Distinctive microRNA expression in early stage nasopharyngeal carcinoma patients.
Ontology highlight
ABSTRACT:
SUBMITTER: Li S
PROVIDER: S-EPMC5134390 | biostudies-other | 2016 Dec
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Radiation encephalopathy (RE) is one of the most severe complications in nasopharyngeal carcinoma (NPC) patients after radiotherapy (RT). However, the morphological alteration of early RE is insufficiently investigated. We aimed to investigate the cortical thickness and surface area alterations in NPC patients with or without RE in the follow-up. A total of 168 NPC patients each underwent a single scan and analysis at various times either Pre-RT (n = 56) or Post-RT (n = 112). We further divided the Post-RT NPC patients into three groups based on the time of the analysis following RT (Post-RTwithin 6 months and Post-RT7-12 months) or whether RE signs were detected in the analysis (Post-RTRE proved in follow-up). We confined the vertex-wise analyses of the cortical thickness and surface area to the bilateral temporal lobes. Interestingly, we revealed a gradual increase in the cortical surface area of the temporal lobe with increasing time after RT within the Post-RTRE proved in follow-up group, consistent with the between-group findings, which showed a significant increase in cortical surface area in the Post-RTRE proved in follow-up group relative to the Pre-RT group and the Post-RTwithin 6 months group. By contrast, such a trend was not observed in the cortical thickness findings. We concluded that the cortical surface area, rather than cortical thickness, may serve as a potential biomarker for early diagnosis of RE.
| S-EPMC6120047 | biostudies-literature
Project description:Background/purposeNasopharyngeal carcinoma (NPC) is a malignant neoplasm of the head and neck. This study aims to use integrated bioinformatics technologies to develop a predictive miRNA-signature correlated with the prognosis of NPC.Materials and methodsInitially, the differentially expressed miRNAs (DEMs) in NPC were identified, and then DEMs related to the prognosis of NPC were further screened. Subsequently, the relatively important DEMs identified by random forest algorithm were used to construct a predictive signature by multivariate COX regression analysis. Moreover, PCA, Kaplan-Meier analysis, time-dependent ROC analysis, and univariate and multivariate COX regression analysis were performed to evaluate the ability of the signature in risk identification and prognosis prediction in NPC.ResultsHsa-miR-29c, hsa-miR-30e and hsa-miR-93 were selected from DEMs to construct a signature, and their abnormal expression was significantly associated with poor prognosis of NPC. The average AUC values of 1- to 5-year OS, DFS and DMFS predicted by the signature were all above 0.7, and showed better clinical independence than other indexes. In addition, 295 differentially expressed mRNAs could be used as potential target genes of the 3 DEMs. Among them, 56 differentially expressed mRNAs were related to PFS. GO and KEGG enrichment analysis indicated that the poor prognosis of NPC was related to the abnormality of chromosomes, cytokines, and chemokines.ConclusionWe constructed a three-miRNA signature with good independent performance in predicting the prognosis for NPC. This study may lay the foundation for exploring new therapeutic targets and improving survival outcomes in NPC patients.
| S-EPMC8740092 | biostudies-literature
Project description:Microarray was used to find out the differentially expressed in tumor sites of early-stage oral squamous cell carcinoma compared with Normal parts. Furthermore, we compared cases of early-stage oral squamous cell carcinoma with lymph node metastasis with cases without lymph node metastasis. The miRNAs obtained may not only serve as predictive biomarkers for lymph node metastasis, but may also be used further to understand disease.
2023-08-22 | GSE241289 | GEO
Project description:MicroRNAs (miRNAs) are a family of small non-coding RNA molecules of about 20-23 nucleotides in length, which negatively regulate protein-coding genes at post-transcriptional level. Using a stem-loop real-time-PCR method, we quantified the expression levels of 270 human miRNAs in 13 nasopharyngeal carcinoma (NPC) samples and 9 adjacent normal tissues, and identified 35 miRNAs whose expression levels were significantly altered in NPC samples. Several known oncogenic miRNAs, including miR-17-92 cluster and miR-155, are among the miRNAs upregulated in NPC. Tumour suppressive miRNAs, including miR-34 family, miR-143, and miR-145, are significantly downregulated in NPC. To explore the roles of these dysregulated miRNAs in the pathogenesis of NPC, a computational analysis was performed to predict the pathways collectively targeted by the 22 significantly downregulated miRNAs. Several biological pathways that are well characterised in cancer are significantly targeted by the downregulated miRNAs. These pathways include TGF-Wnt pathways, G1-S cell cycle progression, VEGF signalling pathway, apoptosis and survival pathways, and IP3 signalling pathways. Expression levels of several predicted target genes in G1-S progression and VEGF signalling pathways were elevated in NPC tissues and showed inverse correlation with the down-modulated miRNAs. These results indicate that these downregulated miRNAs coordinately regulate several oncogenic pathways in NPC.
| S-EPMC2661776 | biostudies-literature
Project description:BackgroundEarly diagnosis of nasopharyngeal carcinoma (NPC) is vital to improve the prognosis of these patients. However, early diagnosis of NPC is typically challenging. Therefore, we explored the pathogenetic roles and associated mechanisms of exosomes in plasma of patients with early-stage NPC.MethodsExosomes in plasma were extracted by ultra-high-speed centrifugation. Western blot and transmission electron microscopy (TEM) were used to verify the purity of exosomes. The sequencing data (6 plasma samples from healthy volunteers vs. 6 NPC plasma samples) were analyzed by principal component analysis (PCA), DESeq2, gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and TargetScan. The differentially expressed miRNAs (DEmiRNAs) were obtained from the dataset (GSE118720) downloaded from the Gene Expression Omnibus (GEO) repository. Additionally, the datasets downloaded from the GEO database (GSE12452, GSE13597, GSE53819, GSE64634) were used to predict the target genes and functions of hsa-miR-1301-3p. qPCR was applied to verify the differences in the expressions of hsa-miR-1301-3p between 10 normal plasma and 10 NPC plasma samples.ResultsWestern blot, TEM, and Nanoparticle Tracking Analysis showed adequate purity of the extracted exosomes. RNA-seq analysis revealed 21 upregulated miRNAs, and 10 downregulated miRNAs in plasma exosomes of early-stage NPC patients. GO analysis showed that the target genes of DEmiRNAs were mainly enriched in DNA synthesis and transcription regulation. KEGG analysis revealed that DEmiRNAs were mainly enriched in PI3K-Akt and MAPK signaling pathways. Moreover, the expression of hsa-mir-1301-3p was verified to be significantly upregulated in enlarged samples of plasma exosomes.ConclusionsWe identified several DEmiRNAs extracted from tumor-derived exosomes between normal plasma and early-stage NPC plasma. Bioinformatics analyses indicated that these DEmiRNAs may be related to NPC development. Our study may provide novel insights into underlying biomarkers and mechanisms of plasma exosomes in early-stage NPC.
| S-EPMC8011216 | biostudies-literature
Project description:The extraocular muscles (EOMs) are a unique group of muscles that are anatomically and physiologically distinct from other muscles. We and others have shown that EOMs have a unique transcriptome and proteome. Here we investigated the expression pattern of microRNAs (miRNAs), as they may play a role in generating the unique EOM allotype. We isolated RNA and screened LC Sciences miRNA microarrays covering the sequences of miRBase 10.0 to define the microRNAome of normal mouse EOM and tibialis anterior (TA) limb muscle. Seventy-four miRNAs were found to be differentially regulated (P value <0.05) of which 31 (14 upregulated, 17 downregulated) were differentially regulated at signal strength >500. Muscle-specific miRNAs miR-206 and miR-499 were upregulated and miR-1, miR-133a, and miR-133b were downregulated in EOM. Quantitative PCR (qPCR) analysis was used to validate the differential expression. Bioinformatic tools were used to identify potential miRNA-mRNA-protein interactions and integrate data with previous transcriptome and proteomic profiling data. Luciferase assays using cotransfection of precursor miRNAs with reporter constructs containing the 3'-untranslated region of predicted target genes were used to validate targeting by identified miRNAs. The definition of the EOM microRNAome complements existing transcriptome and proteome data about the molecular makeup of EOM and provides further insight into regulation of muscle genes. These data will also help to further explain the unique EOM muscle allotype and its differential sensitivity to diseases such as Duchenne muscular dystrophy and may assist in development of therapeutic strategies.
| S-EPMC2869107 | biostudies-literature
Project description:Background: Patients with nasopharyngeal carcinoma (NPC) frequently developed the problem of malnutrition at the time of diagnosis. Chemoradiotherapy (CRT) can even worsen the situation. Therefore, nutritional intervention should be applied to prevent CRT-associated weight loss and interruption of CRT. However, it is still controversial if early nutritional intervention is beneficial to NPC patients with CRT. This study is to investigate the influence of early nutritional intervention on advanced NPC patients with CRT by evaluating the nutritional status and CRT treatment tolerance. Methods: A cohort of 78 stage III-IV nasopharyngeal carcinoma patients was divided into early (n=46) and late (n=32) nutrition intervention groups. The early group of patients received nutritional support at the beginning of CRT, whereas the late group received such a support until development of the side effects, like 50% required oral dietary intake or >10% weight loss. The data were collected and statistically analyzed. Results: There was no significant difference in baseline clinical characteristics between these two groups, suggesting that no selection bias occurred. Both groups of patients had weight loss at the end of CRT and 3 months thereafter. However, at the later time point, the early group started to regain their weight, while the late group continued to lose weight. At both time points, the early group had a lower percentage of weight loss than the late group. Similar results were also obtained for BMI, albumin, and pre-albumin levels (All p<0.05). Besides, the early group showed a lower rate of advanced mucositis, a lower percentage of patients with more than 3 days RT breaks, fewer days of RT delayed for toxicity, and a lower percentage of patients with unplanned hospitalizations (All p<0.05). A linear correlation was also found between the percentage of weight loss and the number of days of RT delayed. Conclusion: Early nutritional intervention provides beneficial outcomes to NPC patients by maintaining their nutritional status and enhancing CRT treatment tolerance. Our results also indicated early nutrition intervention may reduce the hospital cost and improve patients' life quality.
| S-EPMC6636293 | biostudies-literature
Project description:Background and purposeTo investigate effects of radiotherapy on normal brain tissue using in vivo neuroimaging in patients with nasopharyngeal carcinoma (NPC).Methods and materialsWe used longitudinal MRI to monitor structural brain changes during standard radiotherapy in patients newly diagnosed with NPC. We assessed volumetric measures in 63 patients at 2-3 time points before and after radiotherapy, with 20 NPC-free participants as normal controls. Images were processed using validated software (FreeSurfer). Automated results were inspected visually for accuracy. We examined changes in volume of the whole brain, gray matter, white matter, and ventricles, as well as in cerebral volumes partitioned into temporal, frontal, parietal, and occipital lobes. A linear mixed model was used to evaluate longitudinal changes in these measurements. Statistical significance was evaluated at p?<?0.05, which was corrected for multiple comparisons.ResultsVolumes of the gray matter, and bilateral temporal lobes decreased in a time-dependent manner, whereas ventricle volume showed a time-dependent increase after radiotherapy. No volume changes were detected in NPC patients before radiotherapy when compared normal controls. No volume changes were detected in the subcohort of patients after completion of induction chemotherapy but prior to initiation of radiotherapy. Changes of bilateral temporal lobe volume correlated with irradiation dose in this region. Expansion of the ventricles correlated with a reduction in cognition assessment.ConclusionsWe detected significant and progressive radiotherapy-associated structural changes in the brains of patients with NPC who were treated with standard radiotherapy, especially in the bilateral temporal lobe in which the effect was dose-dependent. Expansion of the ventricles can serve as an imaging marker for treatment-related reduction in cognitive function. Future studies with longer follow-ups are needed to evaluate morphometric changes long-term after radiotherapy.
| S-EPMC6051477 | biostudies-literature
Project description:MicroRNAs (miRNAs) are small non-coding RNAs functioning as regulators of hematopoiesis. Their differential expression patterns have been linked with various pathological processes originating from hematopoietic stem cells (HSCs). However, limited information is available regarding the role of miRNAs in myelodysplastic syndrome (MDS). Using miRNA arrays, we measured expression of 1,145 miRNAs in CD34+ bone marrow cells obtained from 39 MDS and acute myeloid leukemia (AML) evolved from MDS patients, and compared them with those of six healthy donors. Differential miRNA expression was analyzed and a panel of upregulated (n=13) and downregulated (n=9) miRNAs were found (P<0.001) in MDS/AML patients. An increased expression of a large miRNA cluster mapped within the 14q32 locus was detected. Differences in miRNA expression of MDS subtypes showed a distinction between early and advanced MDS; an apparent dissimilarity was observed between RAEB-1 and RAEB-2 subtypes. In early MDS, we monitored upregulation of proapoptotic miR-34a, which may contribute to the increased apoptosis of HSCs. Patients with 5q deletion were characterized by decreased levels of miR-143(*) and miR-378 mapped within the commonly deleted region at 5q32. This is an early report describing differential expression in MDS CD34+ cells, likely reflecting their disease-specific regulation.
| S-EPMC3061996 | biostudies-literature
Project description:Discriminating early-stage nasopharyngeal carcinoma (NPC) from benign hyperplasia (BH) on MRI is a challenging but important task for the early detection of NPC in screening programs. Radiomics models have the potential to meet this challenge, but instability in the feature selection step may reduce their reliability. Therefore, in this study, we aim to discriminate between early-stage T1 NPC and BH on MRI using radiomics and propose a method to improve the stability of the feature selection step in the radiomics pipeline. A radiomics model was trained using data from 442 patients (221 early-stage T1 NPC and 221 with BH) scanned at 3T and tested on 213 patients (99 early-stage T1 NPC and 114 BH) scanned at 1.5T. To verify the improvement in feature selection stability, we compared our proposed ensemble technique, which uses a combination of bagging and boosting (BB-RENT), with the well-established elastic net. The proposed radiomics model achieved an area under the curve of 0.85 (95% confidence interval (CI): 0.82-0.89) and 0.80 (95% CI: 0.74-0.86) in discriminating NPC and BH in the 3T training and 1.5T testing cohort, respectively, using 17 features selected from a pool of 422 features by the proposed feature selection technique. BB-RENT showed a better feature selection stability compared to the elastic net (Jaccard index = 0.39 ± 0.14 and 0.24 ± 0.06, respectively; p < 0.001).
| S-EPMC9324280 | biostudies-literature