Design and implementation of cell-based assays to model human disease

Chemical Screening of Nuclear Receptor Modulators

Nuclear receptors are ligand-inducible transcriptional factors that control multiple biological phenomena, including proliferation, differentiation, reproduction, metabolism, and the maintenance of homeostasis. Members of the nuclear receptor superfamily have marked structural and functional similarities, and their domain functionalities and regulatory mechanisms have been well studied. Various modulators of nuclear receptors, including agonists and antagonists, have been developed as tools for elucidating nuclear receptor functions and also as drug candidates or lead compounds. Many assay systems are currently available to evaluate the modulation of nuclear receptor functions, and are useful as screening tools in the discovery and development of new modulators. In this review, we cover the chemical screening methods for nuclear receptor modulators, focusing on assay methods and chemical libraries for screening. We include some recent examples of the discovery of nuclear receptor modulators.

Quantitative Prioritization of Tool Compounds for Phenotypic Screening

Phenotypic screens are increasingly utilized in drug discovery for multiple purposes such as lead and/or tool compound finding, and target discovery. Using potent and selective chemical tool compounds against well-defined targets in phenotypic screens can help elucidate biological processes modulating assay phenotypes. Unfortunately the identification of such tools from large heterogeneous bioactivity databases is nontrivial and there is repeated use of published unselective compounds as phenotypic tools. Here we describe a computational model, the compound-target tool score (TS), which is an evidence-based quantitative confidence metric that can be used to systematically rank tool compounds for targets. The identified selective and nonselective tool compounds have applications in phenotypic assays for target hypothesis validation as well as assay development.

Evidence-Based and Quantitative Prioritization of Tool Compounds in Phenotypic Drug Discovery

The use of potent and selective chemical tools with well-defined targets can help elucidate biological processes driving phenotypes in phenotypic screens. However, identification of selective compounds en masse to create targeted screening sets is non-trivial. A systematic approach is needed to prioritize probes, which prevents the repeated use of published but unselective compounds. Here we performed a meta-analysis of integrated large-scale, heterogeneous bioactivity data to create an evidence-based, quantitative metric to systematically rank tool compounds for targets. Our tool score (TS) was then tested on hundreds of compounds by assessing their activity profiles in a panel of 41 cell-based pathway assays. We demonstrate that high-TS tools show more reliably selective phenotypic profiles than lower-TS compounds. Additionally we highlight frequently tested compounds that are non-selective tools and distinguish target family polypharmacology from cross-family promiscuity. TS can therefore be used to prioritize compounds from heterogeneous databases for phenotypic screening.

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

Drug-induced transcriptional modules (biclusters) were identified and annotated in three human cell lines and rat liver. These were used to assess conservation across systems and to infer and experimentally validate novel drug effects and gene functions.

Biclustering of drug-induced gene expression profiles resulted in modules of drugs and genes, which were enriched in both drug and gene annotations.

Identifying drug-induced transcriptional modules separately in three human cell lines and rat liver allows assessment of their conservation across model systems. About 70% of modules are conserved across cell lines, a lower bound of 15% was estimated for their conservation across organisms, and between the in vitro and in vivo systems.

Drug-induced transcriptional modules can predict novel gene functions. A conserved module associated with (chole)sterol metabolism revealed novel regulators of cellular cholesterol homeostasis; 10 of them were validated in functional imaging assays.

Analysis of drugs clustered into modules can give new insights into their mechanisms of action and provide leads for drug repositioning. We predicted and experimentally validated novel cell cycle inhibitors and modulators of PPARγ, estrogen and adrenergic receptors, with potential for developing new therapies against diabetes and cancer.

In pharmacology, it is crucial to understand the complex biological responses that drugs elicit in the human organism and how well they can be inferred from model organisms. We therefore identified a large set of drug-induced transcriptional modules from genome-wide microarray data of drug-treated human cell lines and rat liver, and first characterized their conservation. Over 70% of these modules were common for multiple cell lines and 15% were conserved between the human in vitro and the rat in vivo system. We then illustrate the utility of conserved and cell-type-specific drug-induced modules by predicting and experimentally validating (i) gene functions, e.g., 10 novel regulators of cellular cholesterol homeostasis and (ii) new mechanisms of action for existing drugs, thereby providing a starting point for drug repositioning, e.g., novel cell cycle inhibitors and new modulators of α-adrenergic receptor, peroxisome proliferator-activated receptor and estrogen receptor. Taken together, the identified modules reveal the conservation of transcriptional responses towards drugs across cell types and organisms, and improve our understanding of both the molecular basis of drug action and human biology.

Multiplexed transposon-mediated stable gene transfer in human cells

Generation of cultured human cells stably expressing one or more recombinant gene sequences is a widely used approach in biomedical research, biotechnology, and drug development. Conventional methods are not efficient and have severe limitations especially when engineering cells to coexpress multiple transgenes or multiprotein complexes. In this report, we harnessed the highly efficient, nonviral, and plasmid-based piggyBac transposon system to enable concurrent genomic integration of multiple independent transposons harboring distinct protein-coding DNA sequences. Flow cytometry of cell clones derived from a single multiplexed transfection demonstrated approximately 60% (three transposons) or approximately 30% (four transposons) stable coexpression of all delivered transgenes with selection for a single marker transposon. We validated multiplexed piggyBac transposon delivery by coexpressing large transgenes encoding a multisubunit neuronal voltage-gated sodium channel (SCN1A) containing a pore-forming subunit and two accessory subunits while using two additional genes for selection. Previously unobtainable robust sodium current was demonstrated through 38 passages, suitable for use on an automated high-throughput electrophysiology platform. Cotransfection of three large (up to 10.8 kb) piggyBac transposons generated a heterozygous SCN1A stable cell line expressing two separate alleles of the pore-forming subunit and two accessory subunits (total of four sodium channel subunits) with robust functional expression. We conclude that the piggyBac transposon system can be used to perform multiplexed stable gene transfer in cultured human cells, and this technology may be valuable for applications requiring concurrent expression of multiprotein complexes.

Pathway Reporter Assays Reveal Small Molecule Mechanisms of Action

Cell-based, phenotypic screening of small molecules often identifies compounds with provocative biological properties. However, determining the cellular target(s) and/or mechanism of action (MoA) of lead compounds remains an extremely challenging and time-consuming exercise. To provide insights into a compound's cellular action and greatly reduce the time required for MoA determination, we have developed a screening platform consisting of an extensive series of reporter gene assays (RGAs). A collection of > 11,000 compounds of known MoA (e.g., World Drug Index entries) were screened against the entire panel. The output provided evidence that an RGA signature could be ascribed to numerous, biologically diverse MoAs. The reference database generated suggested novel biological activity for particular compounds. For example, the profiling data led to the prediction that the cellular target of the natural product terprenin was dihydroorotate dehydrogenase (DHODH), which was confirmed experimentally. The screening methodology developed for this endeavor renders it amenable to the future examination of compounds with unknown MoA, in an automated, inexpensive, and time-efficient manner.

A cellular model of inflammation for identifying TNF-alpha synthesis inhibitors

Neuroinflammation is a common facet of both acute and chronic neurodegenerative conditions, exemplified by stroke and by Alzheimer's and Parkinson's disease, and the presence of elevated levels of the proinflammatory cytokine, tumor necrosis factor-alpha (TNF-alpha), has been documented in each. Although initial TNF-alpha generation is associated with a protective compensatory response, its unregulated chronic elevation is generally detrimental and can drive the disease process. In such circumstances, therapeutic strategies that can both gain access to the brain and target the production of TNF-alpha are predicted to be of clinical benefit. An in vitro mouse macrophage-like cellular screen, utilizing RAW 264.7 cells, was hence developed to identify novel TNF-alpha lowering agents incorporating lipophilic physicochemical characteristics predicted to allow penetration of the blood-brain barrier. Cultured RAW 264.7 cells exposed to lipopolysaccharide (LPS) induced a rapid, marked and concentration-dependent cellular release of TNF-alpha into the cell culture media, which was readily detected by enzyme linked immunosorbent assay (ELISA). The effects of four characterized thalidomide-based TNF-alpha lowering agents were assessed alongside 10 novel uncharacterized compounds synthesized on the same backbone. One of these new analogs possessed activity of sufficient magnitude to warrant further investigation. Activity determined in the cellular model translated to an in vivo rodent model of acute LPS-induced TNF-alpha elevation. The utility of the TNF-alpha cellular assay lies in its simplicity and robust nature, providing a tool for initial pharmacological screening to allow for the rapid identification novel TNF-alpha lowering agents.

Drug-induced liver injury: Is it somehow foreseeable?

The classic view on the pathogenesis of drug-induced liver injury is that the so-called parent compounds are made hepatotoxic by metabolism (formation of neo-substances that react abnormally), mainly by cytochromes P-450 (CYP), with further pathways, such as mitochondrial dysfunction and apoptosis, also playing a role. Risk factors for drug-induced liver injury include concomitant hepatic diseases, age and genetic polymorphisms of CYP. However, some susceptibility can today be predicted before drug administration, working on the common substrate, by phenotyping and genotyping studies and by taking in consideration patients’ health status. Physicians should always think of this adverse effect in the absence of other clear hepatic disease. Ethical and legal problems towards operators in the health care system are always matters to consider.

Myotonic dystrophy: therapeutic strategies for the future

Myotonic dystrophy (DM) is a dominantly inherited neurodegenerative disorder for which there is no cure or effective treatment. Investigation of DM pathogenesis has identified a novel disease mechanism that requires development of innovative therapeutic strategies. It is now clear that DM is not caused by expression of a mutant protein. Instead, DM is the first recognized example of an RNA-mediated disease. Expression of the mutated gene gives rise to an expanded repeat RNA that is directly toxic to cells. The mutant RNA is retained in the nucleus, forming ribonuclear inclusions in affected tissue. A primary consequence of RNA toxicity in DM is dysfunction of two classes of RNA binding proteins, which leads to abnormal regulation of alternative splicing, or spliceopathy, of select genes. Spliceopathy now is known to cause myotonia and insulin resistance in DM. As our understanding of pathogenesis continues to improve, therapy targeted directly at the RNA disease mechanism will begin to replace the supportive care currently available. New pharmacologic approaches to treat myotonia and muscle wasting in DM type 1 are already in early clinical trials, and therapies designed to reverse the RNA toxicity have shown promise in preclinical models by correcting spliceopathy and eliminating myotonia. The well-defined ribonuclear inclusions may serve as convenient therapeutic targets to identify new agents that modify RNA toxicity. Continued development of appropriate model systems will allow testing of additional therapeutic strategies as they become available. Although DM is a decidedly complex disorder, its RNA-mediated disease mechanism may prove to be highly susceptible to therapy.