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Unmasking the True Identity of Gut Stem Cells

A stem cell dividing in two with other cells and DNA helices in the background
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Regenerative medicine may not be living up to its potential due to a case of mistaken identity in gut stem cell research, two independent studies from Columbia University suggest.

Gut stem cells were first identified in 2007 in a discovery hailed as a breakthrough in stem cell science. The research identified Lgr5, a G-protein coupled receptor protein on the cell’s surface involved in the canonical Wnt signaling pathway, as a specific marker for intestinal stem cells.

Using new lineage tracing and computational tools, Columbia researchers have found that Lgr5+ cells are in fact descendants of the gut’s true stem cells. The gut’s true stem cells are found in a different location, produce different proteins and respond to different signals.

“Regenerative medicine has not lived up to its full promise yet. Perhaps one reason for this is that in the gut, we have been targeting the wrong cells,” Dr. Kelley Yan, assistant professor of medicine at Columbia University Vagelos College of Physicians and Surgeons, told Technology Networks.

The role of stem cells in the gut

A layer of epithelium cells lines the inside of the gut. The small intestine epithelium is the largest tissue in the body with an estimated surface area comparable to that of a tennis court. It makes around a million new cells per minute throughout our lifetime to regenerate the tissue every few days. Stem cells work to regenerate the small intestine epithelium under normal conditions to maintain a healthy state and when the tissue is injured and requires repair.

“By better understanding intestinal stem cells and how they manage to be so effective at their job we can hack these cells to better repair the gut in the context of injury and disease,” explained Yan. “Furthermore, we can apply these lessons to hack stem cells in other tissues and organs that are less capable of regeneration.”

Cracks in existing models of regeneration

The existing model for how the intestinal epithelium regenerates states that all Lgr5+ cells are stem cells, and all stem cells are Lgr5+. Over the past decade, discrepancies in the model began to emerge. Yan describes how studies have shown that “When Lgr5+ cells were depleted, the tissue continued to regenerate in much the same way as when the Lgr5+ cells were present.”

Since these findings, many publications have evoked various mechanisms in which the tissues could regenerate without the stem cells to try to explain this paradox. “Some suggest that other mature cells can walk backward in developmental time and regain stem cell characteristics,” said Yan. “Others suggest that there is a dormant population of cells that can become activated upon damage to take over the job of regeneration.”

Identifying the true gut stem cells

Researchers at Columbia University pursuing separate projects realized they were converging on similar conclusions that Lgr5+ cells were not the true gut stem cells.

The lab of Dr. Timothy Wang, the Dorothy L. and Daniel H. Silberberg Professor of Medicine at Columbia University, started a project in collaboration with Dr. Andrea Califano, the former chair of the Systems Biology Department at Columbia, who has developed innovative computational algorithms to reconstruct relationships between cells within a tissue.

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In their study, published in the journal Cell, they focused on the intestinal crypt, the region of the tissue where stem cells are thought to live and divide.

Performing single-cell RNA sequencing to characterize cells within the crypt and feeding this information into computational algorithms, the team discovered the source of “stemness” did not lie within the Lgr5+ cells but in other cells within the crypt.

Moreover, the same stem cells were found in the context of irradiation injury or Lgr5+ cell depletion as in the normal intestinal crypt. This suggests that there is no reversion or activation of cells to account for regeneration when the Lgr5+ cells are lost.

Yan and colleagues aimed to understand other cells outside of Lgr5+ cells that inhabit the crypt. “Despite the fact that other non-Lgr5+ cells are dividing and thought to have some limited potential to regenerate tissue, nobody has been able to study these cells in a rigorous manner as we lacked markers to track or isolate them,” explained Yan.

The study, also published in the journal Cell, identified a population of cells that were proliferative and expressed the gene marker Fgfbp1. This gene encodes a secreted fibroblast growth factor carrier protein. The encoded protein plays a critical role in cell division and migration by potentiating the biological effects of fibroblast growth factors on target cells. Computational analysis showed that the Fgfbp1+ cells give rise to all intestinal cells, including the Lgr5+ cells.

“These findings change our understanding of stem cell identity, their location and their relationship to the other cells in the tissue,” said Yan.

Developing new lines of genetically engineered mice to track and isolate these cells within the intestine enabled the researchers to identify the Fgfbp1+ cells as the crypts cells that reside above the Lgr5+ cell compartment.

“We saw that the Fgfbp1+ cells have all the properties of stem cells,” explained Yan. “Importantly, the experiments showed us that the Lgr5+ cells actually arise from the Fgfbp1, consistent with our computational analysis.”

The future of stem cell research and therapies

The findings have huge implications for the field of gut stem cell research, with past studies potentially needing to be reinterpreted in light of the stem cells’ new identity, the researchers suggest.

By further understanding these outside signals that provide stem cells with instructional cues, the researchers hope to unleash the full regenerative potential of these cells to heal injured tissues.

“Stem cells can be double-edged swords that are beneficial in healing but can also lead to disease,” said Yan.

“It is believed that cancers are wounds that never heal and arise from stem cells that have gone awry,” said Yan. “So, in understanding the identity of the stem cell, we could potentially develop new therapeutics that can prevent cancer development.”

Yan concludes, “Ultimately, we hope to identify a universal pathway that underlies how stem cells work broadly across different tissues so that we can apply the principles from stem cells in the gut who are constantly regenerating toward other tissues like hair, skin, heart, kidney, liver, and brain, etc.”

Dr. Kelley Yan was speaking to Blake Forman, Senior Science Writer for Technology Networks.

About the interviewee:

Dr. Kelley Yan is an assistant professor of medicine at Columbia University Vagelos College of Physicians and Surgeons. Her research interests include understanding tissue renewal in health and disease using the mammalian intestine as a model system to study adult stem cell biology.


Malagola E, Vasciaveo A, Ochiai Y, et al. Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. Cell. 2024;187(12):3056-3071.e17. doi: 10.1016/j.cell.2024.05.004

Capdevila C, Miller J, Cheng L, et al. Time-resolved fate mapping identifies the intestinal upper crypt zone as an origin of Lgr5+ crypt base columnar cells. Cell. 2024;187(12):3039-3055.e14. doi: 10.1016/j.cell.2024.05.001