After almost a year break, we restart our traditional IECB Friday Seminars, now via Zoom.

Join us every Friday (sometimes other days) at 11am on zoom broadcast.

Friday, May 28

11 am

Dr. Julien Gronnier

Center for Plant Molecular Biology (ZMBP), University of Tübingen

Nanoscale regulation of cell-surface receptor signaling

Cell surface receptors survey and relay information to ensure the development and survival of multicellular organisms. In plants, receptor kinases and receptor proteins are the main ligand-binding cell-surface receptors perceiving self, non-self, and modified-self molecules. While over the past decades tremendous efforts led to a detailed understanding of the genetic- and structural-bases underlying ligand-induced formation of receptors complexes for archetypical signaling pathways, their spatial and temporal regulation remains obscure. Taking perception of bacterial flagellin by the immune receptor kinase FLS2 and it’s co-receptor BAK1 as model system we investigate how is cell surface signaling orchestrated. We show that the co-receptor BAK1 is recruited “on demand” into pre-formed FLS2 membrane nanodomains to form signaling active nano-platforms. We unveil that formation of FLS2-BAK1 nanoscale assemblies is regulated by a tri-partite receptor module for endogenous secreted peptides. Our data suggest that plant and mammals evolved distinct spatio-temporal logic to orchestrate cell surface signaling. Finally, we propose a conceptual framework for the formation of nanoscale assemblies regulating cell surface signaling.

Host: Antoine LOQUET

Thursday, June 3

2 pm

Dr. Jonathan Visentin

CHU de Bordeaux, Laboratoire d’Immunologie et Immunogénétique, Hôpital Pellegrin

Université de Bordeaux, Immuno ConcEpT, UMR CNRS 5164

Surface plasmon resonance to study anti-HLA antibodies: transfer of a basic science method to the bedside of organ transplant recipients and beyond

Human leukocyte antigen (HLA) donor-specific antibodies are key serum biomarkers for assessing the outcome of solid organ transplanted patients. The current clinical tools, which are fluorescence-based methods, are semi-quantitative and then lack in-depth characterization of anti-HLA antibodies. We hypothesized that measuring anti-HLA antibodies active concentration, i.e. the fraction that really interacts with donor HLA, and their affinity could help deciphering their pathogenicity. Surface plasmon resonance (SPR) is recognized as the gold-standard for measuring binding kinetics of antibodies but also their active concentration, without calibration curves. Through tight collaboration with the INSERM-CNRS ARNA unit and the IECB’s SPR platform we pushed forward the strategies of immobilization/regeneration to determine the active concentration and binding kinetics of mouse and human monoclonal anti-HLA antibodies. We then correlate binding kinetics of these monoclonal antibodies to the structure of their cognate class I HLA epitopes. We thereafter established a patented method to correct non-specific binding when using SPR with complex samples, in our case patients’ serum. Clinical studies are ongoing to determine whether active concentration of anti-HLA antibodies is a useful biomarker in lung and kidney transplantation. Preliminary results indicate that this SPR-based assay may help to better understand anti-HLA antibodies pathogenicity and to improve solid organ recipients’ management. Beyond anti-HLA antibodies, this assay could be of interest in various fields, especially infectious diseases and vaccines. Our work is another example of how basic science methods can be transferred from the bench to bedside.

Host: Carmelo DI PRIMO

Friday, June 11

11 am

Prof. Pierre Sonveaux &

Prof. Raphaël Frédérick

Université catholique de Louvain (UCLouvain)

Discovery of an oxidative pathway of lactate in cancer and its druggability by inhibitors of lactate dehydrogenase 1 (LDH1) oligomerization

In tumors, cancer cells are most often challenged to evolve and adapt in metabolically hostile microenvironments characterized by low, unstable oxygen and nutrient levels. Among several survival strategies, we identified a metabolic cooperation based on the exchange of lactate between hypoxic/glycolytic cancer cells that produce lactate from glucose (anaerobic glycolysis) and oxygenated/oxidative cancer cells that consume lactate preferentially to glucose to aliment cell respiration. In the cooperation, hypoxic/glycolytic cells gain access to higher amounts of glucose. Interrogating the oxidative side of the cooperation, we further found that oxidative cancer cells using lactate gained an increased rate of autophagy. Indeed, at the core of lactate oxidation, lactate dehydrogenase 1 (LDH1) interacts with vacuolar ATPase (V-ATPase), a proton pump localized at the surface of lysosomes, that it aliments with protons based on the reaction lactate + NAD+ → pyruvate + NADH + H+. Lysosomal acidification promotes autophagy, which for oxidative cancer cells facilitates the recycling of oxidized proteins and organelles. LDH1, encoded by the LDHB gene, is thus at the core of both oxidative lactate metabolism and autophagy in cancer, making it an attractive anticancer target. Accordingly, silencing LDHB with specific shRNAs killed all tested human cancer cell lines but spared all tested human nonmalignant cell lines.

So far, all molecules developed to inhibit LDHs focused on an interaction at the catalytic site and, therefore, suffered from common drawbacks due to the inherent structural features of LDH active sites, so that LDH inhibitors have yet to demonstrate their potential in preclinical and clinical applications. Interestingly, active LDH1 is an obligatory tetramer formed by 4 LDHH monomers. We therefore reasoned that targeting its oligomerization state instead of its active site might reveal a fruitful approach. In good agreement with previous reports, we demonstrated that the epitope for the LDHH tetramerization arm is constituted by the short N-terminal 8 amino acid α-helix that projects key lipophilic residues towards a highly lipophilic pocket. To study this epitope, we designed a protein model of a dimeric LDH-H, and exploited this model through WaterLOGSY nuclear magnetic resonance and microscale thermophoresis. We identified and characterized a set of α-helical peptides and stapled derivatives that specifically target this LDH tetramerization site. We also identified and characterized a new LDH tetrameric interface. Using nanoscale Differential scanning fluorimetry, chemical denaturation and mass photometry, we further identified several residues (E62, D65, L71 and F72) essential for LDH tetrameric stability. Moreover, we identified a family of peptides able to destabilize tetrameric LDHs through binding to this new tetrameric interface. Altogether, our work provides new insights on the LDH tetrameric interface, as well as valuable pharmacological tools for the development of LDH tetramer disruptors.

This seminar will be delivered by two speakers, Prof. Pierre Sonveaux, the Pharmacist who discovered the oxidative pathway of lactate in cancer, and Prof. Raphaël Frédérick, the Medicinal Chemist who harnessed LDH1 oligomerization, further illustrating that symbiosis is an important paradigm in Biomedical Research.

Host: Leon GHOSEZ

Friday, June 25

11 am

Dr. Eric Cornes

Institute Pasteur

Non-coding small RNAs as versatile regulators of germline gene expression programs

The RNA-guided targeting of nucleic acids is an ancient and conserved mechanism of cellular immunity that has been evolutionary adapted and diversified to regulate eukaryotic gene expression. In animal germ cells, PIWI-interacting small RNAs (piRNAs) have been extensively characterized as a defense mechanism targeting transposable elements (TEs) to promote fertility and genome integrity. In a nutshell: loaded into PIWI effector proteins, piRNA sequences provide mRNA targeting specificity by antisense-complementarity, promoting gene silencing through a variety of mechanisms. Yet, piRNA sequences do not necessarily match TEs, pointing to extended possibilities in gene regulation.

Studying piRNA pathway functions in the context of the developing C. elegans germline we show that spermatogenic genes are susceptible to piRNA-mediated transcriptional silencing, and this function is required to ensure proper germline gene expression patterning and germ cell differentiation. In addition, our work revealed an intriguing aspect of small RNA biology: piRNA pathway components localize into diverse and distinct phase separated condensates present in the nuclear periphery. These condensates, also known as germ granules, are enriched in RNA-binding proteins and RNAs and are suspected to regulate post-transcriptional processes important for germ cell fate specification and function. Our results show that the organization of germ granules changes dynamically during development, and only a particular configuration enable nuclear piRNA silencing at a specific time and location in the germline tissue. This suggests that changes in germ granule composition directly influence nuclear processes through the modulation of small RNA related activities.

Overall the results of this work show that the function of piRNAs can be repurposed to regulate endogenous transcriptional programs during development and might contribute to expand the notion that piRNAs do not only function as a cellular immune system but also act as extremely versatile regulators of gene expression in animals.

Host: Denis DUPUY

Full list of speakers is available here.

Previous seminars

January 12, 2021:

Dr. Hervé Vezin (CNRS - Laboratoire Avancé de Spectroscopie pour les Interactions la Réactivité et l'Environnement (LASIRE), Université de Lille)

Title: Advanced EPR spectroscopy in material chemistry for batteries

February 5, 2021:

Dr. Hagen Hofmann (Department of Structural Biology, Weizmann Institute of Science)

Title: Allostery through DNA drives phenotype switching

March 5, 2021:

Prof. Camilo Perez (Biozentrum, University of Basel)

Title: Structure and mechanism of a proton dependent lipid transporter involved in lipoteichoic-acids biosynthesis

March 18, 2021:

Dr. Michael Eck (Dana-Farber Cancer Institute and Harvard Medical School)

Title: Insights into regulation of the Ras/Raf/MAPk pathway from Cryo-EM Structures of BRAF-MEK-14-3-3 Complexes

March 26, 2021:

Dr. Stephan Rauschenbach (University of Oxford)

Title: Electrospray ion beam deposition for single molecule imaging

April 2, 2021:

Prof. Bernard Rentier (Recteur Honoraire, Université de Liège)

Title: Open Science: Excellence revisited

April 15, 2021:

Dr. Nora Vazquez-Laslop (University of Illinois at Chicago)

Title: Macrolide antibiotics as modulators of translation

May 7, 2021:

Dr. Abhishek Chatterjee (Department of Chemistry, Boston College)

Title: Genetically encoded chemistries to read and write biology