T-cell receptor-α CDR3 domain chemical features correlate with survival rates in bladder cancer

Chobrutskiy, Boris I.; Zaman, Saif; Diviney, Andrea; Mihyu, Moody M.; Blanck, George

doi:10.1007/s00432-018-2815-1

Cited by 34 publications

(19 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, high in ltration of memory activated CD4 + T cell subsets were associated with prolonged OS and reduced risk of tumor recurrence in bladder cancer [30]. Chobrutskiy et al demonstrated that lower CDR3 region isoelectric point in T cell receptor was associated with better survival outcomes in bladder cancer [31]. In brief, our data suggested that the 9-lncRNAs signature modulated the development and progression of bladder cancer in a variety of ways.…”

Section: Discussionmentioning

confidence: 51%

Development and verification of immune-related long non-coding RNA prognostic signature in bladder cancer

Lai¹,

Wu²,

Li³

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Bladder cancer is the second most common malignant tumor in urogenital system. The research aimed to investigate the prognostic role of immune-related long non-coding RNA (lncRNA) in bladder cancer. Methods: We extracted 411 bladder cancer samples from The Cancer Genome Atlas database. Single-sample gene set enrichment analysis was employed to assess the immune cell infiltration of these samples. We recognized differentially expressed lncRNAs between tumors and paracancerous tissues, and differentially expressed lncRNAs between the high and low immune cell infiltration groups. Venn diagram analysis detected differentially expressed lncRNAs that intersected the above groups. LncRNAs with prognostic significance were identified by regression analysis and survival analysis. Multivariate Cox analysis was used to establish the risk score model. The nomogram was established and evaluated by receiver operating characteristic (ROC) curve analysis, concordance index (C-index) analysis, calibration chart, and decision curve analysis (DCA). Additionally, we performed gene set enrichment analysis to explore the potential functions of the screened lncRNAs in tumor pathogenesis.Results: Three hundred and twenty differentially expressed lncRNAs were recognized. We randomly divided patients into the training data set and the testing data set at a 2: 1 ratio. In the training data set, 9 immune-related lncRNAs with prognostic significance were identified. The risk score model was constructed to classify patients as high- and low-risk cohorts. Patients in the low-risk cohort had better survival outcomes than those in the high-risk cohort. The nomogram was established based on the indicators including age, gender, TNM stage, and risk score. The model’s predictive performance was confirmed by ROC curve analysis, C-index analysis, calibration chart, and DCA. The testing data set also achieved similar results. Bioinformatics analysis suggested that the 9-lncRNA signature was involved in modulation of various immune responses, antigen processing and presentation, and T cell receptor signaling pathway.Conclusions: The immune-related lncRNAs have the potential to predict the prognosis of bladder cancer and may play a key role in bladder cancer biology.Trial registration: It was a retrospective study and the gene expression data were obtained from the TCGA database. Trial registration was not needed.

show abstract

Section: Discussionmentioning

confidence: 51%

Development and verification of immune-related long non-coding RNA prognostic signature in bladder cancer

Lai¹,

Wu²,

Li³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“… 34 Moreover, high infiltration of memory‐activated CD4 + T cell subsets were associated with prolonged OS and reduced risk of tumor recurrence in bladder cancer. 35 Chobrutskiy et al 36 demonstrated that lower CDR3 region isoelectric point in T cell receptor was associated with better survival outcomes in bladder cancer.…”

Section: Discussionmentioning

confidence: 99%

A robust signature of immune‐related long non‐coding RNA to predict the prognosis of bladder cancer

Lai

et al. 2021

Cancer Medicine

View full text Add to dashboard Cite

show abstract

“…The current software is capable of detecting more recombinations by increasing V and J sequence searches near the N-region diversity section of the recombination (28,29).…”

Section: Discussionmentioning

confidence: 99%

B-cell Receptor Recombinations in Lung Adenocarcinoma Exome Files Correlate With a Higher Overall Survival Rate

Wei

Callahan

et al. 2020

Anticancer Res

Self Cite

View full text Add to dashboard Cite

Background/Aim: While there has been a rapid development in genomic data mining approaches for T-cell receptor recombinations (TcR), less emphasis has been placed on B-cell receptor (BcR) recombinations. Materials and Methods: We obtained lung cancer exome files from the cancer genome atlas (TCGA) and mined the files for TcR and BcR recombination reads. Results: There was a robust detection of BcR light chain recombination reads in lung adenocarcinoma (TCGA-LUAD) samples, and there was a correlation between the detection of light chain recombination reads and a more favorable outcome. This result was supported by analyses of the expression of B-cell markers as indicated by LUAD RNASeq files. Conclusion: BcR and TcR recombination reads recovered from LUAD WXS files, either alone or in combination with the human leukocyte antigen (HLA) type, are likely to have prognostic value.

show abstract

T-cell receptor-α CDR3 domain chemical features correlate with survival rates in bladder cancer

Cited by 34 publications

References 25 publications

Development and verification of immune-related long non-coding RNA prognostic signature in bladder cancer

Development and verification of immune-related long non-coding RNA prognostic signature in bladder cancer

A robust signature of immune‐related long non‐coding RNA to predict the prognosis of bladder cancer

B-cell Receptor Recombinations in Lung Adenocarcinoma Exome Files Correlate With a Higher Overall Survival Rate

Contact Info

Product

Resources

About