I’m late, I’m late, for a very important date deciding the fate of thymic progenitors!

“During development and tissue regeneration, stem and progenitor cells give rise to differentiated cell types in defined numbers and proportions to properly generate and maintain organs and body plans,” shared researchers from the Kueh lab at the University of Washington (UW). But how do stem and progenitor cells know when to differentiate and which cell lineage to produce and to send down the conveyor belt? The answer lies in a gene regulation method called epigenetic switches, which function as key decision makers on the circuit breaker that is the human genome. These switches stand apart from genetic mutations that can control protein expression levels and/or activity. Instead, epigenetics can reduce or enhance gene expression without making changes to the genetic code itself.

Epigenetic regulatory proteins can form complexes with other proteins and typically bind to DNA directly to modify DNA structure, gene expression, and other features of the DNA in either a positive or negative way. Due to this flexibility, these epigenetic regulators behave as the managers instructing the stem and progenitor cells when to grow and which cell lineage to produce. Epigenetic switches can delay the activation of genes required for cell lineage decisions after initial exposure to developmental signals and these delays can be as long as several days or occur over multiple cell generations, explained the researchers from the Kueh lab. Despite these observations, it remained unclear if these delays in gene expression were another important method of regulating the development of specific cell lineages. This is exactly what Dr. Hao Yuan Kueh, an Associate Professor in the Bioengineering Department at UW and Cancer Consortium member, and Nicholas Pease, a PhD student in his lab, wanted to answer. The researchers focused on manipulating the epigenetic lever that regulates the expression of a transcription factor, Bcl11b, that drives T cell generation from precursor progenitor cells. Strikingly, they uncovered that delaying Bcl11b expression reduced production of T cells and increased production of innate lymphoid cells instead! These findings were published in Development. 

The thymus is a gland behind your sternum and centered between the lungs whose central purpose is to produce and train T cells. “After entering the thymus, hematopoietic progenitors maintain a multipotent state for ~7 days, where they are able to give rise to multiple immune cell lineages,” stated the researchers from the Kueh lab. While these cells predominantly differentiate into various T cell lineages, a small subset of these stem cells choose another path, either becoming type 2 innate lymphoid cells (ILC2s) or natural killer (NK) cells. Expression of Bcl11b is known to drive T cell and repress NK cell lineage selections. However, Bcl11b is not expressed in progenitor cells until ~7 days after entering the thymus, aligning with their delayed decision to generate T cell lineages or less frequently ILC2s or NK cells.

To study how this choice is made, the Kueh lab engineered mice to express a fluorescence tagged Bcl11b in a wild-type background and in mice in which the enhancer element that mediates the epigenetic-dependent expression of Bcl11b is mutated—causing a lag in Bcl11b expression beyond its normal delay in thymic progenitor cells. Stem cells from the bone marrow or thymic progenitor cells from the thymus were harvested to determine the outcome of suppressing Bcl11b on thymic progenitor lineage selection. Intriguingly, the researcher uncovered that delayed expression of Bcl11b longer than the typical 7 days following stem cell entry into the thymus resulted in decreased T cell production and an increase in ILC lineage selection. Upon further characterization, the researchers discovered that the absence of Bcl11b enables the expression of another transcription factor, Zbtb16, that drives ILC lineage selection. This epigenetic mechanism within thymic progenitor cells favors T cell lineage selection and results in minimal ILC lineage selection to coordinate a robust immune response and infrequent response to thymic damage, respectively.

In short, epigenetic factors regulate the expression of the Bcl11b transcription factor with a long fuse to trigger T cell lineage selection. Changing this timing of Bcl11b expression provided insight into how the minor population of ILC lineage cells are selected and raises additional questions about how selection of lineage subtypes occurs for T cell, ILCs and NKs. “In further studies, it would be important to more broadly investigate roles for epigenetic timing control in developmental gene regulation and decision making across diverse contexts,” concluded the researchers from the Kueh lab. Timing delays mediated by epigenetics may reveal a hidden network of decisions that cells experience in response to other stimuli as well. 

The spotlighted research was funded by the National Institutes of Health, the National Heart, Lung, and Blood Institute, the National Science Foundation, the John H. Tietze Foundation, and the University of Washington.

Fred Hutch/University of Washington/Seattle Children's Cancer Consortium member Dr. Hao Yuan Kueh contributed to this work.

Pease NA, Denecke KM, Chen L, Gerges PH, Kueh HY. 2024. A timed epigenetic switch balances T and ILC lineage proportions in the thymus. Development. 151(23):dev203016.