Two recent studies by Columbia University scientists reveal a significant flaw in stem cell research: Gut stem cells identified more than 15 years ago are not actual stem cells. New tools have uncovered true stem cells, which are located differently and could reshape the field of regenerative medicine by enabling therapies that repair multiple organs.
Columbia UniversityResearch has uncovered a long-standing error in the identification of intestinal stem cells, finding the true stem cells in a different site, which could revolutionize regenerative medicine by applying these findings to other organs.
Two independent studies by Columbia scientists suggest that research on gut stem cells over the past 15 years has been marred by a case of mistaken identity: Scientists have been studying the wrong cell.
Both studies were published in the journal Cell. Gut stem cells are some of the hardest working stem cells in the body. They work continually throughout our lives to replenish the short-lived cells that line our intestines. About every four days, these cells, which cover an area the size of a tennis court, are completely replaced.
Understanding these workaholic stem cells could help scientists activate less productive stem cells in other organs to repair hearts, lungs, brains, and more. Gut stem cells were supposedly identified more than 15 years ago in a landmark study.
But using new computational and lineage-tracing tools, the Columbia teams, led by Timothy Wang and Kelley Yan, discovered that these cells are descendants of true gut stem cells. True gut stem cells are in a different location, produce different proteins, and respond to different signals.
“The new work is controversial and paradigm-shifting, but it could revitalize (the entire?) field of regenerative medicine,” says Timothy Wang, the Dorothy L. and Daniel H. Silberberg Professor of Medicine.
“We know we are causing a lot of change in this field, but if we want to move forward, we need to identify the true stem cells so we can target these cells for therapies,” says Kelley Yan, the Herbert Irving. Assistant Professor of Medicine.
We recently spoke with Kelley Yan and Timothy Wang about the findings and implications.
Why does the intestine need stem cells?
KY: What’s relevant to this story is a tissue called intestinal epithelium. It is a single layer of cells that lines the intestine and is made up of different types of cells that help digest food, absorb nutrients and fight microbes.
Most cells live only about four days before being replaced, so stem cells must create replacements.
What is really notable about the intestinal lining is its size. If we sliced his intestine open and spread it flat, it would cover the surface of a tennis court.
Gut stem cells may be the hardest working stem cells in the body.
Gut stem cells were supposedly identified in 2007, and the discovery was hailed as a breakthrough in stem cell science. What made you think this was a case of mistaken identity?
TW: For the past 17 years, the intestinal stem cell field has assumed that Lgr5, a protein on the cell surface, is a specific marker for intestinal stem cells. In other words, all Lgr5+ cells are assumed to be stem cells and all stem cells are believed to be Lgr5+. These Lgr5+ cells were located at the bottom of the glands or crypts of the intestinal lining.
However, in the last decade problems began to appear with this model. Removing Lgr5+ cells in mice, using a genetic approach, did not seem to bother the intestine much, and the Lgr5+ stem cells reappeared within a week. Furthermore, the intestine was able to regenerate after severe injury, such as radiation-induced damage, even though the injury destroyed almost all Lgr5+ cells.
KY: By their very definition, stem cells are the cells that regenerate tissues, so these findings created a paradox. Many high-profile papers have evoked different mechanisms to explain the paradox: some suggest that other fully mature intestinal cells can go back in development time and regain the characteristics of stem cells. Others suggest that there is a latent population of stem cells that only functions when the lining is damaged.
No one has really examined the idea that perhaps Lgr5+ cells are not actually stem cells, which is the simplest explanation.
How did your labs identify actual gut stem cells?
TW: My lab collaborated with former chair of Columbia’s systems biology department, Andrea Califano, who developed cutting-edge computational algorithms that can reconstruct the relationships between cells within a tissue. We use a single cell RNA sequencing to characterize all the cells in the crypts, the region of the intestine where stem cells are known to reside, and then fed that data into the algorithms.
These algorithms revealed that the source of the “trunk” in the intestine was not in the Lgr5+ cell group but in another cell type higher up in the crypts in a region known as the isthmus. After eliminating Lgr5+ cells with radiation or genetic ablation, we confirmed that these isthmus cells were intestinal stem cells and capable of regenerating the intestinal lining. We found no evidence that other mature cells could go back in time and become stem cells.
KY: We were not trying to identify stem cells but to understand the other cells in the intestine involved in lining regeneration. No one has been able to define these other progenitor cells in the intestine.
We identified a population of proliferating cells marked by a protein called FGFBP1. When we asked how these cells were related to Lgr5+ cells, our computational analysis told us that these FGFBP1 cells give rise to all intestinal cells, including Lgr5+, the opposite of the accepted model.
My graduate student, Claudia Capdevila, made a mouse that would allow us to determine which cells (Lgr5+ or FGFBP1+) were the true stem cells. In this mouse, every time the FGFBP1 gene is activated in a cell, the cell would express two different fluorescent proteins, red and blue. The red came on immediately and went off immediately, while the blue appeared a little later and stayed for days.
That allowed us to track the cells over time and clearly showed that FGFBP1 cells create Lgr5+ cells, the opposite of what people currently believe. This technique, called time-resolved target mapping, has only been used a few times before, and getting it to work was a pretty incredible achievement, I thought.
How will this affect the stem cell field and the search for stem cell therapies?
TW: This case of mistaken identity may explain why regenerative medicine has not lived up to its promise. We’ve been looking at the wrong cells.
Previous studies will need to be reinterpreted in light of the new identity of stem cells, but eventually this may lead to therapies that help regenerate the intestine in people with intestinal diseases and to possible stem cell transplantation in the future.
KY: Ultimately, we hope to identify a universal pathway underlying stem cell function, so that we can then apply the principles we learn about the gut to other tissues such as skin, hair, brain, heart, lungs , kidneys, liver, etc.
Some cancers are also thought to arise from stem cells that have failed. So, by understanding the identity of the stem cell, we could also develop new therapies that can prevent the development of cancer.
That is why it is so important to understand which cell underlies all this.
References: “Time-resolved fate mapping identifies the intestinal upper crypt zone as the origin of Lgr5+ crypt base columnar cells” by Claudia Capdevila, Jonathan Miller, Liang Cheng, Adam Kornberg, Joel J. George , Hyeonjeong Lee, Theo Botella, Christine S Moon, John W. Murray, Stephanie Lam, Rubén I. Calderón, Ermanno Malagola, Gary Whelan, Chyuan-Sheng Lin, Arnold Han, Timothy C. Wang, Peter A. Sims and Kelley S .Yan,. Cell.
DOI: 10.1016/j.cell.2024.05.001
“Isthmus progenitor cells contribute to homeostatic cell turnover and support regeneration after intestinal injury” by Ermanno Malagola, Alessandro Vasciaveo, Yosuke Ochiai, Woosook Kim, Biyun Zheng, Luca Zanella, Alexander LE Wang, Moritz Middelhoff, Henrik Nienhüser, Lu Deng, Feijing Wu, Quin T. Waterbury, Bryana Belin, Jonathan LaBella, Leah B. Zamechek, Melissa H. Wong, Linheng Li, Chandan Guha, Chia-Wei Cheng, Kelley S. Yan, Andrea Califano, and Timothy C. Wang , , Cell.
DOI: 10.1016/j.cell.2024.05.004
Andrea Califano is a founder, shareholder, and consultant at DarwinHealth Inc., a company that has licensed some of the algorithms used in this manuscript from Columbia University. Columbia University is also a shareholder of DarwinHealth Inc. In connection with this work, US patent number 10,790,040 has been granted, assigned to Columbia University with Andrea Califano as inventor.
The research was funded by the National Institutes of Health and the Burroughs Wellcome Fund.
