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, quantitative proteomics, high content imaging, calcium imaging, and organoid and other co-culture systems. Our research focuses on three main areas:
1) Models of obesity and neurodegeneration
Obesity and neurodegeneration lead to millions of premature deaths each year and lack broadly effective treatments. Obesity is largely caused by the abnormal function of cell populations in the hypothalamus that regulate appetite. We generate human hypothalamic neurons from hPSCs to study how they respond to nutrients and hormones (e.g. leptin) and how disease-associated mutations alter their function. Since human hypothalamic neurons 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, there is an unprecedented opportunity to study the genetic and environmental factors underlying obesity. In addition, we are fascinated by the fact that mid-life obesity is a risk factor for dementia later in life, and caloric restriction, exercise, and certain anti-obesity drugs are neuroprotective, suggesting that there are shared mechanisms between obesity and neurodegeneration. We are exploring these interactions in a new line of investigation for our group, using a combination of in vitro co-culture models and in vivo models. These studies may help bridge the mechanistic gulf between human genetic data and organismic phenotypes, revealing new therapeutic targets.
2) Therapeutic translation
The functionality and scalability of hPSC-derived cellular systems makes them an attractive system for identifying and testing new therapeutic compounds. In particular, we plan to extend our observations from genetic and phenotypic studies of hPSC-derived neurons to test for factors that can reduce disease phenotypes or promote the production of appetite-suppressing neuropeptides such as beta-MSH (Kirwan et al., Mol. Met., 2018) using single-cell transcriptomics and high-content imaging. We then plan to advance promising compounds into in vivo models to test their ability to reduce obesity, or delay the onset or slow the progression of neurodegeneration.
3) Genetic stability in human stem cells
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, we recently showed that 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 carrying out whole genome and whole exome sequencing to understand the effects of gene editing on hPSC genetic architecture and developing novel methods to identify culture conditions that reduce selective pressures in order to reduce the rate at which mutations accumulate.
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. 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. (in press) https://doi.org/10.1101/2020.05.21.103820
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
Merkle FT, Eggan K. Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell. 2013 Jun 6;12(6):656-68. doi: 10.1016/j.stem.2013.05.016. PMID:23746975.
Additional publications are available at: http://www.ncbi.nlm.nih.gov/pubmed/?term=merkle+ft
