Research Interests

The Merkle laboratory aims to uncover the mechanistic basis of human neurological diseases using human pluripotent stem cell (hPSC)-derived culture systems in order to facilitate the development of effective treatments. We use a variety of techniques including CRISPR/Cas9-based genome engineering, single-cell transcriptomics, high content imaging, electrophysiology and calcium imaging, and organoid and other co-culture systems. Our research focuses on three main areas:

1) Cellular models of obesity

Obesity leads to millions of premature deaths each year and lacks broadly effective treatments. It has a strong genetic basis and is caused in part by the abnormal function of cell populations in the hypothalamus that regulate appetite. We generate these human hypothalamic neurons from hPSCs to take advantage of the fact that can be produced in large numbers, are functionally responsive, have a human genome that can be readily edited, and are in culture environment that can be readily controlled. These advantages provide an unprecedented opportunity to study the genetic and environmental factors underlying obesity, and we are using the system to ask several questions: A) how do human neurons respond to metabolic factors and what role do primary cilia play in this process?, B) which genes associated with obesity act in hypothalamic neurons, and how does their dysfunction lead to cellular phenotypes? C) can we develop the hPSC-derived neuronal model system into a cellular platform for drug screens, e.g. for compounds that can promote the production of appetite-suppressing neuropeptides such as beta-MSH?

2) Metabolic and neurodegenerative disease

Mid-life obesity and diabetes has been identified as is a potential risk factor for dementia later in life, and certain anti-obesity drugs are neuroprotective. We are exploring the hypothesis that there are shared mechanisms between these diseases in a new line of investigation for our group, using a combination of in vitro co-culture models and in vivo models. In particular, we are using a prion model of neurodegeneration to understand how diet and/or drugs traditionally used to treat obesity and diabetes mechanistically act to alter disease severity and time course. We are also pursuing targeted CRISPR screens of genes associated with neurodegeneration and/or metabolic disease across a range of cell types to gain insight into cell type-specific cellular phenotypes that could contribute to these disease types. Our ultimate aim is to identify drug treatments that are more potently neuroprotective and could be given to at large scale to human populations.

3) Rational pluripotent cell line selection and genetic stability

HPSCs are widely used to study development or model disease in vitro, and to generate cellular products for human transplantation to restore function lost in disease. However, hPSCs accumulate mutations in culture that could compromise both the reproducibility of in vitro studies and the safety of regenerative medicine approaches. For example, hPSCs recurrently acquire cancer-associated mutations in the tumour suppressor TP53 (p53) that promote growth in culture and would increase the risk of cancer formation from transplanted cells (Merkle et al., Nature, 2017). It is therefore critical to understand which mutations are likely deleterious, and to reduce the rate at these mutations accumulate in culture. In collaboration with the UK Regenerative Medicine Platform we are systematically testing the selective pressures hPSCs experience under different growth conditions, in order to identify conditions to optimise their genomic stability. In parallel with these efforts we are working collaboratively to identify lead cell lines to underpin large-scale collaborative studies, which we hope will lead to greater reproducibility in the field.

I am always happy to hear from outstanding graduate and postdoctoral candidates via email.

 

Selected Publications

Florian T. Merkle, Sulagna Ghosh, Giulio Genovese, Robert E. Handsaker, Seva Kashin, Konrad Karczewski, Colm O’Dushlaine, Carlos Pato, Michele Pato, Daniel G. MacArthur, Steven A. McCarroll, Kevin Eggan. Biological insights from the whole genome analysis of human embryonic stem cells. BioRxiv and in revision https://doi.org/10.1101/2020.10.26.337352

J Jerber, DD Seaton, ASE Cuomo, N Kumasaka, J Haldane, J Steer, M Patel, D Pearce, M Andersson, MJ Bonder, E Mountjoy, M Ghoussaini, MA Lancaster, HipSci Consortium, JC Marioni, FT Merkle, O Stegle, DJ Gaffney. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nature Genetics, 2021 04 March, PMID: 33664506, DOI: 10.1038/s41588-021-00801-6. 

Kirwan P, Kay RG, Brouwers B, Herranz-Pérez V, Jura M, Larraufie P, Jerber J, Pembroke J, Bartels T, White A, Gribble FM, Reimann F, Farooqi IS, O’Rahilly S, Merkle FT^§. Quantitative mass spectrometry for human melanocortin peptides in vitro and in vivo suggests prominent roles for β-MSH and desacetyl α-MSH in energy homeostasis. Mol Metab. Epub Aug21, 2018. DOI: 10.1016/j.molmet.2018.08.006 PMID: 30201275. PMCID:PMC6197775

Merkle FT*, Ghosh S*, Kamataki N, Mitchell J, Avior Y, Mello C, Kashin S, Mekhoubad S, Ilic D, Charlton M, Saphier G, Handsaker RE, Genovese G, Bar S, Benvenisty N, McCarroll S, Eggan K. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature, E-pub. 26 April 2017. DOI 10.1038/nature22312. PMID: 28445466. PMCID:PMC5427175.

Merkle FT*, Neuhausser WM*, Santos D, Valen E, Gagnon JA, Maas K, Sandoe J, Schier AF, Eggan K. Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. Cell Rep. 2015 May 12;11(6):875-83. doi: 10.1016/j.celrep.2015.04.007. PMID: 25937281. PMCID:PMC5533178

Merkle FT, Maroof A, Wataya T, Sasai Y, Studer L, Eggan K, Schier AF. Generation of neuropeptidergic hypothalamic neurons from human pluripotent stem cells. Development. 2015 Feb 15;142(4):633-43. doi: 10.1242/dev.117978. PMID:25670790. PMCID:PMC4325380

Additional publications are available at: http://www.ncbi.nlm.nih.gov/pubmed/?term=merkle+ft