Targeting ARNT attenuates chemoresistance through destabilizing p38α-MAPK signaling in glioblastoma.

Glioblastoma (GBM) is the most aggressive and lethal brain tumor in adults. This study aimed to investigate the functional significance of aryl hydrocarbon receptor nuclear translocator (ARNT) in the pathogenesis of GBM. Analysis of public datasets revealed ARNT is upregulated in GBM tissues compared to lower grade gliomas or normal brain tissues. Higher ARNT expression correlated with the mesenchymal subtype and poorer survival in GBM patients. Silencing ARNT using lentiviral shRNAs attenuated the proliferative, invasive, and stem-like capabilities of GBM cell lines, while ARNT overexpression enhanced these malignant phenotypes. Single-cell RNA sequencing uncovered that ARNT is highly expressed in a stem-like subpopulation and is involved in regulating glycolysis, hypoxia response, and stress pathways. Mechanistic studies found ARNT activates p38 mitogen-activated protein kinase (MAPK) signaling to promote chemoresistance in GBM cells. Disrupting the ARNT/p38α protein interaction via the ARNT PAS-A domain restored temozolomide sensitivity. Overall, this study demonstrates ARNT functions as an oncogenic driver in GBM pathogenesis and represents a promising therapeutic target.

A retrospective analysis of factors associated with the length of hospital stay in COVID-19 patients treated with Nirmatrelvir / Ritonavir.

Objectives: This study reviewed factors influencing the length of hospital stay in adult inpatients with confirmed Coronavirus disease (COVID-19) who were treated with Nirmatrelvir/Ritonavir. Methods: We did a retrospective analysis of data from a cohort of inpatients with confirmed diagnosis of Omicron variant of SARS-CoV-2 infection who were treated with Nirmatrelvir/Ritonavir. We included patients who were treated from 13th March 2022 to 6th May 2022 in various in-patient treatment units in Quanzhou, Fujian Province, China. The primary study outcome was the length of hospital stay. Secondary study outcome was viral elimination defined as negative for ORF1ab and N genes [cycle threshold (Ct) value ≥35 in real-time PCR], according to local guidelines. Hazard ratios (HR) of event outcomes were analyzed using Multivariate Cox regression models. Results: We studied 31 inpatients with high risk for severe COVID-19 who were treated with Nirmatrelvir/Ritonavir. We found that inpatients with shorter length of hospital stay (≤17 days) were mostly females with lower body mass index (BMI) and Charlson Comorbidity Index (CCI) index. Their treatment regimen with Nirmatrelvir/Ritonavir was started within 5 days of diagnosis (p < 0.05). Multivariate Cox regression indicated that inpatients starting treatment of Nirmatrelvir/Ritonavir within 5 days had a shorter length of hospital stay (HR 3.573, p = 0.004) and had a faster clearance of viral load (HR 2.755, p = 0.043). Conclusion: This study assumes relevance during the Omicron BA.2 epidemic as our findings suggest that early treatment with Nirmatrelvir/Ritonavir within 5 days of diagnosis (≤5 days) was highly effective in shortening the length of hospital stay and faster viral load clearance.

GTFtools: a software package for analyzing various features of gene models.

MOTIVATION: Gene-centric bioinformatics studies frequently involve the calculation or the extraction of various features of genes such as splice sites, promoters, independent introns and untranslated regions (UTRs) through manipulation of gene models. Gene models are often annotated in gene transfer format (GTF) files. The features are essential for subsequent analysis such as intron retention detection, DNA-binding site identification and computing splicing strength of splice sites. Some features such as independent introns and splice sites are not provided in existing resources including the commonly used BioMart database. A package that implements and integrates functions to analyze various features of genes will greatly ease routine analysis for related bioinformatics studies. However, to the best of our knowledge, such a package is not available yet. RESULTS: We introduce GTFtools, a stand-alone command-line software that provides a set of functions to calculate various gene features, including splice sites, independent introns, transcription start sites (TSS)-flanking regions, UTRs, isoform coordination and length, different types of gene lengths, etc. It takes the ENSEMBL or GENCODE GTF files as input and can be applied to both human and non-human gene models like the lab mouse. We compare the utilities of GTFtools with those of two related tools: Bedtools and BioMart. GTFtools is implemented in Python and not dependent on any third-party software, making it very easy to install and use. AVAILABILITY AND IMPLEMENTATION: GTFtools is freely available at www.genemine.org/gtftools.php as well as pyPI and Bioconda.

Detection of mutation profiles and tumor mutation burden of cerebrospinal fluid circulating DNA by a cancer genomic panel sequencing in glioma patients.

BACKGROUND AND AIMS: Circulating tumor DNA (ctDNA) has been recognized as a reliable source to reflect the molecular and genetic landscape of corresponding tumors in recent years. In this study, we tested the application of a cancer genomic panel sequencing on the cerebrospinal fluid (CSF)-derived ctDNA for the less invasive detection and diagnosis of glioma. MATERIALS AND METHODS: CtDNA was extracted from 26 CSF samples and subject to a cancer genomic panel sequencing of 520 genes to analyze the mutation profiles and tumor mutation burden (TMB), which were compared with their corresponding tumor DNA samples. Associations between mutations or TMB and clinical characteristics were also evaluated. RESULTS: A high detection rate of ctDNA (24/26, 92.3%) was observed in CSF. CtDNA mutations had high concordance rates with tumor DNA, especially in non-copy number variations and in glioblastoma. CSF ctDNA TMB also exhibited a strong correlation with tumor DNA TMB (R2 = 0.879, P < 0.001), particularly in glioblastoma (R2 = 0.992, P < 0.001). Age was significantly associated with CSF ctDNA TMB in glioma patients. CONCLUSION: We established a less invasive but effective molecular diagnostic approach using a cancer genomic panel sequencing system targeting CSF ctDNA for glioma, especially in glioblastoma.

An integrated analysis of enhancer RNAs in glioma and a validation of their prognostic values.

Glioma, a highly aggressive neuroepithelial malignant brain tumor, is associated with high disability and recurrence rates. Enhancer RNA (eRNA) plays a significant role in tumor proliferation and metastasis; however, their functions in gliomas need further evaluation. We used the computational pipeline, PreSTIGE, to predict tissue-specific enhancer-derived RNAs and the underlying regulatory genes. Using data retrieved from the TCGA and CGGA databases, a LASSO regression analysis and multiCox proportional hazards regression analyses were performed to determine the hub eRNAs associated with glioma prognosis. Quantitative reverse transcription PCR was performed on the glioma samples to evaluate the expression characteristics of the identified hub eRNAs. To construct a risk signature, we selected three eRNAs, including CRNDE, MRPS31P5, and LINC00844, for their significant prognostic values. The predictive value of the risk signature was validated using the CGGA and Rembrandt cohorts. Apart from the risk signature, the nomogram performed well at predicting OS in glioma patients. An eRNA-target gene regulatory network was established, which we evaluated using a target gene enrichment analysis. Pathway and gene ontology (GO) analyses demonstrated that the risk signature is associated with mRNA processing and spliceosome in glioma. Furthermore, we found that hub eRNAs potentially regulate the expressions of numerous splicing factors, such as MOV10 and SEC31B, and are correlated with prognosis-associated alteration splicing (AS). In conclusion, we established a risk signature that comprises three eRNAs, which can accurately be utilized as targets to predict prognosis in glioma patients.

Regulation of prognosis-related Siglecs in the glioma microenvironment.

PURPOSE: The anti-inflammatory environment of glioma reduces the efficacy of immunotherapies. Therefore, it is vital to transform the immunosuppressive microenvironment of glioma into a pro-inflammatory environment. Sialic acid-binding immunoglobulin-type lectins (Siglecs) can serve as immune checkpoint targets that enhance the anti-tumor immune response. However, the roles of Siglecs in the glioma microenvironment are unknown. This study was conducted to identify targets to inhibit the anti-inflammatory environment to improve therapeutic outcomes in patients with glioma. METHODS: We analyzed the regulatory effect of prognosis-related Siglecs identified from data available in The Cancer Genome Atlas database (TCGA) and China Glioma Genome Atlas Data portal on the immunosuppressive microenvironment of glioma. The effects of prognosis-related Siglecs on the glioma microenvironment were investigated by determining the Pearson correlation coefficients of the Siglecs in transcriptome data from the TCGA database. RESULTS: Siglec-1, -9, -10, and -14 were closely associated with the prognosis of patients with glioma. The expression of these four Siglecs was significantly increased in the high-risk group and positively correlated with anti-inflammatory cytokine levels in the glioma microenvironment. CONCLUSION: Our study provides insights into the effects of prognosis-related Siglecs in glioma immunotherapy, suggesting that targeted prognosis-related Siglecs can modify the microenvironment of glioma and improve the sensitivity of patients with glioma to immunotherapy.

Endoscopic Endonasal Approach for Clipping Anterior Communicating Artery Aneurysms From Cadaver Studies and Three-Dimensional Printed Models to a Clinical Case.

OBJECTIVES: Anterior communicating artery (ACoA) aneurysm is one of the most common intracranial aneurysms, and it is also the aneurysm with the highest rupture rate. With the improvement of endoscopic techniques, it is possible to use an endoscopic endonasal approach (EEA) to clip ACoA aneurysms. For further analysis of the EEA for clipping ACoA aneurysms, we used cadaver heads and three-dimensional (3D)-printed models to finish the anatomical study, and we finally selected 1 clinical case to complete the clipping through the EEA. MATERIALS AND METHODS: We first collected 3 cadaver heads to simulate the EEA. Then, the imaging data of 29 real cases of ACoA aneurysm were collected, and the model of an aneurysm was prepared by 3D printing technology; then, the EEA was used to simulate the clipping of the aneurysm model. Finally, a clinical case with 2 ACoA aneurysms was selected to adopt the EEA for clipping. RESULTS: Both the cadaver head and 3D-printed aneurysm model could simulate aneurysm clipping with the EEA. The clinical case of the selected ACoA aneurysm can successfully complete the clipping through the EEA. CONCLUSIONS: 3D-printed models are a good method to study the anatomical characteristics of a surgical approach. For specially selected ACoA aneurysms, the EEA is relatively simple method that can be used to clip the aneurysm successfully. The EEA for clipping ACoA aneurysms is a useful complement to the current traditional craniotomy approaches and endovascular embolization.

Circular RNA circ_0001162 promotes cell proliferation and invasion of glioma via the miR-936/ERBB4 axis.

The biological modulatory roles of many circular RNAs (circRNAs) have been validated in glioma. The current study was designed to research the functional mechanism of circ_0001162 in glioma progression. The quantitative real-time polymerase chain reaction (qRT-PCR) was used for assaying the levels of circ_0001162 and microRNA-936 (miR-936). Cell proliferation and colony formation abilities were evaluated via 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) and colony formation assay, respectively. Transwell assay was applied to assess cell migration and invasion. The impact of circ_0001162 on glioma growth in vivo was performed using xenograft tumor assay. The target binding was affirmed via the dual-luciferase reporter and RNA pull-down assays. All protein expression levels were examined via Western blot. Circ_0001162 was an overexpressed circRNA in glioma. Circ_0001162 promoted glioma cell proliferation, colony formation, migration and invasion in vitro. Tumorigenesis of glioma in vivo was also enhanced by circ_0001162. Circ_0001162 could directly target miR-936 and the biological function of circ_0001162 in glioma was related to the inhibition of miR-936. ErbB2 receptor tyrosine kinase 4 (ERBB4) was a direct target of miR-936. Additionally, miR-936 inhibited the glioma development via targeting ERBB4. The miR-936/ERBB4 axis was responsible for the oncogenic role of circ_0001162 in glioma. The effects of circ_0001162 on glioma cells were also associated with the positive regulation of ERBB4. These results indicated that circ_0001162 contributed to the glioma progression via regulating the miR-936/ERBB4 axis, which laid a foundation for the pathomechanism and molecular treatment of glioma.

Validation of the functions and prognostic values of synapse-associated proteins in lower-grade glioma.

Synapse and synapse-associated proteins (SAPs) play critical roles in various neurodegeneration diseases and brain tumors. However, in lower-grade gliomas (LGG), SAPs have not been explored systematically. Herein, we are going to explore SAPs expression profile and its clinicopathological significance in LGG which can offer new insights to glioma therapy. In the present study, we integrate a list of SAPs that covered 231 proteins with synaptogenesis activity and post synapse formation. The LGG RNA-seq data were downloaded from GEO, TCGA and CGGA database. The prognosis associated SAPs in key modules of PPI (protein-protein interaction networks) was regarded as hub SAPs. Western blot, quantitative reverse transcription PCR (qRT-PCR) and immunochemistry results from HPA database were used to verify the expression of hub SAPs. There were 68 up-regulated SAPs and 44 down-regulated SAPs in LGG tissue compared with normal brain tissue. Data from function enrichment analysis revealed functions of differentially expressed SAPs in synapse organization and glutamatergic receptor pathway in LGGs. Survival analysis revealed that four SAPs, GRIK2, GABRD, GRID2 and ARC were correlate with the prognosis of LGG patients. Interestingly, we found that GABRD were up-regulated in LGG patients with seizures, indicating that SAPs may link to the pathogenesis of seizures in glioma patients. The four-SAPs signature was revealed as an independent prognostic factor in gliomas. Our study presented a novel strategy to assess the prognostic risks of LGGs, based on the expression of SAPs.

Identification of COL6A1 as the Key Gene Associated with Antivascular Endothelial Growth Factor Therapy in Glioblastoma Multiforme.

Background: Vascular endothelial growth factors (VEGFs) are important for glioblastoma multiforme (GBM) growth and development. However, the effects of VEGF-targeting drugs in primary GBM remain poorly understood. Aim: We aimed to explore the key genes correlated with VEGF expression and prognosis and elucidate their potential implications in GBM anti-VEGF therapy. Materials and Methods: RNA-seq data with the corresponding clinicopathological information was retrieved from The Cancer Genome Atlas and the Chinese Glioma Genome Atlas. Weighted gene coexpression network analyses was performed on differentially expressed genes to construct coexpression modules and investigate their correlation with VEGFs. Functional enrichment analyses were performed based on the coexpressed genes from the most promising modules. CytoHubba and Kaplan-Meier analyses were implemented to identify the key genes in the modules of interest. The oncomine database, quantitative reverse transcription PCR, and the Human Protein Atlas were used to investigate the expression characteristics of the identified key genes. Results: Four modules (cyan, green, purple, and tan) correlated significantly with VEGF expression. Enrichment analyses suggested that extracellular matrix-receptor interaction, growth factor binding, and the PI3K-Akt pathways were involved in VEGF expression. Four hub genes (COL6A1, SNRPG, COL3A1, and AHI1) associated with VEGF were identified. Among them, COL6A1 was regarded as the key gene associated with anti-VEGF therapy. Further, COL6A1 was upregulated in GBM compared to that in normal brain tissues. COL6A1 overexpression was associated with a poor prognosis. Conclusion: COL6A1 was identified as the key gene associated with anti-VEGF therapy and may provide novel insight into GBM targeted therapy.

Modified Nasoseptal Rescue Flap Technique for Pituitary Adenoma Resection via Endoscopic Endonasal Approach.

ABSTRACT: Nasoseptal rescue flap (NSRF), which preserves the pedicle of the flap and is harvested as a nasoseptal flap (NSF) when intraoperative leakage of cerebrospinal fluid (CSF) occurs, is an alternative strategy for skull base reconstruction in patients with pituitary adenoma resection via an endoscopic endonasal approach. However, in practice, the original NSRF technique cannot meet the needs during operation. Therefore, the authors aimed to describe a modified NSRF technique for the resection of pituitary adenoma via endoscopic endonasal approach and to examine its utility and outcomes. The authors retrospectively analyzed the medical records of 87 consecutive patients with pituitary adenoma who underwent endoscopic endonasal surgery performed using NSRF technique from September 2019 to August 2020. Data on intraoperative CSF leakage, NSF conversion rate, and reconstruction-related complications were analyzed. The average age of patients was 50.1 years (men, 50.5%). Twenty-five cases of intraoperative CSF leakage were observed: 23 cases of low-flow CSF leakage and two cases of high-flow CSF leakage. NSRF was converted to NSF in 11 cases. Two patients experienced postoperative CSF leakage after reconstruction without NSF and required unplanned reoperation to rebuild the skull base with NSF. In conclusion, this modified NSRF utilized a minimally invasive way to provide sufficient surgical corridor without the need for pedicle retraction, and it can be effectively converted to an NSF for skull base reconstruction in patients with pituitary adenoma.

Timing and Origins of Local and Distant Metastases in Lung Cancer.

INTRODUCTION: Metastasis is the primary cause of lung cancer-related death. Nevertheless, the underlying molecular mechanisms and evolutionary patterns of lung cancer metastases are still elusive. METHODS: We performed whole-exome sequencing for 40 primary tumors (PTs) and 61 metastases from 47 patients with lung cancer, of which 40 patients had paired PTs and metastases. The PT-metastasis genomic divergence, metastatic drivers, timing of metastatic dissemination, and evolutionary origins were analyzed using appropriate statistical tools and mathematical models. RESULTS: There were various degrees of genomic heterogeneity when comparing the paired primary and metastatic lesions or comparing metastases of different sites. Multiple metastasis-selected/enriched genetic alterations were found, such as MYC amplification, NKX2-1 amplification, RICTOR amplification, arm 20p gain, and arm 11p loss, and these results were were also featured in a meta-analysis cross-validated using an independent cohort from Memorial Sloan-Kettering Cancer Center database. To elucidate the metastatic seeding time, we applied a metastatic model and found 61.1% of the tumors were late dissemination, in which the metastatic seeding happened approximately 2.74 years before clinical detection. One exception was lymph node metastases whose dissemination time was relatively early. By analyzing the evolutionary origins, we reported that nonlymph node metastases were mainly seeded by the PT (87.5%) rather than the earlier colonized lymph node metastases. CONCLUSIONS: Our results shed light on the molecular features that potentially drive lung cancer metastases. The distinct temporospatial pattern of disease progression revealed that lung cancer was susceptible to either late dissemination or indolent early lymph node metastases, leaving a potential time window to minimize metastases by early cancer detection.

Wireless phone use and adult meningioma risk: a systematic review and Meta-analysis.

Introduction: Several studies explored the effects of exposure to radiofrequency-electromagnetic field (RF-EMF) and extremely low frequency (ELF) EMF emitted from mobile phones on meningioma among adults. However, the results could not reach an agreement. This meta-analysis was conducted to confirm the relationship between adult meningioma risk and the use of a wireless phone. Methods: Pertinent studies were identified by searching PubMed and Embase up to August 2018. The random- or fixed-effects model was used to combine the results depending on the heterogeneity of the analysis. The publication bias was evaluated using Egger's regression asymmetry test. The subgroup analysis was performed by time since the first use of wireless phone and laterality (ipsilateral/contralateral). Results: Eight studies were enrolled in this meta-analysis. The pooled results suggested that the ever use of wireless phone led to a borderline decreased adult meningioma risk [odds ratio (OR) 0.90; 95% confidence interval (CI) 0.83-0.99] with no heterogeneity (I2 = 5.3%; p = 0.391). A decreased risk of meningioma was seen in short-term (OR = 0.85; 95% CI = 0.77-0.94) users. Neither decreased nor increased risk of meningioma was observed in mid-term (OR = 0.93, 95% CI = 0.75-1.16) and long-term (OR = 1.05, 95% CI = 0.93-1.19) users. Neither ipsilateral (OR = 1.05, 95% CI = 0.90-1.22) nor contralateral (OR = 0.86, 95% CI = 0.62-1.18) wireless phone use was associated with the risk of meningioma. Conclusions: This meta-analysis suggested a relationship between decreased meningioma risk and wireless phone use. However, the findings need further validation.

Intron Retention as a Mode for RNA-Seq Data Analysis.

Intron retention (IR) is an alternative splicing mode whereby introns, rather than being spliced out as usual, are retained in mature mRNAs. It was previously considered a consequence of mis-splicing and received very limited attention. Only recently has IR become of interest for transcriptomic data analysis owing to its recognized roles in gene expression regulation and associations with complex diseases. In this article, we first review the function of IR in regulating gene expression in a number of biological processes, such as neuron differentiation and activation of CD4+ T cells. Next, we briefly review its association with diseases, such as Alzheimer's disease and cancers. Then, we describe state-of-the-art methods for IR detection, including RNA-seq analysis tools IRFinder and iREAD, highlighting their underlying principles and discussing their advantages and limitations. Finally, we discuss the challenges for IR detection and potential ways in which IR detection methods could be improved.

Upregulation of Long Non-Coding RNA GCC2-AS1 Facilitates Malignant Phenotypes and Correlated With Unfavorable Prognosis for Lung Adenocarcinoma.

BACKGROUND: The role played by long noncoding RNA GCC2-AS1 in primary malignant tumors remains poorly understood. This study aimed to determine the expression levels and evaluate the clinical significance and biological effects of GCC2-AS1 in lung adenocarcinoma (LUAD). METHODS: We used data obtained from tissue samples and the TCGA database to determine the levels of GCC2-AS1 expression LUAD patients, and the prognostic value of those levels. Functional experiments were performed to investigate the effect of GCC2-AS1 on LUAD cells. Genes that were differentially expressed in GCC2-AS1-low and -high groups were analyzed by an enrichment analysis. Additionally, a nomogram model was created and subgroup analyses were performed to further determine the prognostic value of GCC2-AS1 in LUAD. RESULTS: GCC2-AS1 expression was significantly upregulated in lung adenocarcinoma tissues as compared with normal tissues. Depletion of GCC2-AS1 inhibited the proliferation and invasion of LUAD cells in vitro. An elevated level of GCC2-AS1 was strongly correlated with shorter overall survival time and was identified as an independent prognostic marker for LUAD patients. Enrichment analyses conducted using GO, KEGG, and GSEA databases were performed to identify biological pathways that might involve GCC2-AS1. Several subgroups were found to have a significant prognostic value for patients in the GCC2-AS1-low and -high groups. CONCLUSIONS: Our findings suggest that GCC2-AS1 can serve as a diagnostic and prognostic biomarker for LUAD patients.

Silencing Smad4 attenuates sensitivity of colorectal cancer cells to cetuximab by promoting epithelial­mesenchymal transition.

The aberrant expression of tumor suppressor Smad4 often occurs in colorectal cancer (CRC), and this phenomenon is believed to be associated with drug resistance. The present study aimed to investigate the effects of Smad4 on the sensitivity of CRC cells to cetuximab, and the possible mechanism underlying such an effect. A total of 629 colorectal adenocarcinoma cases were downloaded from The Cancer Genome Atlas (TCGA) database, and a Smad4 mutation rate of ~21% was demonstrated among the cases. Low expression of Smad4 was present in CRC tissues analyzed by TCGA and in four CRC cell lines, as determined by reverse transcription­quantitative PCR (RT­qPCR) and western blot analysis. Cell Counting kit­8 (CCK­8) was used to measure the effects of different concentrations of cetuximab on SW480 cell viability at 24 and 48 h. The results demonstrated that treatment of SW480 cells with 20 µg/ml cetuximab for 48 h markedly reduced cell viability. In addition, plasmids were transfected into SW480 cells to induce Smad4 silencing or overexpression. Silencing Smad4 attenuated the sensitivity of SW480 CRC cells to cetuximab; this effect was reflected in increased cell viability and slightly increased migration and invasion, as determined by CCK­8, wound scratch and Transwell analyses. RT­qPCR and western blotting was performed to assess the expression levels of apoptosis­ and epithelial­mesenchymal transition (EMT)­related genes. Silencing Smad4 partly reversed the effects of cetuximab on the mRNA and protein expression levels of vimentin, Bax/Bcl­2 and E­cadherin. However, Smad4 overexpression enhanced SW480 cell sensitivity to cetuximab. In conclusion, Smad4 may serve a vital role in the sensitivity of CRC cells to chemotherapeutic drugs by promoting EMT.

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads.

The advent of third-generation sequencing (TGS) technologies, such as the Pacific Biosciences (PacBio) and Oxford Nanopore machines, provides new possibilities for contig assembly, scaffolding, and high-performance computing in bioinformatics due to its long reads. However, the high error rate and poor quality of TGS reads provide new challenges for accurate genome assembly and long-read alignment. Efficient processing methods are in need to prioritize high-quality reads for improving the results of error correction and assembly. In this study, we proposed a novel Read Quality Evaluation and Selection Tool (REQUEST) for evaluating the quality of third-generation long reads. REQUEST generates training data of high-quality and low-quality reads which are characterized by their nucleotide combinations. A linear regression model was built to score the quality of reads. The method was tested on three datasets of different species. The results showed that the top-scored reads prioritized by REQUEST achieved higher alignment accuracies. The contig assembly results based on the top-scored reads also outperformed conventional approaches that use all reads. REQUEST is able to distinguish high-quality reads from low-quality ones without using reference genomes, making it a promising alternative sequence-quality evaluation method to alignment-based algorithms.

MicroRNA-455-3p Inhibits Tumor Cell Proliferation and Induces Apoptosis in HCT116 Human Colon Cancer Cells.

BACKGROUND MicroRNAs have been reported to play significant roles in pathogenesis of colorectal cancer (CRC). In the present study, we aimed to investigate the functional role of microRNA-455-3p (miR-455-3p) in CRC, as well as its underlying mechanisms. MATERIAL AND METHODS Human colon cancer cell line HCT116 cells were transfected with miR-455-3p mimics, inhibitors, or controls. After transfection, the effects of miR-455-3p mimics or inhibitors on cell proliferation were analyzed by 3-(4, 5-dimethyl-2- thiazolyl)-2, 5-diphenyl -2-H-tetrazolium bromide (MTT) assay and BrdU assay, and the effects of miR-455-3p mimics or inhibitors on cell apoptosis were determined. In addition, the underlying mechanisms of cell proliferation and apoptosis were explored by assessing the protein levels of cell cycle regulators and apoptosis-related protein. RESULTS The results showed that overexpression of miR-455-3p significantly inhibited the cell proliferation (P<0.05 or <0.01) in HCT116 cells compared with the control group, but significantly increased the apoptosis (P<0.01). On the contrary, suppression of miR-455-3p significantly increased the cell proliferation but decreased the apoptosis. Moreover, we found that overexpression of miR-455-3p significantly elevated the protein levels of p27 kinase inhibition protein (KIP) 1, Bax, pro-caspase-3, and active caspase-3, and markedly downregulated the levels of B-cell lymphoma-2 (Bcl-2). Contrary results were found by suppression of miR-455-3p. However, there were no significant differences in p21 expression. CONCLUSIONS MiRNA-455-3p functions as an anti-oncogene in HCT116 cells by inhibiting cell proliferation and inducing of apoptosis.