scholarly journals A Novel Expression Signature from the Perspective of Mesenchymal-Epithelial Transition for Hepatocellular Carcinoma with Regard to Prognosis, Clinicopathological Features, Immune Cell Infiltration, Chemotherapeutic Efficacy, and Immunosuppressive Molecules

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Lijun Xu ◽  
Qing Zheng

Purpose. Mesenchymal-epithelial transition (MET), a reverse biological process to epithelial-mesenchymal transition (EMT), is involved in tumor metastasis and invasion. However, the role of MET-related genes (MRGs) in hepatocellular carcinoma (HCC) prognosis remains unclear. Methods. In this research, we obtained MRGs data and clinical information from public databases. In the TCGA dataset, a prognostic signature for HCC was constructed by the least absolute shrinkage and selection operator (LASSO) method and externally verified using the ICGC dataset. Results. There were 148 differentially expressed MRGs (DEMRGs), out of which 37 MRGs were found associated with overall survival (OS) in the univariate Cox analysis. A novel signature integrating of 5 MRGs was constructed, which split patients into high- and low-risk groups. Kaplan–Meier analysis revealed that high-risk patients had unfavorable OS than those low-risk counterparts. Receiver operating characteristic curve (ROC) showed great performance of this signature in predictive ability. Multivariate Cox analysis confirmed that this signature could independently predict HCC prognosis. The analysis of immune cell infiltration demonstrated that immune status varied differently between high- and low-risk groups. The analysis of clinicopathological characteristics suggested that tumor grade, clinical stage, and T stage were different between risk groups. The analysis between this signature and chemotherapeutic efficacy and immunosuppressive molecules indicated that this signature could serve as a promising predictor. Conclusions. In conclusion, we constructed and verified a novel signature from the perspective of MET, which was significantly associated with HCC prognosis, clinicopathological features, immune status, chemotherapeutic efficacy, and immunosuppressive biomarkers.

2021 ◽  
Author(s):  
Jian Xu ◽  
Xiaomin Shen ◽  
Bo Zhang ◽  
Rui Su ◽  
Mingxuan Cui ◽  
...  

Abstract Purpose: To develop a LRP1B gene mutation based prognostic model for hepatocellular carcinoma (HCC) patients risk prediction. Methods: The LRP1B gene mutation rate was calculated from HCC patient samples. Meanwhile, differentially expressed genes according to LRP1B mutant were screened out for prognostic model establishment. Based on this innovative model, HCC patients were categoried into high and low-risk group. The immune status including immune cell infiltration ratio and checkpoints have been explored in two groups. Results: It can be shown here 11 genes demonstrate significant differences according to LRP1B status, which can better predict HCC patient prognosis. The accuracy of the model prediction is evaluated and approved by the AUC value. From the immune cell infiltration ratio analysis, there is a significant difference in the infiltration degree of 7 types of immune cells and 2 immune checkpoints between high and low-risk HCC patients. Meanwhile, LRP1B was tested as a prognostic marker in clinic to predict different stages for HCC with satisfied accurancy. Conclusion: This study has explored a potential prognostic biomarker and developed a novel LRP1B mutation-associated prognostic model for hepatocellular carcinoma, which provides a systematic reference for future better understanding of clinical research.


2022 ◽  
Author(s):  
Qiaonan Guo ◽  
Pengjun Qiu ◽  
Kelun Pan ◽  
Jianpeng Chen ◽  
Jianqing Lin

Abstract Background: Exosomes are nanosized vesicles, play a vital role in breast cancer (BC) occurrence, development, invasion, metastasis, and drug resistance. Nevertheless, studies about exosome-related genes in breast cancer are limited. Besides, the interaction between the exosomes and tumor immune microenvironment (TIME) in BC are still unclear. Hence, we procced to study the potential prognostic value of exosome-related genes and their relationship to immune microenvironment in BC. Methods: 121 exosome-related genes were provided by ExoBCD database and 7 final genes were selected from the intersection of 33 differential expression genes (DEGs) and 19 prognostic genes in BC. Based on the expression levels of the 7 genes, downloaded from The Cancer Genome Atlas (TCGA) database, as well as the regression coefficients, the exosome-related signature was constructed. As a result, the patients in TCGA and GEO database were separated into low- and high- risk groups, respectively. Subsequently, R clusterProfiler package was applied to identify the distinct enrichment pathways between high-risk group and low-risk group. The ESTIMATE method was used to calculate ESTIMATE Score and CIBERSORT was applied to evaluate the immune cell infiltration. Eventually, the different expression levels of immune checkpoint related genes were analyzed between the two risk groups. Results: Results of BC prognosis vary from different risk groups. The low-risk groups were identified with higher survival rate both in TCGA and GEO cohort. The DEGs between high- and low- risk groups were found to enrich in immunity, biological processes, and inflammation pathways. The BC patients with higher ESTIMATE scores were revealed to have better overall survival (OS). Subsequently, CD8+ T cells, naive B cells, CD4+ resting memory T cells, monocytes, and neutrophils were upregulated, while M0 macrophages and M2 macrophages were downregulated in the low-risk group. At last, 4 genes reported as the targets of immune checkpoint inhibitors were further analyzed. The low-risk groups in TCGA and GEO cohorts were indicated with higher expression levels of LAG-3, CD274, TIGIT and CTLA-4. Conclusion: According to this study, exosomes are closely associated with the prognosis and immune cell infiltration of BC patients. These findings may make contributions to improve immunotherapy and bring a new sight for BC treatment strategies.


2021 ◽  
Vol 18 (5) ◽  
pp. 6709-6723
Author(s):  
Xin Yu ◽  
◽  
Jun Liu ◽  
Ruiwen Xie ◽  
Mengling Chang ◽  
...  

<abstract> <sec><title>Objective</title><p>We aimed to construct a novel prognostic model based on N6-methyladenosine (m6A)-related autophagy genes for predicting the prognosis of lung squamous cell carcinoma (LUSC).</p> </sec> <sec><title>Methods</title><p>Gene expression profiles and clinical information of Patients with LUSC were downloaded from The Cancer Genome Atlas (TCGA) database. In addition, m6A- and autophagy-related gene profiles were obtained from TCGA and Human Autophagy Database, respectively. Pearson correlation analysis was performed to identify the m6A-related autophagy genes, and univariate Cox regression analysis was conducted to screen for genes associated with prognosis. Based on these genes, LASSO Cox regression analysis was used to construct a prognostic model. The corresponding prognostic score (PS) was calculated, and patients with LUSC were assigned to low- and high-risk groups according to the median PS value. An independent dataset (GSE37745) was used to validate the prognostic ability of the model. CIBERSORT was used to calculate the differences in immune cell infiltration between the high- and low-risk groups.</p> </sec> <sec><title>Results</title><p>Seven m6A-related autophagy genes were screened to construct a prognostic model: <italic>CASP4</italic>, <italic>CDKN1A</italic>, <italic>DLC1</italic>, <italic>ITGB1</italic>, <italic>PINK1</italic>, <italic>TP63</italic>, and <italic>EIF4EBP1</italic>. In the training and validation sets, patients in the high-risk group had worse survival times than those in the low-risk group; the areas under the receiver operating characteristic curves were 0.958 and 0.759, respectively. There were differences in m6A levels and immune cell infiltration between the high- and low-risk groups.</p> </sec> <sec><title>Conclusions</title><p>Our prognostic model of the seven m6A-related autophagy genes had significant predictive value for LUSC; thus, these genes may serve as autophagy-related therapeutic targets in clinical practice.</p> </sec> </abstract>


2021 ◽  
Author(s):  
zixuan Wu ◽  
Xuyan Huang ◽  
Min-jie Cai ◽  
Peidong Huang ◽  
Zunhui Guan

Abstract Background In 502 Lung squamous cell carcinoma (LUSC) samples from The Cancer Genome Atlas (TCGA) datasets, the predictive significance of ferroptosis-related long non-coding RNAs (lncRNAs) was investigated. In LUSC, we meant to express how ferroptosis-associated lncRNAs interact with immune cell infiltration. Methods Gene expression enrichment was investigated using gene set enrichment analysis in the Kyoto Encyclopedia of Genes and Genomes. The prognostic model was constructed using Lasso regression. To better understand immune cell infiltration in different risk groups and its relationship to clinical outcome, researchers analyzed by modifications in the tumor microenvironment (TME) and immunological association. The expression of lncRNA was intimately connected to that of ferroptosis, according to co-expression analyses. Ferroptosis-related lncRNAs were shown to be partially overexpressed in high-risk patients in the absence of additional clinical signs, suggesting that they may be incorporated into a prediction model to predict LUSC prognosis. GSEA revealed the immunological and tumor-related pathways in the low-risk group. Results According to TCGA, CCR and inflammation-promoting genes were considered to be significantly different between the low-risk and high-risk groups. The expression of C10orf55, AC016924.1, AL161431.1, LUCAT1, AC104248.1, and MIR3945HG were likewise different in the two risk groups. Conclusion LncRNAs linked to ferroptosis are connected to the occurrence and development of LUSC. With the use of matching prognostic models, the prognosis of LUSC patients can be predicted. In LUSC, ferroptosis-related lncRNAs and immune cell infiltration in the TME might be novel therapeutic targets that should be investigated further.


2021 ◽  
Vol 12 ◽  
Author(s):  
Luping Zhang ◽  
Shaokun Wang ◽  
Yachen Wang ◽  
Weidan Zhao ◽  
Yingli Zhang ◽  
...  

BackgroundImbalanced nutritional supply and demand in the tumor microenvironment often leads to hypoxia. The subtle interaction between hypoxia and immune cell behavior plays an important role in tumor occurrence and development. However, the functional relationship between hypoxia and the tumor microenvironment remains unclear. Therefore, we aimed to investigate the effect of hypoxia on the intestinal tumor microenvironment.MethodWe extracted the names of hypoxia-related genes from the Gene Set Enrichment Analysis (GSEA) database and screened them for those associated with colorectal cancer prognosis, with the final list including ALDOB, GPC1, ALDOC, and SLC2A3. Using the sum of the expression levels of these four genes, provided by The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and the expression coefficients, we developed a hypoxia risk score model. Using the median risk score value, we divided the patients in the two databases into high- and low-risk groups. GSEA was used to compare the enrichment differences between the two groups. We used the CIBERSORT computational method to analyze immune cell infiltration. Finally, the correlation between these five genes and hypoxia was analyzed.ResultThe prognosis of the two groups differed significantly, with a higher survival rate in the low-risk group than in the high-risk group. We found that the different risk groups were enriched by immune-related and inflammatory pathways. We identified activated M0 macrophages in TCGA and GEO databases and found that CCL2/4/5, and CSF1 contributed toward the increased infiltration rate of this immune cell type. Finally, we observed a positive correlation between the five candidate genes’ expression and the risk of hypoxia, with significant differences in the level of expression of each of these genes between patient risk groups.ConclusionOverall, our data suggest that hypoxia is associated with the prognosis and rate of immune cell infiltration in patients with colorectal cancer. This finding may improve immunotherapy for colorectal cancer.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shimin Chen ◽  
Wenbo Liu ◽  
Yu Huang

AbstractThe aim of this study was to construct and validate a DNA repair-related gene signature for evaluating the overall survival (OS) of patients with gastric cancer (GC). Differentially expressed DNA repair genes between GC and normal gastric tissue samples obtained from the TCGA database were identified. Univariate Cox analysis was used to screen survival-related genes and multivariate Cox analysis was applied to construct a DNA repair-related gene signature. An integrated bioinformatics approach was performed to evaluate its diagnostic and prognostic value. The prognostic model and the expression levels of signature genes were validated using an independent external validation cohort. Two genes (CHAF1A, RMI1) were identified to establish the prognostic signature and patients ware stratified into high- and low-risk groups. Patients in high-risk group presented significant shorter survival time than patients in the low-risk group in both cohorts, which were verified by the ROC curves. Multivariate analysis showed that the prognostic signature was an independent predictor for patients with GC after adjustment for other known clinical parameters. A nomogram incorporating the signature and known clinical factors yielded better performance and net benefits in calibration plot and decision curve analyses. Further, the logistic regression classifier based on the two genes presented an excellent diagnostic power in differentiating early HCC and normal tissues with AUCs higher than 0.9. Moreover, Gene Set Enrichment Analysis revealed that diverse cancer-related pathways significantly clustered in the high-risk and low-risk groups. Immune cell infiltration analysis revealed that CHAF1A and RMI1 were correlated with several types of immune cell subtypes. A prognostic signature using CHAF1A and RMI1 was developed that effectively predicted different OS rates among patients with GC. This risk model provides new clinical evidence for the diagnostic accuracy and survival prediction of GC.


2021 ◽  
Author(s):  
Jian Xu ◽  
Xiaomin Shen ◽  
Bo Zhang ◽  
Rui Su ◽  
Mingxuan Cui ◽  
...  

Purpose: To develop a LRP1B gene mutation based prognostic model for hepatocellular carcinoma (HCC) patients risk prediction. Methods: The LRP1B gene mutation rate was calculated from HCC patient samples. Meanwhile, differentially expressed genes according to LRP1B mutant were screened out for prognostic model establishment. Based on this innovative model, HCC patients were categoried into high and low-risk group. The immune status including immune cell infiltration ratio and checkpoints have been explored in two groups. The functions of LRP1B and risk factors in the model were verified using both in vivo and in vitro experiments. Results: It could be demonstrated that LRP1B was a potential negative predictor for HCC patients prognosis with high mutation frequency. The functions of LRP1B was verified with ELISA assay and Quantitative Real-time PCR method based on clinical recruited HCC participants. 11 genes displayed significant differences according to LRP1B status, which could better predict HCC patient prognosis. The functions of these genes were examined using HCC cell line HCCLM3, suggesting they played a pivotal role in determining HCC cell proliferation and apoptosis. From the immune cell infiltration ratio analysis, there was a significant difference in the infiltration degree of 7 types of immune cells and 2 immune checkpoints between high and low-risk HCC patients. Conclusion: This study hypothesized a potential prognostic biomarker and developed a novel LRP1B mutation-associated prognostic model for hepatocellular carcinoma, which provided a systematic reference for future understanding of clinical research.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Qian Yan ◽  
Wenjiang Zheng ◽  
Boqing Wang ◽  
Baoqian Ye ◽  
Huiyan Luo ◽  
...  

Abstract Background Hepatocellular carcinoma (HCC) is a disease with a high incidence and a poor prognosis. Growing amounts of evidence have shown that the immune system plays a critical role in the biological processes of HCC such as progression, recurrence, and metastasis, and some have discussed using it as a weapon against a variety of cancers. However, the impact of immune-related genes (IRGs) on the prognosis of HCC remains unclear. Methods Based on The Cancer Gene Atlas (TCGA) and Immunology Database and Analysis Portal (ImmPort) datasets, we integrated the ribonucleic acid (RNA) sequencing profiles of 424 HCC patients with IRGs to calculate immune-related differentially expressed genes (DEGs). Survival analysis was used to establish a prognostic model of survival- and immune-related DEGs. Based on genomic and clinicopathological data, we constructed a nomogram to predict the prognosis of HCC patients. Gene set enrichment analysis further clarified the signalling pathways of the high-risk and low-risk groups constructed based on the IRGs in HCC. Next, we evaluated the correlation between the risk score and the infiltration of immune cells, and finally, we validated the prognostic performance of this model in the GSE14520 dataset. Results A total of 100 immune-related DEGs were significantly associated with the clinical outcomes of patients with HCC. We performed univariate and multivariate least absolute shrinkage and selection operator (Lasso) regression analyses on these genes to construct a prognostic model of seven IRGs (Fatty Acid Binding Protein 6 (FABP6), Microtubule-Associated Protein Tau (MAPT), Baculoviral IAP Repeat Containing 5 (BIRC5), Plexin-A1 (PLXNA1), Secreted Phosphoprotein 1 (SPP1), Stanniocalcin 2 (STC2) and Chondroitin Sulfate Proteoglycan 5 (CSPG5)), which showed better prognostic performance than the tumour/node/metastasis (TNM) staging system. Moreover, we constructed a regulatory network related to transcription factors (TFs) that further unravelled the regulatory mechanisms of these genes. According to the median value of the risk score, the entire TCGA cohort was divided into high-risk and low-risk groups, and the low-risk group had a better overall survival (OS) rate. To predict the OS rate of HCC, we established a gene- and clinical factor-related nomogram. The receiver operating characteristic (ROC) curve, concordance index (C-index) and calibration curve showed that this model had moderate accuracy. The correlation analysis between the risk score and the infiltration of six common types of immune cells showed that the model could reflect the state of the immune microenvironment in HCC tumours. Conclusion Our IRG prognostic model was shown to have value in the monitoring, treatment, and prognostic assessment of HCC patients and could be used as a survival prediction tool in the near future.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12304
Author(s):  
Zhengyuan Wu ◽  
Leilei Chen ◽  
Chaojie Jin ◽  
Jing Xu ◽  
Xingqun Zhang ◽  
...  

Background Cutaneous melanoma (CM) is a life-threatening destructive malignancy. Pyroptosis significantly correlates with programmed tumor cell death and its microenvironment through active host-tumor crosstalk. However, the prognostic value of pyroptosis-associated gene signatures in CM remains unclear. Methods Gene profiles and clinical data of patients with CM were downloaded from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes associated with pyroptosis and overall survival (OS). We constructed a prognostic gene signature using LASSO analysis, then applied immune cell infiltration scores and Kaplan-Meier, Cox, and pathway enrichment analyses to determine the roles of the gene signature in CM. A validation cohort was collected from the Gene Expression Omnibus (GEO) database. Results Four pyroptosis-associated genes were identified and incorporated into a prognostic gene signature. Integrated bioinformatics findings showed that the signature correlated with patient survival and was associated with tumor growth and metastasis. The results of Gene Set Enrichment Analysis of a risk signature indicated that several enriched pathways are associated with cancer and immunity. The risk signature for immune status significantly correlated with tumor stem cells, the immune microenvironment, immune cell infiltration and immune subtypes. The expression of four pyroptosis genes significantly correlated with the OS of patients with CM and was related to the sensitivity of cancer cells to several antitumor drugs. A signature comprising four genes associated with pyroptosis offers a novel approach to the prognosis and survival of patients with CM and will facilitate the development of individualized therapy.


2020 ◽  
Author(s):  
Jianfeng Zheng ◽  
Jinyi Tong ◽  
Benben Cao ◽  
Xia Zhang ◽  
Zheng Niu

Abstract Background: Cervical cancer (CC) is a common gynecological malignancy for which prognostic and therapeutic biomarkers are urgently needed. The signature based on immune‐related lncRNAs(IRLs) of CC has never been reported. This study aimed to establish an IRL signature for patients with CC.Methods: The RNA-seq dataset was obtained from the TCGA, GEO, and GTEx database. The immune scores(IS)based on single-sample gene set enrichment analysis (ssGSEA) were calculated to identify the IRLs, which were then analyzed using univariate Cox regression analysis to identify significant prognostic IRLs. A risk score model was established to divide patients into low-risk and high-risk groups based on the median risk score of these IRLs. This was then validated by splitting TCGA dataset(n=304) into a training-set(n=152) and a valid-set(n=152). The fraction of 22 immune cell subpopulations was evaluated in each sample to identify the differences between low-risk and high-risk groups. Additionally, a ceRNA network associated with the IRLs was constructed.Results: A cohort of 326 CC and 21 normal tissue samples with corresponding clinical information was included in this study. Twenty-eight IRLs were collected according to the Pearson’s correlation analysis between immune score and lncRNA expression (P < 0.01). Four IRLs (BZRAP1-AS1, EMX2OS, ZNF667-AS1, and CTC-429P9.1) with the most significant prognostic values (P < 0.05) were identified which demonstrated an ability to stratify patients into low-risk and high-risk groups by developing a risk score model. It was observed that patients in the low‐risk group showed longer overall survival (OS) than those in the high‐risk group in the training-set, valid-set, and total-set. The area under the curve (AUC) of the receiver operating characteristic curve (ROC curve) for the four IRLs signature in predicting the one-, two-, and three-year survival rates were larger than 0.65. In addition, the low-risk and high-risk groups displayed different immune statuses in GSEA. These IRLs were also significantly correlated with immune cell infiltration. Conclusions: Our results showed that the IRL signature had a prognostic value for CC. Meanwhile, the specific mechanisms of the four-IRLs in the development of CC were ascertained preliminarily.


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