Biological ‘programmers’ crack new code in stem cells

Stem cell colony Wyss Institute James Collins George Daley complexity
Researchers discovered many small nuances in pluripotency states of stem cells by subjecting the cells to various perturbations and then analyzing each individual cell to observe all the different reactions to developmental cues within a stem cell colony. (Credit: Wyss Institute at Harvard University)

Stem cells offer great potential in biomedical engineering because they’re pluripotent—meaning they can multiply indefinitely and develop into any of the hundreds of different kinds of cells and tissues in the body. But in trying to tap these cells’ creative potential, it has so far been hard to pinpoint the precise biological mechanisms and genetic makeups that dictate how stem cells diverge on the path to development.

Part of the challenge, according to James Collins, PhD, a core faculty member at the Wyss Institute for Biologically Inspired Engineering, is that not all stem cells are created the same. “Stem cell colonies contain much variability between individual cells. This has been considered somewhat problematic for developing predictive approaches in stem cell engineering,” he says.

But now, Collins and Boston Children’s Hospital’s George Q. Daley, MD, PhD, have used a new, very sensitive single-cell genetic profiling method to reveal how the variability in pluripotent stem cells runs way deeper than we thought.

While at first glimmer, it could appear this would make predictive stem cell engineering more difficult, it might actually present an opportunity to exert even more programmable control over stem cell differentiation and development than was originally envisioned. “What was previously considered problematic variability could actually be beneficial to our ability to precisely control stem cells,” says Collins.

Collins, Daley and their collaborators—including the study’s lead authors Patrick Cahan, PhD, of Boston Children’s and Roshan Kumar, PhD, of the Wyss—explored the stem cells’ developmental landscape and state of pluripotency by perturbing them in various ways, such as prodding them with different chemicals, growing them in different culture environments and knocking out select genes. Using the single-cell analysis method throughout, they closely monitored how individual stem cells’ unique genetic makeup went through micro-fluctuations during each change to a cell’s pluripotent state.

Their experiments revealed many small nuances in the way internal, chemical and environmental cues influence stem cells, revealing complex “decision-making” circuits that regulate development. These nuances could present an opportune point of entry for scientists to influence which developmental path a cell will follow.

James Collins George Daley sequencing single stem cells
James Collins, PhD, and George Q. Daley, MD, PhD

“These emerging single-cell analytics allow us to classify cells very precisely and identify regulatory circuits that control cell states,” says Kumar, a former postdoctoral fellow in the Collins lab and a current visiting fellow at the Wyss. “The real motivating force behind this study was to understand the causes and consequences of differences between individual stem cells and how the balance of key regulators within a cell can affect that cell’s developmental outcome.”

‘The study was made possible through the use of novel technologies for studying individual cells, which were developed in part by collaborating groups at the Broad Institute, giving our team an unprecedented view of stem cell heterogeneity at the individual cell level,” says Cahan, who is a postdoctoral fellow in the Daley lab.

The researchers now believe that a “code” exists that relates activity patterns in stem cell regulatory circuits to the developmental path a cell ends up taking. By leveraging that code, they hope to manipulate and precisely control which cell and tissue types will develop from an individual pluripotent stem cell or stem cell colony. This could allow them to create specific cell types for a variety of purposes, such as regenerative medicine.

“It’s a very fundamental study but it highlights the wide range of states of pluripotency,” says Daley, who directs Boston Children’s Stem Cell Transplantation Program. “We’ve captured a detailed molecular profile of the different states of stem cells.”

“The ability to understand and program stem cells throughout changing states of pluripotency is a critical necessity for the success of regenerative medicine,” said Donald Ingber, MD, PhD, founding director of the Wyss Institute and the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s. “By making stem cell engineering more predictive, we hope to leverage the versatility of controllable pluripotent stem cells to address a wide range of diseases and injuries.”

Kat J. McAlpine is a science writer at the Wyss Institute for Biologically Inspired Engineering. This post was adapted from a press release issued by the Wyss Institute.