scholarly journals A 5-Gene Signature Is Closely Related to Tumor Immune Microenvironment and Predicts the Prognosis of Patients with Non-Small Cell Lung Cancer

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Jia Li ◽  
Huiyu Wang ◽  
Zhaoyan Li ◽  
Chenyue Zhang ◽  
Chenxing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Risk Group ◽  
Gene Signature ◽  
High Risk Group ◽  
Low Risk ◽  
Egfr Mutations ◽  
Kaplan Meier ◽  
Tumor Immune Microenvironment ◽  
Nsclc Patients

Purpose. Establishing prognostic gene signature to predict clinical outcomes and guide individualized adjuvant therapy is necessary. Here, we aim to establish the prognostic efficacy of a gene signature that is closely related to tumor immune microenvironment (TIME). Methods and Results. There are 13,035 gene expression profiles from 130 tumor samples of the non-small cell lung cancer (NSCLC) in the data set GSE103584. A 5-gene signature was identified by using univariate survival analysis and Least Absolute Shrinkage and Selection Operator (LASSO) to build risk models. Then, we used the CIBERSORT method to quantify the relative levels of different immune cell types in complex gene expression mixtures. It was found that the ratio of dendritic cells (DCs) activated and mast cells (MCs) resting in the low-risk group was higher than that in the high-risk group, and the difference was statistically significant (P<0.001 and P=0.03). Pathway enrichment results which were obtained by performing Gene Set Variation Analysis (GSVA) showed that the high-risk group identified by the 5-gene signature had metastatic-related gene expression, resulting in lower survival rates. Kaplan–Meier survival results showed that patients of the high-risk group had shorter disease-free survival (DFS) and overall survival (OS) than those of the low-risk group in the training set (P=0.0012 and P<0.001). The sensitivity and specificity of the gene signature were better and more sensitive to prognosis than TNM (tumor/lymph node/metastasis) staging, in spite of being not statistically significant (P=0.154). Furthermore, Kaplan–Meier survival showed that patients of the high-risk group had shorter OS and PFS than those of the low-risk group (P=0.0035, P<0.001, and P<0.001) in the validating set (GSE31210, GSE41271, and TCGA). At last, univariate and multivariate Cox proportional hazard regression analyses were used to evaluate independent prognostic factors associated with survival, and the gene signature, lymphovascular invasion, pleural invasion, chemotherapy, and radiation were employed as covariates. The 5-gene signature was identified as an independent predictor of patient survival in the presence of clinical parameters in univariate and multivariate analyses (P<0.001) (hazard ratio (HR): 3.93, 95% confidence interval CI (2.17–7.1), P=0.001, (HR) 5.18, 95% CI (2.6995–9.945), P<0.001), respectively. Our 5-gene signature was also related to EGFR mutations (P=0.0111), and EGFR mutations were mainly enriched in low-risk group, indicating that EGFR mutations affect the survival rate of patients. Conclusion. The 5-gene signature is a powerful and independent predictor that could predict the prognosis of NSCLC patients. In addition, our gene signature is correlated with TIME parameters, such as DCs activated and MCs resting. Our findings suggest that the 5-gene signature closely related to TIME could predict the prognosis of NSCLC patients and provide some reference for immunotherapy.

scholarly journals A Novel Prognostic Signature Based on Cell-In-Cell-Related Genes for Predicting Survival and Tumor Microenvironment in Pancreatic Cancer

2021 ◽  
Author(s):  
Jianlu Song ◽  
Rexiati Ruze ◽  
Yuan Chen ◽  
Ruiyuan Xu ◽  
Xinpeng Yin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
High Risk ◽  
Risk Group ◽  
Gene Signature ◽  
High Risk Group ◽  
Cancer Genome ◽  
Low Risk ◽  
Prognostic Gene ◽  
Prognostic Gene Signature

Abstract Background: Pancreatic cancer (PC) is a highly malignant tumor featured with high intra-tumoral heterogeneity and poor prognosis. Cell-in-cell (CIC) structures have been reported in multiple tumor types, and their presence is thought to promote clonal selection and tumor evolution. Here, we aimed to establish a CIC-related gene signature for predicting the prognosis and evaluating immune microenvironment in PC. Methods: In this study, the gene expression data, as well as corresponding clinicopathological data of PC and normal pancreatic tissues were collected from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) databases. Differential gene expression analysis, random forest screening, least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analysis were performed on 101 CIC-related genes to construct a prognostic gene signature. The effectiveness and robustness of the prognostic gene signature were evaluated by receiver operating characteristic (ROC) curves, Kaplan-Meier survival analysis and establishing the nomogram model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to annotate the biological functions of the differentially expressed genes (DEGs). Quantitative real-time PCR (qRT-PCR), western blotting and immunohistochemistry (IHC) staining were validated the core gene expression in both mRNA and protein levels. Results: A 4-gene signature was constructed to stratify patients into the low-risk and high-risk groups with distinct survival outcomes, somatic mutation profiles and immune features. The high-risk group had poorer prognosis than did the low-risk group. This signature was found to be an independent prognostic factor for PC patients with favorable predictive efficiency. Functional enrichment analyses showed that numerous terms and pathways associated with invasion and metastasis were enriched in the high-risk group. Moreover, the high-risk group had a higher tumor mutation burdens and lower immune cell infiltrations. KRT7, as the most important risk gene, was significantly associated with the worse prognosis of PC. CIC formation assay performing in PC cell lines indicated that KRT7 expression was correlated with CIC frequency. Conclusions: The signature based on four CIC-related genes could be applicable for predicting the prognosis of PC, and targeting CIC processes may be a potential therapeutic option. Further studies are needed to reveal the underlying molecular mechanisms and biological implications of CIC in PC progression.

scholarly journals Identifying and Validating an Acidosis-Related Signature Associated with Prognosis and Tumor Immune Infiltration Characteristics in Pancreatic Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-19
Author(s):  
Pingfei Tang ◽  
Weiming Qu ◽  
Dajun Wu ◽  
Shihua Chen ◽  
Minji Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Pancreatic Carcinoma ◽  
Cox Regression ◽  
Risk Group ◽  
Immune Dysfunction ◽  
Low Risk ◽  
Excellent Performance ◽  
Kaplan Meier ◽  
Prognostic Prediction

Background. Acidosis in the tumor microenvironment (TME) is involved in tumor immune dysfunction and tumor progression. We attempted to develop an acidosis-related index (ARI) signature to improve the prognostic prediction of pancreatic carcinoma (PC). Methods. Differential gene expression analyses of two public datasets (GSE152345 and GSE62452) from the Gene Expression Omnibus database were performed to identify the acidosis-related genes. The Cancer Genome Atlas–pancreatic carcinoma (TCGA-PAAD) cohort in the TCGA database was set as the discovery dataset. Univariate Cox regression and the Kaplan–Meier method were applied to screen for prognostic genes. The least absolute shrinkage and selection operator (LASSO) Cox regression was used to establish the optimal model. The tumor immune infiltrating pattern was characterized by the single-sample gene set enrichment analysis (ssGSEA) method, and the prediction of immunotherapy responsiveness was conducted using the tumor immune dysfunction and exclusion (TIDE) algorithm. Results. We identified 133 acidosis-related genes, of which 37 were identified as prognostic genes by univariate Cox analysis in combination with the Kaplan–Meier method ( p values of both methods < 0.05). An acidosis-related signature involving seven genes (ARNTL2, DKK1, CEP55, CTSV, MYEOV, DSG2, and GBP2) was developed in TCGA-PAAD and further validated in GSE62452. Patients in the acidosis-related high-risk group consistently showed poorer survival outcomes than those in the low-risk group. The 5-year AUCs (areas under the curve) for survival prediction were 0.738 for TCGA-PAAD and 0.889 for GSE62452, suggesting excellent performance. The low-risk group in TCGA-PAAD showed a higher abundance of CD8+ T cells and activated natural killer cells and was predicted to possess an elevated proportion of immunotherapeutic responders compared with the high-risk counterpart. Conclusions. We developed a reliable acidosis-related signature that showed excellent performance in prognostic prediction and correlated with tumor immune infiltration, providing a new direction for prognostic evaluation and immunotherapy management in PC.

scholarly journals Ferroptosis-related gene signature predicts the prognosis of papillary thyroid carcinoma

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jinyuan Shi ◽  
Pu Wu ◽  
Lei Sheng ◽  
Wei Sun ◽  
Hao Zhang
Keyword(s):  
High Risk ◽  
Immune Cells ◽  
Risk Group ◽  
Gene Signature ◽  
High Risk Group ◽  
Low Risk ◽  
Lasso Regression ◽  
Papillary Thyroid ◽  
Related Gene ◽  
Normal Thyroid

Abstract Background Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer (TC), accounting for more than 80% of all cases. Ferroptosis is a novel iron-dependent and Reactive oxygen species (ROS) reliant type of cell death which is distinct from the apoptosis, necroptosis and pyroptosis. Considerable studies have demonstrated that ferroptosis is involved in the biological process of various cancers. However, the role of ferroptosis in PTC remains unclear. This study aims at exploring the expression of ferroptosis-related genes (FRG) and their prognostic values in PTC. Methods A ferroptosis-related gene signature was constructed using lasso regression analysis through the PTC datasets of the Cancer Genome Atlas (TCGA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the bioinformatics functions of significantly different genes (SDG) of ferroptosis. Additionally, the correlations of ferroptosis and immune cells were assessed through the single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT database. Finally, SDG were test in clinical PTC specimens and normal thyroid tissues. Results LASSO regression model was utilized to establish a novel FRG signature with 10 genes (ANGPTL7, CDKN2A, DPP4, DRD4, ISCU, PGD, SRXN1, TF, TFRC, TXNRD1) to predicts the prognosis of PTC, and the patients were separated into high-risk and low-risk groups by the risk score. The high-risk group had poorer survival than the low-risk group (p < 0.001). Receiver operating characteristic (ROC) curve analysis confirmed the signature's predictive capacity. Multivariate regression analysis identified the prognostic signature-based risk score was an independent prognostic indicator for PTC. The functional roles of the DEGs in the TGCA PTC cohort were explored using GO enrichment and KEGG pathway analyses. Immune related analysis demonstrated that the most types of immune cells and immunological function in the high-risk group were significant different with those in the low-risk group. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) verified the SDG have differences in expression between tumor tissue and normal thyroid tissue. In addition, cell experiments were conducted to observe the changes in cell morphology and expression of signature’s genes with the influence of ferroptosis induced by sorafenib. Conclusions We identified differently expressed FRG that may involve in PTC. A ferroptosis-related gene signature has significant values in predicting the patients’ prognoses and targeting ferroptosis may be an alternative for PTC’s therapy.

scholarly journals A nomogram with lymph node status predicts survival and the benefit of postoperative  adjuvant therapy in IIIA-N2 Non-small cell lung cancer patients after surgery

2020 ◽  
Author(s):  
Ye Chen ◽  
Lei Dong ◽  
Minjing Li ◽  
Fei He ◽  
ChenHui Qiu ◽  
...  
Keyword(s):  
High Risk ◽  
Lymph Nodes ◽  
Survival Benefit ◽  
Risk Group ◽  
High Risk Group ◽  
Small Cell ◽  
Low Risk ◽  
Small Cell Lung ◽  
Moderate Risk ◽  
Nsclc Patients

Abstract Objective: This study aimed at establishing a novel nomogram predicting overall survival and investigating the survival benefit of various postoperative adjuvant treatments (POAT) in IIIA-N2 Non-small cell lung cancer (NSCLC) patients after surgery.Methods: Data of IIIA-N2 NSCLC patients between 2004 and 2016 were collected from the Surveillance, Epidemiology, and End Results (SEER). Patients were excluded if the information regarding follow-up time and clinicopathological features were incomplete. Through Univariate and multivariate analyses, independent prognostic factors were identified and integrated into the construction of nomogram. The survival benefit of POAT was evaluated in model-defined low-risk, intermediate-risk, and high-risk subgroups, respectively.Results: In total, 4389 patients were finally included for analysis. Patients’ age, sex, T stage, differentiation grade, examined lymph nodes number (ELN), metastatic lymph nodes number (MLN), and metastatic lymph nodes ratio (LNR) were identified as independent prognostic factors and were integrated into the construction of nomogram. The C-index and calibration curves indicated that the predictive performance of the nomogram was satisfactory. Patients were then categorized into three prognostic groups with the increasing risk of all-cause of death. The prognosis of patients receiving POAT (POCT or PORT plus POCT) and patients receiving surgery alone was comparable in low-risk group, while POCT could significantly prolong survival for IIIA-N2 NSCLC patients after surgery in moderate-risk and high-risk groups. Only patients in high-risk group could benefit from the combination of postoperative radiotherapy (PORT) and postoperative chemotherapy (POCT).Conclusion: In this large-cohort retrospective study, A survival-predicting nomogram and risk stratification model were established to estimate prognosis in IIIA-N2 NSCLC patients. Surgery alone was recommended as the first choice of treatment to patients in low-risk group. POCT was recommended for patients in moderate-risk group, and the combination of PORT and POCT was recommended for patients in high-risk group. This study may provide additional integration, introspection, and improvement for therapeutic decision-making.

scholarly journals Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wei Hu ◽  
Mingyue Li ◽  
Qi Zhang ◽  
Chuan Liu ◽  
Xinmei Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
High Risk ◽  
Risk Score ◽  
Copy Number ◽  
Risk Group ◽  
Gene Signature ◽  
Low Risk ◽  
Breast Cancer Dataset ◽  
Cox Analysis

Abstract Background Copy number variation (CNVs) is a key factor in breast cancer development. This study determined prognostic molecular characteristics to predict breast cancer through performing a comprehensive analysis of copy number and gene expression data. Methods Breast cancer expression profiles, CNV and complete information from The Cancer Genome Atlas (TCGA) dataset were collected. Gene Expression Omnibus (GEO) chip data sets (GSE20685 and GSE31448) containing breast cancer samples were used as external validation sets. Univariate survival COX analysis, multivariate survival COX analysis, least absolute shrinkage and selection operator (LASSO), Chi square, Kaplan-Meier (KM) survival curve and receiver operating characteristic (ROC) analysis were applied to build a gene signature model and assess its performance. Results A total of 649 CNV related-differentially expressed gene obtained from TCGA-breast cancer dataset were related to several cancer pathways and functions. A prognostic gene sets with 9 genes were developed to stratify patients into high-risk and low-risk groups, and its prognostic performance was verified in two independent patient cohorts (n = 327, 246). The result uncovered that 9-gene signature could independently predict breast cancer prognosis. Lower mutation of PIK3CA and higher mutation of TP53 and CDH1 were found in samples with high-risk score compared with samples with low-risk score. Patients in the high-risk group showed higher immune score, malignant clinical features than those in the low-risk group. The 9-gene signature developed in this study achieved a higher AUC. Conclusion The current research established a 5-CNV gene signature to evaluate prognosis of breast cancer patients, which may innovate clinical application of prognostic assessment.

scholarly journals A Four-Gene-Based Prognostic Model Predicts Overall Survival in Patients With Cutaneous Melanoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiaoxia Tong ◽  
Xiaofei Qu ◽  
Mengyun Wang
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Risk Score ◽  
Cutaneous Melanoma ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Low Risk ◽  
Rank Test ◽  
Score Model

BackgroundCutaneous melanoma (CM) is one of the most aggressive cancers with highly metastatic ability. To make things worse, there are limited effective therapies to treat advanced CM. Our study aimed to investigate new biomarkers for CM prognosis and establish a novel risk score system in CM.MethodsGene expression data of CM from Gene Expression Omnibus (GEO) datasets were downloaded and analyzed to identify differentially expressed genes (DEGs). The overlapped DEGs were then verified for prognosis analysis by univariate and multivariate COX regression in The Cancer Genome Atlas (TCGA) datasets. Based on the gene signature of multiple survival associated DEGs, a risk score model was established, and its prognostic and predictive role was estimated through Kaplan-Meier (K-M) analysis and log-rank test. Furthermore, the correlations between prognosis related genes expression and immune infiltrates were analyzed via Tumor Immune Estimation Resource (TIMER) site.ResultsA total of 103 DEGs were obtained based on GEO cohorts, and four genes were verified in TCGA datasets. Subsequently, four genes (ADAMDEC1, GNLY, HSPA13, and TRIM29) model was developed by univariate and multivariate Cox regression analyses. The K-M plots showed that the high-risk group was associated with shortened survival than that in the low-risk group (P &lt; 0.0001). Multivariate analysis suggested that the model was an independent prognostic factor (high-risk vs. low-risk, HR= 2.06, P &lt; 0.001). Meanwhile, the high-risk group was prone to have larger breslow depth (P&lt; 0.001) and ulceration (P&lt; 0.001).ConclusionsThe four-gene risk score model functions well in predicting the prognosis and treatment response in CM and will be useful for guiding therapeutic strategies for CM patients. Additional clinical trials are needed to verify our findings.

Identification of Novel Tumor Microenvironment-Related Long Non-coding RNAs to Predict the Prognosis for Hepatocellular Carcinoma

2021 ◽  
Author(s):  
Shenglan Huang ◽  
Jian Zhang ◽  
Dan Li ◽  
Xiaolan Lai ◽  
Lingling Zhuang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
High Risk ◽  
Tumor Microenvironment ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Low Risk ◽  
Clinicopathological Parameters ◽  
Kaplan Meier ◽  
The Impact

Abstract Introduction: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with poor prognosis. Tumor microenvironment (TME) plays a vital role in the tumor progression of HCC. Thus, we aimed to analyze the association of TME with HCC prognosis, and construct an TME-related lncRNAs signature for predicting the prognosis of HCC patients.Methods: We firstly assessed the stromal/immune /Estimate scores within the HCC microenvironment using the ESTIMATE algorithm based on TCGA database, and its associations with survival and clinicopathological parameters were also analyzed. Then, different expression lncRNAs were filtered out according to immune/stromal scores. Cox regression was performed to built an TME-related lncRNAs risk signature. Kaplan–Meier analysis was carried out to explored the prognostic values of the risk signature. Furthermore, we explored the biological functions and immune microenvironment feathers in high- and low risk groups. Lastly, we probed the association of the risk signature with the treatment responses to immune checkpoint inhibitors (ICIs) in HCC by comparing the immunophenoscore (IPS).Results: Stromal/immune /Estimate scores of HCC patients were obtained based on the ESTIMATE algorithm. The Kaplan-Meier curve analysis showed the high stromal/immune/ Estimate scores were significantly associated with better prognosis of the HCC patients. Then, six TME-related lncRNAs were screened for constructing the prognosis model. Kaplan-Meier survival curves suggested that HCC patients in high-risk group had worse prognosis than those with low-risk. ROC curve and Cox regression analyses demonstrated the signature could predict HCC survival exactly and independently. Function enrichment analysis revealed that some tumor- and immune-related pathways associated with HCC tumorigenesis and progression might be activated in high-risk group. We also discovered that some immune cells, which were beneficial to enhance immune responses towards cancer, were remarkably upregulated in low-risk group. Besides, there was closely correlation of immune checkmate inhibitors (ICIs) with the risk signature and the signature can be used to predict treatment response of ICIs.Conclusions: We analyzed the impact of the tumor microenvironment scores on the prognosis of patients with HCC. A novel TME-related prognostic risk signature was established, which may improve prognostic predictive accuracy and guide individualized immunotherapy for HCC patients.

The Combination of SKY92 and ISS Provides a Powerful Tool to Identify Both High Risk and Low Risk Multiple Myeloma Cases, Validation in Two Independent Cohorts

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2970-2970 ◽  
Author(s):  
Martin van Vliet ◽  
Joske Ubels ◽  
Leonie de Best ◽  
Erik van Beers ◽  
Pieter Sonneveld
Keyword(s):  
Overall Survival ◽  
High Risk ◽  
Research Funding ◽  
Prognostic Markers ◽  
Risk Group ◽  
Risk Groups ◽  
High Risk Group ◽  
Low Risk ◽  
Kaplan Meier ◽  
Standard Risk

Abstract Introduction Multiple Myeloma (MM) is a heterogeneous disease with a strong need for robust markers for prognosis. Frequently occurring chromosomal abnormalities, such as t(4;14), gain(1q), and del(17p) etc. have some prognostic power, but lack robustness across different cohorts. Alternatively, gene expression profiling (GEP) studies have developed specific high risk signatures such as the SKY92 (EMC92, Kuiper et al. Leukemia 2012), which has shown to be a robust prognostic factor across five different clinical datasets. Moreover, studies comparing prognostic markers have indicated that the SKY92 signature outperforms all other markers for identifying high risk patients, both in single and multivariate analyses. Similarly, when assessing the prognostic value of combinations of various prognostic markers, the SKY92 combined with ISS was the top performer, and also enables detection of a low risk group (Kuiper et al. ASH 2014). Here, we present a further validation of the low and high risk groups identified by the SKY92 signature in combination with ISS on two additional cohorts of patients with diverse treatment backgrounds, containing newly diagnosed, previously treated, and relapsed/refractory MM patients. Materials and Methods The SKY92 signature was applied to two independent datasets. Firstly, the dataset from the Total Therapy 6 (TT6) trial, which is a phase 2 trial for symptomatic MM patients who have received 1 or more prior lines of treatment. The TT6 treatment regime consists of VTD-PACE induction, double transplant with Melphalan + VRD-PACE, followed by alternating VRD/VMD maintenance. Affymetrix HG-U133 Plus 2.0 chips were performed at baseline for n=55 patients, and OS was made available previously (Gene Expression Omnibus identifier: GSE57317). However, ISS was not available for this dataset. Secondly, a dataset of patients enrolled at two hospitals in the Czech Republic, and one in Slovakia (Kryukov et al. Leuk&Lymph 2013). Patients of all ages, and from first line up to seventh line of treatment were included (treatments incl Bort, Len, Dex). For n=73 patients Affymetrix Human Gene ST 1.0 array, OS (n=66), and ISS (n=58) was made available previously (ArrayExpress accession number: E-MTAB-1038). Both datasets were processed from .CEL files by MAS5 (TT6), and RMA (Czech), followed by mean variance normalization per probeset across the patients. The SKY92 was applied as previously described (Kuiper et al. Leukemia 2012), and identifies a High Risk and Standard Risk group. In conjunction with ISS, the SKY92 Standard Risk group is then further stratified into low and intermediate risk groups (Kuiper et al. ASH 2014). Kaplan-Meier plots were created, and the Cox proportional hazards model was used to calculate Hazard Ratios (HR), and associated 1-sided p-values that assess whether the SKY92 High Risk group has worse survival than SKY92 Standard Risk group (i.e. HR>1). Results Figure 1 shows the Kaplan Meier plots of the SKY92 High Risk and Standard Risk groups on the TT6 and Czech cohorts. On the TT6 dataset, the SKY92 signature identifies 11 out of 55 patients (20%) as High Risk. In both datasets, the SKY92 High Risk group has significantly worse overall survival, HR=10.3, p=7.4 * 10-6 (TT6), and HR=2.6, p=2.2 * 10-2 (Czech). In addition, the combination of SKY92 with ISS on the Czech dataset identifies a low risk group of 14 out of 61 patients (23%), with a five year overall survival estimate of 100% versus 28.7% in the SKY92 High Risk group (HR=inf). Robustness of the SKY92 signature is further demonstrated by the fact that it validates on both datasets, despite different microarray platforms being used. Conclusions The SKY92 high risk signature has been successfully validated on two independent datasets generated using different microarray platforms. In addition, on the Czech data, the low risk group (SKY92 Standard Risk combined with ISS 1) has been successfully validated. Together, this signifies the robust nature of the SKY92 signature for high and low risk prediction, across treatments, and with applicability in newly diagnosed, treated, and relapsed/refractory MM patients. Figure 1. Kaplan-Meier plots showing a significantly poorer overall survival in patients identified as SKY92 High Risk (red curves), relative to SKY92 Standard Risk, on both the TT6 (left), and Czech (middle) datasets, as well as a low risk group by SKY92 & ISS1 on the Czech dataset (green curve, right). Figure 1. Kaplan-Meier plots showing a significantly poorer overall survival in patients identified as SKY92 High Risk (red curves), relative to SKY92 Standard Risk, on both the TT6 (left), and Czech (middle) datasets, as well as a low risk group by SKY92 & ISS1 on the Czech dataset (green curve, right). Disclosures van Vliet: SkylineDx: Employment. Ubels:SkylineDx: Employment. de Best:SkylineDx: Employment. van Beers:SkylineDx: Employment. Sonneveld:Celgene: Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Karyopharm: Research Funding; SkylineDx: Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Research Funding.

scholarly journals Prognostic utility of neutrophil-to-lymphocyte ratio in patients with metastatic colorectal cancer treated using different modalities

2020 ◽  
Vol 27 (5) ◽  
Author(s):  
G. Nogueira-Costa ◽  
I. Fernandes ◽  
R. Gameiro ◽  
J. Gramaça ◽  
A.T. Xavier ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
High Risk ◽  
Metastatic Colorectal Cancer ◽  
Real World ◽  
Cox Regression ◽  
Risk Group ◽  
High Risk Group ◽  
Low Risk ◽  
First Line ◽  
Kaplan Meier

Introduction Inflammation is a critical component in carcinogenesis. The neutrophil-to-lymphocyte ratio (nlr) has been retrospectively studied as a biomarker of prognosis in metastatic colorectal cancer (mcrc). Compared with a low nlr, a high nlr is associated with worse prognosis. In the present study, we compared real-world survival for patients with mcrc based on their nlr group, and we assessed the utility of the nlr in determining first-line chemo­therapy and metastasectomy benefit. Methods In this retrospective and descriptive analysis of patients with mcrc undergoing first-line chemotherapy in a single centre, the last systemic absolute neutrophil and lymphocyte count before treatment was used for the nlr. A receiver operating characteristic curve was used to estimate the nlr cut-off value, dividing the patients into low and high nlr groups. Median overall survival (mos) was compared using Kaplan–Meier curves and the log-rank test. A multivariate analysis was performed using a Cox regression model. Results The 102 analyzed patients had a median follow-up of 15 months. Regardless of systemic therapy, approx­imately 20% of patients underwent metastasectomy. The nlr cut-off was established at 2.35, placing 45 patients in the low-risk group (nlr < 2.35) and 57 in the high-risk group (nlr ≥ 2.35). The Kaplan–Meier analysis showed a mos of 39.1 months in the low-risk group and 14.4 months in the high-risk group (p < 0.001). Multivariate Cox regression on the nlr estimated a hazard ratio of 3.08 (p = 0.01). Survival analysis in each risk subgroup, considering the history of metastasectomy, was also performed. In the low-risk group, mos was longer for patients undergoing metastasectomy than for those not undergoing the procedure (95.2 months vs. 22.6 months, p = 0.05). In the high-risk group, mos was not statistically different for patients undergoing or not undergoing metastasectomy (24.3 months vs. 12.7 months, p = 0.08). Conclusions Our real-world data analysis of nlr in patients with mcrc confirmed that this biomarker is useful in predicting survival. It also suggests that nlr is an effective tool to choose first-line treatment and to predict the benefit of metastasectomy.

scholarly journals A Hypoxia Signature for Predicting Prognosis and Tumor Immune Microenvironment in Adrenocortical Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Xi Chen ◽  
Lijun Yan ◽  
Yu Lu ◽  
Feng Jiang ◽  
Ni Zeng ◽  
...  
Keyword(s):  
Regression Analysis ◽  
High Risk ◽  
Adrenocortical Carcinoma ◽  
Risk Group ◽  
Gene Signature ◽  
High Risk Group ◽  
Immune Microenvironment ◽  
Gene Sets ◽  
Tumor Immune Microenvironment ◽  
Hypoxia Signature

Adrenocortical carcinoma (ACC) is a rare malignancy with dismal prognosis. Hypoxia is one of characteristics of cancer leading to tumor progression. For ACC, however, no reliable prognostic signature on the basis of hypoxia genes has been built. Our study aimed to develop a hypoxia-associated gene signature in ACC. Data of ACC patients were obtained from TCGA and GEO databases. The genes included in hypoxia risk signature were identified using the Cox regression analysis as well as LASSO regression analysis. GSEA was applied to discover the enriched gene sets. To detect a possible connection between the gene signature and immune cells, the CIBERSORT technique was applied. In ACC, the hypoxia signature including three genes (CCNA2, COL5A1, and EFNA3) was built to predict prognosis and reflect the immune microenvironment. Patients with high-risk scores tended to have a poor prognosis. According to the multivariate regression analysis, the hypoxia signature could be served as an independent indicator in ACC patients. GSEA demonstrated that gene sets linked to cancer proliferation and cell cycle were differentially enriched in high-risk classes. Additionally, we found that PDL1 and CTLA4 expression were significantly lower in the high-risk group than in the low-risk group, and resting NK cells displayed a significant increase in the high-risk group. In summary, the hypoxia risk signature created in our study might predict prognosis and evaluate the tumor immune microenvironment for ACC.

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