In vitro fertilization technology: microfluidic platform for non-invasive embryo reception and characterization

Infertility affects 17.5% of couples of childbearing age. Assisted reproductive technologies (ART), such as in vitro fertilization (IVF), are costly and complex procedures requiring advanced equipments and a highly skilled workforce. Successive embryo manipulations are a source of stress that can impact on embryo quality and viability. But developmental abnormalities and miscarriages are mainly caused by chromosomal number anomalies or aneuploidies. These can be detected by pre-implantation diagnosis of aneuploidies (PGD-A) followed by high-throughput sequencing (NGS). However, PGD-A remains complex and invasive, with embryo biopsy potentially having implications for embryo development.
The question the PhD student will have to answer is: can we design a technological alternative that enables both automated culture of in vitro fertilization (IVF) embryos and their selection by non-invasive methods? The project will focus on automating embryo handling, while minimizing mechanical stress, and on extracting the extra-embryonic medium for circulating DNA analysis.
Expected results include an automated microfluidic platform for handling embryos without human intervention, extraction of extra-embryonic medium for aneuploidy analysis by sequencing, and building the program basis for microfluidic technologies applied to IVF.

Localization and dynamics of key nucleoid-associated proteins during stress-induced bacterial nucleoid remodeling.

Nucleoid remodeling, and in particular, nucleoid compaction, is a common stress response mechanism in bacteria that allows bacteria to rapidly respond to sudden changes in their environment. Using advanced optical microscopy approaches, we recently followed the changes in nucleoid shape and volume induced by exposure to intense UV-C light in the radiation resistant bacterium, Deinococcus radiodurans. This two-step process involves a rapid initial nucleoid condensation step followed by a slower decompaction phase to restore normal nucleoid morphology, before cell growth and division can resume. Nucleoid associated proteins (NAP) are known to be key players in this process, although the details of their implication remain largely elusive. We have started to shed light on the central role of the major NAP, the histone-like HU protein, in this process. The proposed PhD project will extend this work to the study of 5 additional NAPs involved in stress-induced nucleoid remodeling. The PhD student will perform biochemical studies to follow the abundance of these key factors, live cell imaging to map their distribution and single-particle tracking to determine their dynamics. This work will contribute to a better understanding of the fundamental processes that govern bacterial genome organisation and how they are affected by UV radiation and DNA damage.

PPARy, a major player in bone marrow stromal homeostasis and a therapeutic target for myelofibrosis?

Myelofibrosis (MF) is the most severe of the Philadelphia-negative myeloproliferative neoplasias (MPNs), with a median survival of 5-6 years. Whether diagnosed de novo (Primary Myelofibrosis, PMF) or secondary to another MPN, the features of MF are similar. A subpopulation of haematopoietic cells derived from the pathological clone releases pro-inflammatory cytokines and growth factors into the bone marrow microenvironment. In response, the bone marrow microenvironment undergoes remodelling, resulting in osteosclerosis and fibrosis of the mesenchymal stromal cells (MSCs) associated with loss of haematopoietic support. The 2016 WHO classification includes a premyelofibrosis state to facilitate early diagnosis of patients at increased risk of progression. However, although major progress has been made in understanding the pathogenesis of the disease, notably with the description of the so-called "driver" mutations responsible for myeloproliferation (JAK2, CALR and MPL), apart from haematopoietic stem cell allotransplantation, which only concerns a minority of patients, current treatments are mainly symptomatic and have little influence on the natural history of MF.
Recently, we demonstrated that activation of the nuclear receptor PPARy (Peroxisome Proliferator-Activated Receptor-gamma) by its pharmacological ligands (Actos®) or (Pentaza®) reduced the development of osteosclerosis and reticulin fibrosis of the bone marrow (BM) and prevented anaemia resulting from bone marrow remodelling in three preclinical mouse models of MF (Lambert, Saliba et al. 2021). These results position PPARy agonists as interesting therapeutic candidates. However, before considering their therapeutic repositioning in the treatment of MF, it is imperative to characterise the status and function of PPARy within medullary MSCs both at the physiological stage and during the development of NMPs.
In this project, our initial results show that PPARy expression is decreased in murine and human MSCs at the MF stage. In contrast, no change in PPARy expression was observed in MSCs derived from other MPNs. Transcriptomic analyses also demonstrated that TGF-B, a major cytokine in the development of MF, is capable of negatively regulating PPARy expression in MSCs. In order to mimic this expression defect, we invalidated PPAR-y (KO) in two bone marrow MSC lines, the first murine (MS5), the second human (HS5, under characterisation). Under these conditions, basal expression of a panel of genes associated with MF is increased in MSC-KO to the level of wild-type lines stimulated by TGF-B. Expression of this panel was further increased in MSC-KO in the presence of TGF-B, indicating potentiation of the TGF-B-mediated signal in the absence of PPARy. This transcriptomic signature associated with KO-MSCs is found in murine MSCs from the thrombopoietin (TPOhigh) induced MF model as well as in human MSCs from patients with PMF. However, this expression profile was not found in MSCs from patients with another MPN, indicating that it is indeed a sign of a stage of MF.
Invalidation of PPARy does not affect the phenotypic signature of bone marrow MSCs, but their multipotent character is altered with a loss of adipocyte differentiation capacity associated with an increase in osteo-chondrocyte differentiation potential. These histological observations are corroborated by the decrease in the production of adipocyte factors by MSC-KO and an increase in the expression of the osteoblastic factor Runx-2. In addition, the supernatant of the KO line showed a marked increase in osteoprotegerin (OPG), a soluble molecule produced by osteoblasts that leads to apoptosis of osteoclasts. This deregulation of the osteoblast/osteoclast balance in KO conditions could explain the osteosclerosis observed in patients with MF. In addition, the production of CXCL12 (CXC motif Chemokine Ligand 12) and the bone marrow growth factor SCF (c-kit ligand) are greatly reduced in MSC-KO conditions, at both transcriptomic and protein levels. These data recapitulate the results described during transcriptomic analyses of MSC from patients with fibrosis. At the same time, the capacity of MSC-KO to support haematopoiesis, in both the short and long term, is significantly reduced, reflecting the cytopenias associated with MF.
In silico, RNA-Seq analyses were carried out on the MS5-WT and MS5-KO lines. Initial gene set enrichment analyses (GSEA) show that the pathways most significantly affected are inflammation, myogenesis (MSC to myofibroblast transition) and the cell cycle. Comprehensive analyses are now required to identify new therapeutic candidate genes and gain a better understanding of the development of bone marrow fibrosis.
These initial in vitro results support the key role of the PPARy receptor in the homeostasis of the bone marrow microenvironment and in the genesis of its remodelling during the development of myelofibrosis. However, in vitro approaches alone are unable to capture the full complexity of a disease involving multiple players including haematopoietic cells, immunological cells and all the cell types making up the bone marrow microenvironment. To integrate all these parameters, we have established a mouse model in which PPARy expression is reduced (haploinsufficiency) or invalidated (KO) in the medullary MSCs of animals. It is the study of this model that will form the core of the project. Initially, in vivo, it will be used to:
1) Characterise the role of PPARy in the homeostasis of the bone marrow microenvironment.
2) Assess the impact of reduced expression on the development of bone marrow fibrosis.
3) To validate the positioning of PPARy as a therapeutic target in the management of bone marrow fibrosis and to consider the repositioning of its pharmacological agonists (Actos®; Pentaza®) in this pathology.

The presence of medullary pre-fibrosis/fibrosis is a poor prognostic factor in MPN or acute myeloid leukaemia (AML). However, it is difficult to determine whether this condition is simply an indicator or whether it plays an active role in the development of haemopathies. The use of these models (Haplo-insufficient or KO for PPARy in MSCs) in association with preclinical mouse models of MPN (CML (BCR-ABL); PV (JAK2 V617F), ET (CALRDel52)) will allow, in a second phase, to determine whether:
1) The presence of a predisposition to bone marrow fibrosis influences the natural history of haemopathies.
2) In these diseases, which are purely haematopoietic in origin (mutation of the haematopoietic stem cell), it is appropriate to combine treatment targeting the malignant clone with treatment aimed at preventing the development of bone marrow fibrosis (activation of the PPARy receptor by its ligands in the haploinsufficiency condition).

This entire project is part of the Tomorrow's Biotechnologies (F) initiative, which aims to improve patient care through the development of personalised medicine.

Involvement of prokineticins in neurovascular disorders associated with preeclampsia: therapeutic challenge

Pre-eclampsia (PE) is a specific complication of pregnancy associated with hypertension and hypoperfusion of the placenta, leading to an increased risk of adverse fetal and maternal neonatal outcomes and consequences for neurovascular function. However, pre-eclampsia is not limited to pregnancy, and more than 20 years later, women are still at increased risk of stroke and cognitive impairment. Clinical studies have shown that these patients have brain lesions on MRI scans. MAB2's work in a mouse model of PE has demonstrated the direct involvement of prokineticins (PROKs) and their receptors (PROKRs) in the establishment of PE and its symptoms. Our recent results demonstrate a direct link between the preeclamptic event and the onset of late cerebral lesions and inflammation. Finally, we have shown in a cellular model of brain vessels, the blood-brain barrier (BBB), that PROKs modify vascular permeability. The aim of the PhD project is to characterize the vascular changes that occur at the time of PE and their long-term consequences on cognitive function, and to determine whether PROKs and PROKRs may represent therapeutic targets for a preventive treatment of PE. These objectives will be addressed by studies using mouse model of PE and cellular models of the BBB. The studies will rely on the expertise of the MAB2 team and on collaborations with experts in blood-brain interface, MRI and behavioral testing. To correlate our results with the clinic, collaborations with clinicians and hospitals will give us access to blood and tissue samples from patients who have suffered from PE.

Self-organization of cellular microtubule networks

Microtubules produce mechanical forces as they grow and shrink. They also support the forces
produced by molecular motors. The spatial distribution of these two sets of forces orients intra-cellular transport, positions organelles, and thereby determines the cellular compartmentation and polarity.

The architecture of microtubule network depends on two main contributions: the templated
growth, which is defined by the amount and localization of microtubule nucleators, and the selforganization of microtubule and motors, which depends on the concentration of various motors and the number and length of microtubules. This contribution has been much studied in the spindle formed by microtubules during mitosis, but is relatively uncharacterized in interphase although it is central to most cell functions.

We recently managed to define some working conditions allowing us to turn down the
templated growth and highlight the self-organization of microtubule and motors. To our surprise, we found that components could self-pattern themselves into multiple domains, containing either plus-end or minus-end directed motors, separated by bundles of aligned microtubules.

We propose to further explore these conditions and define the phase diagram defining the
number and shape of these domains. This first part will serve as a basis to define a deeper study of this process in various cell types and their evolution as cells progress from a proliferating to a differentiated state (ie as the self-organization progressively replaces the templated growth).

Effects of ionizing radiation and radiosensitizing molecules in a relevant murine model of breast cancer

The project aims at evaluating the efficacy of molecules combined with radiotherapy, in in vitro and in vivo models of breast cancer.
On the one hand, the student will evaluate the radioenhancer effect of bimetallic nanoparticles designed in the laboratory, on a murine model mainly. A clinical, histological, and immune monitoring will confirm the added value of such molecules for combination with radiotherapy. In addition, those innovative nanoparticles have been designed as biodosimeters, using unique physical properties of metallic nanoparticles. Therefore the project includes an evalution of the biodosimetry potential, in collaboration with physicists from CEA, who developed detection tools.
On the other hand, specific inhibitors for DNA repair will be used to block radiation-triggered repair. Thus, damaged cancer cells will be oriented towrads cell death, even in the case of radioresistant cells. The objective of the PhD program is to evaluate these molecules effect on in vitro cellular models, as well as on murine models of breast cancer.
Overall, the research project will benefit from the laboratorys’ collaborations with physicists and chemists, as well as the platforms of IRCM (irradiation, animal experimentation, microscopy, cytometry, etc...)

Molecular and physiological characterization of sugar biosynthetic pathways in brown macroalgae

The aim of this PhD project is to characterize sugar biosynthetic pathways in brown macroalgae at the molecular and physiological levels. Brown macroalgae produce two main types of storage sugars: mannitol (a simple sugar) and laminarin (a polymer made up mainly of glucose units, with the optional addition of a few mannitol units). As these biosynthetic pathways have been poorly described so far, the main aim of this PhD project is to identify and characterize the enzymes responsible for the catalytic activities of these two interconnected biosynthetic pathways in the brown macroalga Ectocarpus. Original molecular and cellular biology approaches, including genome editing, will be used to generate the biological material needed to characterize these biosynthetic pathways and their role in brown macroalgal physiology.