Czech Centre for Phenogenomics
01 2021

Dear Colleagues,

Time is precious! We all know what this means. To help you use your time more efficiently, we have chosen a new format for the CCP Phenogenomics Newsletter. Today, we are happy to announce the first issue of the CCP Phenogenomics eNewsletter. We are delighted to share our recent achievements and updates on mouse phenogenomics, so from now on, the latest developments at CCP will be directly delivered to you via e-mail, with a dedicated website and interesting links for further reading.
As we are rapidly approaching the Festive Season and the end of the year 2021, we will take a look back at the past year in this eNewsletter and also give you some outlooks for 2022, in which we will hopefully soon see the Covid-19 pandemic subsiding.
We hope you will find exciting content in this newsletter. Please also check our other information channels (e.g. and follow our Twitter account @CZphenogenomics.
Enjoy reading!
Radislav Sedlacek and the CCP team

Conferences in 2021

IMPC Conference and workshops

In 2021, the celebration of the 10th anniversary of IMPC was the focus for many activities. Unfortunately, the Covid-19 pandemic made it impossible to meet in person and celebrate this highlight. Therefore, a virtual conference was held in September to bring together all members of IMPC, invited guests, and many interesting people from all over the world to highlight the achievements of IMPC, but also to discuss the activities and necessary developments in the coming years.
In addition to the virtual conference, a series of workshops are being held in 2021 and 2022 for the IMPC 10yr Anniversary, organized by the IMPC working groups to further promote the goals of IMPC. Two workshops have already taken place (IMPC ‘Beyond the Borders” and ‘Exploring the benefit of mammalian lethal genes’). The 3rd workshop will be held on 28th February 2022 entitled ‘IMPC mouse models' contribution to current advances in metabolic and cardiac research’. This workshop will be chaired by Nadine Spielman (Munich, Germany) and Jan Rozman (Prague, Czech Republic) and the Cardiovascular and Metabolism Working Group of the IMPC.

CCP Phenogenomics Conference

In 2021, the CCP Phenogenomics Conference went virtual again. More than 199 participants attended the conference that focused on immunology & infection, disease models, neurosciences, and preclinical developments. The keynote lecturers attracted great interest. We are grateful to Jakub Abramson (Weizmann Institute of Science, Israel), Steve Brown (MRC Harwell Institute, United Kingdom), and Yann Herault (IGBMC, France). The virtual platform allowed lively discussions during the talks, and also the exchanging of participant’s opinions during the poster session, as they would during coffee breaks when meeting in person.
Information about the past event

Improving the robustness of experimental mouse models for human disease

PREMOS and COST Action TEATIME - new networks in behaviour and neuroscience

“PREMOS” is the acronym for the European Brain Research Area Cluster "Predictive Model Systems ". The main goal of PREMOS is to align EU resources for disease model development and expertise in preclinical research with the needs of the clinical and brain research community in academia and industry. PREMOS consists of several large networks and EU-funded consortia that joined forces to advance disease modelling capacity and expertise for neuroscience research. The goals are: improvement of communication, define common research priorities, improve resource and data sharing using European research infrastructures, improve data integration between high-dimensional clinical and modelling data, prioritize predictive preclinical rodent models, harmonize and standardize research protocols, expand networks of disease modelling experts across model systems including in vivo, in vitro, and in silico approaches. CCP is proud to be a partner in PREMOS.
In late October 2021, the new COST Action TEATIME started its activities regarding “Improving biomedical research by automated behaviour monitoring in the animal home-cage”.
This Action aims to team up with European organizations using and developing automated home-cage monitoring (HCM) technologies. TEATIME will develop user guidelines and standard operating procedures and identify needs for further technological development, including analysis of big data. The Action will organize workshops, laboratory rotations to disseminate expertise within and outside the consortium.
TEATIME Working group 3 dealing with the “Development of new technologies, analysis tools and databases” is chaired by James Brown (University of Lincoln, UK) and CCP deputy director Jan Rozman. The deliverables of WG 3 comprise the production of a roadmap for innovations in data analysis, data curation and ontologies existing omics repositories to enable the development of an HCM data repository, identify key researchers in machine learning and neural networks who have an interest in HCM and organise interdisciplinary meetings to determine how to work together, report on the progress of participants sharing software and bioinformatics tools to analyse the output of HCM.

Quality management
Improving reproducibility and repeatability in preclinical research is a critically discussed and highly relevant topic, especially when it comes to ethical considerations in animal research. As a joint outcome of the INFRAFRONTIER Quality Management Group discussions, a paper was recently published in Mammalian Genome addressing internal quality principles in systemic phenotyping of genetically modified mouse models within INFRAFRONTIER. The paper lists and discusses eleven key principles, including general requirements for compliance with existing animal testing guidelines, the need for well-trained personnel, and specific standards such as reference line exchange. The publication provides the specific context, requirements, further recommendations, and key references for each quality principle.

CCP publication highlights in 2021

2021 has been extremely successful regarding publication output either with the involvement of CCP members or with a CCP researcher as the first author. A full list of publications is available on our website. Nonetheless, we would like to briefly introduce three outstanding publications from the expiring year 2021.
Bispecific IgG neutralizes SARS-CoV-2 variants and prevents escape in mice. Nature 2021 Mar 25. De Gasparo R, Pedotti M, Simonelli L, Nickl P, Muecksch F, Cassaniti I, Percivalle E, Lorenzi JCC, Mazzola F, Magrì D, Michalcikova T, Haviernik J, Honig V, Mrazkova B, Polakova N, Fortova A, Tureckova J, Iatsiuk V, Di Girolamo S, Palus M, Zudova D, Bednar P, Bukova I, Bianchini F, Mehn D, Nencka R, Strakova P, Pavlis O, Rozman J, Gioria S, Sammartino JC, Giardina F, Gaiarsa S, Pan-Hammarström Q, Barnes CO, Bjorkman PJ, Calzolai L, Piralla A, Baldanti F, Nussenzweig MC, Bieniasz PD, Hatziioannou T, Prochazka J, Sedlacek R, Robbiani DF, Ruzek D, Varani L
Cytoplasmic polyadenylation by TENT5A is required for proper bone formation.
Cell Rep 2021 35(3): 109015. doi: : 10.1016/j.celrep.2021.109015. Gewartowska O, Aranaz-Novaliches G, Krawczyk PS, Mroczek S, Kusio-Kobiałka M, Tarkowski B, Spoutil F, Benada O, Kofroňová O, Szwedziak P, Cysewski D, Gruchota J, Szpila M, Chlebowski A, Sedlacek R, Prochazka J, Dziembowski A
Expression of human-specific ARHGAP11B in mice leads to neocortex expansion and increased memory flexibility. EMBO J 2021, e107093. [pubmed] [doi]. Xing L, Kubik-Zahorodna A, Namba T, Pinson A, Florio M, Prochazka J, Sarov M, Sedlacek R, Huttner WB.

CCP interacting with users and collaborators

Service User Advisory Committee Managing user expectations is an important project management tool. For this reason, CCP has established a Service User Advisory Committee (SUAC) representing current and potential users of CCP services. The tasks of the SUAC are: advice on service organization, user needs assessment, implementation and evaluation of services.
The SUAC is also involved in discussions about instrumentation and new technologies that may be useful for the user community. The CCP is very much looking forward to collaborating with the SUAC and appreciates the willingness of SUAC members to help improve and develop the CCP portfolio.
Composion of SUAC
CCP Customer Satisfaction Survey
CCP is currently restructuring the user and project management system. Part of the new concept is an online satisfaction survey that is automatically sent as a part of the final report. CCP is seeking feedback, both positive and negative, from our users and collaborators. The feedback will be analyzed and used to improve the management system, phenotyping services, data processing/reporting and other customer services. We promise it will take only a few minutes to answer these questions!
Four simple questions will address your experiences: 1) overall satisfaction with the service; 2) turnaround time for testing; 3) interaction with staff, understanding the report, etc.; 4) our services’ value for money.
A few additional questions are optional and refer to the interactions between CCP and users, as well as general user expectations.

News from the Phenotyping Module

New devices in the Energy Metabolism Lab

Time Domain (TD)-NMR (or qNMR) for body composition analysis in mice and rats. qNMR is non-invasive, does not require anesthesia, and is quick (2-3 min per mouse/rat). Fat and lean mass as well as free liquids can be determined. We established three calibration models: I. mice 5 to 60 g, II. obese mice or small rats 40 to 150 g, and III. rats 40 to 700 g.
qNMR is suitable for longitudinal studies (HF diet, or other treatments), and stands out due to easy data handling and work safety (shielded magnet, no X-ray, no inhalation anesthetic). The method generates high precision data in high-throughput, and improves animal welfare.
CCP is using qNMR body composition analysis in first-line phenotyping as well as customized metabolic studies in mice and rats.

CCP evaluated in the International peer-review of large research infrastructures in the Czech Republic in 2021

In the first half of 2021, the Czech Ministry of Education, Youth and Sports organized an international peer-review of large research infrastructures in the Czech Republic, the results were published in December. According to the evaluation board, CCP represents a unique research infrastructure in terms of expertise in the generation of gene/genome engineered rodent models.

Outlook for 2022

4th CCP Phenogenomics Conference

After the great success of the previous CCP conferences, a CCP Phenogenomics conference will of course be held again next year. Keep your calendar free on September 15 and 16 for the 4th Phenogenomics Conference with the main topic "Rare Diseases - experimental model systems and delivery of therapies". More information will follow early in the new year.
We have reached the end of the first CCP eNewsletter. We would like to conclude by wishing you all a peaceful and relaxing holiday season and all the best, joy and, of course, health for the New Year 2022.
Czech Centre for Phenogenomics
Institute of Molecular Genetics of the
Czech Academy of Sciences
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