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1.
Small Methods ; : e2301585, 2024 May 29.
Artículo en Inglés | MEDLINE | ID: mdl-38807543

RESUMEN

DNA-based data storage is a new technology in computational and synthetic biology, that offers a solution for long-term, high-density data archiving. Given the critical importance of medical data in advancing human health, there is a growing interest in developing an effective medical data storage system based on DNA. Data integrity, accuracy, reliability, and efficient retrieval are all significant concerns. Therefore, this study proposes an Effective DNA Storage (EDS) approach for archiving medical MRI data. The EDS approach incorporates three key components (i) a novel fraction strategy to address the critical issue of rotating encoding, which often leads to data loss due to single base error propagation; (ii) a novel rule-based quaternary transcoding method that satisfies bio-constraints and ensure reliable mapping; and (iii) an indexing technique designed to simplify random search and access. The effectiveness of this approach is validated through computer simulations and biological experiments, confirming its practicality. The EDS approach outperforms existing methods, providing superior control over bio-constraints and reducing computational time. The results and code provided in this study open new avenues for practical DNA storage of medical MRI data, offering promising prospects for the future of medical data archiving and retrieval.

2.
J Biochem Mol Toxicol ; 38(1): e23542, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37712196

RESUMEN

Isoquercitrin has been discovered with various biological properties, including anticancer, anti-inflammation, antioxidation, and neuroprotection. The aim of this study is to explore the efficacy of isoquercitrin in nasopharyngeal carcinoma (NPC) and to disclose its potential regulating mechanisms. CNE1 and HNE1 cells were treated with various concentrations of isoquercitrin. Ferrostatin-1 (Fer-1, a ferroptosis inhibitor) and alpha-lipoic acid (ALA, an activator of the AMP-activated protein kinase [AMPK] pathway) treatments were conducted to verify the effects of isoquercitrin, respectively. Cell viability, proliferation, reactive oxygen species (ROS) generation, and lipid peroxidation were determined, respectively. GPX4 expression and ferroptosis- and pathway-related protein expression were measured. A xenograft tumor model was constructed by subcutaneously inoculating CNE1 cells into the middle groin of each mouse. We found that the IC50 values of CNE1 and HNE1 cells were 392.45 and 411.38 µM, respectively. CNE1 and HNE1 viability and proliferation were both markedly reduced with the increasing concentration of isoquercitrin. ROS generation and lipid peroxidation were both enhanced with declined ferroptosis-related markers under isoquercitrin treatment. The nuclear factor kappa B (NF-κB) pathway, the AMPK pathway, and the interleukin (IL)-1ß expression were all markedly suppressed by isoquercitrin. Moreover, isoquercitrin restrained the tumor growth and enhanced lipid peroxidation and ferroptosis in vivo. Interestingly, both Fer-1 and ALA treatments distinctly offset isoquercitrin-induced effects in vitro and in vivo. These findings indicated that isoquercitrin might enhance oxidative stress and ferroptosis in NPC via AMPK/NF-κB p65 inhibition.


Asunto(s)
Ferroptosis , Neoplasias Nasofaríngeas , Quercetina/análogos & derivados , Humanos , Ratones , Animales , FN-kappa B/metabolismo , Proteínas Quinasas Activadas por AMP/metabolismo , Carcinoma Nasofaríngeo/tratamiento farmacológico , Transducción de Señal , Especies Reactivas de Oxígeno/metabolismo , Estrés Oxidativo , Modelos Animales de Enfermedad
3.
PeerJ ; 11: e16493, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-38025726

RESUMEN

Background: Currently, ferritin heavy chain (FTH1) has been increasingly found to play a crucial role in cancer as a core regulator of ferroptosis, while its role of non-ferroptosis in head and neck squamous cell carcinoma (HNSCC) is still unclear. Methods: Herein, we analyzed the expression level of FTH1 in HNSCC using TCGA database, and FTH1 protein in HNSCC tissues and cell lines was determined by immunohistochemistry (IHC) and western blotting, respectively. Then, its prognostic value and relationship with clinical parameters were investigated in HNSCC patients. Additionally, the biological function of FTH1 in HNSCC was explored. Results: The current study showed that FTH1 is significantly overexpressed in HNSCC tissues and related to poor prognosis and lymph node metastasis of HNSCC. FTH1 knockdown could suppress the metastasis and epithelial-mesenchymal transition (EMT) process of HNSCC. Conclusion: Our findings indicate that FTH1 plays a critical role in the progression and metastasis of HNSCC and can serve as a promising prognostic factor and therapeutic target in HNSCC.


Asunto(s)
Neoplasias de Cabeza y Cuello , Humanos , Carcinoma de Células Escamosas de Cabeza y Cuello/genética , Neoplasias de Cabeza y Cuello/genética , Metástasis Linfática , Pronóstico , Apoferritinas , Ferritinas/genética , Oxidorreductasas
4.
Sensors (Basel) ; 23(19)2023 Oct 08.
Artículo en Inglés | MEDLINE | ID: mdl-37837137

RESUMEN

The grinding grooves of material removal machining and the residues of a machining tool on the key component surface cause surface stress concentration. Thus, it is critical to carry out precise measurements on the key component surface to evaluate the stress concentration. Based on white-light interferometry (WLI), we studied the measurement distortion caused by the reflected light from the steep side of the grinding groove being unable to return to the optical system for imaging. A threshold value was set to eliminate the distorted measurement points, and the cubic spline algorithm was used to interpolate the eliminated points for compensation. The compensation result agrees well with the atomic force microscope (AFM) measurement result. However, for residues on the surface, a practical method was established to obtain a microscopic 3D micro-topography point cloud and a super-depth-of-field fusion image simultaneously. Afterward, the semantic segmentation network U-net was adopted to identify the residues in the super-depth-of-field fusion image and achieved a recognition accuracy of 91.06% for residual identification. Residual feature information, including height, position, and size, was obtained by integrating the information from point clouds and super-depth-of-field fusion images. This work can provide foundational data to study surface stress concentration.

5.
Altern Ther Health Med ; 29(8): 638-643, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37678868

RESUMEN

Objective: In the context of the rising prevalence of eosinophilic chronic sinusitis accompanied by nasal polyps, this study aims toinvestigate the role of CD23 in the pathogenesis of eosinophilic chronic sinusitis with nasal polyps. Methods: The cross-sectional study was conducted, 75 patients with chronic sinusitis and nasal polyps treated in our hospital from January 2019 to May 2021 were selected, including 40 cases of eosinophilic patients with the average age of 29.92 years and 35 cases of non-eosinophilic patients with the average age of 30.05 years and 30 patients with the average age of 30.14 years who underwent skull base benign tumor resection in our hospital were selected as the control group, the expression of CD23 in polyp tissue was detected by immunohistochemistry, and the expression of CD23, p-ERK and CCL20 in polyp tissue were detected by Western blot. Specifically, tissue samples were processed and subjected to staining using specific antibodies targeting CD23. The stained sections were then visualized under a microscope to determine the expression levels of CD23. CD23, p-ERK, and CCL20 expressions in polyp tissue were evaluated via Western blot. Total protein was extracted, separated on a gel, transferred to a membrane, and probed with specific antibodies. Chemiluminescence allowed visualization and quantification of protein expressions. Results: Immunohistochemistry showed that CD23 expression was high in the eosinophilic group but low in the non-eosinophilic and control groups. The relative expression levels of CD23 protein, p-ERK protein, and CCL20 protein in polyp tissue s of the eosinophilic group were (0.892 ± 0.092), (0.733 ± 0.101) and (0.813 ± 0.106), respectively, which were significantly higher than those in non-eosinophilic group and control group (P < .05). The relative expression levels of CD23 protein, p-ERK protein, and CCL20 protein in the non-eosinophilic group were (0.461 ± 0.087), 0.412 ± 0.096) and (0.424 ± 0.098), which were significantly higher than those in the control group (P < .05). The relative expression level of CD23 protein in the eosinophilic group was positively correlated with the relative expression levels of p-ERK protein and CCL20 protein (P < .05). The Lund-Kennedy score in the eosinophilic group was (6.10 ± 1.01), which was significantly higher than that in the non-eosinophilic group (P < .05). The relative expression level of CD23 protein in the eosinophilic group was positively correlated with Lund-Kennedy score (P < .05). Conclusion: Eosinophilic chronic sinusitis with nasal polyp mucosal tissue CD23 expression is up-regulated, which is positively correlated with the ERK signaling pathway and disease severity. This study provides valuable insights into potential therapeutic targets that could be explored to develop future treatment modalities. The potential clinical significance of the study is to reveal the important role of CD23 in the pathogenesis of chronic sinusitis with nasal polyps. The upward adjustment of CD23 is positively related to the severity of the disease, which provides valuable guidance for future treatment strategies. This discovery may provide new ways for the development of CD23 treatment methods, so as to better control the progress of the disease of eosinophilic chronic sinusitis with nasal polyps. Further research can explore the molecular mechanism of CD23 regulation, further verify the feasibility of CD23 as the treatment target, and evaluate the potential value of CD23 as a prognostic logo.


Asunto(s)
Pólipos Nasales , Rinitis , Sinusitis , Humanos , Adulto , Rinitis/complicaciones , Pólipos Nasales/complicaciones , Pólipos Nasales/patología , Estudios Transversales , Sinusitis/complicaciones , Sinusitis/patología , Transducción de Señal , Enfermedad Crónica
6.
Comput Biol Med ; 165: 107404, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37666064

RESUMEN

DNA data storage is a promising technology that utilizes computer simulation, and synthetic biology, offering high-density and reliable digital information storage. It is challenging to store massive data in a small amount of DNA without losing the original data since nonspecific hybridization errors occur frequently and severely affect the reliability of stored data. This study proposes a novel biologically optimized encoding model for DNA data storage (BO-DNA) to overcome the reliability problem. BO-DNA model is developed by a new rule-based mapping method to avoid data drop during the transcoding of binary data to premier nucleotides. A customized optimization algorithm based on a tent chaotic map is applied to maximize the lower bounds that help to minimize the nonspecific hybridization errors. The robustness of BO-DNA is computed by four bio-constraints to confirm the reliability of newly generated DNA sequences. Experimentally, different medical images are encoded and decoded successfully with 12%-59% improved lower bounds and optimally constrained-based DNA sequences reported with 1.77bit/nt average density. BO-DNA's results demonstrate substantial advantages in constructing reliable DNA data storage.


Asunto(s)
Algoritmos , ADN , Simulación por Computador , Reproducibilidad de los Resultados , ADN/genética
7.
Front Genet ; 14: 1158337, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37021008

RESUMEN

DNA is a practical storage medium with high density, durability, and capacity to accommodate exponentially growing data volumes. A DNA sequence structure is a biocomputing problem that requires satisfying bioconstraints to design robust sequences. Existing evolutionary approaches to DNA sequences result in errors during the encoding process that reduces the lower bounds of DNA coding sets used for molecular hybridization. Additionally, the disordered DNA strand forms a secondary structure, which is susceptible to errors during decoding. This paper proposes a computational evolutionary approach based on a synergistic moth-flame optimizer by Levy flight and opposition-based learning mutation strategies to optimize these problems by constructing reverse-complement constraints. The MFOS aims to attain optimal global solutions with robust convergence and balanced search capabilities to improve DNA code lower bounds and coding rates for DNA storage. The ability of the MFOS to construct DNA coding sets is demonstrated through various experiments that use 19 state-of-the-art functions. Compared with the existing studies, the proposed approach with three different bioconstraints substantially improves the lower bounds of the DNA codes by 12-28% and significantly reduces errors.

8.
Endocr Connect ; 12(5)2023 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-36952626

RESUMEN

Background: Fibroblast growth factor 1 (FGF1) is extensively amplified in many tumors and accelerates tumor invasion and metastasis. However, the role and precise molecular mechanism by which FGF1 participates in thyroid cancer (TC) are still unclear. Methods: Quantitative real-time polymerase chain reaction- and western blotting were used to detect the mRNA and protein levels of FGF1, high mobility group A (HMGA1), epithelial-to-mesenchymal transition (EMT)-related factors, and FGFs in both TC tissues and cell lines. Immunohistochemistry was conducted to examine the expression of FGF1 and HMGA1. Immunofluorescence staining was used to detect the coexpression of FGF1 and HMGA1. Transwell and wound healing assays were conducted to evaluate the effects of FGF1 on the capacity of invasion and migration in cells. Results: FGF1 was upregulated in papillary thyroid carcinoma (PTC) tissues and cell lines and was relatively higher in PTC tissues with cervical lymph node metastasis. Furthermore, FGF1 promotes invasion and metastasis through the EMT pathway. Mechanistically, FGF1 promotes EMT through intracellular function independent of FGF receptors. Interestingly, we demonstrated that FGF1 could upregulate HMGA1 in TC cells, and the correlation of FGF1 and HMGA1 was positive in PTC tissues. FGF1 and HMGA1 had obvious colocalization in the nucleus. We further revealed that FGF1 promotes the invasion and migration of TC cells through the upregulation of HMGA1. Conclusion: Intracellular FGF1 could promote invasion and migration in TC by mediating the expression of HMGA1 independent of FGF receptors, and FGF1 may be an effective therapeutic target in TC.

9.
Commun Biol ; 5(1): 1355, 2022 12 09.
Artículo en Inglés | MEDLINE | ID: mdl-36494488

RESUMEN

Circular RNAs (CircRNAs) are a class of noncoding RNAs formed by backsplicing during cotranscriptional and posttranscriptional processes, and they widely exist in various organisms. CircRNAs have multiple biological functions and are associated with the occurrence and development of many diseases. While the biogenesis and biological function of circRNAs have been extensively studied, there are few studies on circRNA degradation and only a few pathways for specific circRNA degradation have been identified. Here we outline basic information about circRNAs, summarize the research on the circRNA degradation mechanisms and discusses where this field might head, hoping to provide some inspiration and guidance for scholars who aim to study the degradation of circRNAs.


Asunto(s)
ARN Circular , ARN , ARN Circular/genética , ARN/genética , ARN/metabolismo , Estabilidad del ARN
10.
Cell Mol Life Sci ; 79(7): 357, 2022 Jun 09.
Artículo en Inglés | MEDLINE | ID: mdl-35680727

RESUMEN

BACKGROUND: Radiation is currently used to be a mainstay of salvage therapy for nasopharyngeal carcinoma (NPC), however, development of radioresistance largely limits the radiation efficacy. Circular RNAs (circRNAs) have been shown to affect NPC progression, but its role in radioresistance remain unclear. METHODS: The circular structure of circFIP1L1(circ_0069740) was verified by RNA-sequencing, RT-PCR based on gDNA or cDNA, RNase R treatment, and actinomycin D treatment. Cellular localization of circFIP1L1 and miR-1253 was detected by nucleoplasmic separation and/or fluorescence in situ hybridization. Expression of non-coding RNAs and mRNAs was detected by qRT-PCR, protein expression was detected by Western blot. Functionally, EdU, CCK-8, and colony formation experiments were employed to assess cell proliferation, flow cytometry was adopted to estimate cell cycle and apoptosis. Xenograft tumor growth was performed to detect the role of circFIP1L1 in vivo. Mechanistically, we examined the interplay between miR-1253 and circFIP1L1 or EIF4A3 through dual-luciferase reporter assay. The potential regulatory impacts of EIF4A3 on circFIP1L1 or PTEN was examined by RNA immunoprecipitation and RNA pull-down assays. RESULTS: CircFIP1L1 overexpression and miR-1253 knockdown repressed NPC cell proliferation, facilitated NPC cell apoptosis, and enhanced NPC radiosensitivity. Mechanistically, circFIP1L1 was revealed to repress miR-1253 by binding to it, and EIF4A3 is a target gene of miR-1253. CircFIP1L1 regulated NPC proliferation, apoptosis, and radiosensitivity through miR-1253/EIF4A3. Moreover, we found that EIF4A3 bound to FIP1L1 mRNA transcript and induced circFIP1L1 formation, and thus stabilizing PTEN mRNA. CONCLUSION: Our findings suggested that EIF4A3-induced circFIP1L1 repressed NPC cell proliferation, facilitated NPC cell apoptosis, and enhanced NPC radiosensitivity by miR-1253.


Asunto(s)
MicroARNs , Neoplasias Nasofaríngeas , Línea Celular Tumoral , Proliferación Celular/genética , ARN Helicasas DEAD-box/genética , Factor 4A Eucariótico de Iniciación/metabolismo , Regulación Neoplásica de la Expresión Génica , Humanos , Hibridación Fluorescente in Situ , MicroARNs/genética , MicroARNs/metabolismo , Carcinoma Nasofaríngeo/genética , Carcinoma Nasofaríngeo/radioterapia , Neoplasias Nasofaríngeas/genética , Neoplasias Nasofaríngeas/metabolismo , Neoplasias Nasofaríngeas/radioterapia , ARN Mensajero , Tolerancia a Radiación/genética
11.
Physiol Genomics ; 54(9): 337-349, 2022 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-35759451

RESUMEN

The interplay between N6-methyladenosine (m6A) modification and microRNAs (miRs) participates in cancer progression. This study is conducted to explore the role of miR-19a-3p in nasopharyngeal carcinoma (NPC) cell proliferation and invasion. Reverse transcription quantitative polymerase chain reaction and Western blot showed that miR-19a-3p was upregulated in NPC tissues and cells and related to poor prognosis, methyltransferase-like 3 (METTL3) was highly expressed, whereas BMP and activin membrane-bound inhibitor (BAMBI) was weakly expressed in NPC tissues and cells. miR-19a-3p downregulation inhibited cell proliferation and invasion, whereas miR-19a-3p overexpression played the opposite role. m6A quantification and m6A RNA immunoprecipitation assays showed that METTL3-mediated m6A modification promoted the processing and maturation of pri-miR-19a via DiGeorge syndrome critical region gene 8 (DGCR8). Dual-luciferase assay showed that BAMBI was a target of miR-19a-3p. The rescue experiments showed that BAMBI downregulation reversed the role of miR-19a-3p inhibition in NPC cells. A xenograft tumor model showed that METTL3 downregulation inhibited tumor growth via the miR-19a-3p/BAMBI in vivo. Overall, our findings elicited that METTL3-mediated m6A modification facilitated the processing and maturation of pri-miR-19a via DGCR8 to upregulate miR-19a-3p, and miR-19a-3p inhibited BAMBI expression to promote NPC cell proliferation and invasion, thus driving NPC progression.


Asunto(s)
MicroARNs , Neoplasias Nasofaríngeas , Animales , Línea Celular Tumoral , Proliferación Celular/genética , Regulación Neoplásica de la Expresión Génica/genética , Humanos , Metiltransferasas/genética , Metiltransferasas/metabolismo , MicroARNs/genética , MicroARNs/metabolismo , Carcinoma Nasofaríngeo/genética , Carcinoma Nasofaríngeo/patología , Neoplasias Nasofaríngeas/genética , Neoplasias Nasofaríngeas/patología , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo
13.
Sci Rep ; 12(1): 8842, 2022 05 25.
Artículo en Inglés | MEDLINE | ID: mdl-35614133

RESUMEN

Today's growing phishing websites pose significant threats due to their extremely undetectable risk. They anticipate internet users to mistake them as genuine ones in order to reveal user information and privacy, such as login ids, pass-words, credit card numbers, etc. without notice. This paper proposes a new approach to solve the anti-phishing problem. The new features of this approach can be represented by URL character sequence without phishing prior knowledge, various hyperlink information, and textual content of the webpage, which are combined and fed to train the XGBoost classifier. One of the major contributions of this paper is the selection of different new features, which are capable enough to detect 0-h attacks, and these features do not depend on any third-party services. In particular, we extract character level Term Frequency-Inverse Document Frequency (TF-IDF) features from noisy parts of HTML and plaintext of the given webpage. Moreover, our proposed hyperlink features determine the relationship between the content and the URL of a webpage. Due to the absence of publicly available large phishing data sets, we needed to create our own data set with 60,252 webpages to validate the proposed solution. This data contains 32,972 benign webpages and 27,280 phishing webpages. For evaluations, the performance of each category of the proposed feature set is evaluated, and various classification algorithms are employed. From the empirical results, it was observed that the proposed individual features are valuable for phishing detection. However, the integration of all the features improves the detection of phishing sites with significant accuracy. The proposed approach achieved an accuracy of 96.76% with only 1.39% false-positive rate on our dataset, and an accuracy of 98.48% with 2.09% false-positive rate on benchmark dataset, which outperforms the existing baseline approaches.


Asunto(s)
Algoritmos , Seguridad Computacional , Benchmarking , Recolección de Datos , Privacidad
14.
Artículo en Inglés | MEDLINE | ID: mdl-35328897

RESUMEN

Breast cancer death rates are higher than any other cancer in American women. Machine learning-based predictive models promise earlier detection techniques for breast cancer diagnosis. However, making an evaluation for models that efficiently diagnose cancer is still challenging. In this work, we proposed data exploratory techniques (DET) and developed four different predictive models to improve breast cancer diagnostic accuracy. Prior to models, four-layered essential DET, e.g., feature distribution, correlation, elimination, and hyperparameter optimization, were deep-dived to identify the robust feature classification into malignant and benign classes. These proposed techniques and classifiers were implemented on the Wisconsin Diagnostic Breast Cancer (WDBC) and Breast Cancer Coimbra Dataset (BCCD) datasets. Standard performance metrics, including confusion matrices and K-fold cross-validation techniques, were applied to assess each classifier's efficiency and training time. The models' diagnostic capability improved with our DET, i.e., polynomial SVM gained 99.3%, LR with 98.06%, KNN acquired 97.35%, and EC achieved 97.61% accuracy with the WDBC dataset. We also compared our significant results with previous studies in terms of accuracy. The implementation procedure and findings can guide physicians to adopt an effective model for a practical understanding and prognosis of breast cancer tumors.


Asunto(s)
Neoplasias de la Mama , Femenino , Humanos , Algoritmos , Mama , Neoplasias de la Mama/diagnóstico , Aprendizaje Automático , Máquina de Vectores de Soporte
15.
Materials (Basel) ; 16(1)2022 Dec 29.
Artículo en Inglés | MEDLINE | ID: mdl-36614667

RESUMEN

As a new surface treatment technology, laser shock peening (LSP) is a multi-point overlay process of single-point laser shock. In this study, the finite element method (FEM) was used to build a model of single-point laser shock, and the model was verified by experiments. The difference in residual stresses between the experimental and simulated results was less than 20%. Then, the effects of the stress field and deformation of 20CrMnTi with different laser shock parameters were simulated and analyzed. According to the mechanical response of 20CrMnTi to different laser shock parameters, the optimal shocking process parameters for single-point shocking via LSP were determined to be a shock energy of 5 J, a laser pulse width of 20 ns, and an impact number of 5. Lastly, a simulation of multi-point laser shock was performed with the optimal parameters, and the residual compressive stress values of multi-point impacts are close to those of single-point impacts under the same process conditions.

16.
Sci Rep ; 11(1): 18063, 2021 09 10.
Artículo en Inglés | MEDLINE | ID: mdl-34508146

RESUMEN

Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention. Consequently, the current DNA storage systems are often not self-contained, implying that they have to resort to external tools for the restoration of the stored DNA data. This may result in high risks in data loss since the required tools might not be available due to the high uncertainty in far future. To address this issue, we propose in this paper a self-contained DNA storage system that can bring self-explanatory to its stored data without relying on any external tool. To this end, we design a specific DNA file format whereby a separate storage scheme is developed to reduce the data redundancy while an effective indexing is designed for random read operations to the stored data file. We verified through experimental data that the proposed self-contained and self-explanatory method can not only get rid of the reliance on external tools for data restoration but also minimise the data redundancy brought about when the amount of data to be stored reaches a certain scale.


Asunto(s)
ADN/genética , Bases de Datos Genéticas , Almacenamiento y Recuperación de la Información/métodos , Algoritmos , ADN/química , Humanos , Modelos Teóricos , Investigación
17.
Aging (Albany NY) ; 12(24): 25778-25804, 2020 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-33232279

RESUMEN

Aging is regarded as a dominant risk factor for cancer. Additionally, inflammation and asthenic immune surveillance with aging may facilitate tumor formation and development. However, few studies have comprehensively analyzed the relationship between aging-related genes (AGs) and the prognosis, inflammation and tumor immunity of head and neck squamous cell carcinoma (HNSCC). Here, we initially screened 41 differentially expressed AGs from The Cancer Genome Atlas (TCGA) database. In the training set, a prognosis risk model with seven AGs (APP, CDKN2A, EGFR, HSPD1, IL2RG, PLAU and VEGFA) was constructed and validated in the TCGA test set and the GEO set (P < 0.05). Using univariate and multivariate Cox regression analyses, we confirmed that risk score was an independent prognostic factor of HNSCC patients. In addition, a high risk score was significantly correlated with immunosuppression, and high expression of PLAU, APP and EGFR was the main factor. Furthermore, we confirmed that a high risk score was significantly associated with levels of proinflammatory factors (IL-1α, IL-1ß, IL-6 and IL-8) in HNSCC samples. Thus, this risk model may serve as a prognostic signature and provide clues for individualized immunotherapy for HNSCC patients.


Asunto(s)
Envejecimiento/genética , Biomarcadores de Tumor/genética , Regulación Neoplásica de la Expresión Génica , Neoplasias de Cabeza y Cuello/genética , Inflamación/genética , Carcinoma de Células Escamosas de Cabeza y Cuello/genética , Envejecimiento/metabolismo , Envejecimiento/patología , Biomarcadores de Tumor/metabolismo , Citocinas/sangre , Femenino , Perfilación de la Expresión Génica , Neoplasias de Cabeza y Cuello/metabolismo , Neoplasias de Cabeza y Cuello/patología , Humanos , Tolerancia Inmunológica/genética , Terapia de Inmunosupresión , Inflamación/metabolismo , Inflamación/patología , Masculino , Persona de Mediana Edad , Pronóstico , Carcinoma de Células Escamosas de Cabeza y Cuello/metabolismo , Carcinoma de Células Escamosas de Cabeza y Cuello/patología
18.
BMC Bioinformatics ; 21(1): 308, 2020 Jul 14.
Artículo en Inglés | MEDLINE | ID: mdl-32664870

RESUMEN

BACKGROUND: Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of potential interactions. RESULTS: We present a novel method, namely priori-fused boosting network inference method (PFBNet), to infer GRNs from time-series expression data by using the non-linear model of Boosting and the prior information (e.g., the knockout data) fusion scheme. Specifically, PFBNet first calculates the confidences of the regulation relationships using the boosting-based model, where the information about the accumulation impact of the gene expressions at previous time points is taken into account. Then, a newly defined strategy is applied to fuse the information from the prior data by elevating the confidences of the regulation relationships from the corresponding regulators. CONCLUSIONS: The experiments on the benchmark datasets from DREAM challenge as well as the E.coli datasets show that PFBNet achieves significantly better performance than other state-of-the-art methods (Jump3, GEINE3-lag, HiDi, iRafNet and BiXGBoost).


Asunto(s)
Algoritmos , Redes Reguladoras de Genes , Área Bajo la Curva , Biología Computacional , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Curva ROC
19.
Kaohsiung J Med Sci ; 36(11): 895-903, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-32668092

RESUMEN

The roles of RNA m6A modification in carcinogenesis have attracted much interest recently. However, the dysregulation of RNA m6A regulators (writers, readers, and erasers) in nasopharyngeal carcinoma (NPC) has never been reported. In this study, we showed that METTL3, one of the writers, was upregulated in NPC. Functional studies revealed that METTL3 promoted the migration and invasion of NPC cells. However, METTL3 knockdown reversed this effect and inhibited the migration, invasion and metastasis of NPC cells. METTL3 activated the luciferase activity of TOPflash (a reporter for beta-catenin/TCF signaling), and downregulation of METTL3 inhibited the expression of beta-catenin/TCF target genes vimentin and N-cadherin, which are two regulators of epithelial-mesenchymal transition. Moreover, dominant negative beta-catenin blocked the migration and invasion of NPC cells. Further mechanistic studies showed that METTL3 silencing decreased the m6A methylation and total mRNA levels of Tankyrase, a negative regulator of axin. Moreover, Tankyrase overexpression abrogated the repressive effects of METTL3 silencing on the migration of NPC cells. Collectively, our study demonstrates the oncogenic roles of METTL3 in NPC, and suggests that METTL3 might be a therapeutic target for NPC.


Asunto(s)
Carcinogénesis/genética , Transición Epitelial-Mesenquimal/genética , Metiltransferasas/genética , Carcinoma Nasofaríngeo/genética , Neoplasias Nasofaríngeas/genética , Adulto , Animales , Antígenos CD/genética , Antígenos CD/metabolismo , Cadherinas/genética , Cadherinas/metabolismo , Carcinogénesis/metabolismo , Carcinogénesis/patología , Línea Celular Tumoral , Movimiento Celular , Proliferación Celular , Femenino , Regulación Neoplásica de la Expresión Génica , Xenoinjertos , Humanos , Metástasis Linfática , Masculino , Metiltransferasas/antagonistas & inhibidores , Metiltransferasas/metabolismo , Ratones , Ratones Desnudos , Persona de Mediana Edad , Carcinoma Nasofaríngeo/metabolismo , Carcinoma Nasofaríngeo/mortalidad , Carcinoma Nasofaríngeo/patología , Neoplasias Nasofaríngeas/metabolismo , Neoplasias Nasofaríngeas/mortalidad , Neoplasias Nasofaríngeas/patología , Estadificación de Neoplasias , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/metabolismo , Transducción de Señal , Análisis de Supervivencia , Vimentina/genética , Vimentina/metabolismo , beta Catenina/genética , beta Catenina/metabolismo
20.
Front Oncol ; 10: 601, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32426279

RESUMEN

Circular RNAs (circRNAs), as a burgeoning sort of non-coding RNAs (ncRNAs), can regulate the expression of parental genes as miRNA sponges. This study was designed to explore the circRNA expression profile of nasopharyngeal carcinoma (NPC). High-throughput sequencing was performed to identify the circRNA expression profile of NPC patients compared with healthy controls. A total of 93 upregulated circRNAs and 77 downregulated circRNAs were identified. The expression levels of the top three upregulated and three downregulated circRNAs annotated by circBase were validated by quantitative real-time PCR (qRT-PCR). GO and KEGG analyses showed that these differentially expressed circRNAs were potentially implicated in NPC pathogenesis. CircRNA-miRNA-target gene network analysis revealed a potential mechanism that hsa_circ_0002375 (circKITLG) may be involved in NPC through sponging up miR-3198 and interfering with its downstream targets. Silencing of circKITLG inhibited NPC cell proliferation, migration, and invasion in vitro. This study provides a leading and fundamental circRNA expression profile of NPC.

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