scholarly journals U-survival for prognostic prediction of disease progression and mortality of patients with COVID-19

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Janne J. Näppi ◽  
Tomoki Uemura ◽  
Chinatsu Watari ◽  
Toru Hironaka ◽  
Tohru Kamiya ◽  
...  

AbstractThe rapid increase of patients with coronavirus disease 2019 (COVID-19) has introduced major challenges to healthcare services worldwide. Therefore, fast and accurate clinical assessment of COVID-19 progression and mortality is vital for the management of COVID-19 patients. We developed an automated image-based survival prediction model, called U-survival, which combines deep learning of chest CT images with the established survival analysis methodology of an elastic-net Cox survival model. In an evaluation of 383 COVID-19 positive patients from two hospitals, the prognostic bootstrap prediction performance of U-survival was significantly higher (P < 0.0001) than those of existing laboratory and image-based reference predictors both for COVID-19 progression (maximum concordance index: 91.6% [95% confidence interval 91.5, 91.7]) and for mortality (88.7% [88.6, 88.9]), and the separation between the Kaplan–Meier survival curves of patients stratified into low- and high-risk groups was largest for U-survival (P < 3 × 10–14). The results indicate that U-survival can be used to provide automated and objective prognostic predictions for the management of COVID-19 patients.

2021 ◽  
Vol 12 ◽  
Author(s):  
ShuQiao Zhang ◽  
XinYu Li ◽  
ChunZhi Tang ◽  
WeiHong Kuang

Background: Gastric carcinoma (GC) is a molecularly and phenotypically highly heterogeneous disease, making the prognostic prediction challenging. On the other hand, Inflammation as part of the active cross-talk between the tumor and the host in the tumor or its microenvironment could affect prognosis.Method: We established a prognostic multi lncRNAs signature that could better predict the prognosis of GC patients based on inflammation-related differentially expressed lncRNAs in GC.Results: We identified 10 differently expressed lncRNAs related to inflammation associated with GC prognosis. Kaplan-Meier survival analysis demonstrated that high-risk inflammation-related lncRNAs signature was related to poor prognosis of GC. Moreover, the inflammation-related lncRNAs signature had an AUC of 0.788, proving their utility in predicting GC prognosis. Indeed, our risk signature is more precise in predicting the prognosis of GC patients than traditional clinicopathological manifestations. Immune and tumor-related pathways for individuals in the low and high-risk groups were further revealed by GSEA. Moreover, TCGA based analysis revealed significant differences in HLA, MHC class-I, cytolytic activity, parainflammation, co-stimulation of APC, type II INF response, and type I INF response between the two risk groups. Immune checkpoints revealed CD86, TNFSF18, CD200, and LAIR1 were differently expressed between lowand high-risk groups.Conclusion: A novel inflammation-related lncRNAs (AC015660.1, LINC01094, AL512506.1, AC124067.2, AC016737.1, AL136115.1, AP000695.1, AC104695.3, LINC00449, AC090772.1) signature may provide insight into the new therapies and prognosis prediction for GC patients.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Quan Jiang ◽  
Hao Chen ◽  
Zhaoqing Tang ◽  
Jie Sun ◽  
Yuanyuan Ruan ◽  
...  

Abstract Objective As a critical feature of cancers, stemness is acknowledged as a contributor to the development of drug resistance in gastric cancer (GC). LncRNAs have been revealed to participate in this process. In this study, we tried to develop a stemness-related lncRNA pair signature as guidance for clinical decisions. Methods The analysis was initiated by collecting stemness-related lncRNAs in TCGA cohort. The differentially expressed stemness-related lncRNAs between normal and tumor tissues in GC patients from TCGA datasets were further collected to establish the signature based on Lasso and Cox regression analyses. The predictive efficacy of the signature for chemotherapy and immunotherapy was also tested. The practicality of this signature was also validated by Zhongshan cohort. Results A 13-DEsrlncRNA pair-based signature was established. The cutoff point acquired by the AIC algorithm divided the TCGA cohort into high and low risk groups. We found that the low-risk group presented with better survival (Kaplan-Meier analysis, p < 0.001). Cox regression analyse was also conducted to confirm the signature as an independent risk factor for GC {p < 0.001, HR = 1.300, 95% CI (1.231–1.373)]}. As for the practicality of this signature, the IC50 of cytotoxic chemotherapeutics was significantly higher in the high-risk group. The low-risk group also presented with higher immunophenoscore (IPS) in both the “CTLA4+ PD1+” (Mann-Whitney U test, p = 0.019) and “CTLA4- PD1+” (Mann-Whitney U test, p = 0.013) groups, indicating higher sensitivity to immunotherapy. The efficacy of the signature was also validated by Zhongshan cohort. Conclusions This study could not only provide a stemness-related lncRNA signature for survival prediction in GC patients but also established a model with predictive potentials for GC patients’ sensitivity to chemotherapy and immunotherapy.


2021 ◽  
Author(s):  
Liyuan Wu ◽  
Feiya Yang ◽  
Nianzeng Xing

Abstract Background Bladder cancer (BC) is a highly heterogeneous disease, which makes the prognostic prediction challenging. Ferroptosis is related to a variety of biological pathways, including those involved in the metabolism of amino acids, lipids, and iron. However, the prognostic value of ferroptosis-related genes in BC remains to be further elucidated. Methods In this study, the mRNA expression profiles and corresponding clinical data of BC patients were downloaded from public databases. The least absolute shrinkage and selection operator (LASSO) Cox regression model was utilized to construct a multigene signature and validated it. Results Our results showed 12 differentially expressed genes (DEGs) were correlated with overall survival (OS) in the univariate Cox regression analysis (all adjusted P< 0.05). A 9-gene signature was constructed to stratify patients into two risk groups. Patients in the high-risk group showed significantly reduced OS compared with patients in the low-risk group (P < 0.001). The risk score was an independent predictor for OS in multivariate Cox regression analyses (HR> 1, P< 0.01). Receiver operating characteristic (ROC) curve analysis confirmed the signature's predictive capacity. Functional analysis revealed that immune-related pathways were enriched, and immune status were different between two risk groups, especially in humoral immune response process. Conclusion In conclusion, a novel ferroptosis-related gene signature can be used for prognostic prediction in BC. Targeting ferroptosis may be a therapeutic alternative for BC.


2020 ◽  
Vol 16 (30) ◽  
pp. 2421-2432 ◽  
Author(s):  
Jiamin Wang ◽  
Han Lin ◽  
Mingda Zhou ◽  
Qian Xiang ◽  
Yihan Deng ◽  
...  

Aim: To construct a survival prediction signature for prostate cancer (PC) based on the RNA N6-methyladenosine (m6A) methylation regulator. Materials & methods: This paper explores the interaction network of differentially expressed m6A RNA methylation regulators in PC by Pearson correlation analysis. Univariate Cox risk regression and LASSO regression analysis were used to construct a predictive signature of PC. Kaplan–Meier survival analysis compared the overall survival of the high- and low-risk groups. Results & Conclusion: We first constructed a prognostic two gene signature for PC based on the m6A RNA methylation regulators MRTTL14 and YTHDF2. The interaction network of m6A RNA methylation regulators in PC was also established.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5526-5526 ◽  
Author(s):  
Sabine Blum ◽  
Norbert Gattermann ◽  
Filipe Martins ◽  
Kathrin Nachtkamp ◽  
Andrea Kuendgen ◽  
...  

Abstract Introduction The IPSS-R (Greenberg et al, Blood 2012) achieved a more accurate definition of risk groups among patients with myelodysplastic syndromes (MDS) by using refined cytogenetic risk assessment and a more sophisticated categorization of bone marrow blast percentages and cytopenias. Like the original IPSS, the IPSS-R was developed from clinical data describing untreated MDS patients, i.e. patients receiving only best supportive care. Our investigation was conducted to see whether the IPSS-R can also predict the survival of patients receiving specific MDS treatment, as is now the case for the majority of patients. Methods We identified in the Duesseldorf MDS Registry 142 patients who completed treatment with either a hypomethylating agent, intensive chemotherapy, allogeneic stem cell transplantation, lenalidomide, or more than one of these therapies, and in whom the IPSS-R could be calculated at the time of diagnosis and at least once after therapy was completed. We used the product-limit method to estimate the probability of survival. Results At diagnosis, the 142 MDS patients were distributed among IPSS-R risk groups as follows: 3 very low risk, 41 low risk, 43 intermediate risk, 27 high risk and 28 very high risk. Figure 1 shows the Kaplan-Meier (KM) survival curves of these groups, which are statistically not significantly separate. In other words, the strong prognostic power of the IPSS-R, which has clearly been demonstrated for untreated patients, was lost in patients receiving disease-modifying treatment. We also applied the IPSS-R after finishing therapy or subsequent to stem cell transplantation. Patients were assigned to the IPSS-R risk groups based on clinical data obtained at least four weeks after treatment. This resulted in Kaplan-Meier survival curves that clearly separated IPSS-R risk groups again (Figure 2). Conclusion Since it was developed on a data base of untreated MDS patients, it is not surprising that, applied at the time of diagnosis, the IPSS-R is not an effective tool to assess the prognosis of patients proceeding to receive disease-modifying treatment. Nevertheless, at the time of diagnosis, the IPSS-R reliably predicts the natural course of disease and thus helps to make appropriate, risk-adapted treatment decisions. After treatment has exerted its influence, mirrored by changes in blood counts, bone marrow blast counts and karyotypes, these changes can lead to re-categorization of patients in the IPSS-R. We demonstrate that such re-assignment is clinically meaningful, as shown by the survival curves in Figure 2. In other words, after disease-modifying treatment the IPSS-R regains its prognostic power and may again be used as an effective tool to support clinical decision making. This does not obviate the need to develop, independent of the IPSS-R, multiple treatment-specific tools to predict the response to various therapies. Disclosures Gattermann: Novartis: Consultancy, Honoraria, Other: travel, accomodation expenses, Research Funding; Celgene: Consultancy, Honoraria, Research Funding. Kobbe:Jansen: Honoraria, Other: travel support; Celgene: Honoraria, Other: travel support, Research Funding.


2020 ◽  
Author(s):  
Heyan Chen ◽  
Shengyu Pu ◽  
Shibo Yu ◽  
Xiaoqin Liao ◽  
Jianjun He ◽  
...  

Abstract Introduction: In recent years, it has been found that the expression of 17 centromere proteins (CENPs) is closely related to malignant tumors. This study intends to investigate the prognostic value of CENPs in breast cancer (BC). Methods: A total of 800 BC patients were included from the TCGA database. The Cox proportional regression models was used to develop a CENPs-related prognostic signature. Furthermore, the mRNA expression and overall survival (OS) of CENPP (centromere protein P) in BC patients with different clinicopathological featureswas analyzed via GEPIA, bcGenExMiner v4.4 and Kaplan-Meier plotter. Finally, the nomogram was established based on the independent predictors recognized by multivariate Cox regression analysis and further validated by receiver-operating characteristic (ROC) curves and calibration plots internally and externally. Results: The result shown that age, Her2 status, pathologic_T stage, pathologic_M stage and CENPP expression with independent prognostic values for BC. CENPP was overexpressed in BC tissues and CENPP high expression was associated with better OS. We then established a nomogram based on those independent predictors, and the calibration curve demonstrated good fitness of the nomogram for OS prediction. In the training set, the AUC of 3−year and 5−year survival were 0.757 and 0.797, respectively. In the validation set, the AUC of 3−year and 5−year survival were 0.727 and 0.71. Conclusion: Our study showed that CENPP is a novel prognostic factor for patients with BC, and the established nomogram can provide valuable information on prognostic prediction for patients with BC.


2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Shalnova ◽  
E Yarovaya ◽  
V Kutsenko ◽  
A Kapustina ◽  
Y.U Makarova ◽  
...  

Abstract Background Angina pectoris (AP) and intermittent claudication (IC) are transient ischemic conditions provoked by exertion due to an imbalance of oxygen supply and demand to the skeletal leg muscle and/or myocardium. They have the similar etiology, both are accepted markers of diffuse atherosclerotic vascular disease and increased mortality risk. But these conditions were rarely studied in community-based cohorts, including comparison with each other or with individuals without symptoms. Aim To investigate the relationship between AP and IC and to evaluate their impact on the survival among Russian men during 30-years follow-up. Methods The data was obtained from representative samples observed in Moscow and Leningrad (now Saint-Petersburg) from 1975 to 1986. Men (10953) aged 35–71 years (mean age 48.8±6.61yrs) were examined by the same core protocol. AP and IC were determined by the original Rose questionnaires. We identified five risk groups of participants: 1) AP and IC; 2) AP without IC; 3) IC without AP; 4) without AP and IC, suffering from chest or leg pain that makes them stop (mixed group); and 5) men without pain, that makes them stop (no pain). During the 31-year follow up period (median time to event – 21.9 years) 7893 deaths from all-causes including 2673 from CHD occurred. We used Kaplan-Meier curves to investigate the relationship between risk groups and survival. Individual impact of AP and IC into mortality was evaluated by multivariate age-adjusted Cox proportional hazards model. For this, we divided participants with AP into three groups: with typical AP, with chest pain that makes them stop, but without AP (mixed group) and other (no pain); and with IC into four groups: with typical IC, with atypical IC, with no pain in legs and all other (mixed group). Results Only 4.8% men with AP had IC, whereas 28.6% with IC had AP. All-cause mortality Kaplan-Meier curves were pairwise different, except groups with “IC without AP” and “AP without IC”. The same results were obtained for CHD mortality. Difference of 17.2 years for median survival times were observed between “no pain” and “AP and IC” groups (Figure 1). We revealed significant impact of each IC and AP group on all-cause mortality. The same results were obtained for CHD mortality except for mixed IC group. Hazard ratios (95% confidence interval) for typical AP and typical IC groups were 1.99 (1.18–2.27) and 2.47 (1.84–3.30) compared to “no pain” group, respectively. They did not significanly differ from each other. Limitations We observed natural history of IC using the original Rose questionnaire in baseline. No modern methods of diagnostics were used that time. Conclusion The greatest decrease in life expectancy of 17.2 years was among participants with “AP and IC”. Survival curves of “IC without AP” and “AP without IC” groups didn't differ. IC and AP significantly independent age-adjusted impacts on all-cause and CHD mortality. Survival curves for all-cause mortality Funding Acknowledgement Type of funding source: None


2020 ◽  
pp. 1-9
Author(s):  
Dong Zhao ◽  
Keming Yang ◽  
Wei Feng ◽  
Shoujun Li ◽  
Jun Yan ◽  
...  

Abstract Objective: This study aimed to investigate the association between long-term survival and different management of major aortopulmonary collateral arteries in patients with pulmonary atresia, ventricular septal defect, and major aortopulmonary collateral arteries. Methods: From November, 2009 to October, 2018, a total of 98 consecutive patients with pulmonary atresia, ventricular septal defect, major aortopulmonary collateral arteries, and hypoplastic pulmonary arteries treated with modified Blalock–Taussig shunt or right ventricle–pulmonary artery connection were included. Fifty-five patients who received occlusion or ligation of major aortopulmonary collateral arteries during or after palliative procedure were occlusion group, and the other 43 patients were no occlusion group. The early and late outcomes were compared. Results: The mean duration of follow-up was 30.9 months in no occlusion group and 49.8 months in the occlusion group (p < 0.001). Multivariate analysis showed that only no occlusion of major aortopulmonary collateral arteries was predictive of total mortality (Hazard Ratio: 4.42, 95% CI: 1.27 to 15.42, p = 0.02). The Kaplan–Meier survival curves confirmed that patients without occlusion of major aortopulmonary collateral arteries demonstrated worse survival as compared with the occlusion group (p = 0.013). The Kaplan–Meier survival curves of patients who underwent different palliative procedures showed no differences. Conclusions: For patients with pulmonary atresia, ventricular septal defect and major aortopulmonary collateral arteries when a primary repair is not feasible, those without occlusion of major aortopulmonary collateral arteries have a higher risk of death following an initial palliative procedure compared with patients who underwent occlusion of major aortopulmonary collateral arteries. The occlusion of major aortopulmonary collateral arteries is not associated with a higher rate of complete repair or better improvement of pulmonary artery growth.


Cancers ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 700 ◽  
Author(s):  
Fabio Zattoni ◽  
Elena Incerti ◽  
Fabrizio Dal Moro ◽  
Marco Moschini ◽  
Paolo Castellucci ◽  
...  

Objectives: To evaluate the ability of 18F-labeled fluoro-2-deoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) to predict survivorship of patients with bladder cancer (BC) and/or upper urinary tract carcinoma (UUTC). Materials: Data from patients who underwent FDG PET/CT for suspicion of recurrent urothelial carcinoma (UC) between 2007 and 2015 were retrospectively collected in a multicenter study. Disease management after the introduction of FDG PET/CT in the diagnostic algorithm was assessed in all patients. Kaplan-Meier and log-rank analysis were computed for survival assessment. A Cox regression analysis was used to identify predictors of recurrence and death, for BC, UUTC, and concomitant BC and UUTC. Results: Data from 286 patients were collected. Of these, 212 had a history of BC, 38 of UUTC and 36 of concomitant BC and UUTC. Patient management was changed in 114/286 (40%) UC patients with the inclusion of FDG PET/CT, particularly in those with BC, reaching 74% (n = 90/122). After a mean follow-up period of 21 months (Interquartile range: 4–28 mo.), 136 patients (47.4%) had recurrence/progression of disease. Moreover, 131 subjects (45.6%) died. At Kaplan-Meier analyses, patients with BC and positive PET/CT had a worse overall survival than those with a negative scan (log-rank < 0.001). Furthermore, a negative PET/CT scan was associated with a lower recurrence rate than a positive examination, independently from the primary tumor site. At multivariate analysis, in patients with BC and UUTC, a positive FDG PET/CT resulted an independent predictor of disease-free and overall survival (p < 0,01). Conclusions: FDG PET/CT has the potential to change patient management, particularly for patients with BC. Furthermore, it can be considered a valid survival prediction tool after primary treatment in patients with recurrent UC. However, a firm recommendation cannot be made yet. Further prospective studies are necessary to confirm our findings.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mouhamad Nasser ◽  
Sophie Larrieu ◽  
Loic Boussel ◽  
Salim Si-Mohamed ◽  
Fabienne Bazin ◽  
...  

Abstract Background There is a paucity of data on the epidemiology, survival estimates and healthcare resource utilisation and associated costs of patients with progressive fibrosing interstitial lung disease (PF-ILD) in France. An algorithm for extracting claims data was developed to indirectly identify and describe patients with PF-ILD in the French national administrative healthcare database. Methods The French healthcare database, the Système National des Données de Santé (SNDS), includes data related to ambulatory care, hospitalisations and death for 98.8% of the population. In this study, algorithms based on age, diagnosis and healthcare consumption were created to identify adult patients with PF-ILD other than idiopathic pulmonary fibrosis between 2010 and 2017. Incidence, prevalence, survival estimates, clinical features and healthcare resource usage and costs were described among patients with PF-ILD. Results We identified a total of 14,413 patients with PF-ILD. Almost half of them (48.1%) were female and the mean (± standard deviation) age was 68.4 (± 15.0) years. Between 2010 and 2017, the estimated incidence of PF-ILD ranged from 4.0 to 4.7/100,000 person-years and the estimated prevalence from 6.6 to 19.4/100,000 persons. The main diagnostic categories represented were exposure-related ILD other than hypersensitivity pneumonitis (n = 3486; 24.2%), idiopathic interstitial pneumonia (n = 3113; 21.6%) and rheumatoid arthritis-associated ILD (n = 2521; 17.5%). Median overall survival using Kaplan–Meier estimation was 3.7 years from the start of progression. During the study, 95.2% of patients had ≥ 1 hospitalisation for respiratory care and 34.3% were hospitalised in an intensive care unit. The median (interquartile range) total specific cost per patient during the follow-up period was €25,613 (10,622–54,287) and the median annual cost per patient was €18,362 (6856–52,026), of which €11,784 (3003–42,097) was related to hospitalisations. Limitations included the retrospective design and identification of cases through an algorithm in the absence of chest high-resolution computed tomography scans and pulmonary function tests. Conclusions This large, real-world, longitudinal study provides important insights into the characteristics, epidemiology and healthcare resource utilisation and costs associated with PF-ILD in France using a comprehensive and exhaustive database, and provides vital evidence that PF-ILD represents a high burden on both patients and healthcare services. Trial registration ClinicalTrials.gov, NCT03858842. ISRCTN, ISRCTN12345678. Registered 3 January 2019—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT03858842


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