Project description:Although multi-agent combination chemotherapy is curative in a significant fraction of childhood acute lymphoblastic leukemia (ALL) patients, 20% of cases relapse and most die due to chemo-refractory disease. Here we used whole-exome and whole-genome sequencing to analyze the mutational landscape and pattern of clonal evolution at relapse in pediatric ALL cases. These analyses showed that ALL relapses originate from a common ancestral precursor clone of the diagnosis and relapsed populations and frequently harbor mutations implicated in chemotherapy resistance. RAS-MAPK pathway activating mutations in NRAS, KRAS and PTPN11 were present in 24/55 (44%) cases in our series. Notably, while some cases showed emergence of RAS mutant clones at relapse, in others, RAS mutant clones present at diagnosis were replaced by RAS wild type populations. Mechanistically, functional dissection of mouse and human wild type Kras and mutant Kras (Kras G12D) isogenic leukemia... (for more see dbGaP study page.)
Project description:Genomic surveys of yeast hybrid species isolated from the wild and from human-related environment, aimed at the reconstruction of the natural evolution of Saccharomyces spp. evolution
Project description:Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, deleterious mutations may also have an important role by promoting adaptive genetic changes that are otherwise inaccessible. Here we study the capacity of the baker’s yeast genome to compensate the complete loss of genes during evolution, and explore the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid yeast genotypes, all of which initially displayed slow growth due to the deletion of a single gene. Compensatory adaptation was rapid and pervasive, and it promoted the genomic divergence of parallel evolving populations. The accumulated mutations did not restore wild type genomic expression states and generated diverse growth phenotypes across environments. Taken together, gene loss initiates genomic changes that can influence evolutionary potential upon environmental change. Evolved yeast-lines were generated by growing strains for 400 doublings during 104 days on YPD medium in 96 wells plates, 8 evolved lines were selected for microarray analysis. Two independent colonies of the wild type control, evolved and corresponding ancestor knock-out strains were grown to early midlog and used for transcription profiling by dual channel array against a common reference.
Project description:miRNA-mediated gene expression silencing has previously been shown to be important for a variety of physiological and pathological processes. Here, we have explored the role of one bona fide human-specific miRNA (miR-941) in evolution of the human-specific expression and function. Using combination of high-throughput sequencing (GSE26545), miRNA transfection and large-scale PCR of various human populations, we have shown that emergence and rapid expansion of miR-941 might take place on the human evolutionary linage between six and one million years ago. Functionally, miR-941 could be associated with hedgehog and insulin signaling pathways, and thus might potentially play a role in evolution of human longevity. Human-specific effects of miR-941 regulation are detectable in human brain and affect genes involved in neurotransmitter signaling. Furthermore, emergence of miR-941 on the human evolutionary linage was accompanied by the accelerated loss of its binding sites. Taken together, these results strongly implicate the contribution of miR-941 in evolution of the human-specific phenotype. Cerebellum mRNA samples from 5 human, 5 chimpanzee and 1 rhesus macaque for Affymetrix Human Exon 1.0 ST Arrays were prepared following the standard GeneChip Whole Transcript (WT) Sense Target Labelling Assay.
Project description:Large-scale genomic profiling efforts have facilitated the characterization of molecular alterations in cancers and aided the development of targeted kinase inhibitors for a wide array of cancer types. However, resistance to these targeted therapies invariably develops and limits their clinical efficacy. Targeting tumours with kinase inhibitors induces complex adaptive survival programs that promote the persistence of a fraction of the original cancer cell population, facilitating the eventual outgrowth of inhibitor-resistant tumour clones following clonal evolution. Here we show that the addition of a newly identified transcriptional repressor, THZ1, to targeted cancer therapy enhances cell killing and impedes the emergence of drug-resistant cell populations in cellular and in vivo cancer models with diverse genetic dependencies. We propose that targeted therapy induces a state of transcriptional dependency in a subpopulation of cells poised to become drug tolerant. THZ1 can exploit this dependency by blocking dynamic transcriptional responses, remodelling of enhancers and key signalling outputs required for tumour cell survival in the setting of targeted cancer therapies. These findings suggest that the addition of THZ1 to targeted cancer therapies is a promising broad-based strategy to hinder the emergence of drug-resistant cancer cell populations. Overall design: RNA-seq in tumor cell lines treated with targeted therapies and/or transcriptional inhibitors
Project description:Large-scale genomic profiling efforts have facilitated the characterization of molecular alterations in cancers and aided the development of targeted kinase inhibitors for a wide array of cancer types. However, resistance to these targeted therapies invariably develops and limits their clinical efficacy. Targeting tumours with kinase inhibitors induces complex adaptive survival programs that promote the persistence of a fraction of the original cancer cell population, facilitating the eventual outgrowth of inhibitor-resistant tumour clones following clonal evolution. Here we show that the addition of a newly identified transcriptional repressor, THZ1, to targeted cancer therapy enhances cell killing and impedes the emergence of drug-resistant cell populations in cellular and in vivo cancer models with diverse genetic dependencies. We propose that targeted therapy induces a state of transcriptional dependency in a subpopulation of cells poised to become drug tolerant. THZ1 can exploit this dependency by blocking dynamic transcriptional responses, remodelling of enhancers and key signalling outputs required for tumour cell survival in the setting of targeted cancer therapies. These findings suggest that the addition of THZ1 to targeted cancer therapies is a promising broad-based strategy to hinder the emergence of drug-resistant cancer cell populations. Overall design: ChIP-Seq for enhancer-binding proteins in multiple tumor cell lines
Project description:Following antifungal treatment, Candida albicans, and other human pathogenic fungi can undergo microevolution, which leads to the emergence of drug resistance. However, the capacity for microevolutionary adaptation of fungi goes beyond the development of drug resistance. Here we used an experimental microevolution approach to show that one of the central pathogenicity mechanisms of C. albicans, the yeast-to-hyphae transition, can be subject to experimental evolution. The C. albicans cph1Δ/efg1Δ mutant is non-filamentous, as central signalling pathways linking environmental cues to hypha formation are disrupted. We subjected this mutant to constant selection pressure in the hostile environment of the macrophage phagosome. In a comparatively short time-frame, the mutant evolved the ability to escape macrophages by filamentation. To investigate the transcriptional response underlying the yeast-to-filament transition in the evolved strain, we applied RNA-Seq technology. Furthermore, RNA-Seq data were used to identify SNPs, which are specific for the evolved strain. For both strains, the cph1Δ/efg1Δ mutant and the Evo-strain, two conditions, one promotes yeast growth the other filamentous growth, were investigated. For each condition three biological replicates were analysed.
Project description:This a model from the article:
Kinetic analysis of a molecular model of the budding yeast cell cycle.
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. Mol Biol Cell
2000 Jan;11(1):369-91 10637314
The molecular machinery of cell cycle control is known in more detail for
budding yeast, Saccharomyces cerevisiae, than for any other eukaryotic organism.
In recent years, many elegant experiments on budding yeast have dissected the
roles of cyclin molecules (Cln1-3 and Clb1-6) in coordinating the events of DNA
synthesis, bud emergence, spindle formation, nuclear division, and cell
separation. These experimental clues suggest a mechanism for the principal
molecular interactions controlling cyclin synthesis and degradation. Using
standard techniques of biochemical kinetics, we convert the mechanism into a set
of differential equations, which describe the time courses of three major
classes of cyclin-dependent kinase activities. Model in hand, we examine the
molecular events controlling "Start" (the commitment step to a new round of
chromosome replication, bud formation, and mitosis) and "Finish" (the transition
from metaphase to anaphase, when sister chromatids are pulled apart and the bud
separates from the mother cell) in wild-type cells and 50 mutants. The model
accounts for many details of the physiology, biochemistry, and genetics of cell
cycle control in budding yeast.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. (2000) - version=1.0
The original CellML model was created by:
The University of Auckland
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
Project description:Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for 200-500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfur transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution. Overall design: All arrays are CGH comparing two genomes using two experimental designs. Control experiments compare differentially labeled DNA from two species to test specificity. The remaining experiments compare the genome content of an experimentally evolved strain with a control.
Project description:microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate. 2 condition experiment, derived experimental evolution strains compared to their ancestor strain. We compared the expression profile of one of the mutator lines (m8) after 6700 generations with its mutator ancestor, and as a control, an evolved non mutator after 6700 generations was compared to to its non-mutator ancestor. In order to prepare cells for expression microarray, glass tubes containing 3 ml of YPD were inoculated from overnight cultures, and grown until the OD600 was approximately 0.3.