Gene Function Validation Research Articles

Upregulation of endogenous ICAM‐1 reduces ovarian cancer cell growth in the absence of immune cells

Ovarian cancer is a difficult-to-treat cancer with a 5-year survival rate of only ∼45%, due to late diagnosis and therapy resistance. In need of new therapeutic approaches, induction of intercellular adhesion molecule (ICAM)-1 expression might be of interest, since the expression of ICAM-1 is lower in ovarian cancer cells compared with healthy ovarian cells and correlated with decreased tumorigenicity. Whereas ICAM-1 expression on tumor cells is of importance for attracting immune cells, ICAM-1 might also induce tumorigenicity and chemoresistance. In ovarian cancer, such a role of ICAM-1 is unclear. Here, we investigated whether ICAM-1 has a cell-biological role by bidirectional modulation of ICAM-1 expression using ICAM-targeting artificial transcription factors. For a panel of ovarian cancer cells, tumor growth and cisplatin sensitivity were evaluated. Induction of ICAM-1 expression (ranging from 3- to 228-fold on mRNA level and 1.7- to 108-fold on protein level) resulted in indications of decreased ovarian cancer cell growth and reduced cisplatin sensitivity. Repression ranged from 48 to 94% on mRNA level and 47 to 91% on protein level. This study shows that, next to its established immunogenic role, ICAM-1 affects cell biological behavior of ovarian cancer cells and, importantly, that reexpression by artificial transcription factors represents a powerful approach for functional validation of genes epigenetically silenced in cancer, such as ICAM-1.

Live-cell high resolution magic angle spinning magnetic resonance spectroscopy for in vivo analysis of Pseudomonas aeruginosa metabolomics

Pseudomonas aeruginosa (PA) is a pathogenic gram-negative bacterium that is widespread in nature, inhabiting soil, water, plants and animals. PA is a prevalent cause of deleterious human infections, particularly in patients whose host defense mechanisms have been compromised. Metabolomics is an important tool used to study host-pathogen interactions and to identify novel therapeutic targets and corresponding compounds. The aim of the present study was to report the metabolic profile of live PA bacteria using in vivo high-resolution magic angle spinning (HRMAS) nuclear magnetic resonance spectroscopy (NMR), in combination with 1- and 2-dimensional HRMAS NMR. This methodology provides a new and powerful technique to rapidly interrogate the metabolome of intact bacterial cells and has several advantages over traditional techniques that identify metabolome components from disrupted cells. Furthermore, application of multidimensional HRMAS NMR, in combination with the novel technique total through-Bond correlation Spectroscopy (TOBSY), is a promising approach that may be used to obtain in vivo metabolomics information from intact live bacterial cells and can mediate such analyses in a short period of time. Moreover, HRMAS 1H NMR enables the investigation of the associations between metabolites and cell processes. In the present study, we detected and quantified several informative metabolic molecules in live PA cells, including N-acetyl, betaine, citrulline, alanine and glycine, which are important in peptidoglycan synthesis. The results provided a complete metabolic profile of PA for future studies of PA clinical isolates and mutants. In addition, this in vivo NMR biomedical approach might have clinical utility and should prove useful in gene function validation, the study of pathogenetic mechanisms, the classification of microbial strains into functional/clinical groups, the testing of anti-bacterial agents and the determination of metabolic profiles of bacterial mutants.

Emerging trends in research on spatial and temporal organization of terpenoid indole alkaloid pathway in Catharanthus roseus: a literature update

Catharanthus roseus (The Madagaskar Periwinkle) plant is commercially valued for harbouring more than 130 bioactive terpenoid indole alkaloids (TIAs). Amongst these, two of the leaf-derived bisindole alkaloids-vinblastine and vincristine-are widely used in several anticancer chemotherapies. The great pharmacological values, low in planta occurrence, unavailability of synthetic substitutes and exorbitant market cost of these alkaloids have prompted scientists to understand the basic architecture and regulation of biosynthesis of these TIAs in C. roseus plant and its cultured tissues. The knowledge gathered over a period of 30years suggests that the TIA biosynthesis is highly regulated by developmental and environmental factors and operates through a complex multi-step enzymatic network. Extensive spatial and temporal cross talking also occurs at inter- and intracellular levels in different plant organs during TIA biogenesis. A close association of indole, methylerythritol phosphate and secoiridoid monoterpenoid pathways and involvement of at least four cell types (epidermis, internal phloem-associated parenchyma, laticifers and idioblasts) and five intracellular compartments (chloroplast, vacuole, nucleus, endoplasmic reticulum and cytosol) have been implicated with this biosynthetic mechanism. Accordingly, the research in this area is primarily advancing today to address and resolve six major issues namely: precise localization and expression of pathway enzymes using modern in situ RNA hybridization tools, mechanisms of intra- and intercellular trafficking of pathway intermediates, cloning and functional validation of genes coding for known or hitherto unknown pathway enzymes, mechanism of global regulation of the pathway by transcription factors, control of relative diversion of metabolite flux at crucial branch points and finally, strategising the metabolic engineering approaches to improve the productivity of the desired TIAs in plant or corresponding cultured tissues. The present literature update has been compiled to provide a brief overview of some of the emerging developments in our current understanding of TIA metabolism in C. roseus.

Abstract 4984: Association of PTEN and p16 mutational status with MITF expression may provide a novel context for a phenotype switch in melanoma

Abstract For the last decade, array-based genomic screening has significantly advanced our understanding of genes involved in cancer development and progression. Moreover, genes identified in those screenings have subsequently been the focus of drug development efforts, ultimately leading to clinical trials. However, the efficient translation of cancer genomics results into the development of more effective therapeutics has been limited in part by the need for robust, high-throughput, functional validation of genes and pathways of interest in well-defined model systems. In order to identify new therapeutic targets in melanoma genomes, we have applied high-throughput RNA interference (RNAi) screening to well-characterized melanoma cell lines. We characterized a panel of 65 melanoma cell lines for genome-wide copy number changes and gene expression, as well as the mutation status of known melanoma genes (BRAF, HRAS, NRAS, KRAS, PTEN, CDKN2A, and TP53). From this panel, 18 cell lines were screened against some 1,250 genes (696 kinases, 550 supplemental; 4 siRNAs per gene) to identify modifiers of melanoma cell survival. A striking finding from our data is that MITF expression appears to be a determinant of invasive context and, furthermore, is associated with changes in both p16 and PTEN status. In the cell lines we examined, high MITF expression correlated with wild-type PTEN status, whereas PTEN was deleted or mutated in 30-35% of cell lines having low MITF expression. Similarly, p16 was unaltered in 40-45% of the cell lines that had high MITF expression but remained unaltered in only 20-25% of low MITF-expressing cell lines. The loss of p16 and PTEN are correlated with an aggressive phenotype in melanoma, and we confirmed by Western analysis that in cell lines with high MITF, p16 is present, but in cell lines with low MITF, p16 expression is absent. In agreement with the current literature, no association could be found with BRAF mutational status. Moreover, these data confirm that MITF is associated with the switch in phenotype from a proliferative to an invasive state in melanoma in a BRAF-independent manner, which in turn is associated with an increase in WNT5A expression, a change we previously have suggested is a critical determinant of melanoma metastasis. Results to be presented, aligned with new studies of sequence variants of MITF (Brown et al., unpublished), may help define a novel context for invasive potential of the important disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4984. doi:10.1158/1538-7445.AM2011-4984

Introduction: Validation methods for function genome annotation

This supplement comprises a report on progress during 2007-10 on an outstanding and continuing problem. What are effective and high throughput methodologies for validating the function of genes, newly displayed within DNA sequences? The display of genomes as DNA sequence is becoming increasingly cheap and fast. Sequence comparison methodologies do serve for computationally recognizing homologues between genes in a newly displayed genome, with those of previously analyzed genomes. This is a first automated step in annotation of newly recognized, candidate genes. But there are abundant examples that follow through experimentation is needed to improve and often also to correct the first outputs of computational annotation. For newly displayed microbial genomes, about a third of the genes do not thus acquire any functional assignment. For the more complex genomes of higher species, gene coverage by automated annotation is even poorer. The DOE Office of Biological and Environmental Research (BER) participated in a 2006 workshop sponsored by the NIH National Center for Biological Information (NCBI). Numerous limitations of computational annotation were discussed. DOE responded with a call for research applications in May 2007: http://www.sc.doe.gov/grants/FAPN07-14.html . Completely solving the long standing problem of validating annotation was certainly not feasible. Rather BER sought methods which could be applied in high throughput modes, with particularly applicability to gene families or genomes related to DOE missions. Validation projects initiated through the FAPN07-14 call and review process are included herein, with complementation by a few cogent projects started earlier. Validation of gene function certainly remains an outstanding problem arena. But the suite of accomplishments and methods reported herein will surely be useful to those considering validation battles.

A Comprehensive Analysis of MicroRNA Expression During Human Keratinocyte Differentiation In Vitro and In Vivo

Here, we report a comprehensive investigation of changes in microRNA (miRNA) expression profiles on human keratinocyte (HK) differentiation in vitro and in vivo. We have monitored expression patterns of 377 miRNAs during calcium-induced differentiation of primary HKs, and have compared these patterns with miRNA expression profiles of epidermal stem cells, transient amplifying cells, and terminally differentiated HKs from human skin. Apart from the previously described miR-203, we found an additional nine miRNAs (miR-23b, miR-95, miR-210, miR-224, miR-26a, miR-200a, miR-27b, miR-328, and miR-376a) that are associated with HK differentiation in vitro and in vivo. In situ hybridization experiments confirmed miR-23b as a marker of HK differentiation in vivo. Additionally, gene ontology analysis and functional validation of predicted miRNA targets using 3'-untranslated region-luciferase assays suggest that multiple miRNAs that are upregulated on HK differentiation cooperate to regulate gene expression during skin development. Our results thus provide the basis for further analysis of miRNA functions during epidermal differentiation.

High-throughput analysis of gene expression on tissue sections by in situ hybridization

Genome-scale sequencing projects, high-throughput RNAi screens, systematic gene targeting, and system-biology-based network predictions all depend on a validation of biological significance in order to understand the relevance of a particular finding. Such validation, for the most part, rests on low-throughput technologies. This article provides protocols that, in combination with suitable instrumentation, make possible a semi-automated analysis of gene expression on tissue sections by means of in situ hybridization. Knowledge of gene expression localization has the potential to aid, and thereby accelerate, the validation of gene functions.

ReGenX AAV Vector Technology: a tool for in vivo screening

Transgenic and knockout mice have been used to create disease models and understand gene function. However, such mice are complex to create, breeding colonies must be established, and some models are not viable. Somatic gene transfer with vectors such as adeno-associated virus (AAV) can overcome these limitations. ReGenX's AAV Vector Technology gives extremely efficient and stable gene expression in neonatal and adult animals, and can be used to create disease models and to study gene function and target validation.

Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot

According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean pi (sil) = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F (ST) = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r (2) = 0.635) within the 700-1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.

Fabrication of a microarray using a combination of the large circular sense and antisense DNA

In the present study, single-stranded large circular (LC)-sense molecules were utilized as probes for DNA microarrays and showed stronger binding signals than those of PCR-amplified cDNA probes. A microarray experiment using 284 LC-sense DNA probes found 6 upregulated and 7 downregulated genes in A549 cells as compared to WI38VA13 cells. Repeated experiments showed largely consistent results, and microarray data strongly correlated with data acquired from quantitative real-time RT-PCR. A large array comprising 5,079 LC-sense DNA was prepared, and analysis of the mean differential expression from dye-swap experiments revealed 332 upregulated and 509 downregulated genes in A549 cells compared to WI38VA13 cells. Subsequent functional analysis using an LC-antisense library of overexpressed genes identified 28 genes involved in A549 cell growth. These experiments demonstrated the proper features of LC-sense molecules as probe DNA for microarray and the potential utility of the combination of LC-sense and -antisense libraries for an effective functional validation of genes.

Assessment of Biomarkers in Acetaminophen-Induced Hepatic Toxicity by siRNA

We investigated global gene expression from both mouse liver and mouse hepatic cell lines treated with acetaminophen (APAP) in order to compare in vivo and in vitro profiles and to assess the feasibility of the two systems. During our analyses of gene expression profiles, we picked up several down-regulated genes, such as the cytochrome P450 family 51 (Cyp51), sulfotransferase family cytosolic 1C member 2 (Sult1c2), 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (Hmgcs1), and several genes that were up-regulated by APAP, such as growth arrest and DNA-damage-inducible 45 alpha (Gadd45a), transformation related protein 53 inducible nuclear protein 1 (Trp53inp1) and zinc finger protein 688 (Zfp688). For validation of gene function, synthesized short interfering RNAs (siRNAs) for these genes were transfected in a mouse hepatic cell line, BNL CL.2, for investigation of cell viability and mRNA expression level. We found that siRNA transfection of these genes induced down-regulation of respective mRNA expression and decreased cell viability. siRNA transfection for Cyp51 and others induced morphological alterations, such as membrane thickening and nuclear condensation. Taken together, siRNA transfection of these six genes decreased cell viability and induced alteration in cellular morphology, along with effective inhibition of respective mRNA, suggesting that these genes could be associated with APAP-induced toxicity. Furthermore, these genes may be used in the investigation of hepatotoxicity, for better understanding of its mechanism.

Transgenic coffee fruits from Coffea arabica genetically modified by bombardment

The genetic modification of Coffea arabica fruits is an important tool for the investigation of physiological characteristics and functional validation of genes related to coffee bean quality traits. In this work, plants of C. arabica cultivar Catuaí Vermelho were successfully genetically modified by bombardment of embryogenic calli. Calli were obtained from 90% of the leaf explants cultivated in a callogenesis-inducing medium modified with 20 μM 2,4-dichlorophenoxyacetic acid (2,4-D). The resulting calli were bombarded with the pBI426 vector containing a uidA and nptII gene fusion that was driven by the double CaMV35s promoter. Kanamycin-selected embryos were positive for β-glucuronidase (GUS) activity in histochemical assays and for target gene amplification by polymerase chain reaction. Integration of the nptII gene was confirmed by Southern blot and showed a low copy number (one to three) of insertions. Transformed plants showed normal development and settled fruits. GUS expression was assessed in the flower and fruit organs demonstrating the capacity of the double CaMV35s promoter to drive long-term stable expression of uidA in C. arabica fruit tissues. Moreover, we obtained a T1 progeny presenting 3:1 Mendelian segregation of the uidA gene. This investigation is the first to report exogenous gene expression in coffee fruits and transgenic inheritance in C. arabica plants.

Pharmacogenomics: candidate gene identification, functional validation and mechanisms.

Pharmacogenetics is the study of the role of inheritance in variation in drug response phenotypes. Those phenotypes can range from life-threatening adverse drugs reactions at one end of the spectrum to equally serious lack of therapeutic efficacy at the other. Over the past half century, pharmacogenetics has--like all of medical genetics--evolved from a discipline with a focus on monogenetic traits to become pharmacogenomics, with a genome-wide perspective. This article will briefly review recent examples of the application of genome-wide techniques to clinical pharmacogenomic studies and to pharmacogenomic model systems that vary from cell line-based model systems to yeast gene deletion libraries. Functional validation of candidate genes and the use of genome-wide techniques to gain mechanistic insights will be emphasized for the establishment of biological plausibility and as essential follow-up steps after the identification of candidate genes.

Robust Hepatic Gene Silencing for Functional Studies Using Helper-Dependent Adenoviral Vectors

RNA interference is currently envisioned as the basis of gene function and drug target validation studies. This novel technology has the advantage of providing a remarkably faster tool for gene silencing than traditional transgenic animal methodologies. In vivo administration of short interfering RNA (siRNA) typically results in reduced target gene expression for approximately 1 week. Viral vectors offer the possibility to express constitutive levels of short hairpin RNA (shRNA) so that the effects of knocking down the target gene can be studied for a few weeks, rather than a few days. Helper-dependent vectors have a significant advantage over previous generations of adenoviral vectors because of their much higher cloning capacity, potential for long-term transgene expression, and enhanced safety profiles on administration in vivo. Therefore, this advanced type of vector is an excellent tool to carry out in vivo studies directed at constitutive expression of shRNA. Here we show it is possible to obtain more than 90% target gene knockdown in an animal model of type 2 diabetes for several weeks, thereby consolidating this technology as an alternative to generating liver-specific knockout animals.

RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome

RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein–protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th.

RNA interference: a pathway to drug target identification and validation in trypanosome

RNA interference (RNAi) is a phenomenon through which double stranded RNA (dsRNA) induces potent sequence-specific degradation of homologous transcripts. Besides its function in cellular defense and developmental regulation, it has emerged as an invaluable tool for elucidation of gene function and drug target validation. This is particularly useful when substantial genome sequence data are available. Gene silencing using RNAi can aid translation of raw genomic sequence data into biologically relevant information toward the development of new and/or improved control strategies. Here, we review the current status of RNAi in trypanosome research focusing on challenges involved in the utilization of the technique as well as its potential application in drug target discovery and validation. Key words: RNA interference, trypanosomes, gene silencing, RNAi library, drug targets

RNAi in primary human chondrocytes: Efficiencies, kinetics, and non-specific effects of siRNA-mediated gene suppression

RNAi-mediated gene silencing is a recent, powerful tool to investigate gene function. Controlling for experimental factors such as transfection efficiencies, siRNA concentration, gene suppression levels, gene suppression kinetics, or non-specific effects is key to robust results. In this methods paper, we compare the efficiencies of different transfection reagents in primary human chondrocytes (PHCs). We investigated TAK1 gene suppression efficiencies and kinetics on the mRNA and protein level depending on the siRNA concentration used. Furthermore, we evaluated PKR, IL-6, and TNF-α induction, as well as IκB degradation and NFκB activation as control parameters of non-specific siRNA effects. PKR and IL-6 proved to be appropriate markers of cellular inflammatory responses resulting from siRNA transfection. In addition, we compared different siRNAs (silencing, non-silencing, classic 21-mer, and 25-mer stealth™ siRNA) with respect to their capacity to induce cellular inflammatory responses. We found the occurrence of cellular responses in PHCs to be a function of the specific siRNA sequence in use. Hence, it is essential to analyze and to compare gene silencing siRNAs and control siRNAs with respect to their off-target effects prior to any functional gene validation.

Strategies for Functional Validation of Genes Involved in Reproductive Stages of Orchids

Plants in the largest family of angiosperms, Orchidaceae, are diverse in both specialized pollination and ecological strategies and provide a rich source for investigating evolutionary relationships and developmental biology. However, studies in orchids have been hindered by several challenges that include low transformation efficiency and long regeneration time. To overcome such obstacles, we selected a symptomless cymbidium mosaic virus (CymMV) isolate for constructing virus-induced gene-silencing vectors. The feasibility of the virus vectors was first assessed with use of an orchid phytoene desaturase gene. The vector was able to induce gene silencing in orchids; however, because of the slow growth of orchids, the commonly used phytoene desaturase gene was not a good visual marker in orchids. We inserted a 150-nucleotide unique region of a B-class MADS-box family gene, PeMADS6, into pCymMV-pro60. The transcription level of PeMADS6 in inoculated Phalaenopsis plants was reduced by up to 73%, but no effect was observed for other MADS-box family genes. In contrast, in Phalaenopsis plants inoculated with CymMV transcripts containing 500 nucleotides of PeMADS6, a conserved region among MADS-box genes, the transcription level of PeMADS6 and the B- and C-class MADS-box genes was reduced by up to 97.8% as compared with plants inoculated with the vector alone. Flower morphology was affected in the MADS-box family gene-silenced plants as well. This in vivo experiment demonstrates an efficient way to study genes involved in the reproductive stage of plants with a long life cycle.

RNA Silencing in the Struggle against Disease

Numerous acquired and hereditary diseases are caused by aberrant cellular or microbial gene expression. As a result of sequencing of the human genome and the genomes of various human pathogens, researchers have gained access to a large number of genes with residual functions. For functional validation of unknown genes, their functions can be specifically inhibited by antisense nucleic acids or small interfering RNAs (siRNAs) and the consequences of the functional loss, that is, the resulting phenotypes, can be analyzed. While antisense nucleic acids block the translation stoichiometrically by docking on the mRNA, siRNAs induce a highly effective cellular mechanism that causes catalytic destruction of several mRNA molecules by a single siRNA molecule. This mechanism, called RNA interference (RNAi), is only intrinsic to eukaryotic cells. Consequently, only eukaryotic target validation is pushed by RNAi whereas time-consuming conventional knockout techniques or the less efficient antisense strategies have to be applied for prokaryotic target validation. We succeeded in triggering gene silencing by siRNA in prokaryotic cells. This opens promising perspectives regarding validation of prokaryotic gene functions.

Activation of the mammalian immune system by siRNAs

Inhibition of gene expression through RNA interference (RNAi) is emerging as a powerful experimental tool for gene function and target validation studies. The potential uses of this technology seem unlimited, extending to the prevention and therapy of human diseases. However, recent work demonstrating that there are unanticipated, different nonspecific effects associated with the use of small interfering RNAs in mammals has raised concerns about the safe use of RNAi in vivo. These nonspecific effects include activation of the immune system, potentially harming the individual. The application of screening assays for nonspecific activation of both innate and acquired immunity will be necessary for further development of RNAi as a therapeutic tool.