Accelerating research through access to technology platforms - - PowerPoint PPT Presentation

1 | C2RT/C2RA – RIIP-America – July 3, 2019

Meeting of the Institut Pasteur International Network American Region – July 3, 2019

Accelerating research through access to technology platforms

2 | C2RT/C2RA – RIIP-America – July 3, 2019

Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. Sidney Brenner

3 | C2RT/C2RA – RIIP-America – July 3, 2019

Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. Sidney Brenner

Core Facilities

4 | C2RT/C2RA – RIIP-America – July 3, 2019

Outline

• Organization of the core facilities and technology offer at

Institut Pasteur, Paris

• How to improve technology networking within the Institut

Pasteur International Network?

5 | C2RT/C2RA – RIIP-America – July 3, 2019

Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. Sidney Brenner

Core Facilities

Center for Technological Resources and Research (C2RT) Center for Animal Resources and Research (C2RA) Units for Technology and Services (4) Technology Platforms (13 + 2)

6 | C2RT/C2RA – RIIP-America – July 3, 2019

Missions of the C2RT and C2RA

Resources

• Structuration and organization of the

facilities, upgrade of instruments

• Advanced technology and animal

resources for biological research

• Services at the highest level (speed and

quality)

• User input and satisfaction
• Proper recognition of personnel in

facilities

Research

• Next generation of equipment and

methods

• Interactions with institutes of technology,

engineering schools, and industry partners

• Collaborations between research units and

facilities

• Technology watch
• Support of innovation

Dissemination

• Training in technologies
• High level network of infrastructures and core facilities within the IPIN and beyond

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The C2RT and C2RA

Center for Technological Resources and Research (C. d’Enfert/A. Kehres) Center for Animal Resources and Research (C. Joubert) 209 employees (90% IP) 14 Scientists 79 Engineers 56 Technicians 23 Zootechnicians 6 Postdocs 5 PhD students 11 Trainees 8 Cadres administratifs 7 Assistants PAD (A. Kehres)

8 | C2RT/C2RA – RIIP-America – July 3, 2019

Structures of the C2RT and C2RA

Center for Technological Resources and Research (C. d’Enfert/A. Kehres) Center for Animal Resources and Research (C. Joubert) PAD (A. Kehres)

Genomics Proteomics Flow cytometry Multiscale imaging (light – cryo) Nanobody discovery Protein production Molecular Biophysics and Structural Biology Screening Microfluidics and organ-on-chips Animal research Genome engineering Parasite production

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Recent technology advances at the C2RT and C2RA

• Long-read sequencing (PacBio, Nanopore)
• Light-sheet imaging
• High-content screening
• Correlated light and eletron microscopy (CLEM) pipelines
• Cryo-EM
• MaMuT: handling of large, multi-view, multi-modality images
• Sorting of nanoparticles
• Experimentation under hypoxia
• Single cell pipelines
• Automation and miniaturization (Ab identification and protein

production)

• Quality assesment and optimization of protein samples
• Analytical centrifugation
• Organ-on-chip
• Germ-free and gnbotobiotic mice (oligo-MM12)
• Mouse/rat models using CRISPR-cas9 technology
• Anopheles mass production

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High-throughput sequencing: Increasing autonomous access

Shared room (Biomics / IP users) Trained user 47 (24 in 2019) 243 (28 in 2019) Utilization (hours)

*estimation based on sequencing runs

100 200 300 400 500 600 700 800 900 janv-19 févr-19 mars-19 avr-19 mai-19 juin-19

Biomics IP users

Users Benefits

• Free training (MOOCs + IRL)
• Simple booking (PPMS)
• Per-use invoicing
• Project accelerator

Biomics Benefits

• Contributes to the maintenance contracts
• Reduces workload

a. 62 projects in autonomy in 2019*

• Response to criticism on the process duration
• Saves time on complex projects

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Exploring biology at different resolutions

Atoms Proteins

100 µm 10 µm 10 nm 1 nm 1Å

Structure size

100 nm 1 µm 1 mm

Viruses Cells

Single Particle cryo-TEM Cryo-electron tomography NMR Light Microscopy X-ray crystallography (XRD) Super Res

RESOLUTION CONTEXT

Mass-spec

Small molecules Tissue

Fluorescence Microscopy

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The time for « single particles » is now

Massive, highly symmetric huge, highly symmetric Large, asymmetric Intermediate, symmetric small, low symmetric helical

90’s 10’s

Cryo-EM maturation

52kD 3.2Å

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Understanding function inside native environment

native COPI coat structure

Images and Movie from Bykov et al., eLife 2017

Subtomogram Averaging

SPA Dock Into Cell

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A building dedicated to cryo-EM

Titan Krios G3 Aquilos Vitrobot Glacios

High resolution imaging of single particles Sample screening/Training

HR SC

Sample preparation for cellular imaging Sample preparation for imaging

• f single particles

Cellular imaging and high resolution imaging

• f single particles
• Acquisition of 4 cryo-electron

microscopes including Titan Krios allowing single particle imaging and cell tomography

• A dedicated building
• Hiring of two PIs (D. Hanein, N.

Volkmann) and creation of a dedicated core facility

• An investment budget of ~15 M€

financed by Institut Pasteur, the Investment for the future Program (Equipex Cacsice) and public generosity

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The Biomaterials & Microfluidics core facility

Organ-on-Chip Technology

emulate™ Gut-on-Chip

• 2. Custom Chips
• 1. Microfabrication

Gentile et al. 2014

Bioengineering Services

• 4. HTS/ 3D cell culture

Ranga et al. 2014

• 3. Cell confinement

Yennek et al. 2014

…

Future Services / Developments

1.Organoids

• 2. Disease-on-Chip

MeningoChip

• 3. Complex Patterning

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Strategic plan 2019-2023: Provide a favorable technological environment

• Expand our nanoimaging initiative by acquiring additional electron microscopes to optimize our

use of the Titan KriosTM for atomic resolution in vitro or in cellulo protein imaging.

• Develop optical imaging methods for the multi-scale study of host-pathogen

interactions: light sheet fluorescence microscopy, planar/cross-sectional imaging microscopy, magnetic

resonance imaging, super-resolution microscopy, etc.

• Optimize our crystallography, nuclear magnetic resonance (NMR), hydrogen exchange mass spectrometry and

biophysics facilities to strengthen our expertise in structural biology.

• Set up a metabolomics platform and/ or research unit to provide a shared infrastructure and

pool our expertise in sample preparation and analysis using mass spectrometry and NMR.

• Develop new single-cell analysis pipelines for transcriptomes, proteomes, metabolomes and
• ther components of the host and microbes.
• Establish a new infrastructure for simultaneous analysis of the host, the vector and

the pathogen under biosafety level 3 containment conditions (animal facility, insectarium, imaging

capabilities).

• Boost our ability to identify novel diagnostic and therapeutic solutions: high-content

imaging, organ-on-a-chip, microfluidics, miniaturization, point-of-care testing, etc.

• Develop high-throughput approaches for antibody identification and production.

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Developments for 2020

• Creation of a metabolomics core facility
• Creation of a humanized mice core facility
• Reinforcement of our screening capabilities

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Scientific animation and contribution to training

• Open Desks (PBI/HAI; Protein-pole)
• User training (MOOCs)
• Technology Seminars
• Technology Workshops
• Pasteur Courses
• Advanced Imunology, Genome analysis,

Protein biochemistry, Mouse Genetics, Fluorescence microscopy,…

• Pasteur network
• Licence, Master,…
• Continuous education
• Host facility for European Core Facility

Management University Diploma

• CTLS workshops: Building a succesful

carreer in a Core Facility

19 | C2RT/C2RA – RIIP-America – July 3, 2019

Outline

• Organization of the core facilities and technology offer at

Institut Pasteur, Paris

• How to improve technology networking within the Institut

Pasteur International Network?

20 | C2RT/C2RA – RIIP-America – July 3, 2019

The situation

• Access to technology has become an essential component of research programs,

supporting the identification and development of novel diagnostic and therapeutic approaches

• Technology networking is poorly organized within the IPIN
• Occasional use of IPP technology platforms by teams of the IPIN (and vice-versa),

influenced by the nature of the technology, impact of the legislation

• Promoted in the frame of Transversal research projects (PTR) or other

collaborative projects

• Some teaching actions: Transgenic Technologies in Modeling Human Diseases:

Principles, Associated Technologies, Animal Management and Ethics – IP Athens; Quantitative Immunology course – IP HongKong

• Needs are varied: access to technology (provided financial support), technology

benchmarking, training, support for implementation, ad hoc technology development…

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An Institut Pasteur Technology Network?

• Based on the example of Alliances for the development of Core Facilities: Core

Technologies for Life Sciences (CTLS); Core for Life (C4L)

• Actions
• Communicate on the IPIN technology offer
• Promote the involvement of core facilities in externally-funded grant applications
• Share good practices for running Core facilities (steering committees, charter,

pricing, HR)

• Support to the establishment of new core facilities
• Share methods
• Provide technology training: theoritical and practical courses, short-term visits
• Help with technology benchmarking
• Promote interactions with technology providers