indices. Moreover, copy number amplifications mostly occurred in cluster 1 tumors and the high-risk group. Additionally, the presence of a CCNE1 deletion was exclusively found in the group of chordoma patients with better outcome, whereas RB1 and CDKN2A/2B deletions were mainly found in the group of chordoma patients with worse outcome. CONCLUSIONS Chordoma prognostic epigenetic subtypes were identified, and their corresponding characteristics were found to be variable.
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Affiliation(s)
- Xulei Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Tengxian Guo
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Ke Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Bohan Yao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Da Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Huan Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Wei Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Liang Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
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Wu Z, Lei K, Li H, He J, Shi E. Transcriptome-based network analysis related to M2-like tumor-associated macrophage infiltration identified VARS1 as a potential target for improving melanoma immunotherapy efficacy. J Transl Med 2022; 20:489. [PMID: 36303162 PMCID: PMC9615154 DOI: 10.1186/s12967-022-03686-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 11/10/2022] Open
Abstract
RATIONALE The M2-like tumor-associated macrophages (TAMs) are independent prognostic factors in melanoma. METHODS We performed weighted gene co-expression network analysis (WGCNA) to identify the module most correlated with M2-like TAMs. The Cancer Genome Atlas (TCGA) patients were classified into two clusters that differed based on prognosis and biological function, with consensus clustering. A prognostic model was established based on the differentially expressed genes (DEGs) of the two clusters. We investigated the difference in immune cell infiltration and immune response-related gene expression between the high and low risk score groups. RESULTS The risk score was defined as an independent prognostic value in melanoma. VARS1 was a hub gene in the M2-like macrophage-associated WGCNA module that the DepMap portal demonstrated was necessary for melanoma growth. Overexpressing VARS1 in vitro increased melanoma cell migration and invasion, while downregulating VARS1 had the opposite result. VARS1 overexpression promoted M2 macrophage polarization and increased TGF-β1 concentrations in tumor cell supernatant in vitro. VARS1 expression was inversely correlated with immune-related signaling pathways and the expression of several immune checkpoint genes. In addition, the VARS1 expression level helped predict the response to anti-PD-1 immunotherapy. Pan-cancer analysis demonstrated that VARS1 expression negatively correlated with CD8 T cell infiltration and the immune response-related pathways in most cancers. CONCLUSION We established an M2-like TAM-related prognostic model for melanoma and explored the role of VARS1 in melanoma progression, M2 macrophage polarization, and the development of immunotherapy resistance.
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Affiliation(s)
- Zhengquan Wu
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Munich, 81377, Munich, Germany.,Walter Brendel Center for Experimental Medicine, University of Munich, 81377, Munich, Germany
| | - Ke Lei
- Department of Dermatology, The Second People's Hospital of Chengdu, 610021, Chengdu, People's Republic of China
| | - Huaizhi Li
- Department of Endocrinology, Shenzhen University General Hospital, Shenzhen University, 518055, Shenzhen, People's Republic of China
| | - Jiali He
- Shenzhen Healthcare Committee Office, 518020, Shenzhen, People's Republic of China
| | - Enxian Shi
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Munich, 81377, Munich, Germany.
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Mei Y, Zhao L, Jiang M, Yang F, Zhang X, Jia Y, Zhou N. Characterization of glucose metabolism in breast cancer to guide clinical therapy. Front Surg 2022; 9:973410. [PMID: 36277284 PMCID: PMC9580338 DOI: 10.3389/fsurg.2022.973410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Background Breast cancer (BRCA) ranks as a leading cause of cancer death in women worldwide. Glucose metabolism is a noticeable characteristic of the occurrence of malignant tumors. In this study, we aimed to construct a novel glycometabolism-related gene (GRG) signature to predict overall survival (OS), immune infiltration and therapeutic response in BRCA patients. Materials and methods The mRNA sequencing and corresponding clinical data of BRCA patients were obtained from public cohorts. Lasso regression was applied to establish a GRG signature. The immune infiltration was evaluated with the ESTIMATE and CIBERSORT algorithms. The drug sensitivity was estimated using the value of IC50, and further forecasted the therapeutic response of each patient. The candidate target was selected in Cytoscape. A nomogram was constructed via the R package of “rms”. Results We constructed a six-GRG signature based on CACNA1H, CHPF, IRS2, NT5E, SDC1 and ATP6AP1, and the high-risk patients were correlated with poorer OS (P = 2.515 × 10−7). M2 macrophage infiltration was considerably superior in high-risk patients, and CD8+ T cell infiltration was significantly higher in low-risk patients. Additionally, the high-risk group was more sensitive to Lapatinib. Fortunately, SDC1 was recognized as candidate target and patients had a better OS in the low-SDC1 group. A nomogram integrating the GRG signature was developed, and calibration curves were consistent between the actual and predicted OS. Conclusions We identified a novel GRG signature complementing the present understanding of the targeted therapy and immune biomarker in breast cancer. The GRGs may provide fresh insights for individualized management of BRCA patients.
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Affiliation(s)
- Yingying Mei
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Lantao Zhao
- Department of Anesthesiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Man Jiang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fangfang Yang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xiaochun Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yizhen Jia
- Core Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Correspondence: Na Zhou Yizhen Jia
| | - Na Zhou
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Correspondence: Na Zhou Yizhen Jia
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14
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Guo R, Zhou Y, Lin F, Li M, Tan C, Xu B. A novel gene signature based on the hub genes of COVID-19 predicts the prognosis of idiopathic pulmonary fibrosis. Front Pharmacol 2022; 13:981604. [PMID: 36147332 PMCID: PMC9489050 DOI: 10.3389/fphar.2022.981604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Increasing evidence has demonstrated that there was a strong correlation between COVID-19 and idiopathic pulmonary fibrosis (IPF). However, the studies are limited, and the real biological mechanisms behind the IPF progression were still uncleared.Methods: GSE70866 and GSE 157103 datasets were downloaded. The weight gene co-expression network analysis (WGCNA) algorithms were conducted to identify the most correlated gene module with COVID-19. Then the genes were extracted to construct a risk signature in IPF patients by performing Univariate and Lasso Cox Regression analysis. Univariate and Multivariate Cox Regression analyses were used to identify the independent value for predicting the prognosis of IPF patients. What’s more, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and gene set enrichment analysis (GSEA) were conducted to unveil the potential biological pathways. CIBERSORT algorithms were performed to calculate the correlation between the risk score and immune cells infiltrating levels.Results: Two hundred thirty three differentially expressed genes were calculated as the hub genes in COVID-19. Fourteen of these genes were identified as the prognostic differentially expressed genes in IPF. Three (MET, UCHL1, and IGF1) of the fourteen genes were chosen to construct the risk signature. The risk signature can greatly predict the prognosis of high-risk and low-risk groups based on the calculated risk score. The functional pathway enrichment analysis and immune infiltrating analysis showed that the risk signature may regulate the immune-related pathways and immune cells.Conclusion: We identified prognostic differentially expressed hub genes related to COVID-19 in IPF. A risk signature was constructed based on those genes and showed great value for predicting the prognosis in IPF patients. What’s more, three genes in the risk signature may be clinically valuable as potential targets for treating IPF patients and IPF patients with COVID-19.
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Affiliation(s)
- Run Guo
- Department of Respiratory Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, China
| | - Yuefei Zhou
- Department of Orthopedics Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Fang Lin
- Department of Respiratory Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, China
| | - Mengxing Li
- Department of Respiratory Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, China
| | - Chunting Tan
- Department of Respiratory Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, China
- *Correspondence: Chunting Tan, ; Bo Xu,
| | - Bo Xu
- Department of Respiratory Medicine, Beijing Friendship Hospital of Capital Medical University, Beijing, China
- *Correspondence: Chunting Tan, ; Bo Xu,
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15
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Xu F, Zou C, Gao Y, Shen J, Liu T, He Q, Li S, Xu S. Comprehensive analyses identify RIPOR2 as a genomic instability-associated immune prognostic biomarker in cervical cancer. Front Immunol 2022; 13:930488. [PMID: 36091054 PMCID: PMC9458976 DOI: 10.3389/fimmu.2022.930488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Cervical cancer (CC) is a malignancy that tends to have a poor prognosis when detected at an advanced stage; however, there are few studies on the early detection of CC at the genetic level. The tumor microenvironment (TME) and genomic instability (GI) greatly affect the survival of tumor patients via effects on carcinogenesis, tumor growth, and resistance. It is necessary to identify biomarkers simultaneously correlated with components of the TME and with GI, as these could predict the survival of patients and the efficacy of immunotherapy. In this study, we extracted somatic mutational data and transcriptome information of CC cases from The Cancer Genome Atlas, and the GSE44001 dataset from the Gene Expression Omnibus database was downloaded for external verification. Stromal components differed most between genomic unstable and genomic stable groups. Differentially expressed genes were screened out on the basis of GI and StromalScore, using somatic mutation information and ESTIMATE methods. We obtained the intersection of GI- and StromalScore-related genes and used them to establish a four-gene signature comprising RIPOR2, CCL22, PAMR1, and FBN1 for prognostic prediction. We described immunogenomic characteristics using this risk model, with methods including CIBERSORT, gene set enrichment analysis (GSEA), and single-sample GSEA. We further explored the protective factor RIPOR2, which has a close relationship with ImmuneScore. A series of in vitro experiments, including immunohistochemistry, immunofluorescence, quantitative reverse transcription PCR, transwell assay, CCK8 assay, EdU assay, cell cycle detection, colony formation assay, and Western blotting were performed to validate RIPOR2 as an anti-tumor signature. Combined with integrative bioinformatic analyses, these experiments showed a strong relationship between RIPOR2 with tumor mutation burden, expression of genes related to DNA damage response (especially PARP1), TME-related scores, activation of immune checkpoint activation, and efficacy of immunotherapy. To summarize, RIPOR2 was successfully identified through comprehensive analyses of the TME and GI as a potential biomarker for forecasting the prognosis and immunotherapy response, which could guide clinical strategies for the treatment of CC patients.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chang Zou
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yueqing Gao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tingwei Liu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qizhi He
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Shaohua Xu, ; Shuangdi Li, ; Qizhi He,
| | - Shuangdi Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Shaohua Xu, ; Shuangdi Li, ; Qizhi He,
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Shaohua Xu, ; Shuangdi Li, ; Qizhi He,
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Wei N, Chao-yang G, Wen-ming Z, Ze-yuan L, Yong-qiang S, Shun-bai Z, Kai Z, Yan-chao M, Hai-hong Z. A ubiquitin-related gene signature for predicting prognosis and constructing molecular subtypes in osteosarcoma. Front Pharmacol 2022; 13:904448. [PMID: 36060009 PMCID: PMC9428517 DOI: 10.3389/fphar.2022.904448] [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: 03/25/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Ubiquitination is medicated by three classes of enzymes and has been proven to involve in multiple cancer biological processes. Moreover, dysregulation of ubiquitination has received a growing body of attention in osteosarcoma (OS) tumorigenesis and treatment. Therefore, our study aimed to identify a ubiquitin-related gene signature for predicting prognosis and immune landscape and constructing OS molecular subtypes. Methods: Therapeutically Applicable Research to Generate Effective Treatments (TARGET) was regarded as the training set through univariate Cox regression, Lasso Cox regression, and multivariate Cox regression. The GSE21257 and GSE39055 served as the validation set to verify the predictive value of the signature. CIBERSORT was performed to show immune infiltration and the immune microenvironment. The NMF algorithm was used to construct OS molecular subtypes. Results: In this study, we developed a ubiquitin-related gene signature including seven genes (UBE2L3, CORO6, DCAF8, DNAI1, FBXL5, UHRF2, and WDR53), and the gene signature had a good performance in predicting prognosis for OS patients (AUC values at 1/3/5 years were 0.957, 0.890, and 0.919). Multivariate Cox regression indicated that the risk score model and prognosis stage were also independent prognostic prediction factors. Moreover, analyses of immune cells and immune-related functions showed a significant difference in different risk score groups and the three clusters. The drug sensitivity suggested that IC50 of proteasome inhibitor (MG-132) showed a notable significance between the risk score groups (p < 0.05). Through the NMF algorithm, we obtained the three clusters, and cluster 3 showed better survival outcomes. The expression of ubiquitin-related genes (CORO6, UBE2L3, FBXL5, DNAI1, and DCAF8) showed an obvious significance in normal and osteosarcoma tissues. Conclusion: We developed a novel ubiquitin-related gene signature which showed better predictive prognostic ability for OS and provided additional information on chemotherapy and immunotherapy. The OS molecular subtypes would also give a useful guide for individualized therapy.
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Affiliation(s)
- Nan Wei
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Gong Chao-yang
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Zhou Wen-ming
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Lei Ze-yuan
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Shi Yong-qiang
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Zhang Shun-bai
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Zhang Kai
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
| | - Ma Yan-chao
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
- *Correspondence: Ma Yan-chao, ; Zhang Hai-hong,
| | - Zhang Hai-hong
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
- Lanzhou University Second Hospital, Lanzhou, China
- *Correspondence: Ma Yan-chao, ; Zhang Hai-hong,
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Dong M, Cui X, Wang G, Zhang Q, Li X. Development of a prognostic signature based on immune-related genes and the correlation with immune microenvironment in breast cancer. Aging (Albany NY) 2022; 14:5427-5448. [PMID: 35793235 PMCID: PMC9320535 DOI: 10.18632/aging.204158] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/30/2022] [Indexed: 11/25/2022]
Abstract
Breast cancer (BC) is an inflammatory tumor caused by a variety of pathological factors, and is still the most common malignant tumor in women. Immune-related genes (IRGs) play a prominent role in the oncogenesis and progression of BC, and are of tumor-specific expression patterns that would benefit the prognosis evaluation. However, there were no systematic studies concerning the possibilities of IRGs in BC prognosis. In this study, the Cancer Genome Atlas (TCGA) database was used to integrate the expression profiles of IRG with the overall survival (OS) rate of 1039 breast cancer patients. The Cox regression analysis was used to predict the survival-related IRGs in BC. Then, we successfully screened a total of 6 IRGs, including PSME2, ULBP2, IGHE, SCG2, SDC1, and SSTR1, and accordingly constructed a prognosis prediction model of BC. Based on the IRG-related model, the BC patients were divided into high- and low-risk groups, and the association between the prognostic model and tumor immune microenvironment (TME) was further explored. The prognostic model reflected the infiltration of various immune cells. Moreover, the low-risk group was found to be with higher immunophenoscore and distinct mutation signatures compared with the high-risk group. The histological validation showed that SDC1, as well as M2 macrophage biomarker CD206, were both of higher abundance in BC samples of high-risk patients, compared with those of low-risk patients. Our results identify the clinically significant IRGs and demonstrate the importance of the IRG-based immune prognostic model in BC monitoring, prognosis prediction, and therapy.
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Affiliation(s)
- Menglu Dong
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoqing Cui
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ge Wang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qi Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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18
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Wang Z, Song J, Azami NLB, Sun M. Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Colon Cancer to Immunotherapy. Front Immunol 2022; 13:802665. [PMID: 35572595 PMCID: PMC9095944 DOI: 10.3389/fimmu.2022.802665] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose To construct an immune-related gene prognostic index (IRGPI) for colon cancer and elucidate the molecular and immune characteristics as well as the benefit of immune checkpoint inhibitor (ICI) therapy in IRGPI-defined groups of colon cancer. Experimental Design Transcriptional and clinical data of colon cancer samples were obtained from The Cancer Genome Atlas (TCGA) (n = 521). Immune-related genes were obtained from ImmPort and InnateDB databases. 21 immune-related hub genes were identified byweighted gene co-expression network analysis (WGCNA). the Cox regression method was used to construct IRGPI and validated with Gene Expression Omnibus (GEO) dataset (n = 584). Finally, the molecular and immune profiles in the groups defined by IRGPI and the benefit of ICI treatment were analyzed. Results 8 genes were identified to construct IRGPI. IRGPI-low group had a better overall survival (OS) than IRGPI-high group. And this was well validated in the GEO cohort. Overall results showed that those with low IRGPI scores were enriched in antitumor metabolism, and collated with high infiltration of resting memory CD4 T cells and less aggressive phenotypes, benefiting more from ICI treatment. Conversely, high IRGPI scores were associated with cell adhesion molecules (CAMs) and chemokine signaling pathways, high infiltration of macrophage M1, suppressed immunity, more aggressive colon cancer phenotypes, as well as reduced therapeutic benefit from ICI treatment. Conclusions IRGPI is a promising biomarker to differentiate the prognostic and molecular profile of colon cancer, as well as the therapeutic benefits of ICI treatment.
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Affiliation(s)
- Zheng Wang
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jingru Song
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nisma Lena Bahaji Azami
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mingyu Sun
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Wu Z, Lei K, Xu S, He J, Shi E. Establishing a Prognostic Model Based on Ulceration and Immune Related Genes in Melanoma Patients and Identification of EIF3B as a Therapeutic Target. Front Immunol 2022; 13:824946. [PMID: 35273605 PMCID: PMC8901887 DOI: 10.3389/fimmu.2022.824946] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 12/13/2022] Open
Abstract
Ulceration and immune status are independent prognostic factors for survival in melanoma patients. Herein univariate Cox regression analysis revealed 53 ulcer-immunity-related DEGs. We performed consensus clustering to divide The Cancer Genome Atlas (TCGA) cohort (n = 467) into three subtypes with different prognosis and biological functions, followed by validation in three merged Gene Expression Omnibus (GEO) cohorts (n = 399). Multiomics approach was used to assess differences among the subtypes. Cluster 3 showed relatively lesser amplification and expression of immune checkpoint genes. Moreover, Cluster 3 lacked immune-related pathways and immune cell infiltration, and had higher proportion of non-responders to immunotherapy. We also constructed a prognostic model based on ulceration and immune related genes in melanoma. EIF3B was a hub gene in the intersection between genes specific to Cluster 3 and those pivotal for melanoma growth (DepMap, https://depmap.org/portal/download/). High EIF3B expression in TCGA and GEO datasets was related to worst prognosis. In vitro models revealed that EIF3B knockdown inhibited melanoma cell migration and invasion, and decreased TGF-β1 level in supernatant compared with si-NC cells. EIF3B expression was negatively correlated with immune-related signaling pathways, immune cell gene signatures, and immune checkpoint gene expression. Moreover, its low expression could predict partial response to anti-PD-1 immunotherapy. To summarize, we established a prognostic model for melanoma and identified the role of EIF3B in melanoma progression and immunotherapy resistance development.
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Affiliation(s)
- Zhengquan Wu
- Walter Brendel Center for Experimental Medicine, University of Munich, Munich, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University of Munich, Munich, Germany
| | - Ke Lei
- Department of Dermatology, The Second People's Hospital of Chengdu, Chengdu, China
| | - Sheng Xu
- Patient Monitor and Life Supporting (PMLS), Shenzhen Mindray Bio-Medical Electronics Co., Ltd, Shenzhen, China
| | - Jiali He
- Department of General Outpatient, Shen zhen Healthcare Committee Office, Shenzhen, China
| | - Enxian Shi
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Munich, Munich, Germany
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20
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Lai W, Li D, Kuang J, Deng L, Lu Q. Integrated analysis of single-cell RNA-seq dataset and bulk RNA-seq dataset constructs a prognostic model for predicting survival in human glioblastoma. Brain Behav 2022; 12:e2575. [PMID: 35429411 PMCID: PMC9120724 DOI: 10.1002/brb3.2575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/20/2022] [Accepted: 03/20/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. For patients with GBM, the median overall survival (OS) is 14.6 months and the 5-year survival rate is 7.2%. It is imperative to develop a reliable model to predict the survival probability in new GBM patients. To date, most prognostic models for predicting survival in GBM were constructed based on bulk RNA-seq dataset, which failed to accurately reflect the difference between tumor cores and peripheral regions, and thus show low predictive capability. An effective prognostic model is desperately needed in clinical practice. METHODS We studied single-cell RNA-seq dataset and The Cancer Genome Atlas-glioblastoma multiforme (TCGA-GBM) dataset to identify differentially expressed genes (DEGs) that impact the OS of GBM patients. We then applied the least absolute shrinkage and selection operator (LASSO) Cox penalized regression analysis to determine the optimal genes to be included in our risk score prognostic model. Then, we used another dataset to test the accuracy of our risk score prognostic model. RESULTS We identified 2128 DEGs from the single-cell RNA-seq dataset and 6461 DEGs from the bulk RNA-seq dataset. In addition, 896 DEGs associated with the OS of GBM patients were obtained. Five of these genes (LITAF, MTHFD2, NRXN3, OSMR, and RUFY2) were selected to generate a risk score prognostic model. Using training and validation datasets, we found that patients in the low-risk group showed better OS than those in the high-risk group. We validated our risk score model with the training and validating datasets and demonstrated that it can effectively predict the OS of GBM patients. CONCLUSION We constructed a novel prognostic model to predict survival in GBM patients by integrating a scRNA-seq dataset and a bulk RNA-seq dataset. Our findings may advance the development of new therapeutic targets and improve clinical outcomes for GBM patients.
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Affiliation(s)
- Wenwen Lai
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
| | - Defu Li
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
| | - Jie Kuang
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China
| | - Libin Deng
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
| | - Quqin Lu
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, China.,Department of Biostatistics and Epidemiology, School of Public Health, Nanchang University, Nanchang, China
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21
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Hu H, Yang M, Dong W, Yin B, Ding J, Huang B, Zheng Q, Li F, Han L. A Pyroptosis-Related Gene Panel for Predicting the Prognosis and Immune Microenvironment of Cervical Cancer. Front Oncol 2022; 12:873725. [PMID: 35574296 PMCID: PMC9099437 DOI: 10.3389/fonc.2022.873725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Cervical cancer (CC) is one of the most common malignant tumors of the female reproductive system. And the immune system disorder in patients results in an increasing incidence rate and mortality rate. Pyroptosis is an immune system-related programmed cell death pathway that produces systemic inflammation by releasing pro-inflammatory intracellular components. However, the diagnostic significance of pyroptosis-related genes (PRGs) in CC is still unclear. Therefore, we identified 52 PRGs from the TCGA database and screened three Differentially Expressed Pyroptosis-Related Genes (DEPRGs) in the prognosis of cervical cancer: CHMP4C, GZMB, TNF. The least absolute shrinkage and selection operator (LASSO) regression analysis and multivariate COX regression analysis were then used to construct a gene panel based on the three prognostic DEPRGs. The patients were divided into high-and low-risk groups based on the median risk score of the panel. According to the Kaplan-Meier curve, there was a substantial difference in survival rates between the two groups, with the high-risk group’s survival rate being significantly lower than the low-risk group’s. The PCA and t-SNE analyses revealed that the panel was able to differentiate patients into high-and low-risk groups. The area under the ROC curve (AUC) shows that the prognostic panel has high sensitivity and specificity. The risk score could then be employed as an independent prognostic factor using univariate and multivariate COX regression analyses paired with clinical data. The analyses of GO and KEGG functional enrichment of differentially expressed genes (DEGs) in the high-and low-risk groups revealed that these genes were primarily engaged in immune response and inflammatory cell chemotaxis. To illustrate immune cell infiltration in CC patients further, we used ssGSEA to compare immune-related cells and immune pathway activation between the high-and low-risk groups. The link between three prognostic DEPRGs and immune-related cells was still being discussed after evaluating immune cell infiltration in the TCGA cohort with “CIBERSORT.” In addition, the GEPIA database and qRT-PCR analysis were used to verify the expression levels of prognostic DEPRGs. In conclusion, PRGs are critical in tumor immunity and can be utilized to predict the prognosis of CC.
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Affiliation(s)
- Haoran Hu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Meiqin Yang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wei Dong
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bo Yin
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianyi Ding
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Baoyou Huang
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qingliang Zheng
- Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Lingfei Han, ; Fang Li, ; Qingliang Zheng,
| | - Fang Li
- Department of Gynecology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Lingfei Han, ; Fang Li, ; Qingliang Zheng,
| | - Lingfei Han
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Lingfei Han, ; Fang Li, ; Qingliang Zheng,
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22
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Hong-bin S, Wan-jun Y, Chen-hui D, Xiao-jie Y, Shen-song L, Peng Z. Identification of an Iron Metabolism-Related lncRNA Signature for Predicting Osteosarcoma Survival and Immune Landscape. Front Genet 2022; 13:816460. [PMID: 35360864 PMCID: PMC8961878 DOI: 10.3389/fgene.2022.816460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) act as epigenetic regulators in the process of ferroptosis and iron metabolism. This study aimed to identify an iron metabolism-related lncRNA signature to predict osteosarcoma (OS) survival and the immune landscape. Methods: RNA-sequencing data and clinical information were obtained from the TARGET dataset. Univariate Cox regression and LASSO Cox analysis were used to develop an iron metabolism-related lncRNA signature. Consensus clustering analysis was applied to identify subtype-based prognosis-related lncRNAs. CIBERSORT was used to analyze the difference in immune infiltration and the immune microenvironment in the two clusters. Results: We identified 302 iron metabolism-related lncRNAs based on 515 iron metabolism-related genes. The results of consensus clustering showed the differences in immune infiltration and the immune microenvironment in the two clusters. Through univariate Cox regression and LASSO Cox regression analysis, we constructed an iron metabolism-related lncRNA signature that included seven iron metabolism-related lncRNAs. The signature was verified to have good performance in predicting the overall survival, immune-related functions, and immunotherapy response of OS patients between the high- and low-risk groups. Conclusion: We identified an iron metabolism-related lncRNA signature that had good performance in predicting survival outcomes and showing the immune landscape for OS patients. Furthermore, our study will provide valuable information to further develop immunotherapies of OS.
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Affiliation(s)
- Shao Hong-bin
- Department of Joint Surgery, The 940 Hospital of PLA Joint Logistics Support Force, Lanzhou, China
| | - Yang Wan-jun
- The Second Affiliated Hospital of Xi’an Medical College, Xi’an, China
| | - Dong Chen-hui
- Department of Joint Surgery, The 940 Hospital of PLA Joint Logistics Support Force, Lanzhou, China
| | - Yang Xiao-jie
- Department of Joint Surgery, The 940 Hospital of PLA Joint Logistics Support Force, Lanzhou, China
| | - Li Shen-song
- Department of Joint Surgery, The 940 Hospital of PLA Joint Logistics Support Force, Lanzhou, China
| | - Zhou Peng
- Department of Joint Surgery, The 940 Hospital of PLA Joint Logistics Support Force, Lanzhou, China
- *Correspondence: Zhou Peng,
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23
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Jiang S, Bu X, Tang D, Yan C, Huang Y, Fang K. A Tumor Suppressor Gene-Based Prognostic Classifier Predicts Prognosis, Tumor Immune Infiltration, and Small Molecule Compounds in Breast Cancer. Front Genet 2022; 12:783026. [PMID: 35186006 PMCID: PMC8850650 DOI: 10.3389/fgene.2021.783026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
Objective: Tumor suppressor genes (TSGs) play critical roles in the cell cycle checkpoints and in modulating genomic stability. Here, we aimed to develop a TSG-based prognostic classifier for breast cancer. Methods: Gene expression profiles and clinical information of breast cancer were curated from TCGA (discovery set) and Gene Expression Omnibus (GEO) repository (GSE12093 and GSE17705 datasets as testing sets). Univariate cox regression analysis and random forest machine learning method were presented for screening characteristic TSGs. After multivariate cox regression analyses, a TSG-based prognostic classifier was constructed. The predictive efficacy was verified by C-index and receiver operating characteristic (ROC) curves. Meanwhile, the predictive independency was assessed through uni- and multivariate cox regression analyses and stratified analyses. Tumor immune infiltration was estimated via ESTIMATE and CIBERSORT algorithms. Small molecule agents were predicted through CMap method. Molecular subtypes were clustered based on the top 100 TSGs with the most variance. Results: A prognostic classifier including nine TSGs was established. High-risk patients were predictive of undesirable prognosis. C-index and ROC curves demonstrated its excellent predictive performance in prognosis. Also, this prognostic classifier was independent of conventional clinicopathological parameters. Low-risk patients exhibited increased infiltration levels of immune cells like T cells CD8. Totally, 48 small molecule compounds were predicted to potentially treat breast cancer. Five TSG-based molecular subtypes were finally constructed, with distinct prognosis and clinicopathological features. Conclusion: Collectively, this study provided a TSG-based prognostic classifier with the potential to predict clinical outcomes and immune infiltration in breast cancer and identified potential small molecule agents against breast cancer.
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Affiliation(s)
- Suxiao Jiang
- Department of Surgery, Yinchuan Maternal and Child Health Hospital, Yinchuan, China
| | - Xiangjing Bu
- Department of Surgery, Yinchuan Maternal and Child Health Hospital, Yinchuan, China
| | - Desheng Tang
- Department of Surgery, The First Affiliated Hospital of Harbin Medical University, Heilongjiang, China
| | - Changsheng Yan
- Department of Surgery, The First Affiliated Hospital of Harbin Medical University, Heilongjiang, China
| | - Yan Huang
- Department of Surgery, Affiliated Hospital of Ningxia Medical University, Ningxia, China
| | - Kun Fang
- Department of Surgery, Yinchuan Maternal and Child Health Hospital, Yinchuan, China
- *Correspondence: Kun Fang,
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24
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Huang C, Zhang C, Sheng J, Wang D, Zhao Y, Qian L, Xie L, Meng Z. Identification and Validation of a Tumor Microenvironment-Related Gene Signature in Hepatocellular Carcinoma Prognosis. Front Genet 2021; 12:717319. [PMID: 34899826 PMCID: PMC8662347 DOI: 10.3389/fgene.2021.717319] [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: 06/16/2021] [Accepted: 10/25/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a typical inflammatory-related malignant tumor with complex immune tolerance microenvironment and poor prognosis. In this study, we aimed to construct a novel immune-related gene signature for the prognosis of HCC patients, exploring tumor microenvironment (TME) cell infiltration characterization and potential mechanisms. Methods: A total of 364 HCC samples with follow-up information in the TCGA-LIHC dataset were analyzed for the training of the prognostic signature. The Least Absolute Shrinkage and Selector Operation (LASSO) regression based on the IRGs was conducted to identify the prognostic genes and establish an immune risk signature. The immune cell infiltration in TME was estimated via the CIBERSORT method. Gene Set Variation Analysis (GSVA) was conducted to compare the biological pathways involved in the low-risk and high-risk groups. Furthermore, paraffin sections of HCC tissue microarrays containing 77 patients from Fudan University Shanghai Cancer Center were used for IHC staining. The clinical characteristics of the 77 HCC patients were collected and summarized for survival analysis validation via the Kaplan-Meier (KM) method. Results: Three-gene signature with close immune correlation (Risk score = EPO * 0.02838 + BIRC5 * 0.02477 + SPP1 * 0.0002044) was constructed eventually and proven to be an effective prognostic factor for HCC patients. The patients were divided into a high-risk and a low-risk group according to the optimal cutoff, and the survival analysis revealed that HCC samples with high-risk immuno-score had significantly poorer outcomes than the low-risk group (p < 0.0001). The results of CIBERSORT suggested that the immune cell activation was relatively higher in the low-risk group with better prognosis. Besides, GSVA analysis showed multiple signaling differences between the high- and low-risk group, indicating that the three-gene prognostic model can affect the prognosis of patients by affecting immune-related mechanisms. Tissue microarray (TMA) results further confirmed that the expression of three genes in HCC tissues was closely related to the prognosis of patients, respectively. Conclusion: In this study, we constructed and validated a robust three-gene signature with close immune correlation in HCC, which presented a reliable performance in the prediction of HCC patients' survival.
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Affiliation(s)
- Changjing Huang
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chenyue Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jie Sheng
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dan Wang
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yingke Zhao
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ling Qian
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lin Xie
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Minimally Invasive Therapy Center, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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25
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Huang H, Hu Y, Guo L, Wen Z. Integrated bioinformatics analyses of key genes involved in hepatocellular carcinoma immunosuppression. Oncol Lett 2021; 22:830. [PMID: 34691257 PMCID: PMC8527569 DOI: 10.3892/ol.2021.13091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a typical inflammation-driven cancer. Chronically unresolved inflammation may remodel the immunosuppressive tumor microenvironment, which is rich in innate immune cells. The mechanisms via which HCC progresses through the evasion of the innate immune surveillance remain unclear. The present study thus aimed to identify key genes involved in HCC immunosuppression and to establish an innate immune risk signature, with the ultimate goal of obtaining new insight into effective immunotherapies. HCC and normal liver tissue mRNA expression and clinicopathological data were obtained from the Cancer Genome Atlas database. The immunosuppressive innate immune-related genes (IIRGs) in HCC were screened using integrated bioinformatics analyses. Gene expression was then validated using the Gene Expression Omnibus database and the Human Protein Atlas database, and tissues were obtained from patients with HCC who underwent surgery. In total, 3,676 genes were identified as differentially expressed mRNAs after comparing the HCC tissues with the normal liver tissues in TCGA. Gene Set Enrichment Analyses revealed 21 highly expressed IIRGs in HCC tissues. A survival analysis and Cox regression model were used to construct an innate immune risk signature, including three IIRGs: Collectin-12 (COLEC12), matrix metalloproteinase-12 (MMP12) and mucin-12 (MUC12) genes. Univariate and multivariate Cox analyses revealed that the signature of the three IIRGs was a robust independent risk factor in relation to the overall survival (OS) of patients with HCC. The expression of the three aforementioned IIRGs was confirmed through external validation. Moreover, COLEC12 and MMP12 expression significantly correlated with that of immune checkpoint molecules or immunosuppressive cytokines. The tumor immune dysfunction and exclusion tool predicted that the increased expression of the three IIRGs in patients with HCC was significantly associated with the efficacy of relatively poor immune checkpoint blockade therapy. Conclusively, a novel innate immune-related risk signature for patients with HCC was constructed and validated. This signature may be involved in immunosuppression, and may be used to predict a poor prognosis, functioning as a potential immunotherapeutic target for patients with HCC.
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Affiliation(s)
- Hongyan Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Youwen Hu
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Li Guo
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhili Wen
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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26
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Wu P, Shi J, Sun W, Zhang H. Identification and validation of a pyroptosis-related prognostic signature for thyroid cancer. Cancer Cell Int 2021; 21:523. [PMID: 34627252 PMCID: PMC8502398 DOI: 10.1186/s12935-021-02231-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Background Pyroptosis is a form of programmed cell death triggered by inflammasomes. However, the roles of pyroptosis-related genes in thyroid cancer (THCA) remain still unclear. Objective This study aimed to construct a pyroptosis-related signature that could effectively predict THCA prognosis and survival. Methods A LASSO Cox regression analysis was performed to build a prognostic model based on the expression profile of each pyroptosis-related gene. The predictive value of the prognostic model was validated in the internal cohort. Results A pyroptosis-related signature consisting of four genes was constructed to predict THCA prognosis and all patients were classified into high- and low-risk groups. Patients with a high-risk score had a poorer overall survival (OS) than those in the low-risk group. The area under the curve (AUC) of the receiver operator characteristic (ROC) curves assessed and verified the predictive performance of this signature. Multivariate analysis showed the risk score was an independent prognostic factor. Tumor immune cell infiltration and immune status were significantly higher in low-risk groups, which indicated a better response to immune checkpoint inhibitors (ICIs). Of the four pyroptosis-related genes in the prognostic signature, qRT-PCR detected three of them with significantly differential expression in THCA tissues. Conclusion In summary, our pyroptosis-related risk signature may have an effective predictive and prognostic capability in THCA. Our results provide a potential foundation for future studies of the relationship between pyroptosis and the immunotherapy response. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02231-0.
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Affiliation(s)
- Pu Wu
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Jinyuan Shi
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China.
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27
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Zhang D, Li Y, Yang S, Wang M, Yao J, Zheng Y, Deng Y, Li N, Wei B, Wu Y, Zhai Z, Dai Z, Kang H. Identification of a glycolysis-related gene signature for survival prediction of ovarian cancer patients. Cancer Med 2021; 10:8222-8237. [PMID: 34609082 PMCID: PMC8607265 DOI: 10.1002/cam4.4317] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/22/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022] Open
Abstract
Background Ovarian cancer (OV) is deemed the most lethal gynecological cancer in women. The aim of this study was to construct an effective gene prognostic model for predicting overall survival (OS) in patients with OV. Methods The expression profiles of glycolysis‐related genes (GRGs) and clinical data of patients with OV were extracted from The Cancer Genome Atlas (TCGA) database. Univariate, multivariate, and least absolute shrinkage and selection operator Cox regression analyses were conducted, and a prognostic signature based on GRGs was constructed. The predictive ability of the signature was analyzed using training and test sets. Results A gene risk signature based on nine GRGs (ISG20, CITED2, PYGB, IRS2, ANGPTL4, TGFBI, LHX9, PC, and DDIT4) was identified to predict the survival outcome of patients with OV. The signature showed a good prognostic ability for OV, particularly high‐grade OV, in the TCGA dataset, with areas under the curve (AUC) of 0.709 and 0.762 for 3‐ and 5‐year survival, respectively. Similar results were found in the test sets, and the AUCs of 3‐, 5‐year OS were 0.714 and 0.772 in the combined test set. And our signature was an independent prognostic factor. Moreover, a nomogram combining the prediction model and clinical factors was developed. Conclusion Our study established a nine‐GRG risk model and nomogram to better predict OS in patients with OV. The risk model represents a promising and independent prognostic predictor for patients with OV. Moreover, our study on GRGs could offer guidance for the elucidation of underlying mechanisms in future studies.
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Affiliation(s)
- Dai Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Air Force Medical University, Xi'an, China
| | - Yiche Li
- Department of Tumor Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Si Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jia Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yujiao Deng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bajin Wei
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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28
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Lei J, Zhang D, Yao C, Ding S, Lu Z. Development of a Predictive Immune-Related Gene Signature Associated With Hepatocellular Carcinoma Patient Prognosis. Cancer Control 2021; 27:1073274820977114. [PMID: 33269615 PMCID: PMC8480351 DOI: 10.1177/1073274820977114] [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] [Indexed: 12/13/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) remains the third leader cancer-associated cause of death globally, but the etiological basis for this complex disease remains poorly clarified. The present study was thus conceptualized to define a prognostic immune-related gene (IRG) signature capable of predicting immunotherapy responsiveness and overall survival (OS) in patients with HCC. Methods: Five differentially expressed IRG associated with HCC were established the immune-related risk model through univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. Patients were separated at random into training and testing cohorts, after which the association between the identified IRG signature and OS was evaluated using the “survival” R package. In addition, maftools was leveraged to assess mutational data, with tumor mutation burden (TMB) scores being calculated as follows: (total mutations/total bases) × 106. Immune-related risk term abundance was quantified via “ssGSEA” algorithm using the “gsva” R package. Results: HCC patients were successfully stratified into low-risk and high-risk groups based upon a signature composed of 5 differentially expressed IRGs, with overall survival being significantly different between these 2 groups in training cohort, testing cohort and overall patient cohort (P = 1.745e-06, P = 1.888e-02, P = 4.281e-07). No association was observed between TMB and this IRG risk score in the overall patient cohort (P = 0.461). Notably, 19 out of 29 immune-related risk terms differed substantially in the overall patient dataset. These risk terms mainly included checkpoints, human leukocyte antigens, natural killer cells, dendritic cells, and major histocompatibility complex class I. Conclusion: In summary, an immune-related prognostic gene signature was successfully developed and used to predict survival outcomes and immune system status in patients with HCC. This signature has the potential to help guide immunotherapeutic treatment planning for patients affected by this deadly cancer.
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Affiliation(s)
- Jiasheng Lei
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Dengyong Zhang
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Chao Yao
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Sheng Ding
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
| | - Zheng Lu
- Department of Hepatobiliary Surgery, BengBu Medical College, BengBu, China
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29
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Xu F, Shen J, Xu S. Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment. Front Genet 2021; 12:663617. [PMID: 34108992 PMCID: PMC8181403 DOI: 10.3389/fgene.2021.663617] [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: 02/03/2021] [Accepted: 04/15/2021] [Indexed: 12/26/2022] Open
Abstract
The cross-talk between tumor cells and the tumor microenvironment (TME) is an important factor in determining the tumorigenesis and progression of cervical cancer (CC). However, clarifying the potential mechanisms which trigger the above biological processes remains a challenge. The present study focused on immune-relevant differences at the transcriptome and somatic mutation levels through an integrative multi-omics analysis based on The Cancer Genome Atlas database. The objective of the study was to recognize the specific immune-related prognostic factors predicting the survival and response to immunotherapy of patients with CC. Firstly, eight hub immune-related prognostic genes were ultimately identified through construction of a protein–protein interaction network and Cox regression analysis. Secondly, 32 differentially mutated genes were simultaneously identified based on the different levels of immune infiltration. As a result, an immune gene-related prognostic model (IGRPM), including six factors (chemokine receptor 7 [CCR7], CD3d molecule [CD3D], CD3e molecule [CD3E], and integrin subunit beta 2 [ITGB2], family with sequence similarity 133 member A [FAM133A], and tumor protein p53 [TP53]), was finally constructed to forecast clinical outcomes of CC. Its predictive capability was further assessed and validated using the Gene Expression Omnibus validation set. In conclusion, IGRPM may be a promising prognostic signature to predict the prognoses and responses to immunotherapy of patients with CC. Moreover, the multi-omics study showed that IGRPM could be a novel therapeutic target for CC, which is a promising biomarker for indicating the immune-dominant status of the TME and revealing the potential mechanisms responsible for the tumorigenesis and progression of CC.
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Affiliation(s)
- Fangfang Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Jiacheng Shen
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Tongji University, Shanghai, China
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Yang S, Yao B, Wu L, Liu Y, Liu K, Xu P, Zheng Y, Deng Y, Zhai Z, Wu Y, Li N, Zhang D, Kang H, Dai Z. Ubiquitin-related molecular classification and risk stratification of hepatocellular carcinoma. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:207-219. [PMID: 34095460 PMCID: PMC8138213 DOI: 10.1016/j.omto.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022]
Abstract
The roles of ubiquitin-related genes in hepatocellular carcinoma (HCC) have not been thoroughly investigated. This study aimed to systematically examine ubiquitin-related genes and identify subtypes and stratify prognosis of HCC by using ubiquitin-related signatures. Survival, biological processes, tumor microenvironment (TME), and genomic alterations of the HCC subtypes were investigated. Patients with HCC were classified into two subtypes (clusters 1 and 2) with distinct survival outcomes, pathways, and genomic alterations. Cluster 2 had better prognosis than did cluster 1. Hepatitis B, hepatitis C, Janus tyrosine kinase (JAK)-signal transducer and activator of transcription (STAT) pathway, and natural killer cell-mediated cytotoxicity were enriched in cluster 1. Moreover, cluster 2 had a higher immune score and immune cell infiltrations, whereas cluster 1 had a lower immune score and immune infiltrations. Additionally, mutations, amplifications, and deletions among the phosphatidylinositol 3-kinase (PI3K)-AKT, p53, and receptor tyrosine kinase (RTK)-RAS pathways more frequently occurred in cluster 1, while those among the Hippo, MYC, and Notch signaling pathways were found in cluster 2. Finally, a prognostic signature, consisting of eight ubiquitin-related genes, was established and validated. In brief, our study established a new classification and developed a prognostic signature for HCC.
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Affiliation(s)
- Si Yang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Bowen Yao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Liming Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yuanxing Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Kang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Xu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Yi Zheng
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Yujiao Deng
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Zhen Zhai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Ying Wu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Na Li
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Dai Zhang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
- Corresponding author Huafeng Kang, Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China.
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
- Corresponding author Zhijun Dai, Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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Peng Y, Liu C, Li M, Li W, Zhang M, Jiang X, Chang Y, Liu L, Wang F, Zhao Q. Identification of a prognostic and therapeutic immune signature associated with hepatocellular carcinoma. Cancer Cell Int 2021; 21:98. [PMID: 33568167 PMCID: PMC7877064 DOI: 10.1186/s12935-021-01792-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most prevalent and inflammation-associated cancers. The tumor microenvironment (TME) plays an essential role in HCC development and metastasis, leading to poor prognosis. The overall TME immune cells infiltration characterizations mediated by immune-related genes (IRGs) remain unclear. In this study, we aimed to investigate whether immune-related genes could be indicators for the prognosis of HCC patients and TME cell infiltration characterization as well as responses to immunotherapy. Methods We obtained differentially expressed immune-related genes (DE IRGs) between normal liver tissues and liver cancer tissues from The Cancer Genome Atlas (TCGA) database. To identify the prognostic genes and establish an immune risk signature, we performed univariable Cox regression survival analysis and the Least Absolute Shrinkage and Selector Operation (LASSO) regression based on the DE IRGs by robust rank aggregation method. Cox regression analysis was used to identify independent prognostic factors in HCC. We estimated the immune cell infiltration in TME via CIBERSORT and immunotherapy response through TIDE algorithm. Results We constructed an immune signature and validated its predictive capability. The immune signature included 7 differentially expressed IRGs: BIRC5, CACYBP, NR0B1, RAET1E, S100A8, SPINK5, and SPP1. The univariate and multivariate cox analysis showed that the 7-IRGs signature was a robust independent prognostic factor in the overall survival of HCC patients. The 7-IRG signature was associated with some clinical features, including gender, vascular invasion, histological grade, clinical stage, T stage. We also found that the 7-IRG signature could reflect the infiltration characterization of different immunocytes in the tumor microenvironment (TME) and had a good correlation with immune checkpoint molecules, revealing that the poor prognosis might be partly due to immunosuppressive TME. The Tumour Immune Dysfunction and Exclusion (TIDE) analysis data showed that the 7-IRG signature had great potential for indicating the immunotherapy response in HCC patients. The mutation analysis demonstrated a significant difference in the tumor mutation burden (TMB) between the high- and low-risk groups, partially explaining this signature's predictive value. Conclusion In a word, we constructed and validated a novel, immune-related prognostic signature for HCC patients. This signature could effectively indicate HCC patients' survival and immunotherapy response. And it might act as potential immunotherapeutic targets for HCC patients.
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Affiliation(s)
- Yanan Peng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Chang Liu
- Department of Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mengting Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Wenjie Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Mengna Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Xiang Jiang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Lan Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China. .,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China. .,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China.
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Yang S, Lin S, Liu K, Liu Y, Xu P, Zheng Y, Deng Y, Zhang D, Zhai Z, Li N, Ren X, Dai Z, Kang H. Identification of an immune-related RNA-binding protein signature to predict survival and targeted therapy responses in liver cancer. Genomics 2021; 113:795-804. [PMID: 33524497 DOI: 10.1016/j.ygeno.2021.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/25/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022]
Abstract
RNA-binding proteins (RBPs) play crucial roles in multiple cancers. However, very few RBPs and their association with immune genes have been systematically studied in liver cancer (LC). We aimed to identify an immune-related RBP signature to predict the survival of LC patients. Bioinformatics methods were used to identify differentially expressed, immune-related, and prognostic RBPs and to develop an immune-related RBP signature based on data from the Cancer Genome Atlas (TCGA) cohort. We obtained eight differentially expressed, immune-related, and prognostic RBPs to construct a risk signature. The signature could effectively distinguish between high- and low-risk patients, and its predictive capacity was validated in the International Cancer Genomics Consortium (ICGC) cohort. We speculated that the high-risk group was more sensitive to targeted therapy. The immune-related RBP signature is an independent prognostic biomarker for LC patients and can expand the application of targeted therapy through patient stratification.
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Affiliation(s)
- Si Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yuanxing Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Peng Xu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yujiao Deng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Dai Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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Zhang D, Zheng Y, Yang S, Li Y, Wang M, Yao J, Deng Y, Li N, Wei B, Wu Y, Zhu Y, Li H, Dai Z. Identification of a Novel Glycolysis-Related Gene Signature for Predicting Breast Cancer Survival. Front Oncol 2021; 10:596087. [PMID: 33489894 PMCID: PMC7821871 DOI: 10.3389/fonc.2020.596087] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
To identify a glycolysis-related gene signature for the evaluation of prognosis in patients with breast cancer, we analyzed the data of a training set from TCGA database and four validation cohorts from the GEO and ICGC databases which included 1,632 patients with breast cancer. We conducted GSEA, univariate Cox regression, LASSO, and multiple Cox regression analysis. Finally, an 11-gene signature related to glycolysis for predicting survival in patients with breast cancer was developed. And Kaplan–Meier analysis and ROC analyses suggested that the signature showed a good prognostic ability for BC in the TCGA, ICGC, and GEO datasets. The analyses of univariate Cox regression and multivariate Cox regression revealed that it’s an important prognostic factor independent of multiple clinical features. Moreover, a prognostic nomogram, combining the gene signature and clinical characteristics of patients, was constructed. These findings provide insights into the identification of breast cancer patients with a poor prognosis.
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Affiliation(s)
- Dai Zhang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yi Zheng
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Si Yang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yiche Li
- Breast Center Department, The Fourth Hospital of Hebei Medical University, Hebei Medical University, Shijiazhuang, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jia Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yujiao Deng
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bajin Wei
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Wu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuyao Zhu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hongtao Li
- Department of Breast Head and Neck surgery, The 3rd Affiliated Teaching Hospital of Xinjiang Medical University (Affiliated Tumor Hospital), Urumqi, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Xu Y, Wang Z, Li F. Survival prediction and response to immune checkpoint inhibitors: A prognostic immune signature for hepatocellular carcinoma. Transl Oncol 2020; 14:100957. [PMID: 33246289 PMCID: PMC7695881 DOI: 10.1016/j.tranon.2020.100957] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/28/2022] Open
Abstract
As is known to us, this is the first immune-gene-related signature of HCC which was validated in various ways. This signature was linked to the mutation status, and we found the difference of mutation between two risk groups. We estimated the association among the signature, TMB and the survival and found the result contrary to previous studies.
Hepatocellular carcinoma (HCC) is one of the most common cancers all over the world. Several studies have explored if immune-related genes and tumor immune microenvironment could play roles in HCC prognoses. This study is aimed at developing a prognostic signature of HCC based on immune-related genes or tumor immune microenvironment to predict survival and response to immune checkpoint inhibitors (ICIs). We constructed a prognostic signature using bioinformatics method and validated its predictive capability. The mechanisms of the signature prediction were explored with The Cancer Immunome Atlas (TCIA) and mutation analysis. We also explored the association between the signature and immunophenoscore (IPS), which is the marker of ICIs response. A 6 immune-related-gene (6-IRG) signature was developed. It was revealed in a multivariate analysis that the 6-IRG signature was an independent prognostic factor of overall survival and progression-free interval among HCC patients. In the high-risk group of 6-IRG signature score, macrophage M0 cells and regulatory T cells, which are observed associated with poor overall survival in our study, were higher. The low-risk group had a higher IPS, which meant a better response to ICIs. Taken together, we constructed a reliable 6-IRG signature for prediction of survival and response to ICIs. The signature needs further testing for clinical application.
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Affiliation(s)
- Ying Xu
- Shanghai University of Traditional Chinese Medicine, No. 1200, Cailun Road, 200120 Shanghai, China; Laboratory of TCM Four Processing, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zheng Wang
- Shanghai University of Traditional Chinese Medicine, No. 1200, Cailun Road, 200120 Shanghai, China; Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fufeng Li
- Shanghai University of Traditional Chinese Medicine, No. 1200, Cailun Road, 200120 Shanghai, China; Laboratory of TCM Four Processing, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Association between tumor mutation burden and immune infiltration in ovarian cancer. Int Immunopharmacol 2020; 89:107126. [PMID: 33189611 DOI: 10.1016/j.intimp.2020.107126] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/02/2020] [Accepted: 10/17/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND It remains unclear whether the tumor mutation burden (TMB) or a TMB-related signature could be prognostic indicators in ovarian cancer (OC), as potential correlations with immune infiltrates and immunotherapy responsiveness remains poorly understood. METHODS Data of 941 OC patients were collected from three datasets, including 587, 260, and 94 patients from The Cancer Genome Atlas (TCGA), GSE32062, and the International Cancer Genome Consortium (ICGC), respectively. TMB was calculated and correlations with clinical outcomes, immune infiltrates, and immunotherapy responsiveness were investigated in the TCGA OC cohort. Weighted gene co-expression network analysis was performed to identify TMB-related genes. A TMB-related signature was constructed and validated. RESULTS Higher TMB was associated with better survival in the TCGA and ICGC OC cohorts. The high-TMB group had higher CD8+ T-cell infiltration than the low-TMB group. No significant correlation was found between TMB and immunotherapy response. Furthermore, we selected 8 prognostic and TMB-related genes to construct a TMB-related signature that could distinguish between the high- and low-risk patients; its predictive power was validated in the GSE32062 and ICGC datasets. SubMap analysis suggested that patients in the low-risk group might have a better response to anti-PD1 therapy. CONCLUSIONS We examined the prognostic value of TMB and its potential association with immune cell infiltration and immunotherapy responsiveness in OC. A TMB-related prognostic signature consisting of 8 genes was developed and verified, which might be a promising prognostic signature for the prognosis of OC patients.
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Chen RL, Zhou JX, Cao Y, Sun LL, Su S, Deng XJ, Lin JT, Xiao ZW, Chen ZZ, Wang SY, Lin LZ. Construction of a Prognostic Immune Signature for Squamous-Cell Lung Cancer to Predict Survival. Front Immunol 2020; 11:1933. [PMID: 33072067 PMCID: PMC7533590 DOI: 10.3389/fimmu.2020.01933] [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: 04/13/2020] [Accepted: 07/17/2020] [Indexed: 12/25/2022] Open
Abstract
Background Limited treatment strategies are available for squamous-cell lung cancer (SQLC) patients. Few studies have addressed whether immune-related genes (IRGs) or the tumor immune microenvironment can predict the prognosis for SQLC patients. Our study aimed to construct a signature predict prognosis for SQLC patients based on IRGs. Methods We constructed and validated a signature from SQLC patients in The Cancer Genome Atlas (TCGA) using bioinformatics analysis. The underlying mechanisms of the signature were also explored with immune cells and mutation profiles. Results A total of 464 eligible SQLC patients from TCGA dataset were enrolled and were randomly divided into the training cohort (n = 232) and the testing cohort (n = 232). Eight differentially expressed IRGs were identified and applied to construct the immune signature in the training cohort. The signature showed a significant difference in overall survival (OS) between low-risk and high-risk cohorts (P < 0.001), with an area under the curve of 0.76. The predictive capability was verified with the testing and total cohorts. Multivariate analysis revealed that the 8-IRG signature served as an independent prognostic factor for OS in SQLC patients. Naive B cells, resting memory CD4 T cells, follicular helper T cells, and M2 macrophages were found to significantly associate with OS. There was no statistical difference in terms of tumor mutational burden between the high-risk and low-risk cohorts. Conclusion Our study constructed and validated an 8-IRG signature prognostic model that predicts clinical outcomes for SQLC patients. However, this signature model needs further validation with a larger number of patients.
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Affiliation(s)
- Rui-Lian Chen
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing-Xu Zhou
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yang Cao
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ling-Ling Sun
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shan Su
- Department of Oncology, Guangzhou Chest Hospital, Guangzhou, China
| | - Xiao-Jie Deng
- Department of Oncology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Jie-Tao Lin
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhi-Wei Xiao
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhuang-Zhong Chen
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Si-Yu Wang
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li-Zhu Lin
- Integrative Cancer Centre, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Wang H, Xu F, Zhang M, Liu J, Wang F, Zhao Q. A Prognostic Immunoscore for Relapse-Free Survival Prediction in Colorectal Cancer. DNA Cell Biol 2020; 39:1181-1193. [PMID: 32397747 DOI: 10.1089/dna.2020.5490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fei Xu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Meng Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
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Noorbakhsh SA, Mahmoodi-Eshkaftaki M, Mokhtari Z. Integrating artificial neural network and scoring systems to increase the prediction accuracy of patient mortality and organ dysfunction. BIOMED ENG-BIOMED TE 2020; 65:/j/bmte.ahead-of-print/bmt-2018-0216/bmt-2018-0216.xml. [PMID: 32598291 DOI: 10.1515/bmt-2018-0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/27/2020] [Indexed: 11/15/2022]
Abstract
The aim of this study was to develop and compare techniques to increase the prediction accuracy of patient mortality and organ dysfunction in the Intensive Care Units (hereinafter ICU) of hospitals. Patient mortality was estimated with two models of artificial neural network (ANN)-backpropagation (BP) and simplified acute physiology score (SAPS). Organ dysfunction was predicted by coupled ANN self-organizing map (SOM) and logistic organ dysfunction score (LODS) method on the basis of patient conditions. Input dataset consisted of 36 features recorded for 4,000 patients in the ICU. An integrated response surface methodology (RSM) and genetic algorithm (GA) was developed to achieve the best topology of the ANN-BP model. Although mortality prediction of the best ANN-BP (MSE = 0.0036, AUC = 0.83, R2 = 0.81) was more accurate than that of the SAPS score model (MSE = 0.0056, AUC = 0.82, R2 = 0.78), the execution time of the former (=45 min) was longer than that of the latter (=20 min). Therefore, the principal component analysis (PCA) was used to reduce the input feature dimensions, which, in turn, reduced the execution time up to 50%. Data reduction also helped to increase the network accuracy up to 90%. The likelihood of organ dysfunction determined by coupled ANN and scoring method technique can be much more efficient than the LODS model alone because the SOM could successfully classify the patients in 64 classes. The primary patient classification plays a major role in increasing the efficiency of an estimator.
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Affiliation(s)
- Seyed Ayoob Noorbakhsh
- Department of Electrical Engineering, Iran University of Science and Technology, Tehran, Iran
| | | | - Zahra Mokhtari
- Community-Oriented Nursing Midwifery Center, Shahrekord University of Medical Science, Shahrekord, Iran
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Yang S, Wu Y, Wang S, Xu P, Deng Y, Wang M, Liu K, Tian T, Zhu Y, Li N, Zhou L, Dai Z, Kang H. HPV-related methylation-based reclassification and risk stratification of cervical cancer. Mol Oncol 2020; 14:2124-2141. [PMID: 32408396 PMCID: PMC7463306 DOI: 10.1002/1878-0261.12709] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/01/2020] [Accepted: 05/09/2020] [Indexed: 12/16/2022] Open
Abstract
Human papillomavirus (HPV) is a clear etiology of cervical cancer (CC). However, the associations between HPV infection and DNA methylation have not been thoroughly investigated. Additionally, it remains unknown whether HPV‐related methylation signatures can identify subtypes of CC and stratify the prognosis of CC patients. DNA methylation profiles were obtained from The Cancer Genome Atlas to identify HPV‐related methylation sites. Unsupervised clustering analysis of HPV‐related methylation sites was performed to determine the different CC subtypes. CC patients were categorized into cluster 1 (Methylation‐H), cluster 2 (Methylation‐M), and cluster 3 (Methylation‐L). Compared to Methylation‐M and Methylation‐L, Methylation‐H exhibited a significantly improved overall survival (OS). Gene set enrichment analysis (GSEA) was conducted to investigate the functions that correlated with different CC subtypes. GSEA indicated that the hallmarks of tumors, including KRAS signaling, TNFα signaling via NF‐κB, inflammatory response, epithelial–mesenchymal transition, and interferon‐gamma response, were enriched in Methylation‐M and Methylation‐L. Based on mutation and copy number variation analyses, we found that aberrant mutations, amplifications, and deletions among the MYC, Notch, PI3K‐AKT, and RTK‐RAS pathways were most frequently detected in Methylation‐H. Additionally, mutations, amplifications, and deletions within the Hippo, PI3K‐AKT, and TGF‐β pathways were presented in Methylation‐M. Genes within the cell cycle, Notch, and Hippo pathways possessed aberrant mutations, amplifications, and deletions in Methylation‐L. Moreover, the analysis of tumor microenvironments revealed that Methylation‐H was characterized by a relatively low degree of immune cell infiltration. Finally, a prognostic signature based on six HPV‐related methylation sites was developed and validated. Our study revealed that CC patients could be classified into three heterogeneous clusters based on HPV‐related methylation signatures. Additionally, we derived a prognostic signature using six HPV‐related methylation sites that stratified the OS of patients with CC into high‐ and low‐risk groups.
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Affiliation(s)
- Si Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ying Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shuqian Wang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Peng Xu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yujiao Deng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tian Tian
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuyao Zhu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Linghui Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Qian JX, Yu M, Sun Z, Jiang AM, Long B. A 17-gene expression-based prognostic signature associated with the prognosis of patients with breast cancer: A STROBE-compliant study. Medicine (Baltimore) 2020; 99:e19255. [PMID: 32282693 PMCID: PMC7220332 DOI: 10.1097/md.0000000000019255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Identification of reliable predictive biomarkers for patients with breast cancer (BC).Univariate Cox proportional hazards regression model was conducted to identify genes correlated with the overall survival (OS) of patients in the TCGA-BRCA cohort. Functional enrichment analysis was conducted to investigate the biological meaning of these survival related genes. Then, patients in TCGA-BCRA were randomly divided into training set and test. Least absolute shrinkage and selection operator (LASSO) penalized Cox regression model was performed and the risk score of BC patients in this model was used to build a prognostic signature. The prognostic performance of the signature was evaluated in the training set, test set, and an independent validation set GSE7390.2519 genes were demonstrated to be significantly associated with the OS of BC patients. Functional annotation of the 2519 genes suggested that these genes were associated with immune response and protein synthesis related gene ontology terms and pathways. 17 genes were identified in the LASSO Cox regression model and used to construct a 17-gene signature. Patients in the 17-gene signature low risk group have better OS and event-free survival compared with those in the 17-gene signature high risk group in the TCGA-BRCA cohort. The prognostic role of the 17-gene signature has been confirmed in the validation cohort. Multivariable Cox proportional hazards regression model suggested the 17-gene signature was an independent prognostic factor in BC.The 17-gene signature we developed could successfully classify patients into high- and low-risk groups, indicating that it might serve as candidate biomarker in BC.
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Affiliation(s)
- Jin-Xian Qian
- Department of Breast Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, People's Republic of China
| | - Min Yu
- Yangtze University, Jingzhou Central Hospital, Galactophore Department, The Second Clinical Medical College, Jingzhou, People's Republic of China
| | - Zhe Sun
- Department of Breast Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, People's Republic of China
| | - Ai-Mei Jiang
- Department of Breast Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, People's Republic of China
| | - Bo Long
- School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
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Tian G, Li G, Liu P, Wang Z, Li N. Glycolysis-Based Genes Associated with the Clinical Outcome of Pancreatic Ductal Adenocarcinoma Identified by The Cancer Genome Atlas Data Analysis. DNA Cell Biol 2020; 39:417-427. [PMID: 31968179 DOI: 10.1089/dna.2019.5089] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadly tumors in digestive tract tumors. Although there has been advancement in PDAC treatment, its prognosis still remains unsatisfactory, mainly because of dismal diagnosis. This article aims to develop new prognostic factors related to energy metabolism in PDAC and to use these genes for novel risk stratification. Hundred fifty messenger RNA (mRNA) expression profiles and clinicopathological data of PDAC were downloaded from The Cancer Genome Atlas dataset. The glycolysis pathway was the significant pathway based on the gene set enrichment analysis. We chose the glycolysis pathway-related 176 genes for further analysis. Multivariate Cox regression analysis and forward stepwise Cox regression model established a novel three-gene glycolytic signature (including MET, B3GNT3, and SPAG4) for PDAC patients' prognosis prediction. All 150 patients were classified into two groups by the median risk score. High-risk group had a worse outcome compared to the low-risk group. The risk score was also significantly correlated with age and radiotherapy. A nomogram, including the glycolytic gene signature, has shown some clinical net benefit for overall survival prediction. We also validated the validity and reliability in the Puleo dataset. This novel gene expression signature may be involved in the pathophysiology and used for risk stratification and prognosis prediction in PDAC.
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Affiliation(s)
- Guangwei Tian
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Guang Li
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Peipei Liu
- Department of Histology and Embryology, Shenyang Medical College, Shenyang, China
| | - Zihui Wang
- Department of Neuroscience, Cleveland Clinic, Cleveland, Ohio
| | - Nan Li
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Shenyang, China
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Yang S, Wu Y, Deng Y, Zhou L, Yang P, Zheng Y, Zhang D, Zhai Z, Li N, Hao Q, Song D, Kang H, Dai Z. Identification of a prognostic immune signature for cervical cancer to predict survival and response to immune checkpoint inhibitors. Oncoimmunology 2019; 8:e1659094. [PMID: 31741756 DOI: 10.1080/2162402x.2019.1659094] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer (CC) is a leading cause of cancer-related death in women. Limited studies have investigated whether immune-related genes (IRGs) or tumor immune microenvironment (TIME) could be indicators for CC prognoses. The aim of this study was to develop an improved prognostic signature for CC based on IRGs or TIME to predict survival and response to immune checkpoint inhibitors (ICIs). A prognostic signature was constructed using bioinformatics method and its predictive capability was validated. The mechanisms underlying the signature's predictive capability were explored with CIBERSORT algorithm and mutation analysis. Immunophenoscore (IPS) is validated for ICIs response, and was therefore explored in relation to the signature. A prognostic signature based on 11 IRGs was developed. A multivariate analysis revealed that the 11-IRG signature was an independent prognostic factor for overall survival (OS) and progression-free interval in CC patients. In the 11-IRG signature high-risk group, CD8 T cells and resting mast cells, which are found to associate with better OS in our study, were lower; activated mast cells, associated with poorer OS, were higher, compared with the low-risk group. An IPS analysis suggested that the 11-IRG signature low-risk group, which possessed a higher IPS, represented a more immunogenic phenotype that was more inclined to respond to ICIs. In short, an 11-IRG prognostic signature for predicting CC patients' survival and response to ICIs was firmly established. The predictive capability of this model in CC requires further testing with the goal of better prognostic stratification and treatment management.
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Affiliation(s)
- Si Yang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ying Wu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yujiao Deng
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Linghui Zhou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pengtao Yang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yi Zheng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dai Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qian Hao
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dingli Song
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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43
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Guo XX, Su J, He XF. A 4-gene panel predicting the survival of patients with glioblastoma. J Cell Biochem 2019; 120:16037-16043. [PMID: 31081973 DOI: 10.1002/jcb.28883] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND To identify independently prognostic gene panel in patients with glioblastoma (GBM). MATERIALS AND METHODS The Cancer Genome Atlas (TCGA)-GBM was used as a training set and a test set. GSE13041 was used as a validation set. Survival associated differentially expression genes (DEGs), derived between GBM and normal brain tissue, was obtained using univariate Cox proportional hazards regression model and then was included in a least absolute shrinkage and selection operator penalized Cox proportional hazards regression model. Thus, a 4-gene prognostic panel was developed based on the risk score for each patient in that model. The prognostic role of the 4-gene panel was validated using univariate and multivariable Cox proportional hazards regression model. RESULTS A total of 686 patients with GBM were included in our study; 724 DEGs was identified, 133 of which was significantly correlated with the overall survival (OS) of patients with GBM. A 4-gene panel including NMB, RTN1, GPC5, and epithelial membrane protein 3 (EMP3) was developed. Kaplan-Meier survival analysis suggested that patients in the 4-gene panel low risk group had significantly better OS than those in the 4-gene panel high risk group in the training set (hazard ratio [HR] = 0.3826; 95% confidence interval [CI]: 0.2751-0.532; P < 0.0001), test set (HR = 0.718; 95% CI: 0.5282-0.9759; P = 0.033) and the independent validation set (HR = 0.6898; 95% CI: 0.4872-0.9766; P = 0.035). Both univariate and multivariable Cox proportional hazards regression analysis suggested that the 4-gene panel was independent prognostic factor for GBM in the training set. CONCLUSION We developed and validated 4-gene panel that was independently correlated with the survival of patients with GBM.
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Affiliation(s)
- Xiao-Xia Guo
- Department of Neurosurgery, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Jiao Su
- Department of Biological Chemistry, Changzhi Medical College, Changzhi, Shanxi, China
| | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
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44
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Shen XY, Liu XP, Song CK, Wang YJ, Li S, Hu WD. Genome-wide analysis reveals alcohol dehydrogenase 1C and secreted phosphoprotein 1 for prognostic biomarkers in lung adenocarcinoma. J Cell Physiol 2019; 234:22311-22320. [PMID: 31074035 DOI: 10.1002/jcp.28797] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/17/2022]
Abstract
To seek out novel promising biomarkers for predicting lung adenocarcinoma (LUAD) prognosis, we conducted this study. First, 279 upregulated and 37 downregulated differentially expressed genes were obtained from LUAD and para-carcinoma tissues by the Affymetrix GeneChip Human Transcriptome Array. Then, we randomly classified samples of LUAD data set GSE31210 as training and testing sets in a 1:1 ratio. Alcohol dehydrogenase 1C (ADH1C) and secreted phosphoprotein 1 (SPP1) were finally identified correlating with the LUAD survival through least absolute shrinkage and selection operator penalized Cox proportion hazards regression model, and applied to build a 2-gene signature related to prognosis in training set. Univariate and multivariable survival analyses suggested that overall survival (OS) and relapse-free survival (RFS) in the 2-gene signature low-risk group were better than the high-risk group. Kaplan-Meier curves proved that elevated ADH1C expression and reduced SPP1 expression were related to better OS and RFS. Besides, the SPP1 expressed higher in LUAD than para-carcinoma tissues using quantitative reverse transcription polymerase chain reaction assay. Finally, the association between the two genes and clinicopathological parameters in 80 LUAD were analyzed, it is suggested that SPP1 was relevant to epidermal growth factor receptor mutation. These findings indicated that ADH1C and SPP1 might be novel promising biomarkers for predicting LUAD prognosis.
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Affiliation(s)
- Xiao-Yan Shen
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors & Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Cong-Kuan Song
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors & Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yu-Jin Wang
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors & Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Sheng Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei-Dong Hu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors & Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
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Liu XP, Yin XH, Meng XY, Yan XH, Wang F, He L. Development and Validation of a 9-Gene Prognostic Signature in Patients With Multiple Myeloma. Front Oncol 2019; 8:615. [PMID: 30671382 PMCID: PMC6331463 DOI: 10.3389/fonc.2018.00615] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/29/2018] [Indexed: 01/21/2023] Open
Abstract
Background: Multiple myeloma (MM) is one of the most common types of hematological malignance, and the prognosis of MM patients remains poor. Objective: To identify and validate a genetic prognostic signature in patients with MM. Methods: Co-expression network was constructed to identify hub genes related with International Staging System (ISS) stage of MM. Functional analysis of hub genes was conducted. Univariate Cox proportional hazard regression analysis was conducted to identify genes correlated with the overall survival (OS) of MM patients. Least absolute shrinkage and selection operator (LASSO) penalized Cox proportional hazards regression model was used to minimize overfitting and construct a prognostic signature. The prognostic value of the signature was validated in the test set and an independent validation cohort. Results: A total of 758 hub genes correlated with ISS stage of MM patients were identified, and these hub genes were mainly enriched in several GO terms and KEGG pathways involved in cell proliferation and immune response. Nine hub genes (HLA-DPB1, TOP2A, FABP5, CYP1B1, IGHM, FANCI, LYZ, HMGN5, and BEND6) with non-zero coefficients in the LASSO Cox regression model were used to build a 9-gene prognostic signature. Relapsed MM and ISS stage III MM was associated with high risk score calculated based on the signature. Patients in the 9-gene signature low risk group was significantly associated with better clinical outcome than those in the 9-gene signature high risk group in the training set, test, and validation set. Conclusions: We developed a 9-gene prognostic signature that might be an independent prognostic factor in patients with MM.
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Affiliation(s)
| | | | | | - Xin-Hui Yan
- Department of Cardiology, the First Hospital of Lanzhou University, Lanzhou, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Li He
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Chen PF, Li QH, Zeng LR, Yang XY, Peng PL, He JH, Fan B. A 4-gene prognostic signature predicting survival in hepatocellular carcinoma. J Cell Biochem 2018; 120:9117-9124. [PMID: 30582205 DOI: 10.1002/jcb.28187] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/12/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To develop an independent prognostic signature for patients with hepatocellular carcinoma (HCC). METHODS HCC gene expression profile the cancer genome atlas-liver hepatocellular carcinoma and GSE14520 were used as discovery and test set, respectively. Differentially expressed genes (DEGs) were identified between HCC tissues and adjacent normal liver tissues. Univariate Cox proportional hazards regression analysis was performed to identify DEGs correlated with survival of HCC patients. A 4-gene-based signature was constructed based on a least absolute shrinkage and selection operator Cox penalized regression model. The predictive value of the signature was analyzed and validated. RESULTS Two hundred sixty-three DEGs were identified between HCC and adjacent liver tissues. After univariate survival analysis, 90 DEGs were found to be significantly correlated with the overall survival (OS) of HCC patients, of which 4 genes (KPNA2, CDC20, SPP1, and TOP2A) with non-zero coefficient were used to construct a prognostic signature. The 4-gene signature was significantly associated with the age (P = 0.046), grade ( P = 0.022), and T stage ( P = 0.023) of HCC patients in the discovery set and it also significantly associated with TNM stage ( P = 0.033), and serum alpha-fetoprotein lever ( P = 0.034). Patients in the 4-gene low-risk group were associated with better OS and recurrence-free survival (RFS) than those in the high-risk group in the discovery and test set. Meanwhile, the 4-gene signature is an independent prognostic factor regarding OS and RFS in the discovery and test set. CONCLUSION We developed a 4-gene-based signature, which could be a candidate prognostic factor for patients with HCC.
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Affiliation(s)
- Peng-Fei Chen
- Department of Gastroenterology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Qing-He Li
- Department of Hepatobiliary Surgery, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Li-Rong Zeng
- Department of Gastroenterology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Xue-Ying Yang
- Department of Medical Records, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Pai-Lan Peng
- Department of Gastroenterology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Jian-Hua He
- Department of Gastroenterology, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
| | - Bin Fan
- Department of Hepatobiliary Surgery, The Central Hospital of Enshi Autonomous Prefecture, Enshi, China
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Grellety E, Golden MH. Severely malnourished children with a low weight-for-height have a higher mortality than those with a low mid-upper-arm-circumference: I. Empirical data demonstrates Simpson's paradox. Nutr J 2018; 17:79. [PMID: 30217205 PMCID: PMC6138885 DOI: 10.1186/s12937-018-0384-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/25/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND According to WHO childhood severe acute malnutrition (SAM) is diagnosed when the weight-for-height Z-score (WHZ) is <-3Z of the WHO2006 standards, the mid-upper-arm circumference (MUAC) is < 115 mm, there is nutritional oedema or any combination of these parameters. Recently there has been a move to eliminate WHZ as a diagnostic criterion on the assertion that children meeting the WHZ criterion are healthy, that MUAC is universally a superior prognostic indicator of mortality and that adding WHZ to the assessment does not improve the prediction; these assertions have lead to a controversy concerning the role of WHZ in the diagnosis of SAM. METHODS We examined the mortality experience of 76,887 6-60 month old severely malnourished children admitted for treatment to in-patient, out-patient or supplementary feeding facilities in 18 African countries, of whom 3588 died. They were divided into 7 different diagnostic categories for analysis of mortality rates by comparison of case fatality rates, relative risk of death and meta-analysis of the difference between children admitted using MUAC and WHZ criteria. RESULTS The mortality rate was higher in those children fulfilling the WHO2006 WHZ criterion than the MUAC criterion. This was the case for younger as well as older children and in all regions except for marasmic children in East Africa. Those fulfilling both criteria had a higher mortality. Nutritional oedema increased the risk of death. Having oedema and a low WHZ dramatically increased the mortality rate whereas addition of the MUAC criterion to either oedema-alone or oedema plus a low WHZ did not further increase the mortality rate. The data were subject to extreme confounding giving Simpson's paradox, which reversed the apparent mortality rates when children fulfilling both WHZ and MUAC criteria were included in the estimation of the risk of death of those fulfilling either the WHZ or MUAC criteria alone. CONCLUSIONS Children with a low WHZ, but a MUAC above the SAM cut-off point are at high risk of death. Simpson's paradox due to confounding from oedema and mathematical coupling may make previous statistical analyses which failed to distinguish the diagnostic groups an unreliable guide to policy. WHZ needs to be retained as an independent criterion for diagnosis of SAM and methods found to identify those children with a low WHZ, but not a low MUAC, in the community.
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Affiliation(s)
- Emmanuel Grellety
- Research Center Health Policy and Systems - International Health, School of Public Health, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Michael H. Golden
- Department of Medicine and Therapeutics, University of Aberdeen, Aberdeen, Scotland
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Li MX, Zhao H, Bi XY, Li ZY, Yao XS, Li H, Huang Z, Han Y, Zhou JG, Zhao JJ, Zhang YF, Zhao DB, Cai JQ. Lactate dehydrogenase is a prognostic indicator in patients with hepatocellular carcinoma treated by sorafenib: results from the real life practice in HBV endemic area. Oncotarget 2018; 7:86630-86647. [PMID: 27880930 PMCID: PMC5349941 DOI: 10.18632/oncotarget.13428] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022] Open
Abstract
Purpose Lactate dehydrogenase (LDH), which was an indirect marker of hypoxia, was a potentially prognostic factor in several malignancies. There is a lack of evidence about the prognostic value of serum LDH level in patients with hepatocellular carcinoma (HCC) receiving sorafenib treatment from hepatitis B virus endemic areas. Materials and Methods A total of 119 HBV-related HCC patients treated by sorafenib from a Chinese center were included into the study. They were categorized into 2 groups according to the cut-off value of pre-treatment LDH, which was determined by the time dependent receiver operating characteristics (ROC) curve for the overall survival. The prognostic value of LDH was evaluated. The relationships between LDH and other clinicopathological factors were also assessed. Results The cut-off value was 221 U/L. With a median follow up of 15 (range, 3-73) months, 91 patients reached the endpoint. Multivariate analysis proved that pre-treatment serum LDH level was an independent prognostic factor for both overall survival (OS) and progression-free survival (PFS). For patients whose pre-treatment LDH ≥ 221 U/L, increased LDH value after 3 months of sorafenib treatment predicted inferior OS and PFS. And patients with elevated pre-treatment LDH level predisposed to be featured with lower serum albumin, presence of macroscopic vascular invasion, advanced Child-Pugh class, advanced T category, higher AFP, and higher serum total bilirubin. Conclusions Serum LDH level was a potentially prognostic factor in HCC patients treated by sorafenib in HBV endemic area. More relevant studies with reasonable study design are needed to further strengthen its prognostic value.
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Affiliation(s)
- Mu-Xing Li
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Hong Zhao
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Xin-Yu Bi
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Zhi-Yu Li
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Xue-Song Yao
- Department of Interventional Therapies, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Huai Li
- Department of Interventional Therapies, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Zhen Huang
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Yue Han
- Department of Interventional Therapies, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Jian-Guo Zhou
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Jian-Jun Zhao
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Ye-Fan Zhang
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Dong-Bin Zhao
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
| | - Jian-Qiang Cai
- Department of Abdominal Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100021, P. R. China
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49
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Zhang X, Li X, Feng Y. A classification performance measure considering the degree of classification difficulty. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2016.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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