A prognostic model of non small cell lung cancer based on TCGA and ImmPort databases

Bioinformatics methods are used to construct an immune gene prognosis assessment model for patients with non-small cell lung cancer (NSCLC), and to screen biomarkers that affect the occurrence and prognosis of NSCLC. The transcriptomic data and clinicopathological data of NSCLC and cancer-adjacent normal tissues were downloaded from the Cancer Genome Atlas (TCGA) database and the immune-related genes were obtained from the IMMPORT database (http://www.immport.org/); then, the differentially expressed immune genes were screened out. Based on these genes, an immune gene prognosis model was constructed. The Cox proportional hazards regression model was used for univariate and multivariate analyses. Further, the correlations among the risk score, clinicopathological characteristics, tumor microenvironment, and the prognosis of NSCLC were analyzed. A total of 193 differentially expressed immune genes related to NSCLC were screened based on the "wilcox.test" in R language, and Cox single factor analysis showed that 19 differentially expressed immune genes were associated with the prognosis of NSCLC (P < 0.05). After including 19 differentially expressed immune genes with P < 0.05 into the Cox multivariate analysis, an immune gene prognosis model of NSCLC was constructed (it included 13 differentially expressed immune genes). Based on the risk score, the samples were divided into the high-risk and low-risk groups. The Kaplan–Meier survival curve results showed that the 5-year overall survival rate in the high-risk group was 32.4%, and the 5-year overall survival rate in the low-risk group was 53.7%. The receiver operating characteristic model curve confirmed that the prediction model had a certain accuracy (AUC = 0.673). After incorporating multiple variables into the Cox regression analysis, the results showed that the immune gene prognostic risk score was an independent predictor of the prognosis of NSCLC patients. There was a certain correlation between the risk score and degree of neutrophil infiltration in the tumor microenvironment. The NSCLC immune gene prognosis assessment model was constructed based on bioinformatics methods, and it can be used to calculate the prognostic risk score of NSCLC patients. Further, this model is expected to provide help for clinical judgment of the prognosis of NSCLC patients.

A novel ferroptosis-related gene signature associated with cell cycle for prognosis prediction in patients with clear cell renal cell carcinoma

Background It is of great urgency to explore useful prognostic markers for patients with clear cell renal cell carcinoma (ccRCC). Prognostic models based on ferroptosis-related gene (FRG) in ccRCC is poorly reported for now. Methods Comprehensive analysis of 22 FRGs were performed in 629 ccRCC samples from two independent patient cohorts. We carried out least absolute shrinkage and selection operator analysis to screen out prognosis-related FRGs and constructed prognosis model for patients with ccRCC. Weighted gene co-expression network analysis was also carried out for potential functional enrichment analysis. Results Based on the TCGA cohort, a total of 11 prognosis-associated FRGs were selected for the construction of the prognosis model. Significantly differential overall survival (hazard ratio = 3.61, 95% CI: 2.68–4.87, p < 0.0001) was observed between patients with high and low FRG score in the TCGA cohort, which was further verified in the CPTAC cohort with hazard ratio value of 5.13 (95% CI: 1.65–15.90, p = 0.019). Subgroup survival analysis revealed that our FRG score could significantly distinguish patients with high survival risk among different tumor stages and different tumor grades. Functional enrichment analysis illustrated that the process of cell cycle, including cell cycle-mitotic pathway, cytokinesis pathway and nuclear division pathway, might be involved in the regulation of ccRCC through ferroptosis. Conclusions We developed and verified a FRG signature for the prognosis prediction of patients with ccRCC, which could act as a risk factor and help to update the tumor staging system when integrated with clinicopathological characteristics. Cell cycle-related pathways might be involved in the regulation of ccRCC through ferroptosis.

A Review of Prognosis Model Associated With Cardiogenic Shock After Acute Myocardial Infarction

Objective: Cardiogenic shock seriously affects the survival rate of patients. However, few prognostic models are concerned with the score of cardiogenic shock, and few clinical studies have validated it. In order to optimize the diagnosis and treatment of myocardial infarction complicated with cardiogenic shock and facilitate the classification of clinical trials, the prognosis score model is urgently needed.Methods: Cardiogenic shock, severe case, prognosis score, myocardial infarction and external verification were used as the search terms to search PubMed, Embase, Web of Science, Cochrane, EBSCO (Medline), Scopus, BMC, NCBI, Oxford Academy, Science Direct, and other databases for pertinent studies published up until 1 August 2021. There are no restrictions on publication status and start date. Filter headlines and abstracts to find articles that may be relevant. The list of references for major studies was reviewed to obtain more references.Results and Conclusions: The existing related models are in urgent need of more external clinical verifications. In the meanwhile, with the development of molecular omics and the clinical need for optimal treatment of CS, it is urgent to establish a prognosis model with higher differentiation and coincidence rates.

The lncRNA Signatures of Genome Instability to Predict Survival in Patients with Renal Cancer

Long noncoding RNAs (lncRNAs) exert an increasingly important effect on genome instability and the prognosis of cancer patients. The present research established a computational framework originating from the mutation assumption combining lncRNA expression profile and somatic mutation profile in the genome of renal cancer to assess the effect of lncRNAs on the gene instability of renal cancer. A total of 45 differentially expressed lncRNAs were evaluated to be genome-instability-associated from the high and low cumulative somatic mutations groups. Then we established a prognosis model based on three genome-instability-associated lncRNAs (AC156455.1, AC016405.3, and LINC01234)-GlncScore. The GlncScore was then verified in testing cohort and the total TCGA renal cancer cohort. The GlncScore was evaluated to have an accurate prediction for the survival of patients. Furthermore, GlncScore was associated with somatic mutation patterns, indicating its capacity of reflecting genome instability in renal cancer. In conclusion, this study evaluated the effect of lncRNAs on genome instability of renal cancer and provided new hidden cancer biomarkers related to genome instability in renal cancer.

Identification of N6-methylandenosine related LncRNAs biomarkers associated with the overall survival of osteosarcoma

Purpose Osteosarcoma (OS) is a differentiation disease caused by the genetic and epigenetic differentiation of mesenchymal stem cells into osteoblasts. OS is a common, highly malignant tumor in children and adolescents. Fifteen to 20 % of the patients find distant metastases at their first visit. The purpose of our study was to identify biomarkers for tracking the prognosis and treatment of OS to improve the survival rate of patients. Materials and methods In this study, which was based on Therapeutically Applicable Research to Generate Effective Treatments (TARGET), we searched for m6A related lncRNAs in OS. We constructed a network between lncRNA and m6A, and built an OS prognostic risk model. Results We identified 14,581 lncRNAs by using the dataset from TARGET. We obtained 111 m6A-related lncRNAs through a Pearson correlation analysis. A network was built between lncRNA and m6A genes. Eight m6A-related lncRNAs associated with survival were identified through a univariate Cox analysis. A selection operator (LASSO) Cox regression was used to construct a prognostic risk model with six genes (RP11-286E11.1, LINC01426, AC010127.3, DLGAP1-AS2, RP4-657D16.3, AC002398.11) obtained through least absolute shrinkage. We also discovered upregulated levels of DLGAP1-AS2 and m6A methylation in osteosarcoma tissues/cells compared with normal tissues/osteoblasts cells. Conclusion We constructed a risk score prognosis model of m6A-related lncRNAs (RP11-286E11.1, LINC01426, AC010127.3, DLGAP1-AS2, RP4-657D16.3, AC002398.11) using the dataset downloaded from TRAGET. We verified the value of the model by dividing all samples into test groups and training groups. However, the role of m6A-related lncRNAs in osteosarcoma needs to be further researched by cell and in vivo studies.

Oxygen Consumption of Resuspended Sediments of the Upper Elbe Estuary: Process Identification and Prognosis

The resuspension of sediment leads to an increased release of nutrients and organic substances into the overlying water column, which can have a negative effect on the oxygen budget. Especially in the warmer months with a lower oxygen saturation and higher biological activity, the oxygen content can reach critical thresholds in estuaries like the upper Elbe estuary. Many studies have dealt with the nutrient fluxes that occur during a resuspension event. However, the sediment properties that influence the oxygen consumption potential (OCP) and the different biochemical processes have not been examined in detail. To fill this gap, we investigated the biogeochemical composition, texture, and OCP of sediments at 21 locations as well as the temporal variability within one location for a period of 2 years (monthly sampling) in the upper Elbe estuary. The OCP of sediments during a seven-day resuspension event can be described by the processes of sulphate formation, nitrification, and mineralisation. Chlorophyll, total nitrogen (Ntotal), and total organic carbon showed the highest correlations with the OCP. Based on these correlations, we developed a prognosis model to calculate the OCP for the upper Elbe estuary with a single sediment parameter (Ntotal). The model is well suited to calculate the oxygen consumption of resuspended sediments in the Hamburg port area during the relevant warmer months and shows a normalised root mean squared error of < 0.11 ± 0.13. Thus, the effect of maintenance measures such as water injection dredging and ship-induced wave on the oxygen budget of the water can be calculated.

Construction and Validation of a Novel Pyroptosis-Related Gene Signature to Predict the Prognosis of Uveal Melanoma

Uveal melanoma is the most common primary intraocular tumor with a poor prognosis. Currently, treatment for UVM is limited, and the development of drug resistance and tumor recurrence are common. Therefore, it is important to identify new prognostic biomarkers of UVM and explore their role in the tumor microenvironment. Pyroptosis is a way of cell programmed death, and related research is in full throttle. However, the role of pyroptosis in UVM is unclear. In this study, we constructed the prognosis model of pyroptosis-related genes of UVM. This model can accurately guide the prognosis of UVM, and different groups differ in immune infiltration. We further verified our results in cell experiments. To some extent, our study can provide new ideas for the diagnosis and treatment of UVM.

Pyroptosis-related Prognosis Model, Immunocyte Infiltration Characterization, and Competing Endogenous RNA Network of Glioblastoma

Background: Glioblastoma (GBM) has a high incidence rate, invasive growth, and easy recurrence, and the current therapeutic effect is less than satisfying. Pyroptosis plays an important role in morbidity and progress of GBM. Meanwhile, the tumor microenvironment (TME) is involved in the progress and treatment tolerance of GBM. In the present study, we analyzed prognosis model, immunocyte infiltration characterization, and competing endogenous RNA (ceRNA) network of GBM on the basis of pyroptosis-related genes (PRGs).Methods: The transcriptome and clinical data of 155 patients with GBM and 120 normal subjects were obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). Lasso (Least absolute shrinkage and selection operator) Cox expression analysis was used in predicting prognostic markers, and its predictive ability was tested using a nomogram. A prognostic risk score formula was constructed, and CIBERSORT, ssGSEA algorithm, Tumor IMmune Estimation Resource (TIMER), and TISIDB database were used in evaluating the immunocyte infiltration characterization and tumor immune response of differential risk samples. A ceRNA network was constructed with Starbase, mirtarbase, and lncbase, and the mechanism of this regulatory axis was explored using Gene Set Enrichment Analysis (GSEA). Results: Five PRGs (CASP3, NLRP2, TP63, GZMB, and CASP9) were identified as the independent prognostic biomarkers of GBM. Prognostic risk score formula analysis showed that the low-risk group had obvious survival advantage compared with the high-risk group, and significant differences in immunocyte infiltration and immune related function score were found. In addition, a ceRNA network of messenger RNA (CASP3, TP63)–microRNA (hsa-miR-519c-5p)–long noncoding RNA (GABPB1-AS1) was established. GSEA analysis showed that the regulatory axis played a considerable role in the extracellular matrix (ECM) and immune inflammatory response.Conclusions: Pyroptosis and TME-related independent prognostic markers were screened in this study, and a prognosis risk score formula was established for the first time according to the prognosis PRGs. TME immunocyte infiltration characterization and immune response were assessed using ssGSEA, CIBERSORT algorithm, TIMER, and TISIDB database. Besides a ceRNA network was built up. This study not only laid foundations for further exploring pyroptosis and TME in improving prognosis of GBM, but also provided a new idea for more effective guidance on clinical immunotherapy to patients and developing new immunotherapeutic drugs.

Construction and Validation of an Immune-Related lncRNA Prognosis Model for Thyroid Cancer

Background: Immune-related long noncoding RNAs (lncRNAs) play an important role in the development of cancer. This study aimed to identify immune-related lncRNAs in thyroid cancer (THCA) and to develop a prognostic model for THCA. Method: We downloaded immune-related gene sets from the Gene Set Enrichment Analysis (GSEA) website and obtained THCA gene expression and clinical data from The Cancer Genome Atlas (TCGA) database. Immune-related lncRNAs were then obtained by performing a correlation analysis on the expression of lncRNAs and immune-related genes. Prognostic model for THCA immune-related lncRNAs was developed though univariate Cox regression and multiple Cox regression analyses. We confirmed the results in clinical samples using quantitative real-time PCR. Results: A totally of 26 immune-related lncRNAs in THCA were obtained. Then we constructed a prognosis model composed of seven lncRNAs (LINC01614, AC017074.1, LINC01184, LINC00667, ACVR2B-AS1, AC090673.1 and LINC00900). Our model can be used as an independent prognostic factor. Principal component analysis displayed that the lncRNAs in the model can distinguish between high and low-risk groups. Clinical correlation analysis showed that the expression levels of AC090673.1 (P<0.05), LINC01184 (P<0.001), and LINC01614 (P<0.001) were related to disease stage, and LINC00900 (P<0.001) and LINC01614 (P<0.001) were related to T stage. We validated this model in cancer and paracancerous tissues from 24 THCA patients. Conclusion: We identified and experimentally validated seven immune-related lncRNAs that can serve as potential biomarkers for THCA prognosis.

A Model for the Prediction of Mortality and Hospitalization in Chinese Heart Failure Patients

Background: Although many risk prediction models have been released internationally, the application of these models in the Chinese population still has some limitations.Aims: The purpose of the study was to establish a heart failure (HF) prognosis model suitable for the Chinese population.Methods: According to the inclusion criteria, we included patients with chronic heart failure (CHF) who were admitted to the Department of Cardiac Rehabilitation of Tongji Hospital from March 2007 to December 2018, recorded each patient's condition and followed up on the patient's re-admission and death. All data sets were randomly divided into derivation and validation cohorts in a ratio of 7/3. Least absolute shrinkage and selection operator regression and Cox regression were used to screen independent predictors; a nomogram chart scoring model was constructed and validated.Results: A total of 547 patients were recruited in this cohort, and the median follow-up time was 519 days. The independent predictors screened out by the derivation cohort included age, atrial fibrillation (AF), percutaneous coronary intervention (PCI), diabetes mellitus (DM), peak oxygen uptake (peak VO2), heart rate at the 8th minute after the cardiopulmonary exercise peaked (HR8min), C-reaction protein(CRP), and uric acid (UA). The C indexes values of the derivation and the validation cohorts were 0.69 and 0.62, respectively, and the calibration curves indicate that the model's predictions were in good agreement with the actual observations.Conclusions: We have developed and validated a multiple Cox regression model to predict long-term mortality and readmission risk of Chinese patients with CHF.Registration Number: ChicTR-TRC-00000235.