Caption: What we remove can shape what grows. These miniature liver tissues were grown in the lab. On the right, SynBITE selectively removed unwanted cells, leaving tissue richer in cells producing albumin, an important liver protein shown in yellow. The tissue on the left developed without this treatment. Blue marks cell nuclei.
By Michael Aubele
Pruning a tree improves its shape and promotes proper growth. University of Pittsburgh researchers say “pruning” aberrant cells when building tissues serves the same purpose. The results of their research, which could have broad applications when studying disease and development in vitro, were published Oct. 22 in Cell Stem Cell.
The body builds tissues through both growth and removal. Like an arborist shaping a maturing shade tree, the Pitt team has shown it can control cell death to mold developing lab-grown tissues by removing cells at the right place and time. They accomplished this through a synthetic biology tool they created, called SynBITE. 
Led by Mo Ebrahimkhani (right), associate professor of pathology, School of Medicine, and director of the Synthetic Morphogenetics and Tissue Ecology Lab, the researchers used SynBITE in a new process they describe as “subtractive tissue engineering” to control engineered tissue architecture and function, including processes such as cavity formation and tissue maturation.
“We think this provides a new way to engineer multicellular systems by combining tissue construction with selective cellular elimination and correction,” Ebrahimkhani says. “And because the concept is quite general, we believe the approach could be applied across organoids, engineered human tissues, multicellular models and other complex biological systems.”
Researchers are leaning into new approach methodologies (NAMs) such as organoids, human tissue models and other in vitro systems as alternatives to animal testing. In their research, Ebrahimkhani and team demonstrated this in liver organoids derived from induced pluripotent human stem cells as well as models of early human development.
Organoids are three-dimensional tissue models that reproduce some features of human organs. But growing them presents a persistent challenge: not all cells develop as intended, leaving a mixture of desired and unwanted cell types.
In part of their work, the team used SynBITE to prune unwanted cells from the lab-grown liver tissue as it formed. SynBITE’s programmable genetic circuits recognize signals about a cell’s identity or developmental state. When researchers activate the system with small molecules, the circuits trigger cell death in selected populations. An additional layer of control can protect cells researchers want to keep.
The body uses this process, called apoptosis, as a programmed form of cell death to clear away unwanted or damaged cells. An example is found in the formation of fingers and toes during embryonic development as the body destroys the webbing that initially is present between the digits.
“We took inspiration from this natural process,” says Mohammad Taheri (right), the paper’s cofirst author and a bioengineering PhD candidate in Ebrahimkhani’s lab, who developed SynBITE.
In the liver organoid, SynBITE not only removed aberrant cells but allowed mature cells to take their place, while a second layer of control kept the tissue’s blood-vessel-like networks intact.
The team also used SynBITE to sculpt a model of early human development, promoting the formation of an internal cavity and improving the organization of surrounding tissues.
“Ultimately, the research could bring lab-grown tissues closer to those in the human body, making them more useful for understanding disease, transplantations and testing how medicines work,” Ebrahimkhani says.
Funding from the University’s Department of Pathology, the National Institutes of Health, the National Science Foundation and Pittsburgh Liver Research Center supported the work.