EUROPEAN REGIMEN ACCELERATOR FOR TUBERCULOSIS

Livrables

Second report on discovery and validation of predictive TB biomarkers

Update of the report will describe the results obtained by the various efforts to identify and/or validate predictive TB biomarkers.

First study subject approvals package for molecule TBAJ587

Includes final version of study protocol as approved by first regulatorethics committees registration number of clinical study in a WHO or ICMJE approved registry and the approvals required for the enrolment of first subject in at least one clinical centre according to EU and national legislation Study protocol will be developed by SERMAS in collaboration with CTUs and EFPIA partners according to ICHE6R2 Guideline For Good Clinical Practice Scheduled CDGO plus 11 months

First report on molecular signatures of anti-TB drug treatment efficacy in the three animal models

This report will describe molecular signature data obtained during antiTB treatment in selected mouse and NHP models Updates M48 M72

Initial report on recommendations for design, dosing and sampling schedule for selected experimental protocols in WPs 2, 3 and 4.

An overview of potential limitations will be presented along with the agreed recommendations for optimisation of experimental protocols Update M36

Second Report on clinical and preclinical datasets standardized and integrated into the DDIM

Second report on the quantity and status of datasets integrated into the DSP This report will also serve to provide best practices and lessons learned to drive continuous improvement in the data collaboration processes

Third Report on clinical and preclinical datasets standardized and integrated into the DDIM

Third report on the quantity and status of datasets integrated into the DSP. This report will also serve to provide best practices and lessons learned to drive continuous improvement in the data collaboration processes.

First Report on implementation of selected mouse models for in vivo evaluation of drug candidates

This report will describe the different mouse models that were established optimized in the partners institutions for the in vivo evaluation of new antiTB compounds Updates M24 M48

Second report on implementation of selected mouse models for in vivo evaluation of drug candidates

This report will describe the different mouse models that were established optimized in the partners institutions for the in vivo evaluation of new antiTB compounds

Project communication plan and initial toolset

A plan for dissemination that includes the communication objectives, target audiences, activities to be carried out and tools that will support their implementation, with connections among these components. It will also include an initial set of communication materials.

Initial standardized templates for collection and reporting of clinical and preclinical data available to consortium members

Initial data collection templates for use by Consortium members for the collection and integration of data. Templates will be generated as soon as possible based on input from Consortium members, and early reviews of the data generated within the Consortium. Data collection templates will evolve throughout the project based on knowledge and experience gained. (Updated M16)

First study subject approvals package

Includes final version of study protocol as approved by first regulator/ethics committee(s), registration number of clinical study in a WHO- or ICMJE- approved registry and the approvals required for the enrolment of first subject in at least one clinical centre according to EU and national legislation. Study protocol will be developed by SERMAS in collaboration with CTUs and EFPIA partners according to ICH-E6(R2) “Guideline For Good Clinical Practice”. Due date will relate to the Commit Decision to GO (CDGO) for each FTIH trial plus 4 months.

Standardized templates for collection and reporting of clinical and preclinical data available to consortium members -interim report

Data collection templates for use by Consortium members for the collection and integration of data

Third report on implementation of selected mouse models for in vivo evaluation of drug candidates

This report will describe the different mouse models that were established / optimized in the partner’s institutions for the in vivo evaluation of new anti-TB compounds.

First Report on clinical and preclinical datasets standardized and integrated into the DDIM

First of a series of periodic report on the quantity and status of datasets integrated into the DSP This report will also serve to provide best practices and lessons learned to drive continuous improvement in the data collaboration processes

First Report on discovery and validation of predictive TB biomarkers

This report will describe the results obtained by the various efforts to identify andor validate predictive TB biomarkers Updates M48 M72

Final report on recommendations for design, dosing and sampling schedule for selected experimental protocols in WPs 2, 3 and 4.

An overview of potential limitations will be presented along with the agreed recommendations for optimisation of experimental protocols.

Report on instantiation of EU-based Drug Development Information Management (DDIM) system

An initial report to provide early status on the deployment of the DDIM and the underlying clinical and preclinical data management systems, image store and common user interface.

Initial molecular imaging systems, procedures and protocols to perform quantitative, dynamic PET/CT and NIR imaging studies in BSL3 conditions in mouse models

Initial report on the molecular imaging systems procedures and protocols to perform quantitative dynamic PETCT and NIR imaging studies in BSL3 conditions in mouse models Updated M70

Project Handbook

Quick reference manual for partners to consult management procedures, including relevant provisions of the GA/CA in an easy to understand language. It will also explain the tools set up to facilitate collaborative work across the Consortium.

Development and optimization of NHP models for TB drug efficacy evaluation

Report on the efforts made to develop and optimize the marmoset and macaque models for evaluating treatment efficacy of new anti-TB compounds under conditions that closer resemble the situation in humans than murine models.

Implementation of HFS-TB in a BSL3 setting in Europe

HFS-TB implementation at UNIZAR to meets industry-level standards for data quality, experimental design and integrity, throughput, analysis, and reporting.

Platform for supervised and automatic image analysis

Imaging platform to define and quantify translational biomarkers from in vivo PET/CT molecular imaging across species (mouse, NHP and human)

Initial molecular imaging systems, procedures and protocols to perform quantitative, dynamic PET/CT studies in BSL3 conditions in NHP models

Initial molecular imaging systems procedures and protocols to perform quantitative dynamic PETCT studies in BSL3 conditions in NHP models Updated M70

Efficient pipeline and logistic resources to image infected tissue

Demonstration of the use of MALDI-MS imaging technologies and means for sharing the samples with no BSL3 SI services constrains to image infected tissues within the pipeline context.

Availability of existing preclinical and clinical TB datasets -interim report

Negotiations with the owners of legacy clinical and preclinical datasets generated prior to the existence of the ERA4TB Consortium or in parallel will be conducted and if permitted will be made available to consortium members This may occur prior to the full implementation of the DDIM so alternative means for dissemination of this data may be used eg via existing data platforms or temporary databases

Publications

The contribution of microfluidics to the fight against tuberculosis

Auteurs: Marina Cañadas-Ortega, Clara Gómez-Cruz, Juan José Vaquero, Arrate Muñoz-Barrutia
Publié dans: Nanotechnology Reviews, Numéro 11, 2022, Page(s) 40-54, ISSN 2191-9097
Éditeur: Walter de Gruyter GmbH
DOI: 10.1515/ntrev-2022-0004

Computer-Aided diagnostic for classifying Chest X-Ray Images Using Deep Ensemble Learning.

Auteurs: Lara Visuña, Dandi Yang, Javier Garcia-Blas and Jesus Carretero
Publié dans: BMC medical imaging, 2022, Page(s) 22, 178., ISSN 1471-2342
Éditeur: BioMed Central
DOI: 10.1186/s12880-022-00904-4

Uptake-independent killing of macrophages by M. tuberculosis aggregates is ESX-1 and PDIM-dependent

Auteurs: Chiara Toniolo, Neeraj Dhar, John D McKinney
Publié dans: EMBO Journal, 2023, ISSN 0261-4189
Éditeur: Nature Publishing Group
DOI: 10.1101/2023.01.11.523669

Breaching the phagosome, the case of the tuberculosis agent

Auteurs: Roxane Simeone, Fadel Sayes, Emeline Lawarée, Roland Brosch
Publié dans: Cellular Microbiology, Numéro 23, 2023, ISSN 1462-5814
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/cmi.13344

In silico designing of vaccine candidate against Clostridium difficile

Auteurs: S. Basak, D. Deb, U. Narsaria, T. Kar, F. Castiglione, I. Sanyal, P. D. Bade, A. P. Srivastava
Publié dans: Scientific Reports, Numéro 11, 2021, Page(s) 14215, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-93305-6

RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness

Auteurs: Griego A, Douché T, Gianetto QG, Matondo M, Manina G.
Publié dans: iScience, 2022, Page(s) Vol. 25Numéro 5, ISSN 1097-4172
Éditeur: Cell Press
DOI: 10.1016/j.isci.2022.104233

Detection and analysis of COVID-19 in medical images using deep learning techniques

Auteurs: Dandi Yang, Cristhian Martinez, Lara Visuña, Hardev Khandhar, Chintan Bhatt, Jesus Carretero
Publié dans: Scientific Reports, Numéro 11/1, 2021, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-99015-3

Implementing best practises on data generation and reporting of Mycobacterium tuberculosis time kill assays: a case study of standardized protocol within the ERA4TB consortium

Auteurs: Rob C van Wijk, Ainhoa Lucía, Pavan Kumar Sudhakar, Lindsay Sonnenkalb, Cyril Gaudin, Eik Hoffmann, Bérénice Dremierre, Diana Angélica Aguilar-Ayala, Michael Dal Molin, Jan Rybniker, Stefano de Giorgi, Laura Cioetto-Mazzabò, Greta Segafreddo, Riccardo Manganelli, Giulia Degiacomi, Deborah Recchia, Maria Rosalia Pasca, Ulrika S H Simonsson, Santiago Ramón-García
Publié dans: Nature Communications, Numéro 11, 2023, Page(s) Volume 26, Numéro 4, 21 April 2023, 106411, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1016/j.isci.2023.106411

Tolerance and Persistence to Drugs: A Main Challenge in the Fight Against Mycobacterium tuberculosis

Auteurs: Francesca Boldrin, Roberta Provvedi, Laura Cioetto Mazzabò, Greta Segafreddo, Riccardo Manganelli
Publié dans: Frontiers in Microbiology, Numéro 11, 2020, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2020.01924

A candidate multi-epitope vaccine against SARS-CoV-2

Auteurs: Tamalika Kar, Utkarsh Narsaria, Srijita Basak, Debashrito Deb, Filippo Castiglione, David M. Mueller, Anurag P. Srivastava
Publié dans: Scientific Reports, Numéro 10/1, 2020, Page(s) 10895, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-67749-1

From Infection to Immunity: Understanding the Response to SARS-CoV2 Through In-Silico Modeling

Auteurs: F. Castiglione, D. Deb, A.P. Srivastava, P. Lio`, A. Liso
Publié dans: Frontiers in Immunology, Numéro 12, 2021, Page(s) 3433-3449, ISSN 1664-3224
Éditeur: Frontiers
DOI: 10.3389/fimmu.2021.646972

Mechanopathology of biofilm-like Mycobacterium tuberculosis cords

Auteurs: Richa Mishra, Melanie Hannebelle, Vishal P. Patil, Anaëlle Dubois, Cristina Garcia-Mouton, Gabriela M. Kirsch, Maxime Jan, Kunal Sharma, Nicolas Guex, Jessica Sordet-Dessimoz, Jesus Perez-Gil, Manu Prakash, Graham W. Knott, Neeraj Dhar, John D. McKinney, Vivek V. Thacker
Publié dans: Cell, Numéro 186, 2023, Page(s) 5135-5150.e28, ISSN 0092-8674
Éditeur: Cell Press
DOI: 10.1016/j.cell.2023.09.016

Difference in persistent tuberculosis bacteria between in vitro and sputum from patients: implications for translational predictions

Auteurs: Alan Faraj, Oskar Clewe, Robin J. Svensson, Galina V. Mukamolova, Michael R. Barer, Ulrika S. H. Simonsson
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-72472-y

Academia and industry agreement on a feasibility tool for first‐time‐in‐human clinical trial units

Auteurs: Paloma Moraga, Paula Prieto, Almari Conradie, Majda Benhayoun, Vicki Rousell, Maria Davy, Uwe Fuhr, Rosa Antonijoan Arbos, Francisco Abad‐Santos, Antonio Portolés, Jolanda Van Duinen, Antonio J. Carcas, Alberto M. Borobia, null null
Publié dans: Clinical and Translational Science, Numéro 16, 2024, Page(s) 2421-2428, ISSN 1752-8054
Éditeur: Wiley-Blackwell
DOI: 10.1111/cts.13655

Microfluidic dose-response platform to track the dynamics of drug response in single mycobacterial cells

Auteurs: Mistretta M, Gangneux N, Manina G.
Publié dans: Scientific Reports, 2022, Page(s) 19578 (2022), ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-24175-9

RHBDL4-triggered downregulation of COPII adaptor protein TMED7 suppresses TLR4-mediated inflammatory signaling

Auteurs: Julia D. Knopf, Susanne S. Steigleder, Friederike Korn, Nathalie Kühnle, Marina Badenes, Marina Tauber, Sebastian J. Theobald, Jan Rybniker, Colin Adrain, Marius K. Lemberg
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-45615-2

Genomic and phenotypic characterization of <i>Mycobacterium tuberculosis’</i> closest-related non-tuberculous mycobacteria

Auteurs: Camille Sous, Wafa Frigui, Alexandre Pawlik, Fadel Sayes, Laurence Ma, Thomas Cokelaer, Roland Brosch
Publié dans: Microbiology Spectrum, Numéro 12, 2024, ISSN 2165-0497
Éditeur: ASM Press
DOI: 10.1128/spectrum.04126-23

Incidence and risk factors for HIV-tuberculosis coinfection in the Cologne–Bonn region: a retrospective cohort study

Auteurs: Isabelle Suárez, Dominic Rauschning, Cora Schüller, Anna Hagemeier, Melanie Stecher, Clara Lehmann, Philipp Schommers, Stefan Schlabe, Jörg-Janne Vehreschild, Carolin Koll, Carolynne Schwarze-Zander, Jan-Christian Wasmuth, Angela Klingmüller, Jürgen Kurt Rockstroh, Gerd Fätkenheuer, Christoph Boesecke, Jan Rybniker
Publié dans: Infection, Numéro 52, 2024, Page(s) 1439-1448, ISSN 0300-8126
Éditeur: Urban und Vogel Medien und Medizin Verlagsgesellschaft mbH
DOI: 10.1007/s15010-024-02215-y

Evaluation of critical parameters in the hollow‐fibre system for tuberculosis: A case study of moxifloxacin

Auteurs: Diana A. Aguilar‐Ayala, Fernando Sanz‐García, Marie Sylvianne Rabodoarivelo, Budi O. Susanto, Rebeca Bailo, Maxime R. Eveque‐Mourroux, Nicolas Willand, Ulrika S. H. Simonsson, Santiago Ramón‐García, Ainhoa Lucía, null null
Publié dans: British Journal of Clinical Pharmacology, Numéro 90, 2024, Page(s) 1711-1727, ISSN 0306-5251
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/bcp.16068

Development of an Inverted Epifluorescence Microscope for Long-Term Monitoring of Bacteria in Multiplexed Microfluidic Devices

Auteurs: Amaro Torres-Simón, María Henar Marino, Clara Gómez-Cruz, Marina Cañadas, Miguel Marco, Jorge Ripoll, Juan José Vaquero, Arrate Muñoz-Barrutia
Publié dans: Sensors, Numéro 20/15, 2020, Page(s) 4140, ISSN 1424-8220
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/s20154140

The Role of Diagnostic Microdevices in the Fight Against Tuberculosis

Auteurs: Marina Cañadas-Ortega, Clara Gómez-Cruz, Juan José Vaquero & Arrate Muñoz-Barrutia
Publié dans: Springer nature, Numéro Integrated Science ((IS,volume 11)), 2023
Éditeur: Springer nature

Effects of Parallel and Distributed Learning on CNN Performance for Lung Disease Classification

Auteurs: Lara Visuña, Javier Garcia-Blas, Jesus Carretero
Publié dans: Lecture Notes in Networks and Systems, Proceedings of the Second International Conference on Advances in Computing Research (ACR’24), 2024, Page(s) 195-205
Éditeur: Springer Nature Switzerland
DOI: 10.1007/978-3-031-56950-0_17

Translational Lung Imaging Analysis Through Disentangled Representations

Auteurs: Pedro M. Gordaliza, Juan José Vaquero, Arrate Muñoz-Barrutia
Publié dans: arXiv, 2022, ISSN 2331-8422
Éditeur: ArXiV
DOI: 10.48550/arxiv.2203.01668

The AMR Accelerator: from individual organizations to efficient antibiotic development partnerships

Auteurs: Josepine Fernow, Marie Olliver, William Couet, Sophie Lagrange, Meindert H. Lamers, Ole F. Olesen, Kristina Orrling, Michel Pieren, Derek J. Sloan, Juan José Vaquero, Timothy J. Miles, Anders Karlén
Publié dans: Nature Reviews Drug Discovery, Numéro 24, 2025, Page(s) 1-2, ISSN 1474-1776
Éditeur: Nature Publishing Group
DOI: 10.1038/d41573-024-00138-9

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