The goal of the Merkle laboratory is to elucidate the molecular and cellular basis of disease in order to improve human health. In particular, we are focused on obesity and neurodegenerative diseases, which are leading causes of death and have no broadly effective treatments. Our vision (see figure above) is to tackle these problems by generating and studying disease-relevant cell populations (see figure below) from human pluripotent stem cells (hPSCs), and then translating discoveries made in vitro into treatments.
In particular, it is now widely accepted that that obesity is largely a disease of the brain and that hypothalamic neurons that are essential regulators of feeding often act abnormally in obesity. However, the disease mechanisms that lead to their aberrant function are unclear, as are the potential mechanisms linking metabolic and neurodegenerative disease. To study how genes and environmental factors associated with these diseases affect the function of human neurons, we employ a range of cutting edge techniques including CRISPR/Cas9-based genome engineering, single-cell transcriptomics, high content imaging, and animal models. We are grateful for the support of the Academy of Medical Sciences, the Wellcome Trust, the Royal Society, the UKRI/Medical Research Council (MRC) the New York Stem Cell Foundation (NYSCF), the Chan Zuckerberg Initiative, and Open Targets.
iPSC-derived hypothalamic cultures, DAPI: Blue, MAP2: Green
Genomic stability and rational selection of human pluripotent stem cell lines. Human pluripotent stem cells (hPSCs) are powerful tools for modelling and treating human disease. To realise the full potential of these tools, sources of variability that compromise reproducibility and correct interpretation of phenotypes must be mimimised. Remarkably, this is usually not done in the field, despite well-known variability in differentiation potential between cell lines, and the recurrent acquisition of genetic variants in culture. These include large structural genetic variants as well as small point mutations affecting genes such as the tumor suppressor TP53 (p53) that likely affect the utility of hPSCs for disease modelling and regenerative medicine. Therefore, we are working as part of the UK Regenerative Medicine Platform (UKRMP) to quantify and minimise selective pressures experienced by hPSCs in vitro, in order to reduce the incidence of acquired mutations. In addition, worked with with an international consortium supported by the Chan Zuckerberg Initiative to identify a ‘C57Bl/6J-like’ reference induced pluripotent stem cell line that displays genomic integrity and good differentiation capacity to form the basis of large-scale genetic engineering and disease modelling efforts. We hope that the widespread distribution and adoption of this cell line, KOLF2.1J, will increase the reproducibility of hiPSC-based studies and enable more direct inter-lab data comparison. It’s readily accessible to both research and commercial partners via the Jackson Laboratories, and has already been distributed to over 200 groups.
Mechanisms of metabolic sensing by human hypothalamic neurons. Neurons in the mediobasal hypothalamus are unique since they receive input from many other brain areas, but also have direct access to circulating nutrients and hormones by virtue of processes or cell bodies that extend outside of the blood-brain barrier. These circulating metabolic signals regulates their activity, which in turn regulates appetite and energy expenditures. Their responses have been largely studied in animals, but the ability to make large numbers of human hypothalamic neurons in vitro provides experimental control over the concentration, duration, and combination of metabolic signals. Indeed, we have shown that the human hypothalamic neurons we produce in vitro respond to the amino acid leucine and the hormone leptin in much the same way as their counterparts in the mouse brain. By characterising how human hypothalamic neurons respond to these signals, we aim to gain insight into the molecular and cellular mechanisms of metabolic signalling in these cells, which could identify new strategies for treating obesity.
Genetic & environmental mechanisms of obesity & neurodegenerative disease. Obesity and neurodegeneration are leading causes of death with no broadly effective treatments. Our aim is to reveal molecular and cellular mechanisms that contribute to these diseases for facilitate the development of more effective treatments. These studies leverage emerging human population sequencing resources that are providing a rapidly growing list of associated genetic variants, the ability to make disease-relevant cell types at scale from human pluripotent stem cells (hPSCs), and the ability to expose these cells to different environmental factors and to edit hPSC genomes using CRISPR/Cas9. We are fortunate to collaborate with three projects funded by Open Targets – an innovative partnership between academia and industry – to study how common genetic variants in 1) neurons and 2) microglia might alter the expression of genes associated with neurodegeneration, and 3) how the loss of these neurodegeneration-associated genes in turn alters cellular phenotypes.
Shared mechanisms in metabolic and neurodegenerative disease. Obesity and neurodegenerative disease are leading causes of death with no broadly effective treatments. Epidemiological evidence links mid-life obesity to dementia later in life, and interventions that reduce obesity (exercise, caloric restriction, and certain anti-obesity drugs) are neuroprotective. Furthermore, the inflammation seen in the rodent mediobasal hypothalamus following consumption of a high-fat diet is reminiscent of that seen surrounding areas of neurodegeneration in the human brain. We therefore hypothesise that there are shared mechanism between obesity and neurodegeneration, and that targeting these mechanisms may reduce the burden of one or both of these diseases. To this end, we are developing both in vitro and in vivo models that are generously supported by the Chan Zuckerberg Initiative’s Neurodegeneration Challenge Network.
Therapeutic translation. Pharmacological treatment of obesity has a mixed history, but recent studies in animal models suggest that targeting the molecular pathways that regulate hunger and energy expenditure have tremendous potential to combat the rising tide of obesity. A scalable, human cellular system should provide an important complementary resource to animal models. We therefore aim to use hPSC-derived hypothalamic neurons to identify nutrients, hormones, and drugs that alter their function in vitro and may reduce food intake and body weight in vivo. We will explore candidate drugs and drug combinations targeting GPCRs enriched in human POMC neurons in studies supported by the Wellcome Trust and The Royal Society, and screen for novel drugs in studies supported by the New York Stem Cell Foundation (NYSCF).