30 Jun PEDIACRIEX CIRCLE, center of excellence in pediatric oncology research, BRIC implications

BRIC Inserm U1312/ Université de Bordeaux teams at the heart of research at PEDIACRIEX CIRCLE, an INCa-certified center of excellence in pediatric oncology research

The French National Cancer Institute (INCa) has just named CIRCLE (Collaboration In between two seas Resistance Cancer Longevity) as the 4th integrated research center of excellence in pediatric oncology, following a call for applications launched in June 2024 (PEDIACRIEX call for projects).

With a total budget of 3 million euros over 5 years, CIRCLE will help to structure pediatric oncology research at the 3 partner sites (Toulouse, Bordeaux and Montpellier) by pooling the expertise of clinicians and researchers around 2 major integrated research programs, with the aim of responding synergistically to the research challenges defined in the new Ten-Year Cancer Strategy (2021-2030).

The CIRCLE center is managed by Prof. Marlène Pasquet (Hematologist and Pediatric Oncologist, Toulouse University Hospital, Inserm, CRCT) and two deputy directors, Prof. Stéphane Ducassou (Hematologist and Pediatric Oncologist, Bordeaux University Hospital, team 11 BRIC) and Prof. Anne Laprie (Radiation Oncologist, Toulouse IUCT-Oncopole and Inserm ToNIC).

CIRCLE – two integrated research programs to which teams from our BRIC unit will contribute.

CIRCLE will enable the deployment of 2 thematic integrated research programs to which 26 research teams from the 3 sites will contribute, covering multiple disciplines and including 3 BRIC teams.

• Team 01 – Tumor and vascular biology laboratory –Lucie BRISSON
• Team 10 –Normal and leukemic hematopoietic stem cells. Amélie GUITART and Jean-max PASQUET
• Team 11 – Cancer and Age -Catherine SAWAI – Stéphane DUCASSOU

These three teams are involved in the first integrated research program coordinated by Dr. Fabienne Meggetto (CRCT, CNRS researcher, Toulouse) and Prof. Nicolas Sirvent (hematologist and pediatric oncologist, Montpellier University Hospital). This program studies autonomous and non-autonomous cell resistance by exploring epigenetic and metabolic reprogramming, as well as the tumor microenvironment. Its aim is to assess how immune and mesenchymal stem cells contribute to treatment resistance. The aim is to develop preclinical models and personalized therapeutic strategies to overcome resistance in hematological and solid tumors in children. Collaboration with pediatric oncology networks will help translate laboratory results into clinical and therapeutic applications.

The program is structured around three workpackages:
WP1. CELL-AUTONOMOUS RESISTANCE
WP2. NON-CELL AUTONOMOUS RESISTANCE
WP3. BRIDGING BIOLOGY TO CLINICAL APPLICATION

Catherine Sawai and BRIC team 11 will be involved in WP1 dedicated to the study of epi-transcriptomic regulation in pediatric acute leukemia and lymphoma.

Epi transcriptomics plays a critical role in cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT). Epi-transcriptomic modifications contribute to treatment resistance through three mechanisms: (i) mRNA modifications; (ii) non-coding RNA modifications; and (iii) post-translational modifications.

More specifically, BRIC team 11 will be in charge of WP1 task 2.1: Function and therapeutic targeting of m6A readers in pediatric AML (acute myeloid leukemia).

Pediatric AML is associated with a worse prognosis than other pediatric hemopathies, with a high relapse rate, underscoring the need to identify new therapeutic targets and/or combination therapies.

RNA methylation, in particular N6-methyladenosine (m6A), is involved in treatment resistance in adult AML, particularly during leukomogenesis… Protein interactions regulating m6A play a key role in the pathophysiology of adult AML. Two reader proteins, IGF2BP2 and IGF2BP3, could be interesting therapeutic targets as they are overexpressed in AML. BRIC Team 11 therefore proposes to explore the role of IGF2BP isoforms in pediatric AML using shRNA KO technologies in cell models and treated patient samples. ex vivo. They will study epigenetic modifications in “IGF2BP-KO” cells cells, global RNA stability and investigate the mechanisms responsible for translation initiation. Finally, the team will investigate the importance of targeting protein interactions regulating m6A methylation in pediatric AML by testing specific IGF2BP inhibitors in vitro and ex vivo.

Amélie Guitart and BRIC team 10 will be involved in WP1 task3: Decoding metabolic resistance in cancer using multi-omics approaches.

Metabolism plays a crucial role in mediating treatment resistance. The researchers involved in this task3 are using next-generation omics approaches to study the mechanisms of treatment-induced metabolic reprogramming in pediatric AML and ependymoma. Their aim is to identify new therapeutic targets capable of overcoming this resistance.

Amélie Guitart and BRIC Team 10 will be in charge of WP1 Task 3.1: Identifying the metabolic features of relapse in pediatric AML.

Among the genetic alterations associated with a poor prognosis in AML are KMT2A (lysine-specific methyltransferase 2A) rearrangements, located on chromosome 11q23, which are observed in 15-20% of pediatric AML cases. A dedicated analysis of NAT8L expression (a single gene encoding the NAA-synthesizing enzyme) in an adult AML cohort from Bordeaux (n= 105), showed a positive correlation between NATL8 expression and unfavorable patient prognosis, as well as an association with KMT2A rearrangements. The team also demonstrated in vivo and ex vivo that the absence of NAA prevents the development of leukemia in 50% of mice. Expression of NAT8L, the only gene responsible for NAA synthesis, therefore correlates with a poor prognosis in adult AML, particularly AML with KMT2A rearrangements. As NAA is produced from acetyl-CoA and aspartate, metabolic adaptations linked to NAA synthesis can significantly affect the Krebs cycle (Tricarboxylic Acid Cycle, TCA), mitochondrial activities and induce epigenetic modifications. To decipher the interaction between epigenetic remodeling and metabolic adaptation, their project proposes to specifically study subpopulations of resistant AML cells in which epigenetic changes have engendered metabolic modifications. They will attempt to (i) elucidate the mechanisms of metabolic dependence of resistant pediatric AML cells, in particular the role of NAA, (ii) determine the impact of treatment-induced metabolic adaptation on epigenetic remodeling in pediatric AML, (iii) specifically target the metabolic and/or epigenetic alterations highlighted in (i) and (ii) (in particular using NATL8 inhibitors identified by HTS and from the team’s previous research).

Jean-Max Pasquet and BRIC team 10 and Lucie Brisson and BRIC team 1 will be involved in WP2, which will be based on the use of pediatric oncology models available in the partner teams to assess the diversity of the tumor microenvironment (TME) in order to elucidate and characterize the functional and molecular interactions between immature microenvironments and tumor progression.

Lucie Brisson and her team will be in charge of WP2 task 3.1: New translational models to study metabolic features in ependymomas and their role in treatment resistance.

Pediatric brain tumors are a heterogeneous group of cancers with different prognoses and therapeutic responses. Among them, pediatric ependymomas constitute a clinically and molecularly distinct group of tumors.

A lipid metabolic signature has been proposed to classify brain cancer types in children, notably ependymomas (Woolman et al., 2024). Lipid absorption, synthesis and storage are often up-regulated, contributing to progression and resistance to treatment. Lipids are highly dynamic, mainly through lipid droplets which are key organelles at the interface between lipid storage and release to maintain lipid homeostasis and plasticity in cancer cells. Interestingly, brain lipid-binding protein (BLPB or FABP7), is a marker of ependymoma stem cells (Taylor et al., 2005), suggesting that lipid dynamics may promote ependymoma progression and resistance.

BRIC Team 1 will aim to understand the role of lipid dynamics (absorption, synthesis and catabolism), in relation to the tumor microenvironment, in ependymoma progression and resistance. To achieve this, they will attempt to modulate lipid uptake, storage and mobilization from lipid droplets in patient-derived cells. They will characterize the effects of these modifications on membrane structure, metabolic plasticity and cell signaling. Metabolic analyses will be carried out in vitro and in vivo to identify the metabolic signatures of ependymoma. They will then evaluate the effect of targeting lipid dynamics on tumor progression alone or in co-treatment with standard therapy, as well as the influence of lipid dynamics on the tumor microenvironment.

This project will provide a better understanding of the role of lipids in ependymoma pathophysiology and their role in treatment resistance.

Jean-Max Pasquet and his team will be in charge of WP2 task 2.1: Role of the bone marrow microenvironment in the progression of pediatric AML.

The specific environment of the bone marrow forming “the hematopoietic niche” favors resistance to therapies, this environment also allows the persistence of LSCs through mechanisms still poorly identified (Medyouf, 2017).

Jean-Max Pasquet’s team, with its expertise in adult AML (Dumas, 2019; Dumas, 2021), will use in vitro and ex vivo models to identify the role of kinases in resistance and persistence mechanisms in AML. The aim will be to uncover the downstream events involved in the persistence or concealment of leukemic stem cells. In line with the signaling pathways characterized, the aim is to assess whether pediatric AML under hematopoietic niche conditions uses these pathways to escape or hide LSCs from therapeutic pressure.

Using pediatric AML cell lines under the specific conditions of the “hematopoietic niche” and 3D culture models (Voxcell platform), the team will use “multi-omics” approaches to analyze molecular responses in the steady state and in the presence of different treatments. The results will lead to in-depth characterization of the transcriptome, which will be completed by characterization of the whole proteome and phosphoproteome. These same approaches can then be used on ex vivo patient samples and on normal hematopoietic progenitors after transduction by lentiviral vectors.

The data from these “multi-omics” analyses, generated in vitro and ex vivo, will make it possible to modify AML cells and/or the microenvironment to study their behavior and response to treatments in vivo, and thus validate the signaling pathways and molecules to be targeted.

All the work carried out by the BRIC teams will be aimed at proposing new therapeutic strategies that can be transferred to the clinic. (WP3, leader Stéphane Ducassou).

Prof. Stéphane Ducassou (équipe 11 BRIC) (team 11 BRIC) will be in charge of WP3: transferring biology to the clinic

Building on the results of WP1 and WP2, the aim of WP3 is to set up innovative preclinical and translational models to explore cell-autonomous and cell-non-autonomous resistance mechanisms. Drawing on CIRCLE’s network of clinical experts, in particular the pediatric oncohaematology department at Bordeaux University Hospital, which has been awarded the ITCC and CLIP2 labels, WP3 aims to transfer translational biology results to the clinic through the implementation of early-phase clinical trial protocols. This WP3 will also benefit from the experiential know-how of partner parents and patient associations, through a “co-construction” approach so that the design of these new clinical trials can be as relevant as possible and have the greatest impact for patients.

More specifically, Prof. Ducassou will be in charge of WP3 task 5: Design and development of early-phase trials in conjunction with CLIP2 and ITCC centers (S Ducassou / R Thiebaut).

Task 5.1. Development of an expert platform for Bayesian adaptive clinical trial design to meet the challenges of low enrolment in early phase clinical trials (EPP) in oncopediatrics

Prof. Ducassou will work with Dr. Eric Frison (USMR, Bordeaux University Hospital) to propose trial designs that meet the statistical, methodological and organizational challenges encountered when implementing EPP, in particular the small numbers involved. These Bayesian designs must be capable of (i) integrate pre-existing adult data; (ii) combine drug safety, efficacy and biological data (iii) take into account the specificities of evaluating treatment combinations, administration schedules and delayed toxicities.

Task 5.2. Development of early-phase trials in conjunction with CLIP2 and ITCC centers

The dual accreditation of Pr Ducassou’s department at Bordeaux University Hospital as a CLIP2 (INCa) and ITCC (Europe) center will be crucial to the CIRCLE project. These labels will enable it to apply for INCa’s CLIP2 calls for projects alongside BRIC translational research teams. One of the aims of WP3 is to propose new translational biology approaches enabling in-depth exploration of the underlying biological mechanisms in pediatric cancers. CIRCLE researchers will have access to new molecules, which will generate new biological data based on the know-how of our research teams, enabling them to be transferred more rapidly to the clinic.

To carry out this work, the Inserm BRIC teams will receive funding of €440k over 5 years to support research staff within their teams, cover their operating costs (purchase of consumables) and purchase shared equipment (hypoxia hood).