Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: prediction and validation

Silencing HIPPI Suppresses Tumor Progression in Non-Small-Cell Lung Cancer by Inhibiting DNA Replication

Introduction

Non-small cell lung cancer (NSCLC) is the most common form of lung cancer, accounting for approximately 80%-85% of all cases of lung cancer. Huntingtin interacting protein-1 interacting protein (HIPPI) is a transcription regulator and plays an important role in apoptotic cell death. However, the role of HIPPI in NSCLC remains unclear.

Methods

Immunohistochemistry (IHC) and qRT-PCR were performed for expression analysis. The roles of HIPPI were studied using cell counting kit-8 (CCK-8), colony formation, flow cytometry, wound healing, Transwell invasion assays and mouse xenograft model. Gene microarray analysis and bioinformatics analysis were used to identify differentially expressed genes after HIPPI silencing.

Results

HIPPI is highly expressed in NSCLC tissues relative to adjacent normal tissues. Targeting HIPPI by RNA interference inhibits NSCLC cell proliferation in vitro and tumor growth in vivo. HIPPI silencing also attenuates cell migration and invasion and enhances cisplatin sensitivity in NSCLC cells. Mechanistic investigation suggests that HIPPI can positively regulate the expression of MCM2, MCM6 and MCM8, which are key regulators of DNA replication. Furthermore, consistent with HIPPI, MCM2, MCM6 and MCM8 are also upregulated in NSCLC tissues.

Conclusion

Our study highlights the importance of HIPPI for tumor biology in NSCLC and suggests that HIPPI may be a potential therapeutic target for NSCLC treatment.

Mechanisms of ciliary targeting: entering importins and Rabs

Primary cilium is a rod-like plasma membrane protrusion that plays important roles in sensing the cellular environment and initiating corresponding signaling pathways. The sensory functions of the cilium critically depend on the unique enrichment of ciliary residents, which is maintained by the ciliary diffusion barrier. It is still unclear how ciliary cargoes specifically enter the diffusion barrier and accumulate within the cilium. In this review, the organization and trafficking mechanism of the cilium are compared to those of the nucleus, which are much better understood at the moment. Though the cilium differs significantly from the nucleus in terms of molecular and cellular functions, analogous themes and principles in the membrane organization and cargo trafficking are notable between them. Therefore, knowledge in the nuclear trafficking can likely shed light on our understanding of the ciliary trafficking. Here, with a focus on membrane cargoes in mammalian cells, we briefly review various ciliary trafficking pathways from the Golgi to the periciliary membrane. Models for the subsequent import translocation across the diffusion barrier and the enrichment of cargoes within the ciliary membrane are discussed in detail. Based on recent discoveries, we propose a Rab-importin-based model in an attempt to accommodate various observations on ciliary targeting.

Trans-activation of small EDRK-rich factor 2 (SERF2) promoter by Heat Shock Factor 1

Heat shock response is an adaptive mechanism of cells characterized by rapid synthesis of a class of proteins popularly known as heat shock proteins (HSPs) by heat-induced activation of Heat Shock Factor 1 (HSF1). In course of our earlier study to show that HSF1 regulates transcription of HYPK (Huntingtin Yeast two-hybrid protein K), a chaperone-like protein, we observed presence of few other genes within 10 kb of HYPK promoter. In an attempt to understand whether adjacent genes of HYPK are co-regulated, we identified that SERF2 (small EDRK-rich factor 2), an upstream neighboring gene of HYPK, is also regulated by heat stress and HSF1. We also showed that SERF2 promoter can be trans-activated by HSF1 due to the presence of functional heat shock element (HSE). Strikingly, HYPK is linked with SERF2 through a Conjoined Gene (CG) albeit the respective proteins have opposite effect on mutant Huntingtin aggregates and subsequent toxicity. Our study provides the first report on regulation of SERF2 expression and thereby depicts a paradigm where two parent genes of a CG are regulated by a common transcription factor despite the fact that they code for proteins having opposite cellular function in a given context.

Transcriptional regulation of microRNA-100, -146a, and -150 genes by p53 and NFκB p65/RelA in mouse striatal STHdh(Q7)/ Hdh(Q7) cells and human cervical carcinoma HeLa cells

MicroRNA (miRNA) genes generally share many features common to those of protein coding genes. Various transcription factors (TFs) and co-regulators are also known to regulate miRNA genes. Here we identify novel p53 and NFκB p65/RelA responsive miRNAs and demonstrate that these 2 TFs bind to the regulatory sequences of miR-100, -146a and -150 in both mouse striatal and human cervical carcinoma cells and regulate their expression. p53 represses the miRNAs while NFκB p65/RelA induces them. Further, we provide evidence that exogenous p53 inhibits NFκB p65/RelA activity by reducing its nuclear content and competing with it for CBP binding. This suggests for the existence of a functional cross-talk between the 2 TFs in regulating miRNA expression. Moreover, promoter occupancy assay reveals that exogenous p53 excludes NFκB p65/RelA from its binding site in the upstream sequence of miR-100 gene thereby causing its repression. Thus, our work identifies novel p53 and NFκB p65/RelA responsive miRNAs in human and mouse and uncovers possible mechanisms of co-regulation of miR-100. It is to be mentioned here that cross-talks between p53 and NFκB p65/RelA have been observed to define the outcome of several biological processes and that the pro-apoptotic effect of p53 and the pro-survival functions of NFκB can be largely mediated via the biological roles of the miRNAs these TFs regulate. Our observation with cell lines thus provides an important platform upon which further work is to be done to establish the biological significance of such co-regulation of miRNAs by p53 and NFκB p65/RelA.

Computational neurobiology is a useful tool in translational neurology: the example of ataxia

Hereditary ataxia, or motor incoordination, affects approximately 150,000 Americans and hundreds of thousands of individuals worldwide with onset from as early as mid-childhood. Affected individuals exhibit dysarthria, dysmetria, action tremor, and diadochokinesia. In this review, we consider an array of computational studies derived from experimental observations relevant to human neuropathology. A survey of related studies illustrates the impact of integrating clinical evidence with data from mouse models and computational simulations. Results from these studies may help explain findings in mice, and after extensive laboratory study, may ultimately be translated to ataxic individuals. This inquiry lays a foundation for using computation to understand neurobiochemical and electrophysiological pathophysiology of spinocerebellar ataxias and may contribute to development of therapeutics. The interdisciplinary analysis suggests that computational neurobiology can be an important tool for translational neurology.

Integration of modeling with experimental and clinical findings synthesizes and refines the central role of inositol 1,4,5-trisphosphate receptor 1 in spinocerebellar ataxia

A suite of models was developed to study the role of inositol 1,4,5-trisphosphate receptor 1 (IP3R1) in spinocerebellar ataxias (SCAs). Several SCAs are linked to reduced abundance of IP3R1 or to supranormal sensitivity of the receptor to activation by its ligand inositol 1,4,5-trisphosphate (IP3). Detailed multidimensional models have been created to simulate biochemical calcium signaling and membrane electrophysiology in cerebellar Purkinje neurons. In these models, IP3R1-mediated calcium release is allowed to interact with ion channel response on the cell membrane. Experimental findings in mice and clinical observations in humans provide data input for the models. The SCA modeling suite helps interpret experimental results and provides suggestions to guide experiments. The models predict IP3R1 supersensitivity in SCA1 and compensatory mechanisms in SCA1, SCA2, and SCA3. Simulations explain the impact of calcium buffer proteins. Results show that IP3R1-mediated calcium release activates voltage-gated calcium-activated potassium channels in the plasma membrane. The SCA modeling suite unifies observations from experiments in a number of SCAs. The cadre of simulations demonstrates the central role of IP3R1.

Remodeling Cildb, a popular database for cilia and links for ciliopathies

Background

New generation technologies in cell and molecular biology generate large amounts of data hard to exploit for individual proteins. This is particularly true for ciliary and centrosomal research. Cildb is a multi–species knowledgebase gathering high throughput studies, which allows advanced searches to identify proteins involved in centrosome, basal body or cilia biogenesis, composition and function. Combined to localization of genetic diseases on human chromosomes given by OMIM links, candidate ciliopathy proteins can be compiled through Cildb searches.

Methods

Othology between recent versions of the whole proteomes was computed using Inparanoid and ciliary high throughput studies were remapped on these recent versions.

Results

Due to constant evolution of the ciliary and centrosomal field, Cildb has been recently upgraded twice, with new species whole proteomes and new ciliary studies, and the latter version displays a novel BioMart interface, much more intuitive than the previous ones.

Conclusions

This already popular database is designed now for easier use and is up to date in regard to high throughput ciliary studies.

Heat shock factor 1 regulates hsa-miR-432 expression in human cervical cancer cell line

Heat shock response pathway is a conserved defense mechanism of mammalian cells to maintain protein homeostasis against proteotoxic environmental conditions. This is characterized by robust synthesis of molecular chaperones mostly by stress-induced activation of heat shock factor 1 (HSF1). MicroRNAs (miRNAs) are a family of small non-coding RNAs that negatively regulate expression of protein-coding genes. Here we report altered expression of a set of miRNAs by thermal stress in HeLa cells. We also show that HSF1 regulates hsa-miR-432 expression in heat shock-dependent manner through its cognate binding site present in hsa-miR-432 upstream sequence. Our report uncovers a novel function of HSF1 and indicates involvement of miRNAs in HSF1-mediated protection of cellular proteome.

Transcription, epigenetics and ameliorative strategies in Huntington's Disease: a genome-wide perspective

Transcriptional dysregulation in Huntington’s disease (HD) is an early event that shapes the brain transcriptome by both the depletion and ectopic activation of gene products that eventually affect survival and neuronal functions. Disruption in the activity of gene expression regulators, such as transcription factors, chromatin-remodeling proteins, and noncoding RNAs, accounts for the expression changes observed in multiple animal and cellular models of HD and in samples from patients. Here, I review the recent advances in the study of HD transcriptional dysregulation and its causes to finally discuss the possible implications in ameliorative strategies from a genome-wide perspective. To date, the use of genome-wide approaches, predominantly based on microarray platforms, has been successful in providing an extensive catalog of differentially regulated genes, including biomarkers aimed at monitoring the progress of the pathology. Although still incipient, the introduction of combined next-generation sequencing techniques is enhancing our comprehension of the mechanisms underlying altered transcriptional dysregulation in HD by providing the first genomic landscapes associated with epigenetics and the occupancy of transcription factors. In addition, the use of genome-wide approaches is becoming more and more necessary to evaluate the efficacy and safety of ameliorative strategies and to identify novel mechanisms of amelioration that may help in the improvement of current preclinical therapeutics. Finally, the major conclusions obtained from HD transcriptomics studies have the potential to be extrapolated to other neurodegenerative disorders.

MicroRNA-124 targets CCNA2 and regulates cell cycle in STHdh(Q111)/Hdh(Q111) cells

Mutation in huntingtin (HTT) gene causes Huntington's disease (HD). Expression of many micro RNAs is known to alter in cell, animal models and brains of HD patients, but their cellular effects are not known. Here, we show that expression of microRNA-124 (miR-124) is down regulated in HD striatal mutant STHdh(Q111)/Hdh(Q111) cells, a cell model of HD compared to STHdh(Q7)/Hdh(Q7) cells. STHdh(Q7)/Hdh(Q7) and STHdh(Q111)/Hdh(Q111) cells express endogenously full length wild type and mutant HTT respectively. We confirmed this result in R6/2 mouse, an animal model of HD, expressing mutant HTT. Gene Ontology terms related to cell cycle were enriched significantly with experimentally validated targets of miR-124. We observed that expression of Cyclin A2 (CCNA2), a putative target of miR-124 was increased in mutant STHdh(Q111)/Hdh(Q111) cells and brains of R6/2 mice. Fraction of cells in S phase was higher in asynchronously growing mutant STHdh(Q111)/Hdh(Q111) cells compared to wild type STHdh(Q7)/Hdh(Q7) cells and could be altered by exogenous expression or inhibition of miR-124. Exogenous expression or knock down of CCNA2, a target of miR-124, also alters proportion of cells in S phase of HD cell model. In summary, decreased miR-124 expression could increase CCNA2 in cell and animal model of HD and is involved in deregulation of cell cycle in STHdh(Q111)/Hdh(Q111) cells.