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Diagnostic and therapeutic RNA technologies for translational genomic medicine

Name of the project

Diagnostic and therapeutic RNA technologies for translational genomic medicine

Key idea (slogan) of the project

Translational research approaches for implementation of genomic medicine (geno-theranostics) based on RNA technologies

Partner organization

National Research Tomsk State University;

Moscow Institute of physics and technology;

RIKEN, Japan;

Fox Chase Cancer Center, USA;

National Agriculture and Food Research Organization, Japan;

JSC Human Stem Cell Institute;

Novosibirsk State University;

Tatarstan Cancer Center;

Medical and Educational Centre of
Lomonosov Moscow State University;

Federal Scientific and Clinical Center of specialized medical Assistance and Medical Technologies of Federal Medico-Biological Agency of RF

Academic supervisor of the project

Hayashizaki Yoshihide  (H-index – 83)

Description of the project

The project is aimed to develop safe and reliable methods of gene diagnostics and gene therapy.
The explosive growth of genomic projects in the world allowed reconstruction of the detailed haplotypes, identification of rare genetic variants, studying their association with diseases and evaluating sensitivity to pharmaceutical drugs. Perhaps the most important question in the field of functional genomics – how the genome structure and its individual sections affect the transcription of RNA. The FANTOM project, is coordinated by the RIKEN Institute, a partner of the Kazan Federal University, is an international consortium established in 2000. Currently, at the fifth stage of the project development, there work is completed on the creation of the largest and most detailed atlas of the activity of promoters and enhancers from 975 human and 399 mouse samples – primary cell lines, cancer lines and tissues. Combined expertise and competence of RIKEN and leading University laboratories, as well as partners in the field of cell technologies allow to set the main objectives of the project. That is to form a research center in Kazan Federal University that is unique for Russia and focuses on using the latest advances in the field of genome-wide RNA technology for the development of four key blocks of competences in SAE 7P Translational Medicine:
Block 1. New levels of biomarkers sensitivity and gene-diagnostics approaches: application and development of RNA technologies in the field of genome-wide identification and characterization of regulatory elements (enhancers and promoters). Also highly sensitive methods for the detection of DNA and nascent RNA in applied research projects that serve are the points of excellence of KFU in the field of translational medicine. This includes:
Implementation of international consortium project MUSCLE-FANTOM: development of scientific and technological platform for understanding the genetic processes at the level of RNA transcription, regulation of differentiation, age-related changes, gravity-induced changes.
The implementation of the Partnership project with TSU (INFLAMATION-FANTOM) for creation of the Atlas of enhancer and promoter activities in macrophages and monoblasts that are specific for different tissues and pathologies.
A partnership project with MIPT will allow development of approaches to personalized therapy of cardiac diseases using iPS. Joint research projects with groups at NSU are focused on characterization of methods and results of genome editing in different models.
Block 2. Development of biomedical technologies on the basis of direct cell reprogramming and preprogramming.
Block 3. Development of gene-therapy therapeutics based on an extensive analysis of the regulatory elements, including the obtaining of constructs with high tissue-specific or cell-specific activity.
Block 4. Scientific and applied projects for identification of targets for non-invasive pre-/post- surgery diagnostics allowing prediction of cancer using analysis of free-circulating RNA and DNA.

Approaches to the implementation of the project

The project has four mutually complementary blocks, each of which contains a number of sub-projects:
In the first block (B1) methods of genome-wide assessment of regulatory elements activity (CAGE, transcriptome analysis of individual cells, open chromatin) will be used to analyze the molecular processes underlying the differentiation of muscles, as well as their functioning and activity in a number of pathologies. The number of sub-projects with partners, including universities participating in 5-100 project, involves using similar highly sensitive methods of genome-wide analysis of the promoter activity – these will be used to identify genetic processes in a wide range of inflammations, and cancer, as well as assessment of cell reprogramming efficiency, development of tissue constructs and genome editing.
The second set of initiatives (B2) includes the strongest competences of teams from Kazan Federal University and other Russian partners in the field of cell technologies. In particular, isolation of mononuclear cells and cancer stem cells, application of genome-wide analysis methods to obtain gene expression profiles in the original and target cell types. Furthermore, integration of the original data with databases of our foreign partners will provide unique protocols of cell reprogramming that will be tested using in vitro and in vivo models in KFU. Evaluation of the approaches efficiency and investigation of obtained induced pluripotent stem cells (IPSC) and also target cell populations will be conducted, including based on deep profiling of transcription processes.
The third block (B3) is aimed to therapeutic application of the obtained genetic knowledge. Recombinant methods will allow creation of next generation gene-therapy drugs (vector constructs), based on activation and effective gene expression that will take place exclusively in target cell types and tissues. In parallel with the increase of specificity of transcription activation, nanomaterials and peptide components will be used to increase stability and efficiency of the expression constructs. The fourth block (B4) will include whole genome DNA and RNA analysis methods for identification of new pathogenic mutations and prospective markers, highly sensitive detection methods for analysis of circulating RNA and DNA to improve the cancer diagnosis. This group of projects is formed on the basis of requests from clinical partners of KFU and the research results in this area will most rapidly be translated into practice.

University’s experience, research and technological preliminary preparatory work

Kazan Federal University created a unique full cycle scientific and technological infrastructure in the field of Biomedicine – from research and development to practical application.
1. University Clinic – a multidisciplinary medical institution with 840 beds, providing high-tech medical care. Importantly, it has a state-accredited department for conducting clinical trials of new methods of diagnostics, treatment and rehabilitation. The clinic has a fully functional laboratory for clinical genomics, powerful sequencers and the laboratory of clinical gene diagnostics that allows to conduct analysis using nucleic acids from clinical samples.
2. Interdisciplinary centre for proteomics and genomics research. The centre is equipped with modern equipment to conduct proteomics, genomics and transcriptomics studies – capillary sequencers and next-generation sequencers, mass spectrometers with liquid and gas chromatography systems (MALDI, Electrospray). Within the framework of the Federal target program “Research and development in priority directions of development of scientific-technological complex of Russia for 2014-2020” KFU carries out two major projects: “Development of proteogenomics based on interdisciplinary core facilities for cell studies, genomic and post-genomic research in the Volga region” and “Development of diagnostics panels for assessment of the qualitative and quantitative compositions of the microbiota from the intestinal contents”.
3. Research and education centre for pharmaceuticals was established within the framework of the Federal program Pharma-2020. The main task is the discovery and development of novel therapeutics: synthesis of pharmaceutical substances, screening for a biological activity, elucidation of the mechanism of action, preclinical studies, manufacturing of finished dosage forms.
4. The competitiveness program of Kazan Federal University builds on the successful work of OpenLab research laboratories and four centers of excellence, namely “Genomics, proteomics and biotechnology”, “Regenerative and translational medicine”, “Neuroscience” (supported by Megagrant from the Russian Government), “Pharmaceuticals”.
5. The research facilities in Kazan Federal University are well equipped for work with cell cultures and animals (in vivarium). Over the last several years the research teams mastered the modern methods of cell programming – this includes work with induced pluripotent stem cells and isolation of stem cancer cells from primary tumors.
In the frame of collaboration with RIKEN, two joint laboratories in the field of translational genomics were established RIKEN (Japan) and KFU (Russia). The laboratories equipped with the park of the most advanced NGS Systems (Illumina). The international team effectively applly the methods of the genome-wide analysis of RNA expression to study promoters networks and to identify activity of enhancers

Achieving of global leadership (excellence), as one of the project results

The project will allow establishment of the competence center “Translational RNA technology” in Kazan Federal University (Strategic Academic Unit). Currently, there are no research centers in Russia that focus on genome-wide technologies for RNA analysis in translational and biomedical fields. The unique nature of the project proposed by Kazan Federal University is based on several modules:
• profiling of cell regulome, as well as generation of personalized target cell lines
• genome profiling of enhancer and promoter activity in muscles (in ontogenesis, norm and pathology), as well as development of prototypes of novel gene-based therapeutics, efficient and safe gene therapy at the level of genome-wide expression in the target tissues and cells.
•identification of ethno-specific profile of cancer mutations and their influcence on RNA expression profile, as well as development of complex non-invasive diagnostics products for prospective analysis of cancer development.
• creation of target-focused libraries of guide RNA for genome editing, as well as identification of diagnostically and therapeutically relevant markers of drug resistance.
In the course of the project a collaborative platform will be established for close partnership with leading Russian scientific centers to create the diagnostics and therapeutics solutions. Important feature of the project is that the team will explore leading RNA-based technologies (CAGE analysis, RNA editing, CRISPR analysis, reprogramming based on performance analysis, analysis of nucleic acids in blood plasma). The project combines unique objects (muscle atlas, pathologies, developments in gene therapy) and objectives (prospective cancer analysis, the safety and efficacy of gene therapy) that will allow us to position Kazan Federal University in the field of fundamental research, with particular focus on ageing, differentiation and regeneration of muscles and nervous system.

Significance, relevance and academic novelty of the project

The prioritized scientific and technical targets of the project are linked to the diagnostics and curing of the main socially significant diseases, first of all – oncological, neuro-muscular and cardiovascular.
The proposed project is rather not the research program for a stand-alone university, but rather process of formation in Russia the consortium of the leading scientific centers, where the combination of expertise will allow to rich the excellency and breakthrough in the field of medical genetics and functional genomics. Also, the proposed plan of the joint research suggest further joint utilization of the results and practical outcome, as well as establishment of the new long-term partnership for further implementation of the consortium-based projects.
Study of the regulation of the genetic processes in the muscles and muscle-derived cell lines of human and model mammals will allow to gradually expand current state of knowledge about formation of neuro-muscle system and the process regulating the cells under different types of pathologies, including germline mutation-based. In addition to the big scientific impact, the project will allow to establish a platform for development of the new generation of gene-therapy approaches.
Both MUSCLE-FANTOM è INFLAMATION-FANTOM projects, will attract the appreciation of the international scientific community, especially, considering its unique approaches and set of samples.
Based on the effective synthesis of the technology of RNA expression analysis and methods of the purification of the cancer stem cells, new unique data of the regulation of the cell differentiation in the process of the cancer will be obtained. Difficult process of the purification and confirmation of the authentic features of the stem cells resulted in absence of the systematic, detailed meta-analysis of the transcriptome profiles of the cancer stem cell. Unique expertise of the center at KFU and collaboration with partners, will allow to create the data bank of the unique promotor-based RNA expression landscape of the tissue-specific endogenous and tumor-derived stem cells. Analytic potential and large data set in FANTOM and Mogrify databases will contribute to the identification of new targets for anti-tumor drugs with low toxicity.
Remarkably, the geographical location of KFU and close partnership with medical institution in the frame of the project, will allow to estimate potential effect of ethnic-based genomic variations in the landscape of driver mutations in cancer and dynamic of RNA-driven genetic regulation of mononuclear cells. Deep analysis of these factors will allow to develop universal and equally effective, disregarding genetic background of the patients, diagnostics and therapeutic solutions.

Relevance and significance of the project in technologies

The concept of the current proposal is the combination of the best expertise’s of KFU and its partners both in Russia and abroad, to develop the new technological platform in medical genomics. It includes well-known excellence of RIKEN (the primary international partner of KFU) in the field of RNA transcription regulation, in combination with a set of unique technologies for both diagnostics and therapeutically use of RNA. The well-developed scientific infrastructure, including joint genomics laboratories in Japan and Russia, and fruitful history of collaboration, of Russian and Japan teams provides a promising background for establishing on the basis of SAU “7P Medicine” unique for Russia Center of Excellence in the field of RNA technologies. The mission of the center is to assist the whole cycles of development of new biomedical genetic technologies from research to end-user oriented diagnostics and therapeutic solutions.
In addition to deep scientific interest, the components of the research programs combining the current proposal were formed in consideration with the needs of industrial and medical partners from Tatarstan and other regions, hosting other participants of the consortium (NSU-TGU-MPhTI). Thus the parts of the research program, including major basic projects MUSCLE-FANTOM and INFLAMATION-FANTOM are also the translational projects, with the expected results to be of use in medical practice.
In collaboration with RIKEN, with its unique menu of technologies for investigation and use of nucleic acids, and contribution of other foreign and Russia-based partners, the project will result in the establishment of ready-to-use for end-users solutions. Thus, in the field of gene-therapy, we will establish a new generation of genetic constructs showing the highest specificity in expression for the target cells and tissues. At the same time, enhanced by the peptide components, it will be more resistant to the nucleases and effective. In the field of cell therapy, especially in the solution using patient-specific iPS, using whole-genome profiling of promoter expression, we will develop a new platform for high precision estimation of the effectiveness of the cell reprogramming technologies.
Another feature of the project is an establishment of multi-step process of the development of innovative biomedical products using in the field of cell and gene therapy. It will allow, to combine the basic and applied research in the stand-alone projects, and preparation of the pre-clinical trials and production of the end-user ready solutions. The expenses of the project is diversified among the participants of the consortium of the translation medicine, including those from main Partners universities. Thus we are focusing on the establishment of the unified platform for research and implementing of new technologies, based on the deep analysis of nucleic acids, gene editing, and cell programming, to combat with socially significant diseases.