scholarly journals Seven Autophagy-Related lncRNAs Associated With Clinical Prognosis in Hepatocellular Carcinoma.

Author(s):  
Yaping Zhou ◽  
Liu Yang ◽  
Xiangxin Zhang ◽  
Xiaotong Zhao ◽  
Jianfeng Fu ◽  
...  

Abstract Background: LncRNA may be involved in the occurrence, metastasis, and chemical reaction of hepatocellular carcinoma (HCC) through various pathways associated with autophagy. Therefore, it is urgent to reveal more autophagy-related lncRNAs, explore these lncRNAs' clinical significance, and find new targeted treatment strategies. Methods: In our study, RNA-seq and clinical data of normal and HCC patients were obtained from the TCGA database, and autophagy genes were obtained from the human autophagy database. Results: The risk prediction model containing seven autophagy-related lncRNAs was constructed. Overall survival (OS) curves show that the high-risk group patients significantly shorter than the low-risk group (P=2.292e-10), and the five years survival rate of the high-risk group (HR 0.286, 95%CI 0.199-0.411) is less than half of the low-risk group (HR 0.694, 95%CI 0.547-0.77). Univariate Cox regression indicated that risk score of the risk prediction model (P<0.001, 95%CI 1.210-1.389 ), T (P<0.001, 95%CI 1.443-2.287), and stage (P<0.001 ,95%CI 1.466-2.408 ) were independent prognostic indicators. However, only the risk score remains the independent prognostic indicator(P<0.001, 95%CI 1.197-1.400 ) based on the multivariate analysis. This risk model's prediction efficiency is significantly higher than other clinicopathological factors for 1-, 3- and 5-year survival rate prediction (AUC are 0.853, 0.794, and 0.764, respectively). Remarkably, the 7 autophagy-related lncRNAs may participate in Spliceosome, Cell cycle, RNA transport, DNA replication, and mRNA surveillance pathway and be related to the biological process of RNA splicing and mRNA splicing. Conclusion: In conclusion, the 7 autophagy-related lncRNAs might be promising prognostic and therapeutic targets for HCC.

2020 ◽  
Vol 7 ◽  
Author(s):  
Muqi Li ◽  
Minni Liang ◽  
Tian Lan ◽  
Xiwen Wu ◽  
Wenxuan Xie ◽  
...  

BackgroundLong non-coding RNA (LncRNA) plays an important role in the occurrence and development of hepatocellular carcinoma (HCC). This study aims to establish an immune-related LncRNA model for risk assessment and prognosis prediction in HCC patients.MethodsHepatocellular carcinoma patient samples with complete clinical data and corresponding whole transcriptome expression were obtained from the Cancer Genome Atlas (TCGA). Immune-related genes were acquired from the Gene Set Enrichment Analysis (GSEA) website and matched with LncRNA in the TCGA to get immune-related LncRNA. Least Absolute Shrinkage and Selection Operator (LASSO) regression was used for screening the candidate LncRNAs and calculating the risk coefficient to establish the prognosis model. Patients were divided into a high-risk group and a low-risk group depending on the median risk score. The reliability of the prediction was evaluated in the validation cohort and the whole cohort. GSEA and principal component analysis were used for function evaluation.ResultsA total of 319 samples met the screening criteria and were randomly distributed across the training cohort and the validation cohort. After comparison with the IMMUNE_RESPONSE gene set and the IMMUNE_SYSTEM_PROCESS gene set, a total of 3094 immune-related LncRNAs were screened. Ultimately, four immune-related LncRNAs were used to construct a formula using LASSO regression. According to the formula, the low-risk group showed a higher survival rate than the high-risk group in the validation cohort and the whole cohort. The receiver operating characteristic curves data demonstrated that the risk score was more specific than other traditional clinical characteristics in predicting the 5-year survival rate for HCC.ConclusionThe four-immune-related-LncRNA model can be used for survival prediction in HCC and guide clinical therapy.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e20553-e20553
Author(s):  
Jianchun Duan ◽  
Hua Bai ◽  
Yiting Sun ◽  
Fei Gai ◽  
Shenya Tian ◽  
...  

e20553 Background: Clinical characters cannot precisely evaluate long-term survival of patients with resectable lung adenocarcinoma. Genomics studies of lung adenocarcinoma (LUAD) have advanced our understanding of LUAD's biology. Thus, genomics-based robust models predicting survival outcome for patients with operatable LUAD needs to be investigated. Here, we aimed to identify new gene signatures to construct a risk prediction model via integrating Omics data from The Cancer Genome Atlas (TCGA) to better evaluate the long-term clinical outcome of LUAD patients. Methods: A cohort of one hundred and eighty-nine stage II-IIIA lung adenocarcinoma cases receiving tumor resection were screened out and downloaded from TCGA database. Tumor samples without survival information and genes with low or no expression were removed. Genes associated with cancer and immune were further narrowed down using a Master Panel Gene Set (Amoydx). Lasso-Cox regression analysis was used to screen gene-survival outcome, and then a risk prediction model was established. LUAD cases were divided into high-risk or low-risk groups as per the scores, to assess differential expressed genes and pathways. Results: A total of 8 most survival outcome related genes (CLEC7A, PAX5, XCR1, KRT7, PLCG1, DKK1, CLEC10A, IKZF3) were identified after Lasso-Cox regression analysis and used for model construction. The overall survival (OS), progression-free survival (PFS) and disease-free survival (DFS) from the subgroups within the high- and low-risk groups were assessed and showed significant prolonged in low-risk group, the hazard ratio (HR) of OS was 2.72 (95%CI: 2.04-3.61, P = 5.91e-12) in high-risk group. Hierarchical clustering analysis, gene ontology (GO) analysis, gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA) revealed that genes involved in immune responses were significantly suppressed in high-risk group, while as genes involved in antioxidative metabolism were activated, which gave us a hint that immune-metabolism interaction might play a vital role in determining the distal survival outcome of LUAD. Conclusions: Our risk prediction model enables precise evaluation of long-term survival for patients with LUAD. Further, it provides a novel and comprehensive understanding of biological impacts on LUAD prognosis, which offers new insights for future development of precise diagnostic and therapeutic approaches.[Table: see text]


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 141-141
Author(s):  
Kristen M. Sanfilippo ◽  
Suhong Luo ◽  
Tzu-Fei Wang ◽  
Tanya Wildes ◽  
Joseph Mikhael ◽  
...  

Abstract Introduction: Venous thromboembolism (VTE) is a common cause of morbidity and mortality among patients with multiple myeloma (MM). Thromboprophylaxis is a safe and effective way to decrease VTE in other high-risk populations. Current guidelines recommend use of thromboprophylaxis in MM patients at high-risk of VTE, but no validated model predicts VTE in MM. A risk prediction model for VTE in MM would allow for use of thromboprophylaxis in MM patients at high-risk of VTE while sparing those at low risk. Therefore, we sought to develop a risk prediction model for VTE in MM. Patients and Methods: Using a nationwide cohort of Veterans, we identified 4,448 patients diagnosed with MM between 1999 and 2014. We retrospectively followed patients for 180 days after start of MM chemotherapy. We identified candidate risk factors through literature review for inclusion into the time-to-event models. We used the methods of Fine and Gray to model time to VTE while accounting for the competing risk of (non-VTE) death. To minimize immortal time bias, all treatment variables were entered as time-varying variables. Using a backward, step-wise approach, we retained variables in the model with a p ≤ 0.05, or with a p < 0.50 with findings consistent with prior literature. Using beta coefficients, we developed a risk score by multiplying by a common factor and rounding to the nearest integer. The risk score for each patient was the sum of all scores for each predictor variable. We assessed model performance with Harrell's c-statistic and with the inverse probability of censoring weighting approach. Through bootstrap analysis, we validated the model internally. We carried out all statistical analyses using SAS version 9.4 (SAS Institute, Cary, NC). Results: The median time from MM diagnosis to start of treatment was 37 days. A total of 53 patients (5.7%) developed VTE within 6 months after start of MM-specific therapy. The mean time from chemotherapy start to VTE was 69 days, with 69% of VTE events occurring in the first 3 months of chemotherapy. The factors associated with VTE were combined to develop the IMPEDE VTE score (IMID 3 points, BMI 1 point, Pathologic fracture pelvis/femur 2 points, ESA 1 point, Dexamethasone (High-dose 4 points, Low-Dose 2 points)/Doxorubicin 2 points, Ethnicity/Race= Asian -3 points, history of VTE 3 points, Tunneled line/CVC 2 points) (Table 1). In addition, use of therapeutic anticoagulation (-5 points) with warfarin or low molecular weight heparin (LWMH) and use of prophylactic LMWH or aspirin (-2 points) were associated with a decreased risk of VTE. The model showed satisfactory discrimination in both the derivation cohort (Harrell's c-statistic = 0.66) and in the bootstrap validation, c-statistic = 0.65 (95% CI: 0.62 - 0.69). Using three risk groups, the incident rate of VTE with the first 6-months of starting chemotherapy was 3.1% for scores ≤ 3 (low-risk), 7.5% for a score of 4-6 (intermediate-risk), and 13.3% for patients with a score of ≥ 7 (high-risk). The risk of developing VTE within 6 months after starting chemotherapy was significantly higher for patients with intermediate- and high-risk scores compared to low-risk (Table 2). Conclusions and Relevance: We developed a risk prediction rule, IMPEDE VTE, which can identify patients with MM at high-risk of developing VTE after starting chemotherapy. IMPEDE VTE could guide clinicians in selecting patients for thromboprophylaxis in MM. Disclosures Sanfilippo: BMS/Pfizer: Speakers Bureau. Wang:Daiichi Sankyo: Consultancy, Other: Travel. Wildes:Janssen: Research Funding. Mikhael:Onyx, Celgene, Sanofi, AbbVie: Research Funding. Carson:Flatiron Health: Employment; Washington University in St. Louis: Employment; Roche: Consultancy.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e24023-e24023
Author(s):  
Shreya Gattani ◽  
Vanita Noronha ◽  
Anant Ramaswamy ◽  
Renita Castelino ◽  
Vandhita Nair ◽  
...  

e24023 Background: Clinical judgement alone is inadequate in accurately predicting chemotherapy toxicity in older adult cancer patients. Hurria and colleagues developed and validated, the CARG score (range, 0–17) as a convenient and reliable tool for predicting chemotherapy toxicity in older cancer patients in America, however, its applicability in Indian patients is unknown. Methods: An observational retrospective and prospective study between 2018 and 2020 was conducted in the Department of Medical Oncology at Tata Memorial Hospital, Mumbai, India. The study was approved by the institutional ethics committee (IEC-III; Project No. 900596) and registered in the Clinical Trials Registry of India (CTRI/2020/04/024675). Written informed consent was obtained in the prospective part of the study. Patients aged ≥ 60 years and planned for systemic therapy were evaluated in the geriatric oncology clinic and their CARG score was calculated. Patients were stratified into low (0-4), intermediate (5-9) and high risk (10-17) based on the CARG scores. The CARG score was provided to the treating physicians, along with the results of the geriatric assessment. Chemotherapy-related toxicities were captured from the electronic medical record and graded as per the NCI CTCAE, version 4.0. Results: We assessed 130 patients, with a median age 69 years (IQR, 60 to 84); 72% patients were males. The common malignancies included gastrointestinal (52%) and lung (30%). Approximately 78% patients received polychemotherapy and 53% received full dose chemotherapy. Based on the CARG score, 28 (22%) patients belonged to low risk, 80 (61%) to intermediate risk and 22 (17%) to the high risk category. The AU-ROC of the CARG score in predicting grade 3-5 toxicities was 0.61 (95% CI, 0.51-0.71). The sensitivity and specificity of the CARG score in predicting grade 3-5 toxicities were 60.8% and 78.6%. Grade 3-5 toxicities occurred in 6/28 patients (21%) in the low risk group, compared to 62/102 patients (61%) in the intermediate /high risk group, p = 0.0002. There was also a significant difference in the time to development of grade 3-5 toxicities, which occurred at a median of 2.5 cycles (IQR, 1-3.8) in the intermediate /high risk group and at a median of 6 cycles (IQR, 3.5-8) in the low risk group, p = 0.0011. Conclusions: In older Indian patients with cancer, the CARG score reliably stratifies patients into low risk and intermediate/high risk categories, predicting both the occurrence and the time to occurrence of grade 3-5 toxicities from chemotherapy. The CARG score may aid the oncologist in estimating the risk-benefit ratio of chemotherapy. An important limitation was that we provided the CARG score to the treating oncologists prior to the start of chemotherapy, which may have resulted in alterations in the chemotherapy regimen and dose and may have impacted the CARG risk prediction model. Clinical trial information: CTRI/2020/04/024675.


Author(s):  
Hui Huang ◽  
Si-min Ruan ◽  
Meng-fei Xian ◽  
Ming-de Li ◽  
Mei-qing Cheng ◽  
...  

Objectives: This study aimed to construct a prediction model based on contrast-enhanced ultrasound (CEUS) ultrasomics features and investigate its efficacy in predicting early recurrence (ER) of primary hepatocellular carcinoma (HCC) after resection or ablation. Methods: This study retrospectively included 215 patients with primary HCC, who were divided into a developmental cohort (n = 139) and a test cohort (n = 76). Four representative images—grayscale ultrasound, arterial phase, portal venous phase and delayed phase —were extracted from each CEUS video. Ultrasomics features were extracted from tumoral and peritumoral area inside the region of interest. Logistic-regression was used to establish models, including a tumoral model, a peritumoral model and a combined model with additional clinical risk factors. The performance of the three models in predicting recurrence within 2 years was verified. Results: The combined model performed best in predicting recurrence within 2 years, with an area under the curve (AUC) of 0.845, while the tumoral model had an AUC of 0.810 and the peritumoral model one of 0.808. For prediction of recurrence-free survival, the 2 year cumulative recurrence rate was significant higher in the high-risk group (76.5%) than in the low-risk group (9.5%; p < 0.0001). Conclusion: These CEUS ultrasomics models, especially the combined model, had good efficacy in predicting early recurrence of HCC. The combined model has potential for individual survival assessment for HCC patients undergoing resection or ablation. Advances in knowledge: CEUS ultrasomics had high sensitivity, specificity and PPV in diagnosing early recurrence of HCC, and high efficacy in predicting early recurrence of HCC (AUC > 0.8). The combined model performed better than the tumoral ultrasomics model and peritumoral ultrasomics model in predicting recurrence within 2 years. Recurrence was more likely to occur in the high-risk group than in the low-risk group, with 2-year cumulative recurrence rates respectively 76.5% and 9.5% (p < 0.0001).


2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Ziwei Wang ◽  
Jun Zhang ◽  
Yan Liu ◽  
Rong Zhao ◽  
Xing Zhou ◽  
...  

Endometrial cancer is one of the most common malignant tumors, lowering the quality of life among women worldwide. Autophagy plays dual roles in these malignancies. To search for prognostic markers for endometrial cancer, we mined The Cancer Genome Atlas and the Human Autophagy Database for information on endometrial cancer and autophagy-related genes and identified five autophagy-related long noncoding RNAs (lncRNAs) (LINC01871, SCARNA9, SOS1-IT1, AL161618.1, and FIRRE). Based on these autophagy-related lncRNAs, samples were divided into high-risk and low-risk groups. Survival analysis showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group. Univariate and multivariate independent prognostic analyses showed that patients’ age, pathological grade, and FIGO stage were all risk factors for poor prognosis. A clinical correlation analysis of the relationship between the five autophagy-related lncRNAs and patients’ age, pathological grade, and FIGO stage was also per https://orcid.org/0000-0001-7090-1750 formed. Histopathological assessment of the tumor microenvironment showed that the ESTIMATE, immune, and stromal scores in the high-risk group were lower than those in the low-risk group. Principal component analysis and functional annotation were performed to confirm the correlations. To further evaluate the effect of the model constructed on prognosis, samples were divided into training (60%) and validation (40%) groups, regarding the risk status as an independent prognostic risk factor. A prognostic nomogram was constructed using patients’ age, pathological grade, FIGO stage, and risk status to estimate the patients’ survival rate. C-index and multi-index ROC curves were generated to verify the stability and accuracy of the nomogram. From this analysis, we concluded that the five lncRNAs identified in this study could affect the incidence and development of endometrial cancer by regulating the autophagy process. Therefore, these molecules may have the potential to serve as novel therapeutic targets and biomarkers.


2021 ◽  
Author(s):  
Ke Han ◽  
Jukun Wang ◽  
Kun Qian ◽  
Teng Zhao ◽  
Yi Zhang

Purpose: ADME genes are those involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs. In this study, a non–small-cell lung cancer (NSCLC) risk prediction model was established using prognosis-associated ADME genes, and the predictive performance of this model was evaluated and verified. In addition, multifaceted difference analysis was performed on groups with high and low risk scores. Methods: An NSCLC sample transcriptome and clinical data were obtained from public databases. The prognosis-associated ADME genes were obtained by univariate Cox and lasso regression analyses to build a risk model. Tumor samples were divided into high-risk and low-risk score groups according to the risk score. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of the differentially expressed genes and the differences in the immune infiltration, mutation, and medication reactions in the two groups were studied in detail. Results: A risk prediction model was established with seven prognosis-associated ADME genes. Its good predictive ability was confirmed by studies of the model’s effectiveness. Univariate and multivariate Cox regression analyses showed that the model’s risk score was an independent prognostic factor for patients with NSCLC. The study also showed that the risk score closely correlated with immune infiltration, mutations, and medication reactions. Conclusion: The risk prediction model established with seven ADME genes in this study can predict the prognosis of patients with NSCLC. In addition, significant differences in immune infiltration, mutations, and therapeutic efficacy exist between the high- and low-risk score groups.


2020 ◽  
Author(s):  
Lumeng Luo ◽  
Minghe Lv ◽  
Xuan Li ◽  
Tiankui Qiao ◽  
Kuaile Zhao ◽  
...  

Abstract Background: Recent advances in immune checkpoint inhibitors (ICIs) have dramatically changed the therapeutic strategy against lung squamous cell carcinoma (LUSC). In the era of immunotherapy, effective biomarkers to better predict outcomes and inform treatment decisions for patients diagnosed with LUSC are urgently needed. We hypothesized that immune contexture of LUSC is potentially dictated by tumor intrinsic events, such as autophagy. Thus, we attempted to construct an autophagy-related risk signature and examine its prediction value for immune phenotype in LUSC.Method: The expression profile of LUSC was obtained from the cancer genome atlas (TCGA) database and the profile of autophagy-related genes (ARGs) was extracted. The survival‑related ARGs (sARGs) was screened out through survival analyses. Random forest was performed to select the sARGs and construct a prognostic risk signature based on these sARGs. The signature was further validated by receiver operating characteristic (ROC) analysis and Cox regression. GEO dataset was used as an independent testing dataset. Patients were divided into high-risk and low-risk group based on the risk score. Then, gene set enrichment analysis (GSEA) was conducted between the two groups. The Single-Sample GSEA (ssGSEA) was introduced to quantify the relative infiltration of immune cells. The correlations between risk score and several main immune checkpoints were examined. And the ESTIMATE algorithm was used to calculate the estimate/immune/stromal scores of the LUSC. Results: Four ARGs (CFLAR, RGS19, PINK1 and CTSD) with the most significant prognostic values were enrolled to construct the risk signature. Patients in high-risk group had better prognosis than the low-risk group (P < 0.0001 in TCGA; P < 0.01 in GEO) and considered as an independent prognosis factor. We also found that high-risk group indicated an immune-suppression status and had higher levels of infiltrating regulatory T cells and macrophages, which are correlated with worse outcome. Besides, risk score showed a significantly positive correlation with the expression of PD-1 and CTLA4, as well as estimate score and immune score.Conclusion: This study established a novel autophagy-related four-gene prognostic risk signature, and the autophagy-related scores are associated with immune landscape of LUSC, with higher score indicating a stronger immune-suppression status.


2020 ◽  
Author(s):  
Qinqin Liu ◽  
Jing Li ◽  
Fei Liu ◽  
Weilin Yang ◽  
Jingjing Ding ◽  
...  

Abstract Background Hepatocellular carcinoma (HCC) is associated with dismal prognosis, and prediction of the prognosis of HCC can assist the therapeutic decisions. More and more studies showed that the texture parameters of images can reflect the heterogeneity of the tumor, and may have the potential to predict the prognosis of patients with HCC after surgical resection. The aim of the study was to investigate the prognostic value of computed tomography (CT) texture parameters for patients with HCC after hepatectomy, and try to develop a radiomics nomograms by combining clinicopathological factors with radiomics signature.Methods 544 eligible patients were enrolled in the retrospective study and randomly divided into training cohort (n=381) and validation cohort (n=163). The regions of interest (ROIs) of tumor is delineated, then the corresponding texture parameters are extracted. The texture parameters were selected by using the least absolute shrinkage and selection operator (LASSO) Cox model in training cohort, and the radiomics score (Rad-score) was generated. According to the cut-off value of the Rad-score calculated by the receiver operating characteristic (ROC) curve, the patients were divided into high-risk group and low-risk group. The prognosis of the two groups was compared and validated in the validation cohort. Univariate and multivariable analyses by COX proportional hazard regression model were used to select the prognostic factors of overall survival (OS). The radiomics nomogram for OS were established based on the radiomics signature and clinicopathological factors. The Concordance index (C-index), calibration plot and decision curve analysis (DCA) were used to evaluate the performance of the radiomics nomogram.Result 7 texture parameters associated with OS were selected in the training, and the radiomics signature was formulated based on the texture parameters. The patients were divided into high-risk group and low-risk group by the cut-off values of the Rad-score of OS. The 1-, 3- and 5-year OS rate was 71.0%, 45.5% and 35.5% in the high-risk group, respectively, and 91.7%, 82.1% and 78.7%, in the low-risk group, respectively, with significant difference (P <0.001). COX regression model found that Rad-score was an independent prognostic factor of OS. In addition, the radiomics nomogram was developed based on five variables: α‐fetoprotein (AFP), platelet lymphocyte ratio (PLR), largest tumor size, microvascular invasion (MVI) and Rad-score. The nomograms displayed good accuracy in predicting OS (C-index=0.747) in the training cohort and was confirmed in the validation cohort (C-index=0.777). The calibration plots also showed an excellent agreement between the actual and predicted survival probabilities. The DAC indicated that the radiomics nomogram showed better clinical usefulness than the clinicopathologic nomogram.Conclusion The radiomics signature is potential biomarkers of the prognosis of HCC after hepatectomy. Radiomics nomogram that integrated radiomics signature can provide more accurate estimate of OS for patients with HCC after hepatectomy.


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