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Department of Physiology, Development and Neuroscience


We investigate the mechanisms that direct cell fate in human embryos and stem cells. This means studying the different factors that tell embryonic cells which type of cell to become. After a human egg is fertilised, the cells multiply as the embryo grows. After five days there are around 100 cells, under 10 of which are embryonic epiblast cells that go on to form the foetus – these are pluripotent cells, as they are capable of becoming any type of cell in the body. The remaining 90 or so cells will go on to form either the placenta or the yolk sac.

We’re trying to understand how these early human pluripotent embryonic cells are established, how they remain pluripotent and how this process if turned off when the cells specialise. We’re trying to map out the complex hierarchy of different genes that control cell activity in early development, determine the influence of factors outside of the cells and understand the similarities and differences between human and mouse development. The processes that underpin early development and stem cell pluripotency are fundamental to human biology. If we knew how these processes worked, this knowledge could inform the understanding and treatment of infertility and developmental disorders. We could also use this knowledge to improve our use of stem cells in both science and medicine.


The goal of our research to understand the molecular mechanisms that control early human development. The mechanisms that regulate early cell fate decisions in human development remain poorly understood, despite their fundamental biological importance and wide-reaching clinical implications for understanding infertility, miscarriages, developmental disorders and therapeutic applications of stem cells. We seek to uncover when and how human embryonic epiblast cells are established and maintained, and to understand the molecular mechanisms that distinguish these pluripotent cells from extra-embryonic cells during embryogenesis. We will further develop pioneering methods to investigate gene function during human embryogenesis using CRISPR-Cas9-mediated genome editing, TRIM-Away protein depletion, constitutively active and kinase dead variants of proteins and small molecule inhibitors and activators. These approaches will enable us to directly test the function of genes involved in signalling pathways, and key transcription factors downstream of these pathways, which we hypothesize are involved in the first and second cell fate decisions. Altogether, we seek to make significant advances in our understanding of the molecular programs that shape early human embryogenesis, which has the potential to provide fundamental insights and to drive clinical translation.

Our laboratory has pioneered approaches to investigate the function of genes that regulate human preimplantation embryo development. To date, we have uncovered a mechanism underlying the first lineage decision in human embryogenesis; discovered gene regulatory networks specific to human embryos, which are not found in mouse embryos; and identified mechanisms that are evolutionarily conserved across mammals. These discoveries validate the need to study human embryos directly. By integrating signalling insights gained from transcriptomic analysis of human blastocysts, we have defined human embryonic stem cell (hESC) culture conditions that more closely recapitulate the embryonic niche. The foundational knowledge we have generated will be informative to further improve ex vivo models to better understand human biology. By applying the knowledge we gained from dissecting the molecular programs in the developing embryo, we are identifying signalling pathways and transcription factors that mediate a cell fate switch from a pluripotent embryonic stem cell (ESC) to yolk sac or placental progenitor cells.


Key publications: 

Claudia GerriAfshan McCarthyGregorio Alanis-LobatoAndrej DemtschenkoAlexandre BruneauSophie Loubersac,
Norah M E Fogarty
Daniel HampshireKay ElderPhil SnellLeila ChristieLaurent DavidHilde Van de VeldeAli A Fouladi-NashtaKathy K Niakan
Initiation of a conserved trophectoderm program in human, cow and mouse embryosNature, In press.

Sissy E WamaithaKatarzyna J GrybelGregorio Alanis-LobatoClaudia GerriSugako OgushiAfshan McCarthyShantha K MahadevaiahLyn HealyRebecca A LeaMiriam Molina-ArcasLiani G DevitoKay ElderPhil SnellLeila ChristieJulian DownwardJames M A TurnerKathy K Niakan
IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche, Nature Communications, 11(1):764

Norah M E FogartyAfshan McCarthyKirsten E SnijdersBenjamin E PowellNada KubikovaPaul BlakeleyRebecca LeaKay ElderSissy E WamaithaDaesik KimValdone MaciulyteJens Kleinjung, Jin-Soo KimDagan WellsLudovic VallierAlessandro BerteroJames M A TurnerKathy K Niakan
Genome editing reveals a role for OCT4 in human embryogenesis, Nature, volume 550, pages67–73

Louise A HyslopPaul BlakeleyLyndsey CravenJessica RichardsonNorah M E FogartyElpida FragouliMahdi LambSissy E WamaithaNilendran PrathalingamQi ZhangHannah O'KeefeYuko TakedaLucia ArizziSamer AlfarawatiHelen A TuppenLaura IrvingDimitrios KalleasMeenakshi ChoudharyDagan WellsAlison P MurdochDouglass M TurnbullKathy K NiakanMary Herbert
Towards clinical application of pronuclear transfer to prevent mitochondrial DNA disease, Nature, 534, pages383–386

Paul BlakeleyNorah M E FogartyIgnacio del ValleSissy E WamaithaTim Xiaoming HuKay ElderPhilip SnellLeila ChristiePaul RobsonKathy K Niakan


Defining the three cell lineages of the human blastocyst by single-cell RNA-seq, Development,

Sissy E WamaithaIgnacio del ValleLily T Y ChoYingying WeiNorah M E FogartyPaul BlakeleyRichard I SherwoodHongkai JiKathy K Niakan

Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells, Genes & Development, 2015. 29: 1239-1255

Mary Marshall and Arthur Walton Professor of Reproductive Physiology
Director, Centre for Trophoblast Research
Chair, Strategic Research Initiative in Reproduction
Picture of Kathy Niakan

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