Nouvelle stratégie de ciblage de la GTPase RhoB : développement d'intracorps conformationnels sélectifs et leur fonctionnalisation en tant qu'inhibiteurs intracellulaires de l'activité de RhoB

La GTPase RhoB partage 85% d'homologie avec RhoA et RhoC. Ces protéines alternent entre deux conformations : une active liée au GTP et une inactive liée au GDP. Des dérégulations de leur expression et de leur activation sont retrouvées dans de nombreux cancers. A ce jour, aucun inhibiteur sélectif de ces GTPases n'a pu être développé afin de bloquer l'activité de l'une ou l'autre de ces Rho. Ce travail doctoral a permis de mettre au point une approche innovante ciblant sélectivement l'état activé de la protéine RhoB. Suite à la caractérisation d'une nouvelle banque d'anticorps à simple domaine, sa validation par phage display contre divers antigènes a fourni de nombreux anticorps de haute fonctionnalité dans plusieurs applications. L'établissement d'une stratégie de sélection directe d'anticorps intracellulaire (intracorps) dirigés contre RhoB a permis d'identifier plusieurs intracorps conformationnels de la forme active de RhoB, dont un discriminant RhoB de ses homologues RhoA et RhoC. La fonctionnalisation d'intracorps par un domaine Fbox conduisant une dégradation de la cible a ensuite fourni la première stratégie efficace d'inhibition sélective de l'activité de RhoB. Ces travaux ont notamment démontré que l'extinction de l'activité de RhoB par intracorps fonctionnalisé augmente la migration et l'invasion de cellules pulmonaires. Ainsi cette avancée permettra de déterminer si l'activité de RhoB peut être une nouvelle cible thérapeutique et ouvre de nouvelles perspectives d'étude fine de l'activité des GTPases.RhoB GTPase shares more than 85% of homology with RhoA and RhoC. These proteins switch between an active conformation bound to GTP and an inactive one bound to GDP. Deregulations of their expression and/or their activity are often found in many cancers. To date, no selective inhibitor of these GTPases has been developed in order to block selectively Rho's activity. This project showed an original approach targeting RhoB's activity. After a new single domain antibody library characterization, its validation using the phage display technology against various antigens gave many highly functional antibodies in many applications. Set up of a new direct screening strategy of intracellular antibody (intrabody) raised against RhoB allowed us to identify several conformational intrabodies of RhoB active form, one of them discriminating RhoB from its homologs RhoA and RhoC. Intrabody functionalization with an Fbox domain driving target to degradation led to the identification of the first efficient selective RhoB activity inhibitory strategy. These work demonstrated that RhoB activity knockdown with functionalized intrabodies increased migration and invasion of pulmonary cells. In conclusion this tool will allow to determine if RhoB activity could be a new therapeutic target and open new perspectives to study GTPases activity

Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment

Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells

A potent KRAS macromolecule degrader specifically targeting tumours with mutant KRAS

International audienceTumour-associated KRAS mutations are the most prevalent in the three RAS-family isoforms and involve many different amino-acids. Therefore, molecules able to interfere with mutant KRAS protein are potentially important for wide-ranging tumour therapy. We describe the engineering of two RAS degraders based on protein macromolecules (macrodrugs) fused to specific E3 ligases. A KRAS-specific DARPin fused to the VHL E3 ligase is compared to a pan-RAS intracellular single domain antibody (iDAb) fused to the UBOX domain of the CHIP E3 ligase. We demonstrate that while the KRAS-specific DARPin degrader induces specific proteolysis of both mutant and wild type KRAS, it only inhibits proliferation of cancer cells expressing mutant KRAS in vitro and in vivo. Pan-RAS protein degradation, however, affects proliferation irrespective of the RAS mutation. These data show that specific KRAS degradation is an important therapeutic strategy to affect tumours expressing any of the range of KRAS mutations

Antibody-Based Approaches to Target Pancreatic Tumours

Pancreatic cancer is an aggressive cancer with a dismal prognosis. This is due to the difficulty to detect the disease at an early and curable stage. In addition, only limited treatment options are available, and they are confronted by mechanisms of resistance. Monoclonal antibody (mAb) molecules are highly specific biologics that can be directly used as a blocking agent or modified to deliver a drug payload depending on the desired outcome. They are widely used to target extracellular proteins, but they can also be employed to inhibit intracellular proteins, such as oncoproteins. While mAbs are a class of therapeutics that have been successfully employed to treat many cancers, they have shown only limited efficacy in pancreatic cancer as a monotherapy so far. In this review, we will discuss the challenges, opportunities and hopes to use mAbs for pancreatic cancer treatment, diagnostics and imagery

Selection and Characterization of a Nanobody Biosensor of GTP-Bound RHO Activities

RHO (Ras HOmologous) GTPases are molecular switches that activate, in their state bound to Guanosine triphosphate (GTP), key signaling pathways, which involve actin cytoskeleton dynamics. Previously, we selected the nanobody RH12, from a synthetic phage display library, which binds the GTP-bound active conformation of RHOA (Ras Homologous family member A). However, when expressed as an intracellular antibody, its blocking effect on RHO signaling led to a loss of actin fibers, which in turn affected cell shape and cell survival. Here, in order to engineer an intracellular biosensor of RHOA-GTP activation, we screened the same phage nanobody library and identified another RHO-GTP selective intracellular nanobody, but with no apparent toxicity. The recombinant RH57 nanobody displays high affinity towards GTP-bound RHOA/B/C subgroup of small GTPases in vitro. Intracellular expression of the RH57 allowed selective co-precipitation with the GTP-bound state of the endogenous RHOA subfamily. When expressed as a fluorescent fusion protein, the chromobody GFP-RH57 was localized to the inner plasma membrane upon stimulation of the activation of endogenous RHO. Finally, the RH57 nanobody was used to establish a BRET-based biosensor (Bioluminescence Resonance Energy Transfer) of RHO activation. The dynamic range of the BRET signal could potentially offer new opportunities to develop cell-based screening of RHOA subfamily activation modulators

RNase H2, mutated in Aicardi‐Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation

RNase H2 is a specialized enzyme that degrades RNA in RNA/DNA hybrids and deficiency of this enzyme causes a severe neuroinflammatory disease, Aicardi Goutières syndrome (AGS). However, the molecular mechanism underlying AGS is still unclear. Here, we show that RNase H2 is associated with a subset of genes, in a transcription-dependent manner where it interacts with RNA Polymerase II. RNase H2 depletion impairs transcription leading to accumulation of R-loops, structures that comprise RNA/DNA hybrids and a displaced DNA strand, mainly associated with short and intronless genes. Importantly, accumulated R-loops are processed by XPG and XPF endonucleases which leads to DNA damage and activation of the immune response, features associated with AGS. Consequently, we uncover a key role for RNase H2 in the transcription of human genes by maintaining R-loop homeostasis. Our results provide insight into the mechanistic contribution of R-loops to AGS pathogenesis

NaLi-H1: A universal synthetic library of humanized nanobodies providing highly functional antibodies and intrabodies

In vitro selection of antibodies allows to obtain highly functional binders, rapidly and at lower cost. Here, we describe the first fully synthetic phage display library of humanized llama single domain antibody (NaLi-H1: Nanobody Library Humanized 1). Based on a humanized synthetic single domain antibody (hs2dAb) scaffold optimized for intracellular stability, the highly diverse library provides high affinity binders without animal immunization. NaLi-H1 was screened following several selection schemes against various targets (Fluorescent proteins, actin, tubulin, p53, HP1). Conformation antibodies against active RHO GTPase were also obtained. Selected hs2dAb were used in various immunoassays and were often found to be functional intrabodies, enabling tracking or inhibition of endogenous targets. Functionalization of intrabodies allowed specific protein knockdown in living cells. Finally, direct selection against the surface of tumor cells produced hs2dAb directed against tumor-specific antigens further highlighting the potential use of this library for therapeutic applications

TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks

International audienceTDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis