scholarly journals Identification of tumour immune microenvironment-related alternative splicing events for the prognostication of pancreatic adenocarcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bo Chen ◽  
Tuo Deng ◽  
Liming Deng ◽  
Haitao Yu ◽  
Bangjie He ◽  
...  
Keyword(s):  
T Cells ◽  
Alternative Splicing ◽  
High Risk ◽  
Pancreatic Adenocarcinoma ◽  
Gene Set Enrichment Analysis ◽  
Prognostic Signature ◽  
Immune Microenvironment ◽  
High Risk Patients ◽  
Risk Patients ◽  
Alternative Splicing Events

Abstract Purpose Pancreatic adenocarcinoma (PAAD) is characterized by low antitumour immune cell infiltration in an immunosuppressive microenvironment. This study aimed to systematically explore the impact on prognostic alternative splicing events (ASs) of tumour immune microenvironment (TIME) in PAAD. Methods The ESTIMATE algorithm was implemented to compute the stromal/immune-related scores of each PAAD patient, followed by Kaplan–Meier (KM) survival analysis of patients with different scores grouped by X-tile software. TIME-related differentially expressed ASs (DEASs) were determined and evaluated through functional annotation analysis. In addition, Cox analyses were implemented to construct a TIME-related signature and an AS clinical nomogram. Moreover, comprehensive analyses, including gene set enrichment analysis (GSEA), immune infiltration, immune checkpoint gene expression, and tumour mutation were performed between the two risk groups to understand the potential mechanisms. Finally, Cytoscape was implemented to illuminate the AS-splicing factor (SF) regulatory network. Results A total of 437 TIME-related DEASs significantly related to PAAD tumorigenesis and the formation of the TIME were identified. Additionally, a robust TIME-related prognostic signature based on seven DEASs was generated, and an AS clinical nomogram combining the signature and four clinical predictors also exhibited prominent discrimination by ROC (0.762 ~ 0.804) and calibration curves. More importantly, the fractions of CD8 T cells, regulatory T cells and activated memory CD4 T cells were lower, and the expression of four immune checkpoints—PD-L1, CD47, CD276, and PVR—was obviously higher in high-risk patients. Finally, functional analysis and tumour mutations revealed that aberrant immune signatures and activated carcinogenic pathways in high-risk patients may be the cause of the poor prognosis. Conclusion We extracted a list of DEASs associated with the TIME through the ESTIMATE algorithm and constructed a prognostic signature on the basis of seven DEASs to predict the prognosis of PAAD patients, which may guide advanced decision-making for personalized precision intervention.

scholarly journals Allogeneic, Off-the-Shelf, Sars-Cov-2-Specific T Cells to Treat High-Risk Patients with COVID-19

2021 ◽  
Vol 27 (3) ◽  
pp. S348-S349
Author(s):  
Spyridoula Vasileiou ◽  
Manik Kuvalekar ◽  
Aster Workineh ◽  
Ayumi Watanabe ◽  
Yovana Velazquez ◽  
...  
Keyword(s):  
T Cells ◽  
High Risk ◽  
High Risk Patients ◽  
Risk Patients

scholarly journals Selective depletion of bone marrow T lymphocytes with anti-CD5 monoclonal antibodies: effective prophylaxis for graft-versus-host disease in patients with hematologic malignancies

Blood ◽  
1991 ◽  
Vol 78 (8) ◽  
pp. 2139-2149 ◽  
Author(s):  
JH Antin ◽  
BE Bierer ◽  
BR Smith ◽  
J Ferrara ◽  
EC Guinan ◽  
...  
Keyword(s):  
Bone Marrow ◽  
T Cells ◽  
High Risk ◽  
Graft Versus Host Disease ◽  
Graft Failure ◽  
Hematologic Malignancies ◽  
Host Disease ◽  
Graft Versus Host ◽  
High Risk Patients ◽  
Risk Patients

Seventy-one patients with hematologic malignancies received bone marrow from a histocompatible sibling (n = 48) or a partially matched relative (n = 23) that had been depleted of CD5+ T cells with either an anti-CD5 mooclonal antibody (MoAb) plus complement (anti-Leu1 + C) or an anti- CD5 MoAb conjugated to ricin A chain (ST1 immunotoxin [ST1-IT]). These patients received intensive chemoradiotherapy consisting of cytosine arabinoside, cyclophosphamide, and fractionated total body irradiation. Both anti-Leu1 + C and ST1-IT ex vivo treatments effectively depleted bone marrow of T cells (97% and 95%, respectively). Overall, primary and late graft failure each occurred in 4% of evaluable patients. The diagnosis of myelodysplasia was a significant risk factor for graft failure (P less than .001), and if myelodysplastic patients were excluded, there were no graft failures in major histocompatibility complex (MHC)-matched patients and 2 of 23 (8.7%) in MHC-mismatched patients. The actuarial risk of grade 2 to 4 acute graft-versus-host disease (GVHD) was 23% in MHC-matched patients and 50% in MHC- mismatched patients. In MHC-matched patients, acute GVHD tended to be mild and treatable with corticosteroids. Chronic GVHD was observed in 6 of 36 (17%) MHC-matched patients and none of 11 MHC-mismatched patients. There were no deaths attributable to GVHD in the MHC-matched group. Epstein-Barr virus-associated lymphoproliferative disorders were observed in 3 of 23 MHC-mismatched patients. The actuarial event-free survival was 38% in the MHC-matched patients versus 21% in the MHC- mismatched patients. However, if outcome is analyzed by risk of relapse, low-risk patients had a 62% actuarial survival compared with 11% in high-risk patients. These data indicate that the use of anti-CD5 MoAbs can effectively control GVHD in histocompatible patients, and that additional strategies are required in MHC-mismatched and high-risk patients.

scholarly journals Identification of A Novel Six Autophagy-Related Genes Signature for The Prognostic and A miRNA-Related Autophagy Predictor for Anti-PD-1 Therapy Responses in Prostate Cancer

2020 ◽  
Author(s):  
Lei Wu ◽  
Guojun Yue ◽  
Wen Quan ◽  
Qiong Luo ◽  
Dongxu Peng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
High Risk ◽  
Regression Model ◽  
Risk Group ◽  
Low Risk ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Prognostic Signature ◽  
Potential Biomarker ◽  
Risk Patients

Abstract Background: Autophagy is a highly conserved homeostatic process in the human body that is responsible for the elimination of aggregated proteins and damaged organelles. Several autophagy-related genes (ARGs) contribute to the process of tumorigenesis and metastasis of prostate cancer (PCa). Also, miRNAs have been proven to modulate autophagy by targeting some ARGs. However, their potential role in PCa still remains unclear.Methods: An univariate Cox proportional regression model was used to identify 17 ARGs associated with the overall survival (OS) of PCa. Then, a multivariate Cox proportional regression model was used to construct a 6 autophagy-related prognostic genes signature. Patients were divided into low-risk group and high-risk group using the median risk score as a cutoff value. High-risk patients had shorter OS than low-risk patients. Furthermore, the signature was validated by ROC curves. Regarding mRNA and miRNA, 12 differentially expressed miRNAs (DEMs) and 1073 differentially expressed genes (DEGs) were detected via the GEO database. We found that miR-205, one of the DEMs, was negatively regulated the expression of ARG (NKX2-3). Based on STRING analysis results, we found that the NKX2-3 was moderately related to the part of genes among the 6 autophagy-related genes prognostic signature. Further, NKX 2-3 was significantly correlated with OS and some clinical parameters of PCa by cBioProtal. By gene set enrichment analysis (GSEA). Lastly, we demonstrated that the association between NKX2-3 and tumor mutation burden (TMB) and PDCD1 (programmed cell death 1) of PCa.Results: We identified that the six ARGs expression patterns are independent predictors of OS in PCa patients. Furthermore, our results suggest that ARGs and miRNAs are inter-related. MiR-205 was negatively regulated the expression of ARG (NKX2-3). Further analysis demonstrated that NKX2-3 may be a potential biomarker for predicting the efficacy of anti-PD-1 therapy in PCa.Conclusions: The current study may offer a novel autophagy-related prognostic signature and may identify a promising miRNA-ARG pathway for predicting the efficacy of anti-PD-1 therapy in PCa.

scholarly journals Bioinformatics Analysis of Autophagy-related LncRNAs in Esophageal Carcinoma

2020 ◽  
Author(s):  
junbai fan ◽  
Dan Wu ◽  
Yi Ding
Keyword(s):  
High Risk ◽  
Esophageal Carcinoma ◽  
Cox Regression ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Diagnostic Value ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
High Risk Patients ◽  
Risk Patients

Abstract Background: Esophageal carcinoma (ESCA) is a malignant tumor with high invasiveness and mortality. Autophagy has multiple roles in the development of cancer; however, there are limited data on autophagy genes associated with long non-coding RNAs (lncRNAs) in ESCA. The purpose of this study was to screen potential diagnostic and prognostic molecules, and to identify gene co-expression networks associated with autophagy in ESCA. Methods: We downloaded transcriptome expression profiles from The Cancer Genome Atlas and autophagy-related gene data from the Human Autophagy Database, and analyzed the co-expression of mRNAs and lncRNAs. In addition, the diagnostic and prognostic value of autophagy-related lncRNAs was analyzed by multivariate Cox regression. Furthermore, Kyoto Encyclopedia of Genes and Genomes analysis was carried out for high-risk patients, and enriched pathways were analyzed by gene set enrichment analysis. Results: The results showed that genes of high-risk patients were enriched in protein export and spliceosome. Based on Cox stepwise regression and survival analysis, we identified seven autophagy-related lncRNAs with prognostic and diagnostic value, with the potential to be used as a combination to predict the prognosis of patients with ESCA. Finally, a co-expression network related to autophagy was constructed. Conclusion: These results suggest that autophagy-related lncRNAs and the spliceosome play important parts in the pathogenesis of ESCA. Our findings provide new insight into the molecular mechanism of ESCA and suggest a new method for improving its treatment.

scholarly journals Bioinformatics Analysis of Autophagy-related lncRNAs in Esophageal Carcinoma

2021 ◽  
Vol 24 ◽  
Author(s):  
Dan Wu ◽  
Yi Ding ◽  
JunBai Fan
Keyword(s):  
High Risk ◽  
Esophageal Carcinoma ◽  
Cox Regression ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Diagnostic Value ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
High Risk Patients ◽  
Risk Patients

Background: Esophageal carcinoma (ESCA) is a malignant tumor with high invasiveness and mortality. Autophagy has multiple roles in the development of cancer; however, there are limited data on autophagy genes associated with long non-coding RNAs (lncRNAs) in ESCA. The purpose of this study was to screen potential diagnostic and prognostic molecules and to identify gene co-expression networks associated with autophagy in ESCA. Methods: We downloaded transcriptome expression profiles from The Cancer Genome Atlas and autophagy-related gene data from the Human Autophagy Database and analyzed the co-expression of mRNAs and lncRNAs. In addition, the diagnostic and prognostic value of autophagy-related lncRNAs was analyzed by multivariate Cox regression. Furthermore, Kyoto Encyclopedia of Genes and Genomes analysis was carried out for high-risk patients, and enriched pathways were analyzed by gene set enrichment analysis. Results: The results showed that genes of high-risk patients were enriched in protein export and spliceosome. Based on Cox stepwise regression and survival analysis, we identified seven autophagy-related lncRNAs with prognostic and diagnostic value, with the potential to be used as a combination to predict the prognosis of patients with ESCA. Finally, a co-expression network related to autophagy was constructed. Conclusion: These results suggest that autophagy-related lncRNAs and the spliceosome play important parts in the pathogenesis of ESCA. Our findings provide new insight into the molecular mechanism of ESCA and suggest a new method for improving its treatment.

CMV-Seropositive Patients Allografted with a CMV-Seronegative Donor Show Delayed or Missing CMV-Specific T-Cell Immune Response and Are at Higher Risk for CMV-Viremia and CMV-Disease.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3249-3249
Author(s):  
Susanne Ganepola ◽  
Chiara Gentilini ◽  
Urte Hilbers ◽  
Goetz Hartung ◽  
Thoralf Lange ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
High Risk ◽  
Cell Response ◽  
T Cell Response ◽  
First Year ◽  
Seronegative Donor ◽  
High Risk Patients ◽  
Risk Patients ◽  
Cmv Disease

Abstract The human cytomegalovirus (CMV) is an important cause for mortality and morbidity after allogeneic stem cell transplantation (allo SCT) especially in patients without a CMV-specific T cell response. CMV seropositive patients allografted with a CMV seronegative donor do not rise up specific CMV-T cell immunity posttransplant and are therefore at great risk for CMV viremia and disease. In a prospective manner, we analyzed blood samples of 38 HLA-A2+ patients with different haematological malignancies for CMV specific T cells. Methods: Frequency of T cells with reactivity against the pp65-peptide (NLVPMVATV) was assessed by ELISPOT assay in 38 patients at defined time points after allo SCT. In patients with high CMV specific T cell frequencies, the T cell phenotype was determined by flow cytometry. Surveillance of CMV viremia was carried out by routine PCR-technique or pp65 Ag staining. Results: In high-risk patients (donor-/recipient+) viremia was observed in 7/9 patients, 3/7 developed clinical severe CMV-disease. In this group, only one patient presented a weak CMV-specific T cell response in the first year after transplantation, although CMV-specific T cells were demonstrated in 5/9 patients before transplantation. In contrast, 64% (11/17) of the CMV seropositive patients having had a CMV seropositive donor showed CMV-specific T cells around day 30. Their T cell frequencies remained stable at a relative high level during the whole time of our investigation period and no CMV disease was observed. CMV seronegative patients allografted with either a CMV seronegative or seropositive donor also remained disease-free. CMV specific T cells were detectable in 2/7 patients of the d+/r− group. FACS analysis revealed that most of the responding cells were of the activated effector phenotype CD8+/CD45RA+/HLA-DR+ with a low expression of CCR7 and CD27. Conclusion: CMV-seropositive patients receiving graft from a seronegative donor are at a high risk and therefore prone for CMV-viremia and -disease. The development of CMV-specific T cells i.e. immune reconstitution in high risk patients remains delayed or is completely missing during the first year post transplant. In contrast, seropositive recipients grafted with a seropositive donor develop a durable T cell response within 3–4 weeks and show no viremia at all. New strategies as donor vaccination and adoptive T cell transfer are warranted to prevent CMV-disease in CMV seropositive patients for whom only a seronegative donor can be found.

scholarly journals Selective depletion of bone marrow T lymphocytes with anti-CD5 monoclonal antibodies: effective prophylaxis for graft-versus-host disease in patients with hematologic malignancies

Blood ◽  
1991 ◽  
Vol 78 (8) ◽  
pp. 2139-2149 ◽  
Author(s):  
JH Antin ◽  
BE Bierer ◽  
BR Smith ◽  
J Ferrara ◽  
EC Guinan ◽  
...  
Keyword(s):  
Bone Marrow ◽  
T Cells ◽  
High Risk ◽  
Graft Versus Host Disease ◽  
Graft Failure ◽  
Hematologic Malignancies ◽  
Host Disease ◽  
Graft Versus Host ◽  
High Risk Patients ◽  
Risk Patients

Abstract Seventy-one patients with hematologic malignancies received bone marrow from a histocompatible sibling (n = 48) or a partially matched relative (n = 23) that had been depleted of CD5+ T cells with either an anti-CD5 mooclonal antibody (MoAb) plus complement (anti-Leu1 + C) or an anti- CD5 MoAb conjugated to ricin A chain (ST1 immunotoxin [ST1-IT]). These patients received intensive chemoradiotherapy consisting of cytosine arabinoside, cyclophosphamide, and fractionated total body irradiation. Both anti-Leu1 + C and ST1-IT ex vivo treatments effectively depleted bone marrow of T cells (97% and 95%, respectively). Overall, primary and late graft failure each occurred in 4% of evaluable patients. The diagnosis of myelodysplasia was a significant risk factor for graft failure (P less than .001), and if myelodysplastic patients were excluded, there were no graft failures in major histocompatibility complex (MHC)-matched patients and 2 of 23 (8.7%) in MHC-mismatched patients. The actuarial risk of grade 2 to 4 acute graft-versus-host disease (GVHD) was 23% in MHC-matched patients and 50% in MHC- mismatched patients. In MHC-matched patients, acute GVHD tended to be mild and treatable with corticosteroids. Chronic GVHD was observed in 6 of 36 (17%) MHC-matched patients and none of 11 MHC-mismatched patients. There were no deaths attributable to GVHD in the MHC-matched group. Epstein-Barr virus-associated lymphoproliferative disorders were observed in 3 of 23 MHC-mismatched patients. The actuarial event-free survival was 38% in the MHC-matched patients versus 21% in the MHC- mismatched patients. However, if outcome is analyzed by risk of relapse, low-risk patients had a 62% actuarial survival compared with 11% in high-risk patients. These data indicate that the use of anti-CD5 MoAbs can effectively control GVHD in histocompatible patients, and that additional strategies are required in MHC-mismatched and high-risk patients.

scholarly journals Analysis of Prognostic Alternative Splicing Reveals the Landscape of Immune Microenvironment in Thyroid Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Jian Wu ◽  
Yifang Sun ◽  
Junzheng Li ◽  
Maomao Ai ◽  
Lihua You ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
High Risk ◽  
Risk Group ◽  
Survival Curve ◽  
Roc Curves ◽  
High Risk Group ◽  
Lasso Regression ◽  
Prognostic Signature ◽  
Immune Microenvironment ◽  
Immune Checkpoint Proteins

BackgroundThe incidence of thyroid cancer (THCA) continues to increase in recent decades. Accumulating evidence showed that the unbalanced alternative splicing (AS) promotes the occurrence of cancers and leads to poor prognosis of patients. However, the research on alternative splicing events in THCA is lacking, and its underlying mechanism is not fully understood. This study identifies a novel prognostic signature based on AS events to reveal the relationship of AS with tumor immune microenvironment.MethodsBased on the AS data, transcriptional data, and clinical information, the differentially expressed alternative splicings (DEASs) were screened out. Least absolute shrinkage and selection operator (LASSO) regression and multi-Cox regression analyses were employed to identify prognostic results related to AS events and establish a prognostic signature. The predictive ability of the signature was assessed by Kaplan-Meier (K-M) survival curve, risk plots, and receiver operating characteristic (ROC) curves. Furthermore, correlations between tumor-infiltrating immune cells, immune checkpoints, immune score and prognostic signature were analyzed.ResultsAccording to the LASSO regression analysis, a total of five AS events were selected to construct the signature. K-M survival curve showed that the higher the risk score, the worse the OS of the patients. Risk plots further confirmed this result. ROC curves indicated the high predictive efficiency of the prognostic signature. As for tumor immune microenvironment, patients in the high-risk group had a higher proportion of immune cells, including plasma cell, CD8+ T cell, macrophages (M0 and M2), and activated dendritic cell. Immune checkpoint proteins, such as PDCD1LG2, HAVCR2, CD274, etc., were significantly higher in the high-risk group. We also found that the ESTIMATE score, stromal score, and immune score were lower in the high-risk group, while the result of tumor purity was the opposite.ConclusionsCollectively, a prognostic signature consisting of five AS events in THCA was established. Furthermore, there was an inextricable correlation between immune cell infiltration, immune checkpoint proteins, and AS events. This study will provide a basis for THCA immunotherapy in the future.

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