scholarly journals The presence of copy number variants in specific topologically associating domains has prognostic value in many cancer types

2019 ◽  
Author(s):  
Lifei Li ◽  
Nicolai K. H. Barth ◽  
Christian Pilarsky ◽  
Leila Taher
Keyword(s):  
Gene Expression ◽  
Prognostic Value ◽  
Gene Expression Regulation ◽  
Cox Regression ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Cancer Genes ◽  
Cox Regression Analysis ◽  
Topologically Associating Domains ◽  
Cancer Types

AbstractThe human genome is organized into topologically associating domains (TADs), which represent contiguous regions with a higher frequency of intra-interactions as opposed to inter-interactions. TADs contribute to gene expression regulation by restricting interactions between regulatory elements, and their disruption by genomic rearrangements can result in altered gene expression and, ultimately, in cancer. Here, we provide a proof-of-principle that mutations within TADs can be used to predict the survival of cancer patients. For this purpose, we first constructed a set of 1,467 TADs representing the three-dimensional organization of genome across 24 normal human tissues. We then used Cox regression analysis to assess the prognostic value of the TADs in different cancer types, and identified a total of 35 TADs that were prognostic for at least one of nine cancer types. Interestingly, only 46% of the prognostic TADs comprised one or more genes with a known causal association with cancer. Moreover, for those TADs encompassing such a gene, the prognostic effect of the TAD was only directed related to the presence/absence of mutations in the gene in 13% of the cases. These observations indicate that the predictive power of a large proportion of the prognostic TADs is independent of whether pan-cancer genes are mutated or not. Furthermore, 34% of the 35 prognostic TADs showed strong structural perturbations in the cancer genome, which might mediate cancer development and progression. This study has important implications for the interpretation of cancer-related non-coding mutations and offer insights to new strategies for personalizing cancer medicine.

scholarly journals Cancer Is Associated with Alterations in the Three-Dimensional Organization of the Genome

Cancers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1886 ◽  
Author(s):  
Lifei Li ◽  
Nicolai K. H. Barth ◽  
Christian Pilarsky ◽  
Leila Taher
Keyword(s):  
Human Genome ◽  
Cancer Patients ◽  
Cancer Progression ◽  
Gene Expression Regulation ◽  
Cox Regression ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Cox Regression Analysis ◽  
Regulatory Mutations ◽  
Coding Variants

The human genome is organized into topologically associating domains (TADs), which represent contiguous regions with a higher frequency of intra-interactions as opposed to inter-interactions. TADs contribute to gene expression regulation by restricting the interactions between their regulatory elements, and TAD disruption has been associated with cancer. Here, we provide a proof of principle that mutations within TADs can be used to predict the survival of cancer patients. Specifically, we constructed a set of 1467 consensus TADs representing the three-dimensional organization of the human genome and used Cox regression analysis to identify a total of 35 prognostic TADs in different cancer types. Interestingly, only 46% of the 35 prognostic TADs comprised genes with known clinical relevance. Moreover, in the vast majority of such cases, the prognostic value of the TAD was not directly related to the presence/absence of mutations in the gene(s), emphasizing the importance of regulatory mutations. In addition, we found that 34% of the prognostic TADs show strong structural perturbations in the cancer genome, consistent with the widespread, global epigenetic dysregulation often observed in cancer patients. In summary, this study elucidates the mechanisms through which non-coding variants may influence cancer progression and opens new avenues for personalized medicine.

scholarly journals Identification of a Ferroptosis Gene Set That Mediates the Prognosis of Squamous Cell Carcinoma of the Head and Neck

2021 ◽  
Vol 12 ◽  
Author(s):  
Chunyan Li ◽  
Xuemin Wang ◽  
Rujia Qin ◽  
Zhaoming Zhong ◽  
Chuanzheng Sun
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Regression Analysis ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Risk Score ◽  
Prognostic Value ◽  
Cox Regression ◽  
Cox Regression Analysis ◽  
Validation Set

Squamous cell carcinoma of the head and neck (HNSCC) is one of the six most common malignancies. HNSCC has both a high incidence and poor prognosis, and its prognostic factors remain unclear. Ferroptosis is a newly discovered form of programmed cell death that is iron-dependent. Increasing evidence indicates that targeting ferroptosis may present a new form of anti-tumor treatment. However, the prognostic value of ferroptosis-related genes (FRGs) in HNSCC is unclear. This study was designed to identify molecular markers associated with ferroptosis that influence prognosis in patients with HNSCC. We used HNSCC tumor and normal data from The Cancer Genome Atlas (TCGA) to identify prognosis-related FRGs. An FRG-based prognostic risk score was constructed, and its prognostic value for patients with HNSCC was evaluated using receiver operating characteristic curve (ROC) and nomogram analyses. The model was validated using the Gene Expression Omnibus (GEO) database. Univariate Cox regression analysis in patients with HNSCC revealed 11 FRGs that were significantly associated with overall survival (OS). We constructed a ferroptosis risk score model based on five genes and divided the patients into different risk groups based on its median value. Kaplan-Meier curve analysis showed that patients with a higher ferroptosis risk score had shorter OS (TCGA training set: P < 0.001, TCGA validation set: P < 0.05,GEO validation set: P < 0.001), and Gene Expression Profiling Interactive Analysis (GEPIA) further verified the relationships between these five genes and prognosis in patients with HNSCC. Multivariate Cox regression analysis showed that the risk score remained an independent predictor of OS after the exclusion of clinical confounders (HR > 1, P < 0.01). Significant differences in gene function enrichment analysis and immune cell infiltration status were identified between the two groups. The prognostic model can be used to predict the prognosis of patients with HNSCC. Moreover, the five FRGs may affect ferroptosis in HNSCC and thereby represent potential treatment targets. These results provide new directions for HNSCC treatment.

scholarly journals Relationship of megakaryocyte size at diagnosis to chemotherapeutic response in children with acute nonlymphocytic leukemia

Blood ◽  
1983 ◽  
Vol 61 (5) ◽  
pp. 867-870 ◽  
Author(s):  
CW Jackson ◽  
GV Dahl
Keyword(s):  
Complete Remission ◽  
Prognostic Value ◽  
Cox Regression ◽  
Time To Failure ◽  
Acute Nonlymphocytic Leukemia ◽  
Spleen Size ◽  
Cox Regression Analysis ◽  
Biopsy Specimens ◽  
Chemotherapeutic Response ◽  
Relationship Of

Abstract Small megakaryocytes are frequently seen in patients with acute nonlymphocytic leukemia (ANLL). In this study, median megakaryocyte diameters were determined in marrow biopsy specimens of 32 children at diagnosis of ANLL and related to platelet count and chemotherapeutic response. The association between median megakaryocyte size and time-to- failure was striking. Seven of 9 patients with median megakaryocyte diameters greater than 20 microns remain in continuous complete remission for more than 3 yr, whereas 20 of 23 patients with smaller median megakaryocyte diameters failed therapy within 15 mo (p = 0.002). By Cox-regression analysis, megakaryocyte size had independent prognostic value (p less than 0.001), surpassing that of spleen size, the only other feature having significant association with time-to- failure. Megakaryocyte size at diagnosis may be useful for predicting the likelihood of prolonged complete remission in ANLL.

scholarly journals Prognostic value of health-related quality of life in patients with acute dyspnea

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
M Belkin ◽  
D Wussler ◽  
I Strebel ◽  
E Michou ◽  
N Kozhuharov ◽  
...  
Keyword(s):  
Prognostic Value ◽  
Cox Regression ◽  
Acute Dyspnea ◽  
Cox Regression Analysis ◽  
Prognostic Accuracy ◽  
Related Quality ◽  
Health Related ◽  
Complete Set ◽  
Eq Vas

Abstract Background Previous studies have shown the prognostic value of health-related quality of life (HRQL) in stable and ambulatory chronic heart failure patients. However, it is unknown whether HRQL can predict all-cause mortality in patients presenting to the emergency department (ED) after acute onset of symptoms. In order to address this unmet need, the aim of this study was to assess the prognostic value of HRQL in patients with acute dyspnea caused by acute heart failure (AHF) and other dyspnea aetiologies for 360-day mortality. Purpose To assess prognostic value of HRQL using the generic EQ-5D and visual analogue scale (EQ VAS) in patients with acute dyspnea. Methods Basics in Acute Shortness of Breath EvaLuation (BASEL V) is a prospective, multicenter, diagnostic study enrolling adult patients presenting with acute dyspnea to the ED. For this analysis, only patients with a complete set of variables necessary for calculation of EQ-5D (range 0–10; with higher score indicating worse HRQL) and EQ VAS (range 0–100; with 100 being the best imaginable health state) at baseline were included. The endpoint was the prognostic value of EQ-5D and EQ VAS at 360 days of follow-up regarding all-cause death. Prognostic accuracy was calculated using c-statistics. In a cox regression analysis EQ-5D was treated as both, a continuous and categorical variable. Adjustments were made for clinically relevant covariates (age, sex, orthopnoea, edema, level of N-terminal pro-B-type natriuretic peptide (NT-proBNP) at presentation, history of coronary artery disease and chronic obstructive pulmonary disease, diuretics, β-blockers and ACE-inhibitors at discharge). Results Among 2605 patients enrolled, 1141 (43,8%) had a complete set of variables allowing the calculation of EQ-5D and EQ VAS. Of these patients 594 (52.1%) had an adjudicated final diagnosis of AHF. 211 (18.5%) patients died within 360 days of follow-up. Median EQ-5D was 3 (interquartile range (IQR) 1.5–5) and median EQ VAS was 50 (IQR 40–70). The prognostic accuracy for 360-day mortality was 0.65 (95% confidence interval ((CI) 0.61–0.69) and 0.58 (95% CI 0.54–0.62) for EQ-5D and EQ VAS, respectively (p=0.002). After combining EQ-5D and EQ VAS in a logistic regression model c-statistics regarding all-cause mortality within 360 days did not improve. The prognostic accuracy of EQ-5D was comparable to that of NT-proBNP (c-statistics 0.69, p=0.385). In an adjusted cox regression analysis the hazard ratio for patients with EQ-5D >4 was 2.2 (95% CI 1.7–2.9; p<0.001). Conclusions In patients presenting with acute dyspnea HRQL is a strong prognostic instrument. Independently of the aetiology of the dyspnea the prognostic value of the generic EQ-5D for 360-day mortality is comparable to NT-proBNP. Patients with an EQ-5D >4 are at significantly higher risk for mortality within 360 days. Figure 1. Prognostic value of HRQL Funding Acknowledgement Type of funding source: Public grant(s) – National budget only. Main funding source(s): Swiss National Science Foundation, Swiss Heart Foundation

Cognitive impairment predicts conversion to multiple sclerosis in clinically isolated syndromes

2009 ◽  
Vol 16 (1) ◽  
pp. 62-67 ◽  
Author(s):  
Valentina Zipoli ◽  
Benedetta Goretti ◽  
Bahia Hakiki ◽  
Gianfranco Siracusa ◽  
Sandro Sorbi ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Cognitive Impairment ◽  
Prognostic Value ◽  
Cox Regression ◽  
Cox Regression Analysis ◽  
Clinically Isolated Syndromes ◽  
Kaplan Meier ◽  
Sizable Proportion ◽  
One Year ◽  
Therapeutic Decision Making

Significant cognitive impairment has been found in 20—30% of patients with clinically isolated syndromes suggestive of multiple sclerosis. In this study we aimed to assess the prognostic value of the presence of cognitive impairment for the conversion to multiple sclerosis in patients with clinically isolated syndromes. All patients with clinically isolated syndromes consecutively referred to our centre since 2002 and who had been followed-up for at least one year underwent cognitive assessment through the Rao’s Battery and the Stroop test. Possible predictors of conversion to clinically definite multiple sclerosis were evaluated through the Kaplan Meier curves and Cox regression analysis. A total of 56 patients (41 women; age 33.2 ± 8.5 years; expanded disability scale score 1.2 ± 0.7) were recruited. At baseline, 32 patients (57%) fulfilled McDonald’s criteria for dissemination in space. During the follow-up (3.5 ± 2.3 years), 26 patients (46%) converted to a diagnosis of multiple sclerosis. In particular, 64% of patients failing ≥ 2 tests and 88% of patients failing ≥ 3 tests converted to multiple sclerosis. In the Cox regression model, the failure of at least three tests (HR 3.3; 95% CI 1.4—8.1; p = 0.003) and the presence of McDonald’s dissemination in space at baseline (HR 3.8; 95% CI 1.5—9.7; p = 0.005), were found to be predictors for conversion to multiple sclerosis. We conclude that cognitive impairment is detectable in a sizable proportion of patients with clinically isolated syndromes. In these subjects cognitive impairment has a prognostic value in predicting conversion to multiple sclerosis and may therefore play a role in therapeutic decision making.

Identification and Validation of a Seven m6A-related lncRNAs Signature Predicting Prognosis of Ovarian Cancer

2021 ◽  
Author(s):  
Yan Li ◽  
Xiaoying Wang ◽  
Yue Han ◽  
Xun Li
Keyword(s):  
Ovarian Cancer ◽  
Regression Analysis ◽  
Correlation Analysis ◽  
Prognostic Value ◽  
Cox Regression ◽  
Risk Group ◽  
Pearson Correlation ◽  
Regression Analyses ◽  
Cox Regression Analysis ◽  
Pearson Correlation Analysis

Abstract Background: Long non-coding RNAs (lncRNAs) play an important role in angiogenesis, immune response, inflammatory response and tumor development and metastasis. m6 A (N6 - methyladenosine) is one of the most common RNA modifications in eukaryotes. The aim of our research was to investigate the potential prognostic value of m6A-related lncRNAs in ovarian cancer (OC).Methods: The data we need for our research was downloaded from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. Pearson correlation analysis between 21 m6A regulators and lncRNAs was performed to identify m6A-related lncRNAs. Univariate Cox regression analysis was implemented to screen for lncRNAs with prognostic value. A least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox regression analyses was used to further reduct the lncRNAs with prognostic value and construct a m6A-related lncRNAs signature for predicting the prognosis of OC patients. Results: 275 m6A-related lncRNAs were obtained using pearson correlation analysis. 29 m6A-related lncRNAs with prognostic value was selected through univariate Cox regression analysis. Then, a seven m6A-related lncRNAs signature was identified by LASSO Cox regression. Each patient obtained a riskscore through multivariate Cox regression analyses and the patients were classified into high-and low-risk group using the median riskscore as a cutoff. Kaplan-Meier curve revealed that the patients in high-risk group have poor outcome. The receiver operating characteristic curve revealed that the predictive potential of the m6A-related lncRNAs signature for OC was powerful. The predictive potential of the m6A-related lncRNAs signature was successfully validated in the GSE9891, GSE26193 datasets and our clinical specimens. Multivariate analyses suggested that the m6A-related lncRNAs signature was an independent prognostic factor for OC patients. Moreover, a nomogram based on the expression level of the seven m6A-related lncRNAs was established to predict survival rate of patients with OC. Finally, a competing endogenous RNA (ceRNA) network associated with the seven m6A-related lncRNAs was constructed to understand the possible mechanisms of the m6A-related lncRNAs involed in the progression of OC.Conclusions: In conclusion, our research revealed that the m6A-related lncRNAs may affect the prognosis of OC patients and identified a seven m6A-related lncRNAs signature to predict the prognosis of OC patients.

scholarly journals Expression of LOX Suggests Poor Prognosis in Gastric Cancer

2021 ◽  
Vol 8 ◽  
Author(s):  
Jinfeng Zhu ◽  
Chen Luo ◽  
Jiefeng Zhao ◽  
Xiaojian Zhu ◽  
Kang Lin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Logistic Regression ◽  
Regression Analysis ◽  
Poor Prognosis ◽  
Cox Regression ◽  
Gene Set Enrichment Analysis ◽  
High Expression ◽  
Expression Level ◽  
Cox Regression Analysis

Background: Lysyl oxidase (LOX) is a key enzyme for the cross-linking of collagen and elastin in the extracellular matrix. This study evaluated the prognostic role of LOX in gastric cancer (GC) by analyzing the data of The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) dataset.Methods: The Wilcoxon rank-sum test was used to calculate the expression difference of LOX gene in gastric cancer and normal tissues. Western blot and immunohistochemical staining were used to evaluate the expression level of LOX protein in gastric cancer. Kaplan-Meier analysis was used to calculate the survival difference between the high expression group and the low expression group in gastric cancer. The relationship between statistical clinicopathological characteristics and LOX gene expression was analyzed by Wilcoxon or Kruskal-Wallis test and logistic regression. Univariate and multivariate Cox regression analysis was used to find independent risk factors affecting the prognosis of GC patients. Gene set enrichment analysis (GSEA) was used to screen the possible mechanisms of LOX and GC. The CIBERSORT calculation method was used to evaluate the distribution of tumor-infiltrating immune cell (TIC) abundance.Results: LOX is highly expressed in gastric cancer tissues and is significantly related to poor overall survival. Wilcoxon or Kruskal-Wallis test and Logistic regression analysis showed, LOX overexpression is significantly correlated with T-stage progression in gastric cancer. Multivariate Cox regression analysis on TCGA and GEO data found that LOX (all p < 0.05) is an independent factor for poor GC prognosis. GSEA showed that high LOX expression is related to ECM receptor interaction, cancer, Hedgehog, TGF-beta, JAK-STAT, MAPK, Wnt, and mTOR signaling pathways. The expression level of LOX affects the immune activity of the tumor microenvironment in gastric cancer.Conclusion: High expression of LOX is a potential molecular indicator for poor prognosis of gastric cancer.

scholarly journals The diagnostic and prognostic value of H2AFY in hepatocellular carcinoma

2020 ◽  
Author(s):  
xuyang ma ◽  
Ying Ding ◽  
Li Zeng
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Poor Prognosis ◽  
Prognostic Value ◽  
Clinical Characteristics ◽  
Cox Regression ◽  
Normal Liver ◽  
Diagnostic Value ◽  
The Relationship ◽  
Diagnostic And Prognostic Value

Abstract Background: The potential correlation between H2AFY (also known as MacroH2A1) and the clinical characteristics of hepatocellular carcinoma (HCC) patients was analysed through gene expression profiles and clinical data in The Cancer Genome Atlas (TCGA) database, and the diagnostic and prognostic value of H2AFY in HCC was discussed. Methods: The gene expression data of HCC and the corresponding clinical characteristics of HCC patients were downloaded from the TCGA database. The differences in H2AFY in normal liver tissues and HCC were analysed. The relationship between H2AFY and clinical characteristics was analysed by Wilcoxon signed-rank test, logistic regression and Kruskal-Wallis test. The Kaplan-Meier method and the Cox regression method were used to analyse the relationship between overall survival and clinical characteristics of the patients. An ROC curve was used to predict the diagnostic value of H2AFY in HCC. Gene set enrichment analysis (GSEA) was used to analyse the pathway enrichment of H2AFY. Result: Compared with normal liver tissues, H2AFY was significantly highly expressed in HCC. H2AFY was positively correlated with the age, clinical stage, G stage (grade) and T stage (tumor stage) of liver cancer patients. Higher H2AFY expression predicted a poor prognosis in HCC patients. Cox regression analysis suggested that H2AFY was an independent risk factor for the prognosis of HCC patients. The ROC curve suggested that H2AFY had certain diagnostic value in HCC. GSEA suggested that H2AFY was correlated with lipid metabolism and a variety of tumour pathways. Conclusion: Our study showed that H2AFY was significantly overexpressed in HCC. H2AFY may be a potential diagnostic and prognostic marker for HCC, and high expression of H2AFY predicts a poor prognosis in patients with HCC.

scholarly journals The Prognostic Value of the m6A Score in Multiple Myeloma Based on Machine Learning

2021 ◽  
Vol 1 (3) ◽  
pp. 77-87
Author(s):  
Gong Xiao ◽  
Qiongjing Yuan ◽  
Wei Wang
Keyword(s):  
Multiple Myeloma ◽  
Cancer Progression ◽  
Risk Score ◽  
Prognostic Value ◽  
Risk Model ◽  
Cox Regression ◽  
Microarray Dataset ◽  
Immune Checkpoints ◽  
Bioinformatics Analyses ◽  
Cox Regression Analysis

Background: Multiple myeloma (MM) is one of the most common cancers of the blood system. N6-methyladenosine (m6A) plays an important role in cancer progression. We aimed to investigate the prognostic relevance of the m6A score in multiple myeloma through a series of bioinformatics analyses. Methods: The microarray dataset GSE4581 and GSE57317 used in this study were downloaded from the Gene Expression Omnibus (GEO) database. The m6A score was calculated using the GSVA package. The Random forests, univariate Cox regression analysis and Lasso analyses were performed for the differentially expressed genes (DEGs). Kaplan–Meier analysis and an ROC curve were used to diagnose the effectiveness of the model. Results: The GSVA R software package was used to predict the function. A total of 21 m6A genes were obtained, and 286 DEGs were identified between high and low m6A score groups. The risk model was constructed and composed of PRX, LBR, RB1, FBXL19-AS1, ARSK, MFAP3L, SLC44A3, UNC119 and SHCBP1. Functional analysis of risk score showed that with the increase in the risk score, Activated CD4 T cells, Memory B cells and Type 2 T helper cells were highly infiltrated. Conclusions: Immune checkpoints such as HMGB1, TGFB1, CXCL9 and HAVCR2 were significantly positively correlated with the risk score. We believe that the m6A score has a certain prognostic value in multiple myeloma.

scholarly journals Actively translated uORFs reduce translation and mRNA stability independent of NMD in Arabidopsis

2021 ◽  
Author(s):  
Hsin-Yen Larry Wu ◽  
Polly Yingshan Hsu
Keyword(s):  
Gene Expression ◽  
Mrna Stability ◽  
Gene Expression Regulation ◽  
Regulatory Elements ◽  
Expression Regulation ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Nonsense Mediated Decay ◽  
Protein Levels ◽  
Eukaryotic Genes

ABSTRACTUpstream ORFs (uORFs) are widespread cis-regulatory elements in the 5’ untranslated regions of eukaryotic genes. Translation of uORFs could negatively regulate protein synthesis by repressing main ORF (mORF) translation and by reducing mRNA stability presumably through nonsense-mediated decay (NMD). While the above expectations were supported in animals, they have not been extensively tested in plants. Using ribosome profiling, we systematically identified 2093 Actively Translated uORFs (ATuORFs) in Arabidopsis seedlings and examined their roles in gene expression regulation by integrating multiple genome-wide datasets. Compared with genes without uORFs, we found ATuORFs result in 38%, 14%, and 43% reductions in translation efficiency, mRNA stability, and protein levels, respectively. The effects of predicted but not actively translated uORFs are much weaker than those of ATuORFs. Interestingly, ATuORF-containing genes are also expressed at higher levels and encode longer proteins with conserved domains, features that are common in evolutionarily older genes. Moreover, we provide evidence that uORF translation in plants, unlike in vertebrates, generally does not trigger NMD. We found ATuORF-containing transcripts are degraded through 5’ to 3’ decay, while NMD targets are degraded through both 5’ to 3’ and 3’ to 5’ decay, suggesting uORF-associated mRNA decay and NMD have distinct genetic requirements. Furthermore, we showed ATuORFs and NMD repress translation through separate mechanisms. Our results reveal that the potent inhibition of uORFs on mORF translation and mRNA stability in plants are independent of NMD, highlighting a fundamental difference in gene expression regulation by uORFs in the plant and animal kingdoms.

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