Integrative analysis of multi-omics data reveals a pseudouridine-related lncRNA signature for prediction of glioma prognosis and chemoradiotherapy sensitivity.

BACKGROUND: Glioblastoma is the most common type of glioma with a high incidence and poor prognosis, and effective medical treatment remains challenging. Pseudouridine (Ψ) is the first post-transcriptional modification discovered and one of the most abundant modifications to RNA. However, the prognostic value of Ψ-related lncRNAs (ΨrLs) for glioma patients has never been systematically evaluated. This study aims to construct a risk model based on ΨrLs signature and to validate the predictive efficiency of the model. METHOD: Transcriptomic data, genomic data, and relevant clinical data of glioma patients were extracted from the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). ΨrLs with significant correlation with Ψ-related genes were identified, and univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression, and multivariate Cox regression were used to further select biomarkers and construct a ΨrLs signature risk model. Then, the expression of lncRNAs of ΨrLs signature in multiple glioma cell lines was detected by qPCR. Further, ROC analysis, stratification analysis, correlation analysis, survival analysis, nomogram, enrichment analysis, immune infiltration analysis, chemoradiotherapy sensitivity analysis, somatic mutation, and recurrent copy number variation (CNV) analysis were used to validate the predictive efficiency of ΨrLs signature in TCGA and CGGA datasets. RESULTS: A four-lncRNA ΨrLs signature (DNAJC27-AS1, GDNF-AS1, ZBTB20-AS4, and DNMBP-AS1) risk model was constructed. By ROC analysis, stratified analysis, correlation analysis, survival analysis, and nomogram, the signature showed satisfactory predictive efficiency. Functional enrichment analysis revealed the differences in immune-related biological processes between high- and low-risk groups. Immune infiltration analysis showed that the high-risk group had lower tumor purity and higher stromal, immune and ESTIMATE scores. Mitoxantrone was identified as effective drug for low-risk group of glioma patients. Key genes in glioma development, including IDH1, EGFR, PTEN, etc., were differentially mutated between risk groups. The main recurrent CNVs in low-risk groups were 19q13.42 deletion and 7q34 amplification; 10q23.31 deletion and 12q14.1 in the high-risk group. CONCLUSIONS: Our study identified a four-lncRNA ΨrLs signature that effectively predicts the prognosis of glioma patients and may serve as a diagnostic tool. Risk scores of glioma patients generated by the signature is associated with immune-related biological processes and chemoradiotherapy sensitivity. These findings may inform the development of more targeted and effective therapies for glioma patients.

A novel immune-related prognostic signature based on Chemoradiotherapy sensitivity predicts long-term survival in patients with esophageal squamous cell carcinoma.

Background: There is a heterogenous clinical response following chemoradiotherapy (CRT) in esophageal squamous cell carcinoma (ESCC). Therefore, we aimed to study signaling pathway genes that affect CRT sensitivity and prognosis. Methods: Gene expression analyses were performed in the GEO and TCGA datasets. A immunohistochemistry (IHC) analysis was performed in pretreatment biopsies. Results: MMP13 was found to be highly expressed in the "Pathologic Complete Response (pCR)" and "Complete Remission (CR)" and "Alive" groups. Th17 cells and MMP9/13 showed a negative correlation in immune infiltration analysis. In GSEA analysis, IL-4 and IL-13 signaling pathways were highly enriched in patients exhibiting high MMP expression in pCR and CR groups. IHC results suggested higher MMP13 & IL-4 and lower IL-17A & RORC expression in the CR group compared to the 0.70, and the model could well distinguish high-risk and low-risk subgroups. Conclusion: The above results may provide guidance for developing novel treatment and prognostic strategies in ESCC patients.

Preliminary study of the detection of genes related to sensitivity to concurrent chemoradiotherapy based on circulating free DNA in locally advanced esophageal squamous cell carcinoma / 中华放射肿瘤学杂志

Objective:To explore the genes and molecular markers related to the sensitivity to concurrent chemoradiotherapy in patients with locally advanced esophageal squamous cell carcinoma.Methods:The peripheral blood sample of 31 patients with locally advanced esophageal squamous cell carcinoma receiving radical concurrent chemoradiotherapy was collected and the plasma circulating free DNA (cf-DNA) was extracted before treatment. The target gene capture sequencing technology based on NovaseQ6000 high-throughput sequencing platform was employed to detect the changes of target genes and tumor mutation burden (TMB). According to the short-term efficacy of chemoradiotherapy, all patients were divided into the chemoradiotherapy-sensitive group (CR+ PR) and chemoradiotherapy-resistant group (SD+ PD). Bioinformatics and clinical data were adopted to analyze the differences of gene mutation and TMB between two groups.Results:In the sequencing data of 31 patients, the tumor-related genes with a mutation frequency above 10% were Tp53, Notch1, BRAF, FGFR4, CDKN2A, ATRX and Axin2, which were almost equally distributed between the CR+ PR and SD+ PD groups. High-frequency mutant genes were associated with 7 signaling pathways, mainly involved in the RTK/RAS signaling pathways. The TMB value in the CR+ PR group was higher than that in the SD+ PD group ( P=0.04), however, the mutation rate of GXYLT1 and KRT18 genes in the SD+ PD group was higher than that in the CR+ PR group ( P<0.05). Conclusions:Tp53, Notch1 and CDKN2A may be the high-frequency mutant genes associated with the incidence and progression of esophageal squamous cell carcinoma. KRT18, GXYLT1 and TMB are closely correlated with the sensitivity to concurrent chemoradiotherapy of patients with locally advanced esophageal squamous cell carcinoma.

Study of sensitization effect of hydroxyurea on chemoradiotherapy of human glioma U251 cells / 中华放射肿瘤学杂志

Objective:To investigate the effect of hydroxyurea (HU) combined with temozolomide (TMZ) and radiotherapy (RT) on the sensitivity of human glioma U251 cells to chemoradiotherapy (CRT).Methods:Human glioma U251 cell line was cultured in vitro. CCK8 cell assay was used to detect the proliferation activity of U251 cells treated with different concentrations of HU/TMZ under different conditions. Flow cytometry was utilized to detect apoptosis rate and cell cycle distribution of U251 cells. Transwell chamber assay and scratch test were performed to evaluate the changes of cell invasion and migration. The expression levels of apoptosis proteins were determined by Western blot. Colony formation assay was adopted to detect the cell survival fraction . Results:HU concentration at 50μmol/L and below did not affect the proliferation of human glioma U251 cells ( P>0.05). Low-dose HU combined with CRT significantly inhibited cell proliferation ( P<0.05), invasion ( P<0.01) and migration (12h P<0.001, 24h P<0.01), and promoted cell apoptosis ( P<0.01) compared with the use of CRT alone. Application of 50μmol/L HU combined with RT increased the radiosensitivity of cells (SER=1.49), significantly prolonged the cell cycle of S phase and G 2 phase (both P<0.05), considerably up-regulated the expression levels of the apoptosis-associated proteins of Caspase-3 and Bax and significantly down-regulated the expression level of anti-apoptosis protein of Bcl-2(all P<0.001). Conclusions:Compared with CRT, HU combined with CRT can further inhibit the proliferation, invasion and migration of human glioma U251 cells, promote cell apoptosis, increase the radiosensitivity and prolong the cell cycle of S and G 2 phases, thereby enhancing the sensitivity of human glioma U251 cells to CRT.

Candidate genes and potential mechanisms for chemoradiotherapy sensitivity in locally advanced rectal cancer.

The aim of the present study was to investigate candidate genes for chemoradiotherapy (CRT) sensitivity in patients with locally advanced rectal cancer (LARC), and the potential mechanisms of their action. A microarray dataset (GSE98959) was obtained from the Gene Expression Omnibus database that included microRNA (miRNA, miR) expression profiling of 22 samples from patients with LARC who had received preoperative radiotherapy and chemotherapy. Of these patients, 10 responded to the treatment and 12 did not. Differentially expressed miRNAs (DEMs) were identified, followed by the construction of an miRNA-gene network. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) function analyses were performed on the target genes in the miRNA-gene network. Furthermore, a protein-protein interaction (PPI) network was constructed on the basis of the target genes, followed by GO function enrichment and KEGG pathway analysis. A total of 30 DEMs were identified between the responder and non-responder groups. Thiamine metabolism (including miR-371a-3p) was the pathway with the highest enrichment of DEMs. The pathway that was most markedly enriched in the target genes of upregulated miRNAs was the pluripotency of stem cells pathway, as indicated by phosphoinositide-4,5-bisphosphate 3-kinase γ (PIK3CG) and anaphase-promoting complex subunit 2 (APC2). Pathways in cancer exhibited the highest enrichment in the set of target genes of downregulated miRNAs. KEGG pathway and GO function analysis indicated that target genes in the PPI network were enriched in the glioma pathway and assembled in the intracellular signaling cascade function, as indicated by the proto-oncogene NRAS. miR-371a-3p may be a candidate miRNA for CRT sensitivity in LARC via the thiamine metabolism pathway. PIK3CG and APC2 may contribute to CRT sensitivity via signaling pathways regulating the pluripotency of stem cells. Furthermore, NRAS may serve an important role in mediating CRT sensitivity via an intracellular signaling cascade.