Hunting for computational approaches for stem cells at ISSCR2017

By Cátia Bandeiras, PhD Student at University of Lisbon, Portugal and Massachusetts Institute of Technology. See tweets from the conference using #ISSCR2017 @apulgarita

I just wrapped up my stay at the Annual Meeting of ISSCR 2017, which happened in Boston. I decided to take advantage of the fact that I am living in Boston at the moment and go to the largest stem cell research conference to present my work. As a matter of fact, I am not the usual PhD student in stem cell research. I don’t do lab work at all, my working hours are spent coding a simulation model for stem cell manufacturing. Given my background as a programmer, I went there with the very specific mission of finding the hottest trends in computational research for stem cells.

I was present in a varied mix of plenary and concurrent sessions. My focus was related to expansion and differentiation of induced pluripotent stem cells (iPSCs), in particular into endodermal lineages, mesenchymal stem cells (MSCs), clinical trials and research translation and ethical considerations in stem cell research, which are all topics aligned with my project. While most of the talks were interesting, to me there were two from the ones I saw that stood out:

• Shinya Yamanaka from the Center for iPS Cell Research and Application (it’s not every day I could say I was witnessing a Nobel Prize awardee talk) gave a compelling lecture on the methodologies for allogeneic therapies produced from iPSCs, focusing on the recently initiated clinical trial with allogeneic iPSCs-derived retinal pigment epithelium cells. The need for allogeneic pluripotent stem cell derived therapies is driven by the prohibitive costs of autologous manufacturing for these therapies, reaching costs of over $1 million per patient, as mentioned by Hardy Kagimoto from Healios K.K.
• George Daley from the Boston Children’s Hospital (and awardee with this ISSCR edition Public Service Award) focused on the “brave new world” of emerging biomedical technologies. He mentioned how gene editing of animal embryos looked like science fiction until some years ago, with the advent of CRISPR/Cas9 technology, and how human embryos will be able to be edited. Daley discussed the ethical considerations behind human gene editing, as well as mitochondrial DNA replacement in case of mitochondrial diseases and how it can only be done in male embryos, and the very recent growth of goat fetuses in an extrauterine system. He mentioned the new ISSCR guidelines for stem cell research, released in 2016, and how technology is always ahead of the guidelines.

In none of the talks I watched much attention was paid to computational methodologies for research of result analysis, even from a bioinformatics point of view, which is the most common use to evaluate the up or down regulation of gene expression during culture events. Therefore, I decided to take a closer look into the poster sessions and to look carefully into the list of abstracts for computational approaches. While most of the posters that included computational methodologies were focused on computational biology and gene clustering, I found some other interesting projects. I learned about the SyMBioSys consortium, an initiative led by Sakis Mantalaris from University College of London focused on building kinetic models to explain functional behavior from varying concentrations in cell components, through a metabolic model reconstruction of umbilical cord blood mesenchymal stem cell during osteogenic differentiation. I also learned how the migration of implanted neural stem cells (NSCs) is made along the white matter of the brain and how the directions and velocity of migration can be modeled through imaging and fluid dynamics modeling with researchers from the City of Hope National Cancer Center. Finally, I was captivated by the Stem Cell Commons open source bioinformatics platform created by researchers from the Harvard Stem Cell Institute, aiming to help wet lab scientists to process, share and visualize data in stem cell research. I talked with some of the poster presenters and there were two groups: one, where the presenters are experimental researchers and have to devote the limited amount of time available to computational analysis, and another where there are specialized computational biologists or mathematicians to analyze the experimental work of their group colleagues. I am in the latter group, and I generally tend to think that this is a more productive approach to research. From the feedback I got from my poster, there seems to be a lot of interest for new computational methods that are ready to use, open source, and user-friendly for experimental scientists. It is upon us to develop these tools with reliability and reproducibility to help advance stem cell research even further.

I was very pleased with my first experience at ISSCR and hope to be able to present in the future. This was only a very quick overview of my experience, focused on my research field, but I was impressed with the amount of innovation and recent successes with pre-clinical and clinical trials presented there. As Sally Temple, president of ISSCR said in the opening session, “This is our Century”. I hope for our community that we can keep on working on bringing safe and effective stem cell therapies to the clinic, as well as better disease models and drug screening platforms, with the collaboration of professionals with many different expertises.