Yeast, flies, worms, and fish in the study of human disease

Protective effects of Phaseolus vulgaris lectin against viral infection in Drosophila

Phytohemagglutinin (PHA) isolated from the family of Phaseolus vulgaris beans is a promising agent against viral infection; however, it has not yet been demonstrated in vivo. We herein investigated this issue using Drosophila as a host. Adult flies were fed lectin approximately 12 h before they were subjected to a systemic viral infection. After a fatal infection with Drosophila C virus, death was delayed and survival was longer in flies fed PHA-P, a mixture of L4, L3E1, and L2E2, than in control unfed flies. We then examined PHA-L4, anticipating subunit L as the active form, and confirmed the protective effects of this lectin at markedly lower concentrations than PHA-P. In both experiments, lectin feeding reduced the viral load prior to the onset of fly death. Furthermore, we found a dramatic increase in the levels of the mRNAs of phagocytosis receptors in flies after feeding with PHA-L4 while a change in the levels of the mRNAs of antimicrobial peptides was marginal. We concluded that P. vulgaris PHA protects Drosophila against viral infection by augmenting the level of host immunity.

Model systems inform rare disease diagnosis, therapeutic discovery and pre-clinical efficacy

Model systems have played a large role in understanding human diseases and are instrumental in taking basic research findings to the clinic; however, for rare diseases, model systems play an even larger role. Here, we outline how model organisms are crucial for confirming causal associations, understanding functional mechanisms and developing therapies for disease. As diseases that have been studied extensively through genetics and molecular biology, cystic fibrosis and Rett syndrome are portrayed as primary examples of how genetic diagnosis, model organism development and therapies have led to improved patient health. Considering which model to use, yeast, worms, flies, fish, mice or larger animals requires a careful evaluation of experimental genetic tools and gene pathway conservation. Recent advances in genome editing will aid in confirming diagnoses and developing model systems for rare disease. Genetic or chemical screening for disease suppression may reveal functional pathway members and provide candidate entry points for developing therapies. Model organisms may also be used in drug discovery and as preclinical models as a prelude to testing treatments in patient populations. Now, model organisms will increasingly be used as platforms for understanding variation in rare disease severity and onset, thereby informing therapeutic intervention.

Intercellular cooperation and competition in brain cancers: lessons from Drosophila and human studies

Glioblastoma (GBM) is a primary brain cancer with an extremely poor prognosis. GBM tumors contain heterogeneous cellular components, including a small subpopulation of tumor cells termed glioma stem cells (GSCs). GSCs are characterized as chemotherapy- and radiotherapy-resistant cells with prominent tumorigenic ability. Studies in Drosophila cancer models demonstrated that interclonal cooperation and signaling from apoptotic clones provokes aggressive growth of neighboring tumorigenic clones, via compensatory proliferation or apoptosis induced proliferation. Mechanistically, these aggressive tumors depend on activation of Jun-N-terminal kinase (upstream of c-JUN), and Drosophila Wnt (Wg) in the apoptotic clones. Consistent with these nonmammalian studies, data from several mammalian studies have shown that c-JUN and Wnt are hyperactivated in aggressive tumors (including GBM). However, it remains elusive whether compensatory proliferation is an evolutionarily conserved mechanism in cancers. In the present report, we summarize recent studies in Drosophila models and mammalian models (e.g., xenografts of human cancer cells into small animals) to elucidate the intercellular interactions between the apoptosis-prone cancer cells (e.g., non-GSCs) and the hyperproliferative cancer cells (e.g., GSCs). These evolving investigations will yield insights about molecular signaling interactions in the context of post-therapeutic phenotypic changes in human cancers. Furthermore, these studies are likely to revise our understanding of the genetic changes and post-therapeutic cell-cell interactions, which is a vital area of cancer biology with wide applications to many cancer types in humans.

The role of the Hippo pathway in human disease and tumorigenesis

Understanding the molecular nature of human cancer is essential to the development of effective and personalized therapies. Several different molecular signal transduction pathways drive tumorigenesis when deregulated and respond to different types of therapeutic interventions. The Hippo signaling pathway has been demonstrated to play a central role in the regulation of tissue and organ size during development. The deregulation of Hippo signaling leads to a concurrent combination of uncontrolled cellular proliferation and inhibition of apoptosis, two key hallmarks in cancer development. The molecular nature of this pathway was first uncovered in Drosophila melanogaster through genetic screens to identify regulators of cell growth and cell division. The pathway is strongly conserved in humans, rendering Drosophila a suitable and efficient model system to better understand the molecular nature of this pathway. In the present study, we review the current understanding of the molecular mechanism and clinical impact of the Hippo pathway. Current studies have demonstrated that a variety of deregulated molecules can alter Hippo signaling, leading to the constitutive activation of the transcriptional activator YAP or its paralog TAZ. Additionally, the Hippo pathway integrates inputs from a number of growth signaling pathways, positioning the Hippo pathway in a central role in the regulation of tissue size. Importantly, deregulated Hippo signaling is frequently observed in human cancers. YAP is commonly activated in a number of in vitro and in vivo models of tumorigenesis, as well as a number of human cancers. The common activation of YAP in many different tumor types provides an attractive target for potential therapeutic intervention.

Normal morphogenesis of epithelial tissues and progression of epithelial tumors

Epithelial cells organize into various tissue architectures that largely maintain their structure throughout the life of an organism. For decades, the morphogenesis of epithelial tissues has fascinated scientists at the interface of cell, developmental, and molecular biology. Systems biology offers ways to combine knowledge from these disciplines by building integrative models that are quantitative and predictive. Can such models be useful for gaining a deeper understanding of epithelial morphogenesis? Here, we take inventory of some recurring themes in epithelial morphogenesis that systems approaches could strive to capture. Predictive understanding of morphogenesis at the systems level would prove especially valuable for diseases such as cancer, where epithelial tissue architecture is profoundly disrupted.

Drosophila and Galleria insect model hosts: new tools for the study of fungal virulence, pharmacology and immunology

Over recent years we have witnessed the emergence of several non-vertebrate mini-hosts as alternative pathosystems for the study of fungal disease. These heterologous organisms have unique advantages, as they are economical, ethically expedient, and facile to use. Hence, they are amenable to high-throughput screening studies of fungal genomes for identification of novel virulence genes and of chemical libraries for discovery of new antifungal compounds. In addition, because they have evolutionarily conserved immunity they offer the opportunity to better understand innate immune responses against medically important fungi. In this review, we discuss how the insects Drosophila melanogaster and Galleria mellonella can be employed for the study of various facets of host-fungal interactions as complementary hosts to conventional vertebrate animal models.

Analysis of cell proliferation, senescence, and cell death in zebrafish embryos

Proper control of cell proliferation is critical for normal development, growth, differentiation, and tissue homeostasis. Dysregulation of cell division and cell death underlies almost all cancers, and contributes to the pathology of birth defects and degenerative diseases. The zebrafish has proved to be an excellent system for elucidating the roles of the cell cycle in normal development, and ways in which dysregulation of cell proliferation contributes to disease. This chapter describes the methods for studying the cell cycle in zebrafish embryos, including protocols to examine cell proliferation, DNA damage, senescence, and cell death.

Modeling human diseases in Caenorhabditis elegans

Genes linked to human diseases often function in evolutionarily conserved pathways, which can be readily dissected in simple model organisms. Because of its short lifespan and well-known biology, coupled with a completely sequenced genome that shares extensive homology with that of mammals, Caenorhabditis elegans is one of the most versatile and powerful model organisms. Research in C. elegans has been instrumental for the elucidation of molecular pathways implicated in many human diseases. In this review, we introduce C. elegans as a model organism for biomedical research and we survey recent relevant findings that shed light on the basic molecular determinants of human disease pathophysiology. The nematode holds promise of providing clear leads towards the identification of potential targets for the development of new therapeutic interventions against human diseases.

Similarly strong purifying selection acts on human disease genes of all evolutionary ages

A number of studies have showed that recently created genes differ from the genes created in deep evolutionary past in many aspects. Here, we determined the age of emergence and propensity for gene loss (PGL) of all human protein–coding genes and compared disease genes with non-disease genes in terms of their evolutionary rate, strength of purifying selection, mRNA expression, and genetic redundancy. The older and the less prone to loss, non-disease genes have been evolving 1.5- to 3-fold slower between humans and chimps than young non-disease genes, whereas Mendelian disease genes have been evolving very slowly regardless of their ages and PGL. Complex disease genes showed an intermediate pattern. Disease genes also have higher mRNA expression heterogeneity across multiple tissues than non-disease genes regardless of age and PGL. Young and middle-aged disease genes have fewer similar paralogs as non-disease genes of the same age. We reasoned that genes were more likely to be involved in human disease if they were under a strong functional constraint, expressed heterogeneously across tissues, and lacked genetic redundancy. Young human genes that have been evolving under strong constraint between humans and chimps might also be enriched for genes that encode important primate or even human-specific functions.

Autophagy in Drosophila melanogaster

Macroautophagy (autophagy) is a bulk cytoplasmic degradation process that is conserved from yeast to mammals. Autophagy is an important cellular response to starvation and stress, and plays critical roles in development, cell death, aging, immunity, and cancer. The fruit fly Drosophila melanogaster provides an excellent model system to study autophagy in vivo, in the context of a developing organism. Autophagy (atg) genes and their regulators are conserved in Drosophila, and autophagy is induced in response to nutrient starvation and hormones during development. In this review we provide an overview of how Drosophila research has contributed to our understanding of the role and regulation of autophagy in cell survival, growth, nutrient utilization, and cell death. Recent Drosophila research has also provided important mechanistic information about the role of autophagy in protein aggregation disorders, neurodegeneration, aging, and innate immunity. Differences in the role of autophagy in specific contexts and/or cell types suggest that there may be cell-context-specific regulators of autophagy, and studies in Drosophila are well-suited to yield discoveries about this specificity.

Invertebrate and fungal model organisms: emerging platforms for drug discovery

Early-stage translational research programs have increasingly exploited yeast, worms and flies to model human disease. These genetically tractable organisms represent flexible platforms for small molecule and drug target discovery. This review highlights recent examples of how model organisms are integrated into chemical genomic approaches to drug discovery with an emphasis on fungal yeast, nematode Caenorhabditis elegans and fruit fly Drosophila melanogaster. The roles of these organisms are expanding as novel models of human disease are developed and novel high-throughput screening technologies are created and adapted for drug discovery.

Orthology and functional conservation in eukaryotes

In recent years, it has become clear that all of the organisms on the Earth are related to each other in ways that can be documented by molecular sequence comparison. In this review, we focus on the evolutionary relationships among the proteins of the eukaryotes, especially those that allow inference of function from one species to another. Data and illustrations are derived from specific comparison of eight species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Saccharomyces cerevisiae, and Plasmodium falciparum.

Regulation of Imaginal Disc Growth by Tumor-Suppressor Genes inDrosophila

Inactivating mutations in the Drosophila tumor-suppressor genes result in tissue overgrowth. This can occur because the mutant tissue either grows faster than wild-type tissue and/or continues to grow beyond a time when wild-type tissue stops growing. There are three general classes of tumor-suppressor genes that regulate the growth of imaginal disc epithelia. Mutations in the hyperplastic tumor-suppressor genes result in increased cell proliferation but do not disrupt normal tissue architecture. These genes include pten, Tsc1, Tsc2, and components of the hippo/salvador/warts pathway. Mutations in a second class of genes, the neoplastic tumor-suppressor genes, disrupt proteins that function either as scaffolds at cell-cell junctions (scribble, discs large, lgl) or as components of the endocytic pathway (avalanche, rab5, ESCRT components). For the third group, the nonautonomous tumor-suppressor genes, mutant cells stimulate the proliferation of adjacent wild-type cells. Understanding the interactions between these three classes of genes will improve our understanding of how cell and tissue growth are coordinated during organismal development and perturbed in disease states such as cancer.

TILLING is an effective reverse genetics technique for Caenorhabditis elegans

Background

TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetic technique based on the use of a mismatch-specific enzyme that identifies mutations in a target gene through heteroduplex analysis. We tested this technique in Caenorhabditis elegans, a model organism in which genomics tools have been well developed, but limitations in reverse genetics have restricted the number of heritable mutations that have been identified.

Results

To determine whether TILLING represents an effective reverse genetic strategy for C. elegans we generated an EMS-mutagenised population of approximately 1500 individuals and screened for mutations in 10 genes. A total of 71 mutations were identified by TILLING, providing multiple mutant alleles for every gene tested. Some of the mutations identified are predicted to be silent, either because they are in non-coding DNA or because they affect the third bp of a codon which does not change the amino acid encoded by that codon. However, 59% of the mutations identified are missense alleles resulting in a change in one of the amino acids in the protein product of the gene, and 3% are putative null alleles which are predicted to eliminate gene function. We compared the types of mutation identified by TILLING with those previously reported from forward EMS screens and found that 96% of TILLING mutations were G/C-to-A/T transitions, a rate significantly higher than that found in forward genetic screens where transversions and deletions were also observed. The mutation rate we achieved was 1/293 kb, which is comparable to the mutation rate observed for TILLING in other organisms.

Conclusion

We conclude that TILLING is an effective and cost-efficient reverse genetics tool in C. elegans. It complements other reverse genetic techniques in this organism, can provide an allelic series of mutations for any locus and does not appear to have any bias in terms of gene size or location. For eight of the 10 target genes screened, TILLING has provided the first genetically heritable mutations which can be used to study their functions in vivo.

Caenorhabditis elegans : modèle d'étude in vivo de la virulence bactérienne

The nematode Caenorhabditis elegans presents many advantages as a model system. The worm has recently emerged as a potentially useful tool for the study of host-pathogen interactions. This paper presents advantages and inconveniences of this model, the variety of bacterial pathogens studied, and its use to monitor virulence of Extraintestinal Escherichia coli strains.

Mating worms and the cystic kidney: Caenorhabditis elegans as a model for renal disease

Polycystic kidney disease (PKD) is caused by a group of variably inherited human disorders that are major causes of end-stage renal disease in both children and adults. The genetic culprits responsible for autosomal-dominant PKD (ADPKD), the polycystins, have been identified, yet still little is known about the molecular mechanisms that result in the disease phenotype. Polycystin homologs have been isolated in the model genetic organism Caenorhabditis elegans and, interestingly, play a specific role in C. elegans male mating behavior. Despite the recruitment of the polycystins for divergent functions in worms and humans it appears that the fundamental molecular and genetic interactions of these genes are evolutionarily conserved. In addition, studies in the worm have contributed to an understanding of the emerging role for cilia in the function of the polycystin pathway, expanding a promising frontier in PKD research. C. elegans has also been used to identify a gene family which may have significance for understanding the formation and maintenance of renal tubules.

A microbial TRP-like polycystic-kidney-disease-related ion channel gene

Ion channel genes have been discovered in many microbial organisms. We have investigated a microbial TRP (transient receptor potential) ion channel gene which has most similarity to polycystic-kidney-disease-related ion channel genes. We have shown that this gene (pkd2) is essential for cellular viability, and is involved in cell growth and cell wall synthesis. Expression of this gene increases following damage to the cell wall. This fission yeast pkd2 gene, orthologues of which are found in all eukaryotic cells, appears to be a key signalling component in the regulation of cell shape and cell wall synthesis in yeast through an interaction with a Rho1-GTPase. A model for the mode of action of this Schizosaccharomyces pombe protein in a Ca2+ signalling pathway is hypothesized.

Death and taxis: what non-mammalian models tell us about sphingosine-1-phosphate

Sphingosine-1-phosphate (S1P) is a signaling molecule that regulates critical events including mammalian cell proliferation, survival, migration and cell-cell interactions. Most of these signals are triggered by engagement of sphingosine-1-phosphate receptors of the Edg family. However, accumulating evidence derived from investigation of non-mammalian models that lack Edg receptors suggests that sphingosine-1-phosphate-like molecules can act through alternative mechanisms and thereby contribute to morphogenesis, development, reproduction and survival. This review provides an overview of sphingosine-1-phosphate metabolism, the isolation of genes in this pathway employing yeast genetics, the evidence for its influence on non-mammalian development, and the pertinence of these findings to human disease.

The human life span is not that limited: the effect of multiple longevity phenotypes

There is an ongoing debate as to whether or not human longevity is approaching its limits. The debate and its outcome are important since they might affect public policy. We review the evidence presented by both schools. We add our empirical observation that there exist multiple longevity phenotypes, each of which arises from the alteration of fundamental aging processes. The current debate only considers two of the three known mammalian longevity phenotypes. The overlooked phenotype is the delayed onset of senescence phenotype, which can be induced by various interventions, including pharmaceuticals. The existence of multiple phenotypes means that an overview of potential life expectancy outcomes for a species should be based on the analysis of all longevity phenotypes likely to occur in that species.

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes

BACKGROUND

Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities. The availability of the human, mouse and, most recently, the rat genome sequences now permit the comprehensive investigation of the rodent orthologs of genes associated with human disease. Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change.

RESULTS

Human disease genes are unevenly distributed among human chromosomes and are highly represented (99.5%) among human-rodent ortholog sets. Differences are revealed in evolutionary conservation and selection between different categories of human disease genes. Although selection appears not to have greatly discriminated between disease and non-disease genes, synonymous substitution rates are significantly higher for disease genes. In neurological and malformation syndrome disease systems, associated genes have evolved slowly whereas genes of the immune, hematological and pulmonary disease systems have changed more rapidly. Amino-acid substitutions associated with human inherited disease occur at sites that are more highly conserved than the average; nevertheless, 15 substituting amino acids associated with human disease were identified as wild-type amino acids in the rat. Rodent orthologs of human trinucleotide repeat-expansion disease genes were found to contain substantially fewer of such repeats. Six human genes that share the same characteristics as triplet repeat-expansion disease-associated genes were identified; although four of these genes are expressed in the brain, none is currently known to be associated with disease.

CONCLUSIONS

Most human disease genes have been retained in rodent genomes. Synonymous nucleotide substitutions occur at a higher rate in disease genes, a finding that may reflect increased mutation rates in the chromosomal regions in which disease genes are found. Rodent orthologs associated with neurological function exhibit the greatest evolutionary conservation; this suggests that rodent models of human neurological disease are likely to most faithfully represent human disease processes. However, with regard to neurological triplet repeat expansion-associated human disease genes, the contraction, relative to human, of rodent trinucleotide repeats suggests that rodent loci may not achieve a 'critical repeat threshold' necessary to undergo spontaneous pathological repeat expansions. The identification of six genes in this study that have multiple characteristics associated with repeat expansion-disease genes raises the possibility that not all human loci capable of facilitating neurological disease by repeat expansion have as yet been identified.

Global Mapping of the Yeast Genetic Interaction Network

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

After the genome--the phenome?

What next? The Human Genome Project signifies complexity rather than simplification in the relationship between genotype and phenotype. Genotypes are embedded in genomes. Individuality in phenotypes is embedded in components of the phenome (transcriptome, metabolome, proteome, etc.). The phenome, its layers, and its nodes, links and networks, require elucidation; there is a need for a Human Phenome Project (Freimer and Sabatti 2003). Biology has largely been a reductive science in the recent past; integrative biology lies ahead. Clinician-scientists (including human biochemical geneticists) will be recognized as key participants in the 'medical' Phenome Project as it reveals components of individuality, and their contributions, in simple or combinatorial fashion, to Mendelian and complex traits; better ways to treat 'genetic disease' will be by-products of the project. Although the Word is common to all, most men live as if each had a private wisdom of his own.Herakleitos