Novel drosophila transcription factor ortholog of BCL11A/BCL11B is crucial for regulating intestinal stem cell quiescence and preventing GUT dysfunction during aging

The National Institute of Diabetes and Digestive and Kidney Diseases awarded Baylor College of Medicine $149,190 on December 6, 2025, under the Diabetes, Digestive, and Kidney Diseases Extramural Research program (CFDA 93.847) to conduct basic research modeling intestinal stem cell regulation during aging.

The recipient will use Drosophila melanogaster to investigate mechanisms controlling the transition between active and quiescent states in intestinal stem cells, with particular focus on a transcription factor ortholog designated chronophage (CPH). CPH is the Drosophila equivalent of human BCL11A and BCL11B genes, both of which show specific expression in mammalian intestinal stem cells. The research employs bioinformatics-guided genetic screening and leverages existing single-cell sequencing datasets from the Fly Cell Atlas and Aging Fly Cell Atlas to characterize Drosophila intestinal stem cells and their age-related changes. Preliminary findings indicate that loss of CPH impairs intestinal stem cell proliferation and differentiation, suggesting the gene's role in maintaining stem cell function and preventing gut dysfunction during aging.

The award is structured as a project grant with a period of performance from December 6, 2025, through June 5, 2028. Work is performed in Houston, Texas.

Abstract

And abstract stem cells are essential for tissue homeostasis following environmental challenges. During aging however, these stem cells lose this ability to maintain tissue integrity. Dysregulation in the proliferation and the differentiation of stem cells are implicated in several pathologies such as cancer, hematological disorders, and gastrointestinal disease. Intestinal stem cells (iscs) reside in the digestive tract epithelium and their balance between active and quiescent states is disrupted during aging. Several signaling pathways that are dysregulated in aging iscs have been characterized, however, the mechanism by which iscs transit between active and quiescent states during an organism's lifetime is relatively unknown. Here i propose using drosophila melanogaster to model the regulation of quiescent and active states with their drosophila ISC (disc) population given the excellent orthology with miscs. Drosophila have the advantage of being inexpensive, reproducing rapidly, short-lived, and having plentiful genetic resources available. There are many datasets available to characterize discs and their changes during aging. These resources include single cell sequencing datasets from young and old fly guts developed in the lab: the fly cell atlas (2022 science) and the aging fly cell atlas (2022 science). Using a bioinformatics analysis-guided genetic screen approach i identified an uncharacterized transcription factor required for proper regulation in discs, chronophage (CPH, "time-eater"). This gene is an ortholog of two essential genes in humans: BCL11A and BCL11B, which also have specific expression in miscs from curation of mammalian scrna-SEQ datasets. Preliminary evidence from the screen showed an defect for iscs to proliferate and differentiate when CPH was lost. Additionally, this gene's expression is reduced in aged discs, suggesting a potential role in GUT degeneration during aging. The role of CPH has only been defined in neural stem cells and muscle cell progenitors, showing the critical function of CPH for proliferation and differentiation in these cell types. Therefore, i hypothesize CPH is required for the homeostasis and proper regulation of discs between active and quiescent states, and is indispensable for GUT maintenance during aging. For aim 1, i will characterize the cellular and molecular mechanism this occurs by generating a new reporter line and driving cell-specific KD of CPH, characterizing potential regulators of CPH, and then apply a novel single cell multiome sequencing approach to identify genes that CPH regulates and how dysfunction impacts the microenvironment. In aim 2, i will study the age-associated decrease of CPH and explore whether and how its decline contributes to GUT degeneration. This work will have significant implications for how aging impacts ISC function and how stem cells regulate the transition between active and quiescent states.