Enhanced DNA repair through droplet formation and p53 oscillations

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P53脉冲的研究现状与展望

P53脉冲是指细胞内p53蛋白水平周期性或重复性的涨落.该脉冲产生的途径是调节p53的各种正负反馈环,其核心的两个负反馈环是p53-Mdm2环和Wip1-ATM-p53环.这些负反馈环能产生极限环振荡,在极限环振荡区,P53水平成脉冲型变化.随着P53脉冲的增多,不同形式的p53蛋白和促凋亡蛋白逐渐积累并到达一定阈值水平,可打开凋亡"开关",引发不可逆的细胞命运.除了P53脉冲的数目,其频率、振幅、波形等物理学参数也与细胞命运存在密切关系.这一研究进展对阐明诸多疾病发生机理和防治研究有重要意义.     

Novel recurrent neural network for modelling biological networks: Oscillatory p53 interaction dynamics

Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system – a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more quantitative data become available on individual proteins, the RNN would be able to refine parameter estimation and mapping of temporal dynamics of individual signalling molecules as well as signalling networks as a system. Moreover, RNN can be used to modularise large signalling networks.     

A minimal model for decoding of time-limited Ca2+ oscillations

Calcium oscillations regulate several cellular processes by activating particular proteins. Most theoretical studies focused on the idealized situation of infinitely long oscillations. Here we analyze information transfer by time-limited calcium spike trains. We show that proteins can be selectively activated in a resonance-like manner by time-limited spike trains of different frequencies, while infinitely long oscillations do not show this resonance phenomenon. We found that proteins are activated more specifically by shorter oscillatory signals with narrower spikes.     

p53蛋白多肽片段在大肠杆菌中的表达

在所有研究过的人体肿瘤组织或细胞中,ｐ５３似乎是突变频率最高的一个基因,研究和检测ｐ５３基因及其编码产物的变化将具有重要的意义。我们将野生型ｐ５３基因编码区３’端７０３ｂｐ的ｃＤ－ＮＡ片段插入到大肠杆菌表达载体ｐＢＶ２２０中,得到了一个重组体表达质粒ｐＲＲ３３,经热诱导表达,用ＳＤＳ－ＰＡＧＥ和Ｗｅｓｔｅｒｎ印迹法证实ｐ５３蛋白多肽在大肠杆菌中得到了表达,它不仅可用于抗ｐ５３蛋白抗体的制备,而且也可用于对ｐ５３蛋白羧基端多肽功能的研究。     

Polymorphisms in p53 and the p53 pathway: roles in cancer susceptibility and response to treatment

The p53 tumour suppressor protein lies at the crossroads of multiple cellular response pathways that control the fate of the cell in response to endogenous or exogenous stresses and inactivation of the p53 tumour suppressor signalling pathway is seen in most human cancers. Such aberrant p53 activity may be caused by mutations in the TP53 gene sequence producing truncated or inactive mutant proteins, or by aberrant production of other proteins that regulate p53 activity, such as gene amplification and overexpression of MDM2 or viral proteins that inhibit or degrade p53. Recent studies have also suggested that inherited genetic polymorphisms in the p53 pathway influence tumour formation, progression and/or response to therapy. In some cases, these variants are clearly associated with clinico-pathological variables or prognosis of cancer, whereas in other cases the evidence is less conclusive. Here, we review the evidence that common polymorphisms in various aspects of p53 biology have important consequences for overall tumour susceptibility, clinico-pathology and prognosis. We also suggest reasons for some of the reported discrepancies in the effects of common polymorphisms on tumourigenesis, which relate to the complexity of effects on tumour formation in combination with other oncogenic changes and other polymorphisms. It is likely that future studies of combinations of polymorphisms in the p53 pathway will be useful for predicting tumour susceptibility in the human population and may serve as predictive biomarkers of tumour response to standard therapies.     

p53基因及其功能研究进展

p53基因是一种肿瘤抑制基因,野生型p53对细胞周期和细胞凋亡起重要作用。其编码的蛋白P53相对分子质量为53×103,可刺激Cipt基因产生相对分子质量为21×103的蛋白,该蛋白可以抑制促使细胞通过细胞周期进入有丝分裂的酶的活性,进而抑制细胞生长表达而调控细胞生长,对于预防和治疗胆管癌、肝癌、胃癌等疾病有重要作用。我们在此简要阐述国内外对p53基因及其编码产物的结构、作用机制、检测、功能等方面的研究进展。     

Regulation of p53 in embryonic stem cells

Despite an increasing interest in the role of the p53 tumour suppressor protein in embryonic stem cells, not much is known about its regulation in this cell type.We show that the relatively high amount of p53 protein correlates with a higher amount of p53 RNA in ES cells compared to differentiated cells. Moreover, p53 RNA is more stable in embryonic stem cells and the p53 protein is more often transcribed. This is at least partly due to decreased expression of miRNA-125a and 125b in embryonic stem cells. Despite its cytoplasmic localisation, p53 is degraded in 26S proteasomes in embryonic stem cells. This process is controlled by Mdm2, the deubiquitinating enzyme Hausp and Ubc13. In contrast, the E3 ligase PirH2 appears to be less important for the control of p53 in embryonic stem cells. During differentiation, p53 protein and RNA levels are decreased which corresponds to increased expression of miRNA-125a and miRNA-125b.     

Network modelling of gene regulation

Gene regulatory network (GRN) modelling has gained increasing attention in the past decade. Many computational modelling techniques have been proposed to facilitate the inference and analysis of GRN. However, there is often confusion about the aim of GRN modelling, and how a gene network model can be fully utilised as a tool for systems biology. The aim of the present article is to provide an overview of this rapidly expanding subject. In particular, we review some fundamental concepts of systems biology and discuss the role of network modelling in understanding complex biological systems. Several commonly used network modelling paradigms are surveyed with emphasis on their practical use in systems biology research.     

Over-expression of the human MDM2 p53 binding domain by fusion to a p53 transactivation peptide

MDM2 binds to the tumor suppressor protein p53 and regulates the level of p53 in cells. Although it is possible to prepare a small amount of the region of MDM2 that binds to p53, the expression level of this fragment of MDM2 is relatively low, limiting the studies involving this protein. Here, we describe a construct for the optimized bacterial expression and purification of the MDM2 p53 binding domain. We found that the expression level of the soluble MDM2 p53 binding domain in bacteria was increased dramatically by fusing it to its interaction partner, the p53 transactivation peptide. Attachment of the p53 transactivation peptide (residues 17-29) to the N-terminus of MDM2 resulted in a more than 200-fold increase of soluble protein expression of the p53 binding domain in bacteria. To obtain the final MDM2 p53 binding domain (residues 5-109) we inserted a tobacco etch virus protease recognition site between the P53 peptide and the MDM2 p53 binding domain. To weaken the protein/peptide interaction and facilitate the separation of the protein from the complex, we introduced a point mutation of one of the key interaction residues (F19A or W23A) in the p53 peptide. The advantages of our new construct are high yield and easy purification of the MDM2 protein.     

小鼠成纤维细胞凋亡过程中P53与bcl-2表达的时序性

为探讨细胞凋亡过程中,ｂｃｌ－２与Ｐ５３,这两种凋亡关键性基因的相互关系,用５－氟尿嘧啶（５－Ｆｕ）诱导小鼠正常与恶性转化的成纤维细胞的凋亡,观察了这两种基因在凋亡过程中表达变化的时序．经流式细胞计检测,这两种细胞在５－Ｆｕ作用２４ｈ均出现了凋亡峰,细胞存活率随之下降,ＤＮＡ电泳显现梯状断裂．Ｎｏｒｔｈｅｒｎ杂交结果显示,在５－Ｆｕ作用６ｈ后两种细胞Ｐ５３ｍＲＮＡ水平已明显增高,而ｂｃｌ－２ｍＲＮＡ水平则在作用１２ｈ方明显降低．Ｐ５３上调与ｂｃｌ－２下调的明显时序性,说明Ｐ５３具备作为ｂｃｌ－２基因负调控转录因子的条件．由此,为进一步了解凋亡过程的ｂｃｌ－２基因下调机理提供了线索     

Control of Boolean networks: hardness results and algorithms for tree structured networks

Finding control strategies of cells is a challenging and important problem in the post-genomic era. This paper considers theoretical aspects of the control problem using the Boolean network (BN), which is a simplified model of genetic networks. It is shown that finding a control strategy leading to the desired global state is computationally intractable (NP-hard) in general. Furthermore, this hardness result is extended for BNs with considerably restricted network structures. These results justify existing exponential time algorithms for finding control strategies for probabilistic Boolean networks (PBNs). On the other hand, this paper shows that the control problem can be solved in polynomial time if the network has a tree structure. Then, this algorithm is extended for the case where the network has a few loops and the number of time steps is small. Though this paper focuses on theoretical aspects, biological implications of the theoretical results are also discussed.     

Common conformational effects of p53 mutations

The tumor suppressor gene p53 has been identified as the most frequent target of genetic alterations in human cancers. Most of these mutations occur in highly conserved regions in the DNA-binding core domain of the p53 protein, suggesting that the amino acid residues in these regions are critical for maintaining normal p53 structure and function. We previously used molecular dynamics calculations to demonstrate that several amino acid substitutions in these regions that are induced by environmental carcinogens and found in human tumors produce certain common conformational changes in the mutant proteins that differ substantially from the wild-type structure. In order to determine whether these conformational changes are consistent for other p53 mutants, we have now used molecular dynamics to determine the structure of the DNA-binding core domain of seven other environmentally induced, cancer-related p53 mutants, namely His 175, Asp 245, Asn 245, Trp 248, Met 249, Ser 278, and Lys 286. The results indicate that all of these mutants differ substantially from the wild-type structure in certain discrete regions and that some of these conformational changes are similar for these mutants as well as those determined previously. The changes are also consistent with experimental evidence for alterations in structure in p53 mutants determined by epitope detectability using monoclonal antibodies directed against these regions of predicted conformational change.     

Ad-P53癌基因治疗制剂质量分析研究

采用酶切图谱及ＰＣＲ法分析了Ａｄ－Ｐ５３癌基因治疗制剂中Ｐ５３基因的插入顺序;用ＰＣＲ及病变法检查产品中是否污染野生型腺病毒;用Ｗｅｓｔｅｒｎｂｌｏｔ验证Ｐ５３基因的表达。用分子生物学方法从几个主要方面对产品的安全性及有效性作出质量评价     

Quasi-periodic behaviour in a model for the lithium-induced,electrical oscillations of frog skin

The fact that oscillations can be induced in studies of the maintenance of the electrical potential of frog skin by addition of lithium allowed evaluation of several parameters fundamental to the functioning of the system in vivo (e.g. relative volumes of internal compartments, characteristic times of ionic exchanges between compartments). A realistic model was thus proposed under the form of a set of ordinary differential equations. In the past, numerical simulations using such a model reproduced the periodic experimental oscillations and was able to provide an explanation for the global synchronised oscillations of the whole skin. In that paper, new numerical simulations reproduce the non-periodic oscillations which were observed two decades ago, but not reproduced by the model. Moreover, the dynamical process under which all the local oscillators are synchronised is explained in terms of a tangent bifurcation.