Modern humans have existed for over 200,000 years, and each new generation has begun with a single cell—dividing, changing shape and function, organizing into tissues, organs, and limbs. With slight variations, the process has repeated billions of times with remarkable fidelity to the same body plan.

Researchers at Tufts have been on a quest to understand the code guiding individual cells to create the architecture of a human being, and to create a foundation for regenerative medicine. As they learn more about that code, they are also looking at how to build living structures from human cells that have totally new forms and capabilities—without genetic manipulation.

To decipher that code, they took a cell from the human body and allowed it to grow in a novel environment to observe how the rules of self-organization play out.

In 2023, Michael Levin, Vannevar Bush Professor of Biology, and then Ph.D. candidate Gizem Gumuskaya, AG23, created Anthrobots, tiny multicellular organisms grown from a single human tracheal cell and assembled into new forms—spherical, oblong, covered with cilia on all or part of their surfaces, capable of swimming and repairing “wounds” in plated neurons.

In a new study recently published in the journal Advanced Science, Gumuskaya and Levin reveal what is going on inside the Anthrobot cells as they create a new living construct. The researchers discovered that human cells freed from their evolutionary obligations will turn back the clock to express both ancient genes, which are shared with our predecessors as far back as single celled organisms, and embryonic genes, including those that guide emerging symmetry, layering, and folding of cells and tissues. 

With a new mission to create tiny bots instead of entire humans, the cells changed their expression of over 9,000 genes—almost half the genome—without any interventions like synthetic biology circuits or genetic engineering. 

Beyond creating new synthetic constructs, understanding how human cells take on new shapes can shine light into developmental diseases, such as birth defects. Levin and his lab want to better understand the rules of self-assembly to perhaps someday help prevent birth defects, grow new tissues and organs for regenerative medicine, and create tiny functional organisms like Anthrobots from the patient’s own cells that could treat disease and repair damage without triggering immune system responses.

Cell Hardware and Software

“Anthrobots are made from adult donor cells, so it was striking to see that those cells were also expressing embryonic genes,” said Gumuskaya. That included genes that help make the embryonic mesoderm-ectoderm transition—a process that takes outer layer cells to create a middle layer that ends up forming interior tissues and organs, as well as genes for making anterior-posterior (head to tail), and dorsal-ventral (back to belly) patterns.

What did not come up were embryonic genes involved in left-right patterning—the kind that helps create mirror symmetry with arms, eyes, legs, lungs, and kidneys on either side of a body. 

“The Anthrobots are mostly spherical, so at this point it’s hard to say without further study what role each of these embryonic genes played in their bodies’ construction,” says Levin.

Even if the researchers take a knife to the Anthrobots and cut open a wound, they exhibit a kind of functional shape memory that allows them to heal back to their original form.

Levin points out that this emerging model illustrates that the genes determine the cell’s hardware—making receptors, enzymes, ion pumps, and more—while emergent features of that hardware, such as electrical fields, chemical signals, and biomechanical forces experienced by the tissues taking shape, are the software instructions that guide the body into its final form. The software, he says, can change depending on the starting conditions and environment, in turn influencing the hardware. 

Detecting biological clock reversal in Anthrobots relied on tracking the accumulation of modifications and damage to DNA as we get older. The addition of methyl chemical groups to DNA is a measurable quantity that contributes to our “epigenetic age,” which can end up being older or younger than our chronological age. One donor for the Anthrobot study was 21 years old, but the epigenetic age of his cells was 25. Remarkably, when the cells were used to grow Anthrobots, their epigenetic age dropped to 18.7 years. Anthrobots were biologically 25% younger than their cells of origin. 

“The fact that these bots become biologically younger than the adult cells they’re made from suggests that the process of organizing into a new shape alone can reset the cellular aging clock—without any genetic reprogramming,” says Gumuskaya. 

Levin offered a hypothesis for dialing back biological clocks. “I think that cell collectives are fundamentally information-processing agents,” he said. “The developmental genes being activated, the physical forces from their new shape and other aspects of their self-construction can be interpreted by cells as embryogenesis, which conflicts with their actual age. So they end up reversing some of the DNA markers of aging to be consistent with their current state. I call this the ‘age evidencing’ hypothesis.”

What exactly are the cues that convince cells to roll back the Anthrobot’s epigenetic clock? Could they be harnessed to rejuvenate tissues in our own bodies? “We’re working on it,” says Levin.