High throughput functional genomics: Identification of novel genes with tumor suppressor phenotypes

Dissecting mitochondrial apoptosis pathways by gain-of-function cell culture screens

While more primitive organism such as Caenorhabditis elegans and Drosophila melanogaster feature a limited, and by now probably mostly known, array of basic cell death factors, the mammalian cell is replete with additional regulators of the cell's demise. This abundance of apoptosis mediators has made it imperative to set up a systematic inventory of mammalian cell death genes. Genetic screens in this biological system have recently uncovered the rich diversity of cell death signalling and have in particular highlighted mitochondria as an organelle loaded with apoptosis regulators. Many of the screens that have addressed this utilised the novel technique of RNA interference but some also looked at gain-of-functions with transfected cDNAs. Here we give an overview of the rationale for the latter approach, present the genes discovered by this strategy and in particular describe the involvement of mitochondria and their signalling pathways defined by those genes.

Cancer cell senescence: a new frontier in drug development

Senescence forms a universal block to tumorigenesis which impacts on all hallmarks of cancer, making it an attractive target for drug discovery. Therefore a strategy must be devised to focus this broad potential into a manageable drug discovery programme. Several issues remain to be addressed including the lack of robust senescence-inducing compounds and causally related biomarkers to measure cellular response. Here, we review the latest progress in translating senescence as a target for cancer therapy and some promising approaches to drug and biomarker discovery. Finally, we discuss the potential application of a senescence-induction therapy in a clinical setting.

Determining signalling nodes for apoptosis by a genetic high-throughput screen

BACKGROUND

With the ever-increasing information emerging from the various sequencing and gene annotation projects, there is an urgent need to elucidate the cellular functions of the newly discovered genes. The genetically regulated cell suicide of apoptosis is especially suitable for such endeavours as it is governed by a vast number of factors.

METHODOLOGY/PRINCIPAL FINDINGS

We have set up a high-throughput screen in 96-well microtiter plates for genes that induce apoptosis upon their individual transfection into human cells. Upon screening approximately 100,000 cDNA clones we determined 74 genes that initiate this cellular suicide programme. A thorough bioinformatics analysis of these genes revealed that 91% are novel apoptosis regulators. Careful sequence analysis and functional annotation showed that the apoptosis factors exhibit a distinct functional distribution that distinguishes the cell death process from other signalling pathways. While only a minority of classic signal transducers were determined, a substantial number of the genes fall into the transporter- and enzyme-category. The apoptosis factors are distributed throughout all cellular organelles and many signalling circuits, but one distinct signalling pathway connects at least some of the isolated genes. Comparisons with microarray data suggest that several genes are dysregulated in specific types of cancers and degenerative diseases.

CONCLUSIONS/SIGNIFICANCE

Many unknown genes for cell death were revealed through our screen, supporting the enormous complexity of cell death regulation. Our results will serve as a repository for other researchers working with genomics data related to apoptosis or for those seeking to reveal novel signalling pathways for cell suicide.

A high-throughput platform for lentiviral overexpression screening of the human ORFeome

In response to the growing need for functional analysis of the human genome, we have developed a platform for high-throughput functional screening of genes overexpressed from lentiviral vectors. Protein-coding human open reading frames (ORFs) from the Mammalian Gene Collection were transferred into lentiviral expression vector using the highly efficient Gateway recombination cloning. Target ORFs were inserted into the vector downstream of a constitutive promoter and upstream of an IRES controlled GFP reporter, so that their transfection, transduction and expression could be monitored by fluorescence. The expression plasmids and viral packaging plasmids were combined and transfected into 293T cells to produce virus, which was then used to transduce the screening cell line. We have optimised the transfection and transduction procedures so that they can be performed using robotic liquid handling systems in arrayed 96-well microplate, one-gene-per-well format, without the need to concentrate the viral supernatant. Since lentiviruses can infect both dividing and non-dividing cells, this system can be used to overexpress human ORFs in a broad spectrum of experimental contexts. We tested the platform in a 1990 gene pilot screen for genes that can increase proliferation of the non-tumorigenic mammary epithelial cell line MCF-10A after removal of growth factors. Transduced cells were labelled with the nucleoside analogue 5-ethynyl-2′-deoxyuridine (EdU) to detect cells progressing through S phase. Hits were identified using high-content imaging and statistical analysis and confirmed with vectors using two different promoters (CMV and EF1α). The screen demonstrates the reliability, versatility and utility of our screening platform, and identifies novel cell cycle/proliferative activities for a number of genes.

BASP1 promotes apoptosis in diabetic nephropathy

Apoptosis contributes to the development of diabetic nephropathy (DN), but the mechanisms that lead to diabetes-induced cell death are not fully understood. Here, we combined a functional genomics screen for cDNAs that induce apoptosis in vitro with transcriptional profiling of renal biopsies from patients with DN. Twelve of the 138 full-length cDNAs that induced cell death in human embryonic kidney cells matched upregulated mRNA transcripts in tissue from human DN. Confirmatory screens identified induction of BASP1 in tubular cross sections of human DN tissue. In vitro, apoptosis-inducing conditions such as serum deprivation, high concentrations of glucose, and proinflammatory cytokines increased BASP1 mRNA and protein in human tubular epithelial cells. In normal cells, BASP1 localized to the cytoplasm, but in apoptotic cells, it colocalized with actin in the periphery. Overexpression of BASP1 induced cell death with features of apoptosis; conversely, small interfering RNA (siRNA)-mediated knockdown of BASP1 protected tubular cells from apoptosis. Supporting possible involvement of BASP1 in renal disease other than DN, we also observed significant upregulation of renal BASP1 in spontaneously hypertensive rats and a trend toward increased tubulointerstitial BASP1 mRNA in human hypertensive nephropathy. In summary, a combined functional genomics approach identified BASP1 as a proapoptotic factor in DN and possibly also in hypertensive nephropathy.

Effects of TWEAK (TNF superfamily member 12) on differentiation, metabolism, and secretory function of human primary preadipocytes and adipocytes

Expansion of adipose tissue mass by hypertrophy and hyperplasia is the hallmark of obesity. An automated cDNA screen was established to identify secreted human proteins with an inhibitory effect on adipocyte differentiation and, thereby, a potential inhibitory effect on adipose tissue growth. A member of the TNF superfamily, TNF-like weak inducer of apoptosis (TWEAK; TNF superfamily 12) was identified by means of high-throughput screening with the lipophilic dye Nile Red as an inhibitor of murine adipocyte differentiation and, subsequently, also of human adipocyte differentiation. TWEAK inhibited lipid deposition in a dose-dependent manner without causing cytotoxic effects. This inhibitory action was mimicked by an agonistic antibody of the TWEAK receptor. The TWEAK receptor (fibroblast growth factor inducible 14; CD266) was expressed on human primary preadipocytes and mature adipocytes. Knockdown of TWEAK receptor by short-hairpin RNA abolished the inhibitory effect of TWEAK on cell differentiation, demonstrating that the effects of TWEAK are mediated by its specific receptor. Inhibition of differentiation was the result of interference at an early step of transcriptional activation as assessed by decreased peroxisome proliferator-activated receptor-gamma, CCAAT enhancer-binding protein alpha (C/EBPalpha), and CCAAT enhancer-binding protein beta (C/EBPbeta) mRNA expression. In contrast to TNFalpha, basal and insulin-stimulated glucose uptake and lipolysis of terminally differentiated mature adipocytes and secretion of proinflammatory cytokines were not altered in the presence of TWEAK, and nuclear factor kappa B activity was only weakly induced. We conclude from our findings that TWEAK and the corresponding agonistic antibody have the potential to prevent adipose tissue growth without adversely influencing central metabolic pathways or proinflammatory cytokine secretion in adipose tissue.

Functional screening revisited in the postgenomic era

Functional screening can reveal a hidden function of a gene. cDNA library-based functional screening has flourished in various fields of biology so far, such as cancer biology, developmental biology and neuroscience. In the postgenomic era, however, various sequence database and public full-length cDNA resources are available, which now allow us to perform more straightforward, gene-oriented screening. Furthermore, the advent of RNA interference techniques has made it possible to perform effective loss-of-function screening. Gene-based functional screening is able to bridge the gap between genes and biological phenomena and raise important biological questions which should be tackled by integration of 'omic' datasets. These possible roles of functional screening will become more and more important in modern molecular biology moving toward the system level understanding of living organisms.

Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models

MOTIVATION

The development of gene expression microarray technology has allowed the identification of differentially expressed genes between different clinical phenotypic classes of cancer from a large pool of candidate genes. Although many class comparisons concerned only a single phenotype, simultaneous assessment of the relationship between gene expression and multiple phenotypes would be warranted to better understand the underlying biological structure.

RESULTS

We develop a method to select genes related to multiple clinical phenotypes based on a set of multivariate linear regression models. For each gene, we perform model selection based on the doubly-adjusted R-square statistic and use the maximum of this statistic for gene selection. The method can substantially improve the power in gene selection, compared with a conventional method that uses a single model exclusively for gene selection. Application to a bladder cancer study to correlate pre-treatment gene expressions with pathological stage and grade is given. The methods would be useful for screening for genes related to multiple clinical phenotypes.

AVAILABILITY

SAS and MATLAB codes are available from author upon request.

Identification of proangiogenic genes and pathways by high-throughput functional genomics: TBK1 and the IRF3 pathway

A genome-wide phenotype screen was used to identify factors and pathways that induce proliferation of human umbilical vein endothelial cells (HUVEC). HUVEC proliferation is a recognized marker for factors that modulate vascularization. Screening "hits" included known proangiogenic factors, such as VEGF, FGF1, and FGF2 and additional factors for which a direct association with angiogenesis was not previously described. These include the kinase TBK1 as well as Toll-like receptor adaptor molecule and IFN regulatory factor 3. All three proteins belong to one signaling pathway that mediates induction of gene expression, including a mixture of secreted factors, which, in concert, mediate proliferative activity toward endothelial cells. TBK1 as the "trigger" of this pathway is induced under hypoxic conditions and expressed at significant levels in many solid tumors. This pattern of expression and the decreased expression of angiogenic factors in cultured cells upon RNA-interference-mediated ablation suggests that TBK1 is important for vascularization and subsequent tumor growth and a target for cancer therapy.

Common denominator procedure: a novel approach to gene-expression data mining for identification of phenotype-specific genes

MOTIVATION

We have established a novel data mining procedure for the identification of genes associated with pre-defined phenotypes and/or molecular pathways. Based on the observation that these genes are frequently expressed in the same place or in close proximity at about the same time, we have devised an approach termed Common Denominator Procedure. One unusual feature of this approach is that the specificity and probability to identify genes linked to the desired phenotype/pathway increase with greater diversity of the input data.

RESULT

To show the feasibility of our approach, the Cancer Genome Anatomy Project expression data combined with a defined set of angiogenic factors was used to identify additional and novel angiogenesis-associated genes. A multitude of these additional genes were known to be associated with angiogenesis according to published data, verifying our approach. For some of the remaining candidate genes, application of a high-throughput functional genomics platform (XantoScreen) provided further experimental evidence for association with angiogenesis.

Bioinformatic tools for cancer geneticists

Early detection is essential for the control and prevention of many diseases, particularly cancer, which is the reason why the need for new disease markers with improved sensitivity and specificity continues to grow. Utilization of sophisticated bioinformatic tools enables the increased specificity and a relatively large quantity of high quality assays for any gene of interest. Understanding the molecular characteristics of diseases, such as cancer and the detection of mutations or changes in gene expression patterns that occur as a result of the disease, will bring researchers one step closer to achieving the predictive power needed for the development of new therapies, the design of clinical trials, and specific patient treatment planning. Genetic screening is one of the fastest moving areas of medical science, particularly in oncology, and as more genes are cloned, and more disease-associated mutations discovered, the workload is set to increase considerably with the utilization of bioinformatics tools used in integration and analysis of genomic, proteomic and metabolomic profiles of cancer. .