A fate-mapped human pluripotent stem cell library for designer organoids

Modern technologies that capture details of single cells across a large population of cells are shedding new light on many avenues of mammalian biology. Nozomu Yachie, Ph.D., Nika Shakiba, Ph.D., and Josef Penninger, M.D., are leading a project to apply these technologies to the study and improvement of organoids, lab-grown mini-organs grown from human stem cells. By tracing the “family trees” of cell fates as stem cells grow and form, the team hopes to better understand the complex tissues inside these mini-organs, ultimately to the point of directing cell fate in different directions to faithfully engineer different types of organoids. The team is also working to introduce a blood vessel system to organoids, merging vascular organoids with other types of organoids, to give the tissues supplies of nutrients and oxygen that will keep them alive in the lab for longer.  

Affiliated Investigators

Nozomu Yachie, Ph.D.

University of British Columbia

Nozomu Yachie is an Associate Professor and Canada Research Chair in Synthetic Biology at the School of Biomedical Engineering (SBME) at the University of British Columbia (UBC). Combining technologies in cell engineering, genome editing, and computational biology, Yachie’s team is developing new technologies to measure the dynamics of molecules and cells in complex biological systems, including mammalian development and cell differentiation. Previously, Yachie was an Associate Professor at the University of Tokyo’s Research Center for Advanced Science and Technology (RCAST) and also served as the Director of the Laboratories for Systems Biology and Medicine (LSBM).

Yachie received his Ph.D. in Systems Biology from Keio University in 2009. He then completed postdoctoral training with Dr. Frederick Roth at Harvard Medical School and the University of Toronto where he received a Banting Fellowship. Yachie is also a recipient of JSPS fellowships DC1, PD and "Research Abroad" awarded by the Japan Society for the Promotion of Science, the PRESTO Researchership awarded by the Japan Science and Technology Agency (2014-2018), and the Young Scientists Award by the Minister of Education, Culture, Sports, Science and Technology, Japan (2020).

Nika Shakiba, Ph.D.

University of British Columbia

Nika Shakiba is an Assistant Professor in the School of Biomedical Engineering (SBME) at the University of British Columbia. Her lab is interested in the “social lives” of stem cells: how these cells interact to influence one another’s survival and cell fate decisions, both in culture and embryonic development. Dr. Shakiba’s team uses systems and synthetic biology to understand the genetic rules that encode cooperative and competitive interactions between stem cells. Leveraging genetic engineering, her lab seeks to program these interactions to drive predictable growth and differentiation outcomes and enable robust bioprocesses for manufacturing stem cell-derived cell therapies.

Dr. Shakiba completed her Ph.D. under the supervision of Dr. Peter Zandstra at the University of Toronto. She then conducted her postdoctoral training under the co-supervision of Dr. Ron Weiss and Dr. Domitilla Del Vecchio in the Synthetic Biology Center at Massachusetts Institute of Technology, supported by a Postdoctoral Fellowship from NSERC. Through these experiences, she has bridged experiment-to-theory by using genetic technologies to track single cell behaviors, using mathematical models to deconvolve complex datasets, and generating novel predictions. Dr. Shakiba is also passionate about providing equity in mentorship and multi-directional advice-sharing through her latest project, Advice to a Scientist.

Josef Penninger, Ph.D.

University of British Columbia

Josef Martin Penninger, born in Gurten, Austria, is a world-renowned geneticist and the Canada 150 Research Chair in Functional Genetics. Dr. Penninger is currently the Director of the Life Sciences Institute (LSI) at the University of British Columbia. He studied medicine at the University of Innsbruck in Austria. From 1990 to 1994 he worked as post-doctoral fellow at the Ontario Cancer Institute, thereafter until 2002 at the Department of Immunology and Medical Biophysics at the University of Toronto. As Principal Investigator of Amgen, his independent lab contributed to the development of the antibody Denosumab for bone loss and also found the first connection for RANKL to mammary gland development in pregnancy and breast cancer. In 2002, he moved to Vienna, Austria to start and develop the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), which has become one of the prime research centers in the world. Dr. Penninger envisions to recreate this environment at the LSI to nurture and train the best and brightest young minds of UBC scholars. His major accomplishments include pioneering insights into the molecular basis of osteoporosis and breast cancer, and demonstrating a critical role for ACE2 as the cellular receptor for the SARS Coronavirus infections and linking ACE2 to lung failure in such infections.  He has published extensively in several multidisciplinary scientific journals, with over 60 publications in Cell, Nature, and Science. Josef has received numerous awards including the Wittgenstein Prize of the Austrian Federal Government, the Descartes Prize for Research, the Ernst Jung Prize for Medical Excellence, the Innovator Award of the US Department of Defense, and the Austrian Cross of Honor for Science and Art First Class.