The Merkle laboratory studies the molecular and cellular basis of human disease, in particular obesity and the sleep disorder narcolepsy. Obesity and narcolepsy are both associated with the aberrant function of specific neuron types in the hypothalamus, an evolutionarily ancient brain region that regulates essential physiological and behavioural processes. My laboratory uses a range of cutting edge techniques to elucidate disease mechanisms including: directed differentiation of human stem cells, genome engineering, high content imaging, single-cell transcriptomics, and animal models. Research in my laboratory revolves around three areas:
1) Basic biology of human hypothalamic neurons
Since human hypothalamic neurons have been effectively inaccessible, we are interested in understanding how their similarities and differences to rodent neurons, and their responsiveness to biologically important factors such as leptin. Over the past 18 months, my group has established itself and we have improved the efficiency and consistency of hypothalamic differentiation. Single-cell RNA sequencing of the differentiated population revealed a broad diversity of behaviourally and physiologically relevant neuropeptidergic hypothalamic cell types. We are analysing the properties of several of these neuron types with a particular emphasis on POMC neurons. We are interested in the following areas: pro-hormone processing into bioactive peptides, responsiveness to exogenous cues such as leptin, development of novel cellular assays to measure signal transduction and cellular activity, calcium imaging, transcriptomics, proteomics, and gene editing.
2) Genetics of appetite regulation
The study of rare and highly penetrant mutations has revealed the importance of the leptin and melanocortin systems in human obesity, but the mechanisms and cell types in which most mutations associated with human obesity act are poorly understood. We have identified obesity-associated genes that are enriched in hypothalamic neurons such as POMC neurons, and will use CRISPR/Cas9 to introduce these candidate genetic variants into hPSCs. These will then be differentiated into hypothalamic neurons the transcriptional and functional consequences of these mutations will be compared to isogenic controls using the functional assays described above. In parallel with these studies, we will use single-cell RNA sequencing to examine the effect of common genetic variants associated with obesity on gene expression in different sub-populations of human hypothalamic neurons.
3) Translation and in vivo models
In previous studies, we have shown that human hypothalamic neurons survive transplantation into the mouse brain. To test the functionality of human stem cell-derived neurons in an in vivo context, we transplant purified hypothalamic neuron populations into the adult mouse brain. Our ultimate goals are to rescue animal models of obesity via transplantation, and to develop transplantation as an way to examine the effect of human mutations on organismic phenotypes such as feeding behaviour.
Outstanding graduate and postdoctoral candidates interested in joining our team are encouraged to write me directly.
1) 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, in press).
2) Santos D, Kiskinis E, Eggan K, and Merkle, FT. Comprehensive protocols for CRISPR/Cas9-based gene editing in human pluripotent stem cells. Current Protocols in Stem Cell Biology. 2016 Aug 17, pp5B. 6.1-5B. 6.60.
3) 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.
4) 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.
5) Merkle FT, Fuentealba LC, Sanders TA, Magno L, Kessaris N, Alvarez-Buylla A.
Adult neural stem cells in distinct microdomains generate previously unknown interneuron types. Nat Neurosci. 2014 Feb;17(2):207-14. doi: 10.1038/nn.3610.
6) Merkle FT, Eggan K. Modeling human disease with pluripotent stem cells: fromb genome association to function. Cell Stem Cell. 2013 Jun 6;12(6):656-68. doi: 10.1016/j.stem.2013.05.016.
7) Merkle FT, Mirzadeh Z, Alvarez-Buylla A. Mosaic organization of neural stem cells in the adult brain. Science. 2007 Jul 20;317(5836):381-4.
Additional publications are available at: http://www.ncbi.nlm.nih.gov/pubmed/?term=merkle+ft