Research Valeriya Malysheva

Abstract

Adult neurogenesis plays an essential role in normal cognitive function including in memory formation, learning, pattern separation and mood regulation and is disrupted in neurodegenerative disorders. Adult neurogenesis primarily occurs in two regions of the adult brain: the dentate gyrus (DG) of the hippocampus, and the subventricular zone. In the DG, neural stem cells slowly give rise to neural intermediate progenitor cells, neuroblasts and ultimately new neurons. Intriguingly, NSCs are thought to be almost entirely quiescent, expressing no markers for active proliferation, with the detection of any proliferating cells often proving difficult. Yet, NSCs are maintained throughout adulthood. This apparent contradiction emphasises our current lack of understanding of the regulatory mechanisms underlying NSC transition from a state of quiescence to a state of proliferation. It is vital that we understand these processes, and identify the key factors regulating it, so that we know how exactly and why neurogenesis is impaired in disease, and how we can intervene to treat it. Changes in the 3D structure of chromatin are essential for coordinating the transition from quiescence to self-renewal in other stem cell populations including in hematopoietic stem cells. Yet no study has ever investigated the role of the changing 3D structure of chromatin in the NSCs in the DG. This is a significant shortcoming as changes in chromatin organisation often precede transcriptional changes, with gene promoters interacting with 'primed' or 'poised' enhancer regulatory elements prior to activation. I therefore hypothesise that NSCs exist in functionally distinct states, distinguishable at the level of 3D chromatin organisation, and that changes in chromatin organisation coordinate the transition from quiescence to self-renewal, shaping cell fate trajectories during adult neurogenesis in the DG. To investigate these hypotheses I propose the first ever study of chromatin organisation in the human DG. For this we will develop a novel technology (scSPRITE-IP) for profiling multiway chromatin hubs at high-resolution in single cells and apply it to detect the regulatory chromatin interactions governing the NSC transition from quiescence to self-renewal state. Importantly, to understand adult neurogenesis, regulated at so many intrinsic and extrinsic levels, a holistic approach which can integrate information across scales and modalities must be taken. Therefore, we will integrate the scSPRITE-IP data with single-cell gene expression, chromatin accessibility and disease risk-variants (GWAS) data in a novel bespoke computational inference framework and identify key factors regulating adult neurogenesis. Our group's dual expertise in the development of novel experimental methods for profiling chromatin organisation in rare cell populations, as well as development of multimodal, integrative network inference methods and statistical analysis tools is essential to the success of this project and ensures its success. Through the development of novel experimental and computational approaches this highly innovative proposal carries transformative potential both in the field of neurogenesis and well beyond stem cell research in the brain, enabling the advance of research into cell fate acquisition in other tissues and organisms, in health and disease.

Researcher(s)

• Promoter: Malysheva Valeriya

Research team(s)

• VIB CMN - Computational Neurobiology

Project type(s)

• Research Project

Abstract

Isoform expression is highly cell type-specific, drives cell fate trajectories, profoundly influences drug responses and its dysregulation is a cause of disease. Despite research traditionally focusing on alternative splicing, the use of alternative transcription start sites (TSSs) and termination sites (TTSs) accounts for the majority of transcriptional diversity in humans. Yet little is known about what governs alternative TSS and TTS isoform choice. Our preliminary data show chromatin organisation, via 3D isoform-enhancer interactions, likely plays a crucial role, but no in-depth research has been done. We hypothesise that chromatin organisation is a central coordinator of isoform choice. As the brain contains the widest isoform diversity it is ideal for addressing this question. I will use experimental methods including the chromatin organisation technology patented by Prof. Malysheva, which is the only method capable of detecting isoform-level 3D chromatin organisation interactions in rare cell populations at high resolution, as well as computational methods for integrative regulatory network inference to identify the drivers of isoform choice in the major cell types of the human frontal cortex. This project will reveal the ground rules of isoform choice, which, in the long run, will be a game-changer for understanding the role of isoforms in health and disease and shift the regulatory paradigm from gene-centric to isoform-centric.

Researcher(s)

• Promoter: Malysheva Valeriya
• Fellow: De Broeck Noémie

Research team(s)

• VIB CMN - Computational Neurobiology

Project type(s)

• Research Project

Abstract

Over the last decade, organoids emerged as an attractive middle ground between 2D cell cultures, which do not fully recapitulate the 3D environment and animal models, which pose technical and ethical limits. In particular, cerebral organoids are emerging as the next step in patient-derived in vitro models for both neurodevelopmental as well as neurodegenerative diseases. However, cerebral organoids have mostly been based on neuronal cells alone, while evidence increases that the role of non-neuronal types (microglia, astrocytes, endothelial cells) is critical in these conditions. Integration of these cell types will more closely mimic the in vivo cellular environment in health and disease and constitutes the major challenge of this project. The established neuroimmune organoid technology will find a wide range of applications as models for studying fundamental mechanisms underlying cellular biology and genetic pathophysiology as well as for efficient drug screening.

Researcher(s)

• Promoter: Sleegers Kristel
• Co-promoter: Jordanova Albena
• Co-promoter: Malysheva Valeriya
• Co-promoter: Mancuso Renzo
• Co-promoter: Weckhuysen Sarah

Research team(s)

• VIB CMN - Genetics of Alzheimer’s Disease

Project type(s)

• Research Project