scholarly journals Immune-Related lncRNA Correlated with Transcription Factors Provide Strong Prognostic Prediction in Gliomas

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Yixin Tian ◽  
Yi-Quan Ke ◽  
Yanxia Ma

Glioma is the most common and deadly tumor in central nervous system. According to previous studies, long noncoding RNAs (lncRNA) and transcription factors were significant factors of gliomas progression by regulating gliomas immune microenvironment. In our study, we built two independent cohorts from CGGA and TCGA. And we extracted 253 immune-related lncRNA correlated with prognosis. After LASSO analysis and multivariate Cox regression analysis, 8 immune-related lncRNA were used to construct classifier. The effectiveness of classifier was confirmed in both CGGA (AUC = 0.869) and TCGA (AUC = 0.902) cohorts. The correlation between transcription factors and immune-related lncRNA was calculated by WCGNA. Eventually, we built a network between 8 lncRNA and transcription factors. The function of core immune-related lncRNA in gliomas immune microenvironment was also investigated by CIBERTSORT. Our research provided a strong classifier of immune-related lncRNA to predict gliomas patient outcome. We also found the correlation between core immune-related lncRNA and transcription factors. These results may stimulate new strategy of immunotherapy in gliomas patients.

2021 ◽  
Vol 11 ◽  
Author(s):  
Guoxu Fang ◽  
Jianhui Fan ◽  
Zongren Ding ◽  
Rong Li ◽  
Kongying Lin ◽  
...  

PurposeDigestive system carcinoma is one of the most devastating diseases worldwide. Lack of valid clinicopathological parameters as prognostic factors needs more accurate and effective biomarkers for high-confidence prognosis that guide decision-making for optimal treatment of digestive system carcinoma. The aim of the present study was to establish a novel model to improve prognosis prediction of digestive system carcinoma, with a particular interest in transcription factors (TFs).Materials and MethodsA TF-related prognosis model of digestive system carcinoma with data from TCGA database successively were processed by univariate and multivariate Cox regression analyses. Then, for evaluating the prognostic prediction value of the model, ROC curve and survival analysis were performed by external data from GEO database. Furthermore, we verified the expression of TFs expression by qPCR in digestive system carcinoma tissue. Finally, we constructed a TF clinical characteristics nomogram to furtherly predict digestive system carcinoma patient survival probability with TCGA database.ResultsBy Cox regression analysis, a panel of 17 TFs (NFIC, YBX2, ZBTB47, ZNF367, CREB3L3, HEYL, FOXD1, TIGD1, SNAI1, HSF4, CENPA, ETS2, FOXM1, ETV4, MYBL2, FOXQ1, ZNF589) was identified to present with powerful predictive performance for overall survival of digestive system carcinoma patients based on TCGA database. A nomogram that integrates TFs was established, allowing efficient prediction of survival probabilities and displaying higher clinical utility.ConclusionThe 17-TF panel is an independent prognostic factor for digestive system carcinoma, and 17 TFs based nomogram might provide implication an effective approach for digestive system carcinoma patient management and treatment.


Author(s):  
Chunliang Shang ◽  
Jiaming Huang ◽  
Hongyan Guo

The tumor metabolic reprogramming contributes to the progression and prognosis of cervical cancer (CC). However, the potential remodeling mechanisms of tumor metabolism in the immune microenvironment of CC remain largely unknown. In this study, we first performed microarray analysis to identify differential metabolic gene expression. A novel 5-metabolic-related genes (MRGs) signature comprising P4HA1, P4HA2, ABL2, GLTP, and CYP4F12 was established to better predict prognosis of CC using LASSO-Cox regression analysis. This signature could reveal the metabolic features and monitor the immune status of tumor microenvironment (TME). Among them, P4HA2 was significantly upregulated in CC tissues and negatively correlated with CD8+T cells. Knockdown of P4HA2 inhibited lipid droplets (LDs) accumulation and cancer cells invasion. Moreover, P4HA2 knockdown significantly suppressed PD-L1 expression. This study provides a new and feasible method for evaluating the prognosis of CC and explores the potential value to navigate metabolic pathways to enhance anti-tumor immunity and immunotherapy.


2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jun-Le Liu ◽  
Jian-Wen Jin ◽  
Zhong-Meng Lai ◽  
Jie-Bo Wang ◽  
Jian-Sheng Su ◽  
...  

Abstract Background The prognosis of hospitalized patients after emergent endotracheal intubation (ETI) remains poor. Our aim was to evaluate the 30-d hospitalization mortality of subjects undergoing ETI during daytime or off-hours and to analyze the possible risk factors affecting mortality. Methods A single-center retrospective study was performed at a university teaching facility from January 2015 to December 2018. All adult inpatients who received ETI in the general ward were included. Information on patient demographics, vital signs, ICU (Intensive care unit) admission, intubation time (daytime or off-hours), the department in which ETI was performed (surgical ward or medical ward), intubation reasons, and 30-d hospitalization mortality after ETI were obtained from a database. Results Over a four-year period, 558 subjects were analyzed. There were more male than female in both groups (115 [70.1%] vs 275 [69.8%]; P = 0.939). A total of 394 (70.6%) patients received ETI during off-hours. The patients who received ETI during the daytime were older than those who received ETI during off-hours (64.95 ± 17.54 vs 61.55 ± 17.49; P = 0.037). The BMI of patients who received ETI during the daytime was also higher than that of patients who received ETI during off-hours (23.08 ± 3.38 vs 21.97 ± 3.25; P < 0.001). The 30-d mortality after ETI was 66.8% (373), which included 68.0% (268) during off-hours and 64.0% (105) during the daytime (P = 0.361). Multivariate Cox regression analysis found that the significant factors for the risk of death within 30 days included ICU admission (HR 0.312, 0.176–0.554) and the department in which ETI was performed (HR 0.401, 0.247–0.653). Conclusions The 30-d hospitalization mortality after ETI was 66.8%, and off-hours presentation was not significantly associated with mortality. ICU admission and ETI performed in the surgical ward were significant factors for decreasing the risk of death within 30 days. Trial registration This trial was retrospectively registered with the registration number of ChiCTR2000038549.


2020 ◽  
Author(s):  
Pin Li ◽  
Huixia Zhou ◽  
Hualin Cao ◽  
Tao Guo ◽  
Weiwei Zhu ◽  
...  

Abstract Background To elucidate the bladder rhabdomyosarcoma clinicopathological characteristics and reveal the prognostic factors. Methods We screened data from SEER database (1975-2016) stratified by age group, evaluated the differences between groups with Chi-square and Fisher’s test, conducted the Kaplan-Meier survival analysis and plotted the survival curve. The significant factors were brought into Cox regression analysis and calculated the HR(95%CI). Results About half of the patients who develop bladder RMS will be younger than 2 years of age. Embryonal RMS account for 76% of all histopathology types. Age at diagnosis more than 16-y (HR=6.595,95%CI:3.62-12.01, p=7.04e-10), NOT embryonal rhabdomyosarcoma (HR=3.61, 95%CI:1.99-6.549, p =4.1e-06), without radiotherapy combined or surgery alone (HR=4.382, 95%CI:1.99-6.549, p =2.4e-05) and not performed the surgery (HR=2.982,95%CI:1.263-7.039, p =0.0126) were negatively correlated with 5-year survival time, while race( p =0.341), whether performed the lymphadenectomy( p =0.722) showed no influence on survival time. Cox regression results show that age, histology, SEER stage, treatment combined or alone influence the clinical outcomes. Conclusions We demonstrated the demographic and characteristic of bladder rhabdomyosarcoma, identified and excluded the prognostic factors for the 5-year overall survival and clinical outcomes.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 5551-5551
Author(s):  
Jake Towriss ◽  
Prosanta Mondal ◽  
Waleed Sabry ◽  
Mohamed Elemary ◽  
Hadi Alphonse Goubran ◽  
...  

Abstract Background: The addition of anti-CD20 monoclonal antibodies to chemotherapy regimens for Chronic Lymphocytic Leukemia (CLL) has led to significant improvements in response and survival (Burger, O'Brian, Nat Rev Clin Oncol 2018). However, toxicities with treatment exist and real world evidence suggests that tolerability of treatment protocols may differ than those established by clinical trials (Mato et. al. Am Soc Hematology 2017), making clinical treatment decisions challenging. This study retrospectively reviewed the tolerability of three front line chemo-immunotherapy options utilized at the Saskatchewan Cancer Agency (SCA): Fludarabine, Cyclophosphamide and Rituximab (FCR) for fit patients, Bendamustine plus Rituximab (BR) for older but fit patients or younger but frail and Obinutuzumab plus Chlorambucil (O-Chlor) for older and/or frail patients. SCA guidelines suggest the choice of treatment regimen should be based on patient age and fitness, a surrogate for ability to tolerate full dose treatment. However, neither these two criteria nor what constitutes tolerability is defined, resulting in a subjective assessment of fitness, a common problem in real world settings (Bouret et al, Hematologica 2013). We hypothesized that choice of treatment without these definitions would lead to poor choice of regimen selection and inferior patient outcome. Methods: We retrospectively reviewed the electronic medical records of CLL patients receiving front line chemo immunotherapy treatment at the SCA between 2015-2018. Patients' ability to tolerate treatment was assessed by the number of cycles completed, total dose intensity received, dose delays or change in therapy. Regimen tolerability was compared to physician calculated Cumulative Illness Rating Scale (CIRS) scores (an objective fitness measure) however, this was calculated after treatment regimen was determined. Kaplan-Meier analysis, univariable and multivariable Cox regression models were utilized to analyze the effect of tolerability and regimen received on patient outcome as defined by death due to CLL or progressive disease. Results: Ninety-six patient charts were reviewed. Regimen tolerability is shown in Table 1. A dose intensity of ≥ 75% was achieved by 91.3%, 69.9% and 48.7% of patients treated with FCR, BR and O-Chlor respectively. Dose intensity was statistically different among all 3 treatments (p=0.002) and specifically between FCR and BR (p=0.048). The number of cycles received for the 3 treatment groups were also statistically different most notably between FCR and O-Chlor (p=0.01) CIRS score of ≤ or > 6 was not different between the 3 groups. Median survival was statistically different between FCR (34.5 mo.), BR (36.1 mo.) and O-Chlor (25.4mo), (p=0.02) by Kaplan Meir Analysis. Univariate Cox regression analysis demonstrated the following statistically significant risk differences for death from CLL or disease progression; 1) Higher risk for O-Chlor versus BR [Hazard Ratio (HR)= 5.16, 95% confidence interval (CI): (1.65-16.13), P=0.004), 2) Lower risk for DI ≥ 75% for a 3 regimens [HR=0.19, 95% CI: (0.08-0.44), P=0.001], 3) each additional cycle of treatment received lowered the risk of death from CLL or disease progression by 33% [HR=0.67, 95% CI:(0.56-0.80), P<0.0001] and 4) if an additional cycle of treatment required dose reduction, the event rate decreased by 23% [HR=0.77, 95% CI: (0.59-0.99), P=0.047]. Multivariable Cox regression analysis demonstrated that only the regimen received and not specific tolerability remained statistically significant for patient outcomes. Conclusions: Dose intensity and the number of cycles received independently affected patient outcome indicating that certain aspects of regimen tolerability are important to consider when making treatment decisions. These results add to the growing body of real world evidence for front line CLL chemo immunotherapy. Disclosures Elemary: Roche: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Lundbeck: Membership on an entity's Board of Directors or advisory committees.


2021 ◽  
Vol 8 ◽  
Author(s):  
Mingqin Ge ◽  
Jie Niu ◽  
Ping Hu ◽  
Aihua Tong ◽  
Yan Dai ◽  
...  

Objective: This study aimed to construct a prognostic ferroptosis-related signature for thyroid cancer and probe into the association with tumor immune microenvironment.Methods: Based on the expression profiles of ferroptosis-related genes, a LASSO cox regression model was established for thyroid cancer. Kaplan-Meier survival analysis was presented between high and low risk groups. The predictive performance was assessed by ROC. The predictive independency was validated via multivariate cox regression analysis and stratified analysis. A nomogram was established and verified by calibration curves. The enriched signaling pathways were predicted via GSEA. The association between the signature and immune cell infiltration was analyzed by CIBERSORT. The ferroptosis-related genes were validated in thyroid cancer tissues by immunohistochemistry and RT-qPCR.Results: A ferroptosis-related eight gene model was established for predicting the prognosis of thyroid cancer. Patients with high risk score indicated a poorer prognosis than those with low risk score (p = 1.186e-03). The AUCs for 1-, 2-, and 3-year survival were 0.887, 0.890, and 0.840, respectively. Following adjusting other prognostic factors, the model could independently predict the prognosis (p = 0.015, HR: 1.870, 95%CI: 1.132–3.090). A nomogram combining the signature and age was constructed. The nomogram-predicted probability of 1-, 3-, and 5-year survival approached the actual survival time. Several ferroptosis-related pathways were enriched in the high-risk group. The signature was distinctly associated with the immune cell infiltration. After validation, the eight genes were abnormally expressed between thyroid cancer and control tissues.Conclusion: Our findings established a prognostic ferroptosis-related signature that was associated with the immune microenvironment for thyroid cancer.


Author(s):  
Zhengdong Deng ◽  
Xiangyu Li ◽  
Yuanxin Shi ◽  
Yun Lu ◽  
Wei Yao ◽  
...  

Autophagy is an important bioprocess throughout the occurrence and development of cancer. However, the role of autophagy-related lncRNAs in pancreatic cancer (PC) remains obscure. In the study, we identified the autophagy-related lncRNAs (ARlncRNAs) and divided the PC patients from The Cancer Genome Atlas into training and validation set. Firstly, we constructed a signature in the training set by the least absolute shrinkage and selection operator penalized cox regression analysis and the multivariate cox regression analysis. Then, we validated the independent prognostic role of the risk signature in both training and validation set with survival analysis, receiver operating characteristic analysis, and Cox regression. The nomogram was established to demonstrate the predictive power of the signature. Moreover, high risk scores were significantly correlated to worse outcomes and severe clinical characteristics. The Pearson’s analysis between risk scores with immune cells infiltration, tumor mutation burden, and the expression level of chemotherapy target molecules indicated that the signature could predict efficacy of immunotherapy and targeted therapy. Next, we constructed an lncRNA–miRNA–mRNA regulatory network and identified several potential small molecule drugs in the Connectivity Map (CMap). What’s more, quantitative real-time PCR (qRT-PCR) analysis showed that serum LINC01559 could serve as a diagnostic biomarker. In vitro analysis showed inhibition of LINC01559 suppressed PC cell proliferation, migration, and invasion. Additionally, silencing LINC01559 suppressed gemcitabine-induced autophagy and promoted the sensitivity of PC cells to gemcitabine. In conclusion, we identified a novel ARlncRNAs signature with valuable clinical utility for reliable prognostic prediction and personalized treatment of PC patients. And inhibition of LINC01559 might be a novel strategy to overcome chemoresistance.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fei Li ◽  
Dongcen Ge ◽  
Shu-lan Sun

Abstract Background Ferroptosis is a newly discovered form of cell death characterized by iron-dependent lipid peroxidation. This study aims to investigate the potential correlation between ferroptosis and the prognosis of lung adenocarcinoma (LUAD). Methods RNA-seq data were collected from the LUAD dataset of The Cancer Genome Atlas (TCGA) database. Based on ferroptosis-related genes, differentially expressed genes (DEGs) between LUAD and paracancerous specimens were identified. The univariate Cox regression analysis was performed to screen key genes associated with the prognosis of LUAD. LUAD patients were divided into the training set and validation set. Then, we screened out key genes and built a prognostic prediction model involving 5 genes using the least absolute shrinkage and selection operator (LASSO) regression with tenfold cross-validation and the multivariate Cox regression analysis. After dividing LUAD patients based on the median level of risk score as cut-off value, the generated prognostic prediction model was validated in the validation set. Moreover, we analyzed the somatic mutations, and estimated the scores of immune infiltration in the high-risk and low-risk groups. Functional enrichment analysis of DEGs was performed as well. Results High-risk scores indicated the worse prognosis of LUAD. The maximum area under curve (AUC) of the training set and the validation set in this study was 0.7 and 0.69, respectively. Moreover, we integrated the age, gender, and tumor stage to construct the composite nomogram. The charts indicated that the AUC of LUAD cases with the survival time of 1, 3 and 5 years was 0.698, 0.71 and 0.73, respectively. In addition, the mutation frequency of LUAD patients in the high-risk group was significantly higher than that in the low-risk group. Simultaneously, DEGs were mainly enriched in ferroptosis-related pathways by analyzing the functional results. Conclusions This study constructs a novel LUAD prognosis prediction model involving 5 ferroptosis-related genes, which can be used as a promising tool for decision-making of clinical therapeutic strategies of LUAD.


2020 ◽  
Author(s):  
Ruihua Fang ◽  
Lin Chen ◽  
Jing Liao ◽  
Jierong Luo ◽  
Chenchen Zhang ◽  
...  

Abstract Background: Head and neck squamous cell carcinoma (HNSCC), the most frequent subtype of head and neck cancer, continues to have a poor prognosis with no improvement. Growing evidence has demonstrated that the immune system plays a crucial role in the development and progression of HNSCC. The goal of our study was to develop an immune-related signature for accurately predicting the survival of HNSCC patients. Methods: Gene expression profiles were established from a total of 546 HNSCC and normal tissues to establish a training set and 83 HNSCC tissues for a validation set. Differentially expressed prognostic immune genes were identified by univariate Cox regression analysis and a corresponding network of differentially expressed transcription factors (TFs) were identified using Cytoscape. The immune-related gene signature was established and validated by univariate Cox regression analysis, least absolute shrinkage and selector operation (LASSO), and multivariate Cox regression analyses. In addition, the prognostic value of the immune-related signature was analyzed by survival and Cox regression analysis. Finally, the correlation between the immune-related signature and the immune microenvironment was established.Results: In this study, the TF-mediated network revealed that Foxp3 plays a central role in the regulatory mechanism of most immune genes. A prognostic signature based on 10 immune-related genes, which divided patients into high and low risk groups, was developed and successfully validated using two independent databases. Our prognostic signature was significantly related to worse survival and predicted prognosis in patients with different clinicopathological factors. A nomogram including clinical characteristics was also constructed for accurate prediction. Furthermore, it was determined that our prognostic signature may act as an independent factor for predicting the survival of HNSCC patients. ROC analysis also revealed that our signature had superior predictive value compared with TNM stage. As for the immune microenvironment, our signature showed a positive correlation with activated mast cells and M0 macrophages, a negative correlation with Tregs, and immune checkpoint molecules PD-1 and CLTA-4. Conclusions: Our study established an immune-related gene signature, which not only provides a promising biomarker for survival prediction, but may be evaluated as an indicator for personalized immunotherapy in patients with HNSCC.


2021 ◽  
Author(s):  
Jianfeng Huang ◽  
Wenzheng Chen ◽  
Changyu Chen ◽  
Tao Xiao ◽  
Zhigang Jie

Abstract BackgroundN6-methyladenosine (m6A) RNA modification plays an important role in regulating tumor microenvironment (TME) infiltration. However, the relationship between the expression pattern of m6A-related long non-coding RNAs (lncRNAs) and the immune microenvironment of gastric cancer (GC) is unclear. MethodsIn this study, 23 m6A-related lncRNAs were identified by Pearson’s correlation analysis and univariate Cox regression analysis. According to the expression of these lncRNAs, we identified two distinct molecular clusters by consensus clustering and compared the differences of the TME and enriched pathways between the two clusters. We further constructed a prognostic risk signature and verified it using The Cancer Genome Atlas training and testing cohorts. ResultsThe results showed that cluster 1 was associated with tumor-related and immune activation-related pathways. In addition, cluster 1 was also associated with higher ImmuneScore, StromalScore, and ESTIMATEScore. The results of the stratified survival analysis and independent prognosis analysis indicated that the risk signature is an independent prognostic indicator for patients with GC. In addition, it can effectively predict survival status in patients with different clinical characteristics. Furthermore, our risk model showed that low risk scores were significantly correlated with high expression of programmed death-1 (PD-1) and cytotoxic T-lymphocyte associated protein 4 (CTLA4), as well as sensitivity to chemotherapeutic drugs (e.g., paclitaxel and oxaliplatin). ConclusionsThis evidence contributes to our understanding of the regulation of TME infiltration by m6A-related lncRNAs and my lead to more effective immunotherapy and chemotherapy for patients with GC.


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