急性和慢性髓性白血病细胞中可变剪接事件的识别

目的：为揭示异常的可变剪接在肿瘤中发挥的作用,着重研究急性髓性白血病（ AML）与慢性髓性白血病（CML）内显著差异的可变剪接事件以及剪接异构体。方法基于CML（K562）和AML（THP1、HL－60）细胞系的全转录组测序数据,在全基因组范围内采用TopHat、MATS和Cufflinks计算识别可变剪接事件、重构剪接异构体和分析其差异表达。结果在AML和CML细胞间识别的130个基因在CML细胞系中特异性高表达,80个基因在AML两株细胞系内均表达上调。在CML与AML之间识别了337个差异表达的剪接异构体以及35个差异可变剪接事件。结论 AML与CML细胞系间存在显著差异的可变剪接事件和剪接异构体。白血病相关的可变剪接事件可作为其潜在的标志物或药物靶标。     

The adaptive deep brain stimulation challenge

Sub-optimal clinical outcomes of conventional deep brain stimulation (cDBS) in treating Parkinson's Disease (PD) have boosted the development of new solutions to improve DBS therapy. Adaptive DBS (aDBS), consisting of closed-loop, real-time changing of stimulation parameters according to the patient's clinical state, promises to achieve this goal and is attracting increasing interest in overcoming all of the challenges posed by its development and adoption. In the design, implementation, and application of aDBS, the choice of the control variable and of the control algorithm represents the core challenge. The proposed approaches, in fact, differ in the choice of the control variable and control policy, in the system design and its technological limits, in the patient's target symptom, and in the surgical procedure needed. Here, we review the current proposals for aDBS systems, focusing on the choice of the control variable and its advantages and drawbacks, thus providing a general overview of the possible pathways for the clinical translation of aDBS with its benefits, limitations and unsolved issues.     

Cross‐relaxation parameters in cortical bone assessed with different MR sequences

This study aimed to show evidence of MR cross‐relaxation effects in cortical bone and to compare different MR sequences for the quantification of cross‐relaxation parameters. Measurements were performed on bovine diaphysis samples with spectroscopic methods (inversion‐recovery, off‐resonance saturation) and with a variable flip angle (VFA) UTE imaging method on a 4.7 T laboratory‐assembled scanner. Cross‐relaxation parameter assessment was carried out via a two‐pool model simulation with a matrix algebra approach. A proton signal amplitude of 28 Mol/L was observed (equivalent water fraction of 25%). It was attributed to collagen‐bound water, with values of ~ 0.3 ms, a “long‐T₂” proton pool, in exchange with protons from the collagen macromolecules ( of 10–20 μs). Magnetization transfer (MT) effects were detected with all sequences. The best precision of model parameters was obtained with off‐resonance saturation; the fraction of collagen methylene protons was found in the range of 22–28% and the transverse relaxation time for collagen methylene protons was 11 μs (1% precision). The model parameters obtained were compatible with VFA‐UTE results but could not be assessed with acceptable accuracy and precision using this method. In vivo MT quantification using off‐resonance saturation with a single B₁ amplitude and offset frequency may provide information about the relative amount of collagen per unit volume in cortical bone.     

Epitope mapping of the White Spot Syndrome Virus (WSSV) VP28 monoclonal antibody through combined in silico and in vitro analysis reveals the potential antibody binding site

White Spot Syndrome Virus (WSSV) infecting shrimp is an enveloped double-stranded DNA virus. The WSSV is a member of the genus Whispovirus. The envelope protein VP28 is the most investigated protein of WSSV. In the present study, the epitope mapping of the monoclonal antibody (MAb) C-33 was carried out. Based on the epitope mapping results, an antigen-antibody interaction model was derived. Peptide scanning and confirmation of epitopes of MAb C-33 were carried out using the sequence data. The MAb was reactive to the epitope of both recombinant VP28 and the whole virus. The results of the study indicated the presence of an epitope region. The epitope region is found positioned within two peptides, covering 13 amino acids. Framework and CDR (complementarity determining regions) of heavy and light chain (VH & VL) sequences showed identity to germline immunoglobulin sequences. The Web Antibody Modelling (WAM) selected for further evaluation based on a comparative analysis of WAM and Rosetta server-generated models of the Fv region. The docking study using WAM generated model revealed that the residues from LEU98 to GLY105 are active in antibody binding. The findings of this study could form a structural basis for further research in VP28 based diagnostics and therapeutics or vaccine discovery.     

Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia

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丝氨酸/精氨酸富有剪接因子1、核因子κB在前列腺癌中的表达及与患者临床特征的关系

目的探讨前列腺癌组织中丝氨酸/精氨酸富有剪接因子1(SRSF1)、核因子κB(NF-κB)的表达情况及与患者临床特征的关系。方法选取前列腺癌患者和前列腺良性增生患者,各70例,取前列腺癌组织和前列腺良性增生组织。免疫组化法检测前列腺癌组织和前列腺良性增生组织SRSF1、NF-κB蛋白的阳性表达率,并分析不同临床特征前列腺癌患者前列腺癌组织中SRSF1、NF-κB蛋白的表达情况。结果前列腺癌组织中SRSF1、NF-κB蛋白的阳性表达率均高于前列腺良性增生组织,差异均有统计学意义(P﹤0.05)。不同前列腺特异性抗原(PSA)水平前列腺癌患者前列腺癌组织中SRSF1蛋白的阳性表达率比较,差异无统计学意义(P﹥0.05);不同TNM分期、淋巴结转移情况、Gleason评分前列腺癌患者前列腺癌组织中SRSF1蛋白的阳性表达率比较,差异均有统计学意义(P﹤0.05)。不同PSA水平、Gleason评分前列腺癌患者前列腺癌组织中NF-κB蛋白的阳性表达率比较,差异均无统计学意义(P﹥0.05);不同TNM分期、淋巴结转移情况前列腺癌患者前列腺癌组织中NF-κB蛋白的阳性表达率比较,差异均有统计学意义(P﹤0.05)。结论前列腺癌组织中的SRSF1、NF-κB蛋白表达水平和阳性表达率均较高,SRSF1蛋白的表达可能与TNM分期、淋巴结转移情况和Gleason评分,NF-κB蛋白的表达可能与TNM分期和淋巴结转移情况有关。     

High-throughput alternative splicing detection using dually constrained correspondence analysis (DCCA)

Alternative splicing is an important component of tumorigenesis. Recent advent of exon array technology enables the detection of alternative splicing at a genome-wide scale. The analysis of high-throughput alternative splicing is not yet standard and methodological developments are still needed. We propose a novel statistical approach—Dually Constrained Correspondence Analysis—for the detection of splicing changes in exon array data. Using this methodology, we investigated the genome-wide alteration of alternative splicing in patients with non-small cell lung cancer treated by bevacizumab/erlotinib. Splicing candidates reveal a series of genes related to carcinogenesis (SFTPB), cell adhesion (STAB2, PCDH15, HABP2), tumor aggressiveness (ARNTL2), apoptosis, proliferation and differentiation (PDE4D, FLT3, IL1R2), cell invasion (ETV1), as well as tumor growth (OLFM4, FGF14), tumor necrosis (AFF3) or tumor suppression (TUSC3, CSMD1, RHOBTB2, SERPINB5), with indication of known alternative splicing in a majority of genes. DCCA facilitates the identification of putative biologically relevant alternative splicing events in high-throughput exon array data.     

Asymptotic accuracy of Bayesian estimation for a single latent variable

In data science and machine learning, hierarchical parametric models, such as mixture models, are often used. They contain two kinds of variables: observable variables, which represent the parts of the data that can be directly measured, and latent variables, which represent the underlying processes that generate the data. Although there has been an increase in research on the estimation accuracy for observable variables, the theoretical analysis of estimating latent variables has not been thoroughly investigated. In a previous study, we determined the accuracy of a Bayes estimation for the joint probability of the latent variables in a dataset, and we proved that the Bayes method is asymptotically more accurate than the maximum-likelihood method. However, the accuracy of the Bayes estimation for a single latent variable remains unknown. In the present paper, we derive the asymptotic expansions of the error functions, which are defined by the Kullback–Leibler divergence, for two types of single-variable estimations when the statistical regularity is satisfied. Our results indicate that the accuracies of the Bayes and maximum-likelihood methods are asymptotically equivalent and clarify that the Bayes method is only advantageous for multivariable estimations.