Specialised phenotyping - metabolic phenotyping pipeline

INFRAFRONTIER2020 project - Trans-national Access call

March 2019

 

Context and aims of the call

Main objective of this INFRAFRONTIER2020 Trans-national Access call is to facilitate access for the wider biomedical research community to the unique infrastructure and scientific expertise of the participating INFRAFRONTIER mouse clinic, where mouse mutant lines can be tested through phenotyping pipelines with special focus on metabolic functions.

As an example, disturbed energy balance regulation results in obesity and in numerous related metabolic disorders - such as type 2 diabetes mellitus. We offer specialised phenotyping pipelines comprising state-of-the-art test assays monitoring disease related parameters.

Access will be granted based on scientific excellence and supports the development and in-depth characterisation of mouse models for investigating gene function and human pathophysiology.  INFRAFRONTIER will provide open access to all characterised disease models and phenotyping data.

 

The call is open till 15 April, 2019

Click here for the application form.

 

Access modalities
  • The EC Horizon 2020 funded INFRAFRONTIER2020 project (2017 – 2020) supports eligible customers with a free-of-charge mouse model specialised phenotyping service implemented as a Trans-national Access activity supporting a total of 3 projects in this call.
  • The access unit offered covers the specialised metabolic phenotyping of a mouse mutant line, and the preparation of a comprehensive phenotyping report.  
  • Participating mouse clinic is the Czech Centre for Phenogenomics (CCP), IMG AS CR v.v.i.
  • Centre specific collaboration agreements will be established between applicants and the mouse clinic. 
  • Starting material for the phenotyping projects is a breeding nucleus and then cohorts are bred by the CCP. Mouse mutants from various sources (transgenes, knockout mice, mutants from mutagenesis screens like ENU) and of different genetic backgrounds can be accepted.
  • The phenotyping pipeline to be used will be a specialised metabolic phenotyping pipeline based on published IMPReSS SOPs (IMPReSS: http://www.mousephenotype.org/impress), or on local mouse clinic SOPs. Details of the CCP metabolic phenotyping pipeline are described below.
  • Support will be provided by the CCP to analyse and interpret the phenotyping data.
  • The analysed mouse models and the generated phenotyping data will be made available to the scientific community. An optional grace period of up to 1 year for mouse resources and phenotype data may apply, with immediate release of mouse resources and data after expiry of the grace period. A phenotyping report with all phenotyping data will be prepared, and data will also be uploaded onto a public phenotype database of the mouse clinics and / or onto the IMPC portal at http://www.mousephenotype.org. Mouse mutant lines will be deposited into the INFRAFRONTIER/EMMA repository for subsequent use by the scientific community, and will be distributed using the applicant’s institutional MTAs.
  • Costs: The access to the INFRAFRONTIER2020 phenotyping service is free of charge. However, the shipment cost of mouse mutant lines to the CCP in Prague must be borne by the applicants.
  • Eligibility: The INFRAFRONTIER2020 Trans-national Access call is open and proposals can be submitted from applicants around the world
  • Application: Requests for the INFRAFRONTIER2020 specialised phenotyping service can be made via an application form. Applications for the Trans-national Access activity must include a short description of the research plans for utilising the phenotyped mouse model that is being characterised by the INFRAFRONTIER2020 TA service.
  • Selection procedure: Proposals from eligible customers for free of charge access to the INFRAFRONTIER2020 specialised phenotyping service will be subject to a review procedure. The review will be based on short descriptions of the projects involving the mouse mutants that will be phenotyped by the TA service. A mixed panel of members of INFRAFRONTIER and of an external Evaluation Committee will assess service requests supported by the TA activity. In addition to scientific merit of applicants, relevance and quality of preliminary data, soundness of the proposal and research plans, and the project objectives and prospects for exploitation of phenotype data will be assessed. In a further step experts of the mouse clinics will assess the technical feasibility of projects. Applicants will be informed on the outcome of the evaluation within 6 weeks after the end of the call for which the TA application was submitted. All applications will be handled with strict confidentiality.
  • Acknowledgements: Please do acknowledge any support under this scheme in all resulting publications with ‘Part of this work has been funded by the European Union Research and Innovation programme Horizon 2020 (Grant Agreement Number 730879)’, and by LM2015040 (Czech Centre for Phenogenomics), CZ.1.05/2.1.00/19.0395, and CZ.105/1.1.00/02.0109 funded by the Ministry of Education, Youth and Sports and the European Regional Development Fund. The participating infrastructure, which provided the service, should be specifically mentioned in any publication resulting from the service.
  • Timeline: Closing of call on 15 April 2019   -   Evaluation process until 15 May 2019.
Specialised phenotyping pipeline

Czech Centre for Phenogenomics (CCP, www.phenogenomics.cz)

In-depth metabolic phenotyping

The CCP can support three projects in this TA call

The Czech Centre for Phenogenomics offers a comprehensive primary phenotyping pipeline in combination with secondary screens based on metabolic challenges established in our laboratories. The challenges focus on global metabolomics approaches with deep profiling of small metabolites. The secondary screens will include mouse cohort preparation, which should contain 10 +10 mutant mice for each sex compared to the same number of wild-type controls.  The experimental cohort will be prepared either by rederivation of imported live animals or from frozen embryos or sperms.

Basic metabolism assessment and metabolomics analysis

We will provide a primary metabolism screen combined with one secondary test based on a metabolic challenge. The primary metabolism pipeline consists of growth curve analysis, IPGTT, comprehensive 48h indirect calorimetry measurement in a PhenoMaster indirect calorimetry system, body composition analysis by in-vivo micro CT, with possibilities to quantify fat tissue deposition (visceral, subcutaneous, brown adipose tissue), clinical biochemistry panel from blood and urine samples and metabolome screen using Q-TOF with following non-targeted metabolomics analysis.

Portfolio of secondary test

The portfolio of secondary tests comprises a diet and liver injury based metabolic challenge including high-calorie diet (e.g. high fat diet), methionine choline-deficient (MCD) diet, or custom-tailored diet, or an intoxication model based on tetrachloride injection, or by diet supplemented with 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). Taking advantage of a climate control system during the indirect calorimetry measurements, we can also include temperature or the circadian rhythm as additional experimental factors.

The experimental animal cohorts will be assessed for clinical biochemistry blood parameters, and by a complete histopathology.