Current & Upcoming

Research in our lab focuses on understanding how cells in the early embryo integrate genetic and epigenetic information to initiate and orchestrate a new developmental programme. After fertilisation of the oocyte by the sperm, the resulting zygote acquires the unique capacity to form a complete new organism. This is a universal principle across species and is fundamental for the preservation of species and for multicellularity. At these early developmental stages, genetic, epigenetic and mechanical mechanisms are in place. Yet, how these regulatory layers are integrated at the molecular level remains still a poorly understood, yet exciting area of research. I will present our work investigating how the pervasive presence of transposable elements in mammalian genomes, chromatin function, and genome nuclear organisation are integrated with nuclear mechanics to shape and regulate early developmental programmes. I will also illustrate how we leverage these findings to restore cellular plasticity for reprogramming cell fates.

Maintaining negatively supercoiled (-SC) topological homeostasis in the bacterial chromosome is essential for genome stability, replication fidelity, and transcriptional regulation. As DNA and RNA polymerases track along the double helix, they generate mechanical stress, producing downstream positive supercoils (+SC) that can stall macromolecular machineries. In bacteria, the type II topoisomerase DNA gyrase uniquely relieves this topological strain through a tightly regulated homeostatic feedback loop, modulating gyrA and gyrB expression in response to DNA relaxation. While gyrase is known to be biochemically versatile, catalyzing ATP-dependent negative supercoiling, ATP-dependent positive supercoil relaxation, and ATP-independent negative supercoil relaxation, its catalytic efficacy depends entirely on its capacity to distinguish between these topological states. Despite extensive biochemical characterization, the structural basis governing how DNA gyrase senses DNA chirality and selectively engages supercoiled substrates has remained fundamentally unresolved. To address this question, this study presents high-resolution cryo-electron microscopy structures of DNA gyrase trapped in complex with (+) and (–) supercoiled minicircle DNA substrates. By capturing these distinct topological assemblies, the resulting reconstructions reveal the critical C-terminal domain (CTD) interactions and large-scale conformational transitions that mediate chirality discrimination and dictate the directionality of strand passage. Furthermore, this study reports the structural determination of a novel DNA-free conformation of DNA gyrase, a resting state intermediate hypothesized from kinetic experiments but never previously visualized at near-atomic resolution. Together, these findings define the conformational steps leading to supercoil chirality sensing, establishing a definitive mechanistic model for how DNA gyrase maintains topological integrity within the bacterial cell.

The mechanical stiffness of the nucleus regulates its deformation under force, making it an emerging central mechanosensor of the cell, which interacts with numerous signaling macromolecules and pathways. In particular, Yes-Associated Protein (YAP), is a key transcription factor in diverse physiology and disease whose activity is in part regulated by nuclear compression. This makes downstream activity of YAP in diverse contexts directly regulated by the forces applied to the nucleus, as well as the nucleus’s mechanical properties. Previous studies have related nuclear mechanics with YAP activity, but we still lack an understanding of what nuclear deformation specifically regulates YAP, and its relationship with mechanical stimuli. In this talk I will discuss some of our ongoing work and recent findings related to YAP mechanosensing in the nucleus. Our lab has shown that nuclear compression from diverse sources of substrate stiffness mediated contractile force to external osmotic pressure reveal an identical scaling of YAP activity as a function of nuclear volume. I will discuss how examining the details of nuclear deformation in mesenchymal stem cells (MSCs), we find that specifically nuclear curvature is a clear predictor for YAP mechanosensing in the nucleus. By controlling the nuclear curvature, we are able to precisely direct the differentiation lineage of MSCs in culture, with numerous potential therapeutic applications. Beyond differentiation, we have also revealed how nuclear deformation mediated YAP activity regulates cellular senescence. Examining Hutchinson Gilford Progeria Syndrome (HGPS) cells with healthy wild type fibroblasts, we find that HGPS nuclei are stiffer and wrinkled due to the nucleoplasmic spoke-like structure of lamin A/C in HGPS nuclei. We find that increased nuclear stiffness is correlated with reduced YAP activity, which in turn promotes cellular aging as assessed by biomarkers. Directly mechanically compressing stiff cells lead to a dramatic increase in YAP activity and a reduction in cellular aging. These studies of nuclear mechanics reveal its role in YAP mechanotransduction with broad impact across diverse cell functions and pathology.

How do cells and tissues encode and exchange information to coordinate multicellular behaviour? Our work on somitogenesis showed that the temporal organization of signalling matters for development: the relative timing between oscillating pathways is functionally important for embryonic segmentation. We then asked whether temporal signalling could also regulate cell fate in a homeostatic tissue. In the intestinal epithelium, we found that changing the frequency of signalling oscillations alters cell-type composition, establishing frequency encoding as a mechanism of tissue homeostasis. More recently, we turned to communication between embryonic and maternal tissues during human implantation. While initially aiming to study signalling between these tissues, we made an unexpected observation: embryonic and endometrial cells form heterokaryons. Following this finding mechanistically led us to identify Syncytin-2/MFSD2A as a mediator of this interaction. Together, these studies explore how information is encoded within tissues and exchanged between them to coordinate multicellular behaviour.

Halloween requires the presence of blood and horror (as well as drinks and sometimes bats). In my talk I will cover all four aspects. Bed bugs binge drink (about three times their body weight), and they only drink blood. For females, drinking blood comes with sex, which, as I will present, denotes the horror part (if that is insufficient for horror, I will bring a picture from a heavily infested room). Sex is traumatic for females – copulatory wounding occurs at every mating - and I will quantify the trauma and show what females do about that. Traumatic insemination also lead to some unusual sperm biology. I will examine some of the sperm biology separately for the two genetically separated clades of bed bugs that either drink human or bat blood. Human and bat blood produce bed bug sperm that differ predictably in lipid profiles, and in sperm metabolism. This contrasts with Drosophila, where we find that, in the testes, sperm are protected from incorporating dietary lipids but instead take them up from lipid vesicles in the seminal fluid (called microcarriers). Sperm then shuttle dietary sterols to the offspring where they seem to enhance offspring growth, possibly because sterols are the precursor for the insect growth hormone.

Eukaryotic cells produce thousands of different lipids—collectively known as the lipidome—whose composition is tailored to cellular needs. Lipids are distributed unevenly throughout biological systems, where they accumulate locally, forming membranes with specific compositions and thereby determining the identity and functional specialization of organelles. Due to their hydrophobicity, lipids cannot move freely out of cellular membranes through the cell’s aqueous environment and require transporters—lipid transfer proteins, or LTPs—to carry them. LTPs are soluble molecular machines responsible for transporting lipids, and they are found in all kingdoms of life. They have diverse structures, but many share a common mode of action: they extract specific lipids from membrane bilayers and load them into a hydrophobic pocket, forming water-soluble protein-lipid complexes that isolate cargoes from the aqueous phase. In addition to their cargo, some LTPs mobilize auxiliary lipids that function as exchange currencies or cofactors. They facilitate the uptake or release of the cargo, which would determine the direction of transport and its coupling to metabolism. However, for most LTPs, the identity of cargo and auxiliary lipids remains unknown. The fundamental biochemistry of LTPs remains poorly understood, limiting our ability to study how they function within cells. Our goal is to begin addressing this gap; I will present a recent systematic analysis of the lipid binding properties of human LTPs and discuss the general principles that we have derived from it.