Pathprinting: An integrative approach to understand the functional basis of disease

New strategies to combat complex human disease require systems approaches to biology that integrate experiments from cell lines, primary tissues and model organisms. We have developed Pathprint, a functional approach that compares gene expression profiles in a set of pathways, networks and transcriptionally regulated targets. It can be applied universally to gene expression profiles across species. Integration of large-scale profiling methods and curation of the public repository overcomes platform, species and batch effects to yield a standard measure of functional distance between experiments. We show that pathprints combine mouse and human blood developmental lineage, and can be used to identify new prognostic indicators in acute myeloid leukemia. The code and resources are available at http://​compbio.​sph.​harvard.​edu/​hidelab/​pathprin

Genetically modified food products: peculiarities of genetic identification

Our research goal was to perform a genetic analysis of food stuffs produced in Russia in order to determine whether ge-netically modified components, predominantly soya, occurred in them. We also set a task to draw up an optimal list of genetic modifiers for sausages and soya products; this list was to be applied as a tool for monitoring of undeclared GMO and for providing biological safety of food stuffs. We applied polymerase chain reaction in real-time mode to analyze certain food prod-ucts (sausages and soya products); the analysis was to reveal genetically modified organisms. The task was to identify the fol-lowing GMO genes: promoters (p35SCaMV, P-SSuAra, Ubi1, ract1, hsp70, TA29 tobacco promoter), terminators (nos3, T-E9, T-g7, T-OCS), reporter genes (nptll, qHptFP308, bar, pat_10-P), bio-pesticides Bacillus Thuringensis (Bt) or Cry-toxins (Cry1Ab/Ac), reporter gene of β-glucuronidase (GUS-gene). Analysis of some sausage samples allowed us to identify the following GMO genes: Cry1Ab/Ac, P-FMV, P-nos, bar, gus_9-P, Т-nos3, nptii, P-TA29, T-E9, T-g7, T-OCS. The research performed on food products revealed GMO in 56 % of the analyzed sausage samples. Genetic modification of the analyzed food samples had its peculiarities; a set of identified genes that included promoter genes P-FMV, terminators (nos3, T-g7, T-OCS), Cry1Ab/Ac endo-toxin, and a reporter of GMO bar was one of them. We recommend to use the following candidate genes for GMO contents in food products: Cry1Ab/Ac, P-FMV, P-nos, bar, gus_9-P, Т-nos3, nptii, P-TA29, T-E9, T-g7, T-OCS. They all are evidence that genetic modifications took place and they all can be applied as marker genes for control over food products safety as per GMO contents criterion

Development of methodical approach to the identification of the features of the genetic polymorphisms and gene expression in children under influence of chemical environmental factors on the example of strontium

Methodological approaches evaluating the features of genetic polymorphism associated with exposure to chemical etiology factors for the identification of genetic susceptibility markers were developed. The technologies, methodological aspects of the use of polymerase chain reaction, DNA sequencing fragments, studies of spontaneous and induced strontium expression of candidate genes that help identify changes in the genome and transcriptome in order to identify early disorders of adaptation processes in chronic environmental burden to prove the injury and assessment of individual exposure risk chemical factors were suggested

Polymorphism’s assessment of children’s candidate genes associated with low-level long-term exposure to strontium in drinking water

A sequencing of the candidate genes of the pupils, exposed to strontium by the method of targeted resequencing has been performed. It is shown, that under conditions of increased revenues of strontium in drinking water the number of polymorphonuclear altered portions of candidate genes increases. As a result of the targeted resequencing in conditions of strontium exposure, the maximum polymorph modifications of the following genes are defined: sulfotransferase 1A1 (SULT1A1) and methylenetetrahydrofolate. It was shown that the structure of the mutations in conditions of the strontium exposure was characterized by the formation of defects in the gene mapping detoxification (38.5 % of all mutations) and immunoregulation (22.5 %). Analysis of the cause-effect relationships in the system "factor - the number of mutations" revealed that candidate genes reflecting strontium exposure conditions (content of strontium in drinking water is 1.3 MAC), are genes: cytochrome P450, glutathione - transaminase (detoxification); dopamine (CNS), interleukin 17 and the major histocompatibility complex (immune system), methylene-tetra-hydro-folate-reductase (reproduction)

Therapeutic targeting of preleukemia cells in a mouse model of mutant acute myeloid leukemia

The initiating mutations that contribute to cancer development are sometimes present in premalignant cells. Whether therapies targeting these mutations can eradicate premalignant cells is unclear. Acute myeloid leukemia (AML) is an attractive system for investigating the effect of preventative treatment because this disease is often preceded by a premalignant state (clonal hematopoiesis or myelodysplastic syndrome). In mutant knock-in mice, a model of AML development, leukemia is preceded by a period of extended myeloid progenitor cell proliferation and self-renewal. We found that this self-renewal can be reversed by oral administration of a small molecule (VTP-50469) that targets the MLL1-Menin chromatin complex. These preclinical results support the hypothesis that individuals at high risk of developing AML might benefit from targeted epigenetic therapy in a preventative setting

EVI1 is critical for the pathogenesis of a subset of MLL-AF9-rearranged AMLs

The proto-oncogene EVI1 (ecotropic viral integration site-1), located on chromosome band 3q26, is aberrantly expressed in human acute myeloid leukemia (AML) with 3q26 rearrangements. In the current study, we showed, in a large AML cohort carrying 11q23 translocations, that ∼ 43% of all mixed lineage leukemia (MLL)-rearranged leukemias are EVI1pos. High EVI1 expression occurs in AMLs expressing the MLL-AF6, -AF9, -AF10, -ENL, or -ELL fusion genes. In addition, we present evidence that EVI1pos MLL-rearranged AMLs differ molecularly, morphologically, and immunophenotypically from EVI1neg MLL-rearranged leukemias. In mouse bone marrow cells transduced with MLL-AF9, we show that MLL-AF9 fusion protein maintains Evi1 expression on transformation of Evi1pos HSCs. MLL-AF9 does not activate Evi1 expression in MLLAF9- transformed granulocyte macrophage progenitors (GMPs) that were initially Evi1neg. Moreover, shRNA-mediated knockdown of Evi1 in an Evi1pos MLL-AF9 mouse model inhibits leukemia growth both in vitro and in vivo, suggesting that Evi1 provides a growth-promoting signal. Using the Evi1pos MLL-AF9 mouse leukemia model, we demonstrate increased sensitivity to chemotherapeutic agents on reduction of Evi1 expression. We conclude that EVI1 is a critical player in tumor growth in a subset of MLL-rearranged AMLs