scholarly journals A Innovative Prognostic Symbol Based on Autophagy-Related Long Noncoding RNAs Signature Predicts in Low-Grade Glioma

Author(s):  
Aierpati Maimaiti ◽  
Mirezhati Tuerhong ◽  
Yongxin Wang ◽  
Maimaitili Aisha ◽  
Lei Jiang ◽  
...  

Abstract Autophagy is a highly conserved lysosomal degradation process essential in tumorigenesis. However, the involvement of autophagy-related lncRNA in low-grade gliomas (LGG) remains a pending question. Efforts were made to establish an autophagy-related lncRNA signature prognostic in LGG patients, and to explore the behind potential function. We used Univariate Cox, Least Absolute Shrinkage and Selection Operator (Lasso), and Multivariate Cox regression models were designed to establish an autophagy-related lncRNA prognostic signature. Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curve, nomogram, C-index, calibration curve and clinical decision-making curve were adopted to assess the predictive capability of the identified signature.A signature comprising 9 autophagy-related lncRNAs (AL136964.1, ARHGEF26-AS1, PCED1B-AS1, AS104072.1, PRKCQ-AS1, LINC00957, AS125616.1, PSMB8-AS1, and AC087741.1) was identified as a prognostic model. LGG patients were allocated into high- and low-risk cohorts depending on the median model-based Riskscore. The survival analysis showed a 10-year survival rate of 9.3% (95% CI: 1.91-45.3%) in high-risk LGG patients and 48.4% (95% CI: 24.7-95.0%) in low-risk individuals in the training set. While those of patients in the validation set were 13.48% (95% CI: 4.52-40.2%) for high-risk LGG patients and 48.4% (95% CI: 28.04-83.4%) for low-risk LGG patients, respectively. This suggested a relatively low survival in high-risk cases compared to low-risk individuals. In addition, LncRNA signature was independently prognostic and potentially associated with the progression of LGG. Taken together, our constructed 9 autophagy-related lncRNA signature may play a crucial part in the diagnosis and treatment for LGG, which may guide to open up a new avenues for tumor targeted therapy.

2021 ◽  
Vol 09 (03) ◽  
pp. E348-E355
Author(s):  
David L. Diehl ◽  
Harshit S. Khara ◽  
Nasir Akhtar ◽  
Rebecca J. Critchley-Thorne

Abstract Background and study aims The TissueCypher Barrett’s Esophagus Assay is a novel tissue biomarker test, and has been validated to predict progression to high-grade dysplasia (HGD) and esophageal adenocarcinoma (EAC) in patients with Barrett’s esophagus (BE). The aim of this study was to evaluate the impact of TissueCypher on clinical decision-making in the management of BE. Patients and methods TissueCypher was ordered for 60 patients with non-dysplastic (ND, n = 18) BE, indefinite for dysplasia (IND, n = 25), and low-grade dysplasia (LGD, n = 17). TissueCypher reports a risk class (low, intermediate or high) for progression to HGD or EAC within 5 years. The impact of the test results on BE management decisions was assessed. Results Fifty-two of 60 patients were male, mean age 65.2 ± 11.8, and 43 of 60 had long segment BE. TissueCypher results impacted 55.0 % of management decisions. In 21.7 % of patients, the test upstaged the management approach, resulting in endoscopic eradication therapy (EET) or shorter surveillance interval. The test downstaged the management approach in 33.4 % of patients, leading to surveillance rather than EET. In the subset of patients whose management plan was changed, upstaging was associated with a high-risk TissueCypher result, and downstaging was associated with a low-risk result (P < 0.0001). Conclusions TissueCypher was used as an adjunct to support a surveillance-only approach in 33.4 % of patients. Upstaging occurred in 21.7 % of patients, leading to therapeutic intervention or increased surveillance. These results indicate that the TissueCypher test may enable physicians to target EET for TissueCypher high-risk BE patients, while reducing unnecessary procedures in TissueCypher low-risk patients.


2021 ◽  
Vol 2021 ◽  
pp. 1-19
Author(s):  
Pingfei Tang ◽  
Weiming Qu ◽  
Dajun Wu ◽  
Shihua Chen ◽  
Minji Liu ◽  
...  

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.


2020 ◽  
Author(s):  
Wei Ma ◽  
Qing Cao ◽  
Wandong She

Abstract Background: The mechanism of transition from low-grade to high-grade head and neck carcinomas (HNC) still remains unclear. The aim of this study was to explore the genes expression profiles that drive malignancy from low to high-grade HNC, as well as analyze their correlations with the survival.Methods: Gene expressions and clinical data of HNC were downloaded from the Gene Expression Omnibus (GEO) repository. The significantly differential genes (SDGs) between low and high-grade HNC were screened by GEO2R and R software. Bioinformatics functions of SDGs were investigated by the enrichment analyses. Univariate and multivariate cox regressions were performed to identify prognostic SDGs of progression free survival (PFS) and disease specific survival (DSS). ROC curve was established to evaluate the ability to predict the prognosis. Then, the correlations between SDGs and clinical features were evaluated. The genes were experimentally validated by RT-PCR in clinical specimens’ tissues at last.Results: Thirty-five SDGs were identified in 47 low-grade and 30 high-grade HNC samples. Enrichment analysis showed these SDGs were mainly enriched in the DNA repair pathway and the regulation of I−kappaB kinase/NF−kappaB signaling pathway. Cox regression analyses showed that CXCL14, SLC44A1 and UBD were significantly associated with DSS, and PPP2R2C and SLC44A1 were associated with PFS. Patients at a high-risk or low-risk for prognosis were established based on genes signatures. High-risk patients had significantly shorter DSS and PFS than low-risk patients (P=0.033, 0.010 respectively). Multivariate cox regression showed HPV (P=0.033), lymph node status (P=0.032) and residual status (P<0.044) were independent risk factors for PFS. ROC curves showed the risk score had better efficacy to predict survival both for DSS and PFS (AUC=0.858, 0.901 respectively). In addition, we found UBD, PPP2R2C and risk score were significantly associated with HPV status (all P<0.05). The experiment results showed CXCL14 and SLC44A1 were significantly overexpressed in the HNC grade I/II tissues and the UBD were overexpressed in the HNC grade III/IV tissues.Conclusions: Our results suggested that SDGs had different expression profiles between the low-grade and high-grade HNC, and these genes may serve as prognostic biomarker to predict the survival.


2021 ◽  
Author(s):  
Shenglan Huang ◽  
Jian Zhang ◽  
Dan Li ◽  
Xiaolan Lai ◽  
Lingling Zhuang ◽  
...  

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.


1999 ◽  
Vol 84 (1) ◽  
pp. 114-116 ◽  
Author(s):  
DeAnna L. Mori ◽  
Wayne Klein ◽  
Patricia Gallagher

Psychosocial factors are presented which affect clinical decision-making regarding the allocation of renal organs. Patients were rated as being either High Risk or Low Risk transplant candidates High Risk candidates were scored as being significantly different from the Low Risk candidates on many psychosocial variables. Interestingly, significant differences were not found between these two groups on either the MMPI–2 or the Beck Depression Inventory. The validity of using information from these inventories to allocate organs is discussed.


2020 ◽  
Vol 27 (5) ◽  
Author(s):  
G. Nogueira-Costa ◽  
I. Fernandes ◽  
R. Gameiro ◽  
J. Gramaça ◽  
A.T. Xavier ◽  
...  

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.


Author(s):  
Jing Zhu ◽  
Yong Mou ◽  
Shenglan Ye ◽  
Hongling Hu ◽  
Rujuan Wang ◽  
...  

Given the importance of solute carrier (SLC) proteins in maintaining cellular metabolic homeostasis and that their dysregulation contributes to cancer progression, here we constructed a robust SLC family signature for lung adenocarcinoma (LUAD) patient stratification. Transcriptomic profiles and relevant clinical information of LUAD patients were downloaded from the TCGA and GEO databases. SLC family genes differentially expressed between LUAD tissues and adjacent normal tissues were identified using limma in R. Of these, prognosis-related SLC family genes were further screened out and used to construct a novel SLC family-based signature in the training cohort. The accuracy of the prognostic signature was assessed in the testing cohort, the entire cohort, and the external GSE72094 cohort. Correlations between the prognostic signature and the tumor immune microenvironment and immune cell infiltrates were further explored. We found that seventy percent of SLC family genes (279/397) were differentially expressed between LUAC tissues and adjacent normal. Twenty-six genes with p-values &lt; 0.05 in univariate Cox regression analysis and Kaplan-Meier survival analysis were regarded as prognosis-related SLC family genes, six of which were used to construct a prognostic signature for patient classification into high- and low-risk groups. Kaplan-Meier survival analysis in all internal and external cohorts revealed a better overall survival for patients in the low-risk group than those in the high-risk group. Univariate and multivariate Cox regression analyses indicated that the derived risk score was an independent prognostic factor for LUAD patients. Moreover, a nomogram based on the six-gene signature and clinicopathological factors was developed for clinical application. High-risk patients had lower stromal, immune, and ESTIMATE scores and higher tumor purities than those in the low-risk group. The proportions of infiltrating naive CD4 T cells, activated memory CD4 T cells, M0 macrophages, resting dendritic cells, resting mast cells, activated mast cells, and eosinophils were significantly different between the high- and low-risk prognostic groups. In all, the six-gene SLC family signature is of satisfactory accuracy and generalizability for predicting overall survival in patients with LUAD. Furthermore, this prognostics signature is related to tumor immune status and distinct immune cell infiltrates in the tumor microenvironment.


2021 ◽  
Vol 8 ◽  
Author(s):  
Shenglan Huang ◽  
Jian Zhang ◽  
Xiaolan Lai ◽  
Lingling Zhuang ◽  
Jianbing Wu

Introduction: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with poor prognosis. The tumor microenvironment (TME) plays a vital role in HCC progression. Thus, this research was designed to analyze the correlation between the TME and the prognosis of HCC patients and to construct a TME-related long noncoding RNA (lncRNA) signature to determine HCC patients’ prognosis and response to immunotherapy.Methods: We assessed the stromal–immune–estimate scores within the HCC microenvironment using the ESTIMATE (Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data) algorithm based on The Cancer Genome Atlas database, and their associations with survival and clinicopathological parameters were also analyzed. Thereafter, differentially expressed lncRNAs were filtered out according to the immune and stromal scores. Cox regression analysis was performed to build a TME-related lncRNA risk signature. Kaplan–Meier analysis was used to explore the prognostic value of the risk signature. Furthermore, we explored the biological functions and immune microenvironment features in the high- and low-risk groups. Lastly, we probed the association of the risk model with treatment responses to immune checkpoint inhibitors (ICIs) in HCC.Results: The stromal, immune, and estimate scores were obtained utilizing the ESTIMATE algorithm for patients with HCC. Kaplan–Meier analysis showed that high scores were significantly correlated with better prognosis in HCC patients. Six TME-related lncRNAs were screened to construct the prognostic model. The Kaplan–Meier curves suggested that HCC patients with low risk had better prognosis than those with high risk. Receiver operating characteristic (ROC) curve and Cox regression analyses indicated that the risk model could predict HCC survival exactly and independently. Functional enrichment analysis revealed that some tumor- and immune-related pathways were activated in the high-risk group. We also revealed that some immune cells, which were important in enhancing immune responses toward cancer, were significantly increased in the low-risk group. In addition, there was a close correlation between ICIs and the risk signature, which can be used to predict the treatment responses of HCC patients.Conclusion: We analyzed the influence of the stromal, immune, and estimate scores on the prognosis of HCC patients. A novel TME-related lncRNA risk model was established, which could be effectively applied as an independent prognostic biomarker and predictor of ICIs for HCC patients.


2003 ◽  
Vol 13 (2) ◽  
pp. 137-142 ◽  
Author(s):  
Christine L. Shanahan ◽  
Nigel J. Wilson ◽  
Tom L. Gentles ◽  
Jonathan R. Skinner

Aims: To determine the accuracy of data relating to pulmonary vascular resistance data in patients with a bidirectional Glenn anastomosis as calculated using predicted versus measured uptake of oxygen. Methods: We studied retrospectively the data from 33 patients with a bidirectional Glenn anastomosis who underwent cardiac catheterisation prior to surgery to complete the Fontan circulation. Their weight ranged from 5.4 to 51.7 kg, and they were aged up to 12 years. Uptake of oxygen was measured using the Deltatrac II metabolic monitor. From the calculated indexed pulmonary vascular resistance, cases were stratified according to the risk of failure of the subsequent Fontan circulation. The six patients with a resistance of greater than 4 Um2 were deemed at high risk, the six with a resistance from 3 to 4 Um2 at moderate risk, and the 21 patients with a resistance less than 3 Um2 at low risk. Uptake of oxygen was also estimated from the predictive formulas of Lindahl, Lundell et al. and LaFarge and Miettinen. The indexed resistance was similarly calculated using these formulas and a comparable stratification of risk made from this data. Results: The predicted values for uptake of oxygen were consistently higher than those measured, leading to an underestimation of indexed resistance, with mean difference between −0.62 and −1.57 Um2. This difference resulted in misclassification of between five and nine of the 12 patients considered at moderate or high risk as being at low-risk. No other haemodynamic data could reliably separate the subjects deemed at low-risk from those considered to be at high-risk. A transpulmonary gradient of greater than 7 mm of mercury was found to be 100 percent specific for elevated indexed resistance, but only 60 percent sensitive. Conclusions: In patients with bidirectional Glenn anastomoses, all formulas based on predictive uptake of oxygen lead to underestimation of the true indexed pulmonary vascular resistance, to an extent that could significantly influence clinical decision-making. The transpulmonary gradient is not a reliable surrogate for indexed pulmonary vascular resistance.


Author(s):  
Valentin H. Meissner ◽  
Mira Woll ◽  
Donna P. Ankerst ◽  
Stefan Schiele ◽  
Jürgen E. Gschwend ◽  
...  

Abstract Purpose The safety of active surveillance (AS) in favorable intermediate-risk (FIR) prostate cancer (PCa) remains uncertain. To provide guidance on clinical decision-making, we examined long-term and pathological outcomes of low-risk and intermediate-risk PCa patients after radical prostatectomy (RP). Methods The study involved 5693 patients diagnosed between 1994 and 2019 with low-risk, FIR, and unfavorable intermediate-risk (UIR) PCa (stratification according to the AUA guidelines) who underwent RP. Pathological outcomes were compared, and Kaplan–Meier analysis determined biochemical recurrence-free survival (BRFS) and cancer-specific survival (CSS) at 5, 10, 15, and 20 years. Multiple Cox regression was used to simultaneously control for relevant confounders. Results Those at FIR had higher rates of upgrading and upstaging (12.8% vs. 7.2%, p < 0.001; 19.8% vs. 12.0%, p < 0.001) as well as pathological tumor and node stage (≥ pT3a: 18.8% vs. 11.6%, p < 0.001; pN1: 2.7% vs. 0.8%, p > 0.001) compared to patients at low risk. The 20-year BRFS was 69%, 65%, and 44% and the 20-year CSS was 98%, 95%, and 89% in low-risk, FIR, and UIR patients. On multiple Cox regression, FIR was not associated with a worse BRFS (HR 1.07, CI 0.87–1.32), UIR was associated with a worse BRFS (HR 1.49, CI 1.20–1.85). Conclusion Patients at FIR had only slightly worse pathological and long-term outcomes compared to patients at low risk, whereas the difference compared to patients at UIR was large. This emphasizes AS in these patients as a possible treatment strategy in well-counseled patients.


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