Gfi1-expressing Paneth cells revert to stem cells following intestinal injury

Chen, M.-S.; Lo, Y.-H.; Butkus, J.; Zou, W.; Tseng, Y.-J.; Jen, H.-I.; Patel, S.; Groves, A.; Estes, M.; Sahin, E.; Frey, M.; Dempsey, P.; Shroyer, N.

doi:10.1101/364133

bioRxiv · 10.1101/364133

Gfi1-expressing Paneth cells revert to stem cells following intestinal injury

Chen, M.-S.·Lo, Y.-H.·Butkus, J.·Zou, W.·Tseng, Y.-J.·Jen, H.-I.·Patel, S.·Groves, A.·Estes, M.·Sahin, E.·Frey, M.·Dempsey, P.·Shroyer, N.

View original source ↗Export metadata ↓

Abstract

BackgroundAimChemotherapy drugs harm rapidly dividing normal healthy cells such as those lining the gastrointestinal tract, causing morbidity and mortality that complicates medical treatment modalities. Growth Factor-Independent 1 (GFI1) is a zinc finger transcriptional repressor implicated in the differentiation of secretory precursors into Paneth and goblet cells in the intestinal epithelium. We hypothesize that stimulating the reversion of Gfi1+ secretory cells into stem cells will improve intestinal epithelial regeneration and mitigate injury.\n\nMethodsGfi1 reporter mice (Gfi1cre/+; ROSA26 LSL-YFP) were treated with Doxorubicin, radiation, anti-CD3 antibody, and rotavirus to induce intestinal injury. Mice and intestinal organoids (enteroids) were used to investigate cellular repair mechanisms following injury.\n\nResultsUnder homeostatic conditions, Gfi1-lineage cells are Paneth and goblet cells, which were non-proliferative and not part of the stem cell pool. After injury, Gfi1+ secretory cells can re-enter the cell cycle and give rise to all cell lineages of the intestinal epithelium including stem cells. Reversion of Gfi1-lineage cells was observed in other injury model systems, including irradiation and anti-CD3 treatment, but not in ISC-sparing rotavirus infection. Our results also demonstrated that PI3kinase/AKT activation improved cell survival, and elevated WNT signaling increased the efficiency of Gfi1+ cell reversion upon injury.\n\nConclusionsThese findings indicate that Gfi1+ secretory cells display plasticity and reacquire stemness following severe damage. Moreover, PI3kinase/AKT and WNT are key regulators involved in injury-induced regeneration. Our studies identified potential therapeutic intervention strategies to mitigate the adverse effects of chemotherapy-induced damage to normal tissues and improve the overall effectiveness of cancer chemotherapy.

Explore related subjects

cell biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Chen, M.-S., Lo, Y.-H., Butkus, J., Zou, W., Tseng, Y.-J., Jen, H.-I., Patel, S., Groves, A., Estes, M., Sahin, E., Frey, M., Dempsey, P., Shroyer, N.. 2018-07-16. Gfi1-expressing Paneth cells revert to stem cells following intestinal injury. https://doi.org/10.1101/364133

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Fatty acid synthase coordinates mTOR signaling and histone crotonylation during cardiomyocyte hypertrophy

Background: Epigenetic modifications are central to the regulation of cardiac gene expression during disease. Among these, histone crotonylation (Kcr) has recently emerged as a key modulator of chromatin structure and transcriptional activity. Here, we identify a novel signaling axis linking fatty acid synthase (FASN) to mTOR activation and hypertrophic gene expression through histone crotonylation. Methods: FASN expression, mTOR activation, and histone crotonylation were assessed in mouse hearts and isolated cardiomyocytes using immunoblotting. FASN was silenced by siRNA or inhibited pharmacologically using TVB-2640. Hypertrophic gene expression was quantified by RT-qPCR. Cardiomyocyte hypertrophy was evaluated by immunofluorescence-based cell size analysis. p300 acetylation and crotonylation were assessed by immunoprecipitation and immunoblotting. CUT&RUN-seq and RNA-seq were performed to identify FASN- and Histone H3K18cr-regulated genes during hypertrophic stimulation. Bioinformatic analyses of human RNA-seq and genome-wide association study (GWAS) data were conducted to investigate the clinical relevance of these findings. Results: Histone crotonylation was markedly elevated in hypertrophic myocardium and cardiomyocytes. This increase was driven by upregulated FASN expression in response to hypertrophic stimuli. Genetic or pharmacological inhibition of FASN suppressed histone crotonylation, hypertrophic gene expression, and cardiomyocyte enlargement. Mechanistic studies suggested that FASN regulates histone crotonylation through mTOR-associated signaling and changes in p300 activity. Transcriptomic analyses further revealed that FASN enhances the expression of hypertrophy-associated genes enriched for histone crotonylation marks. Analysis of human sequencing datasets demonstrated a positive association between FASN expression and molecular markers of hypertrophy in patients with hypertrophic cardiomyopathy (HCM). Furthermore, GWAS analysis identified a variant at the FASN locus associated with heart failure as the underlying cause of death and increased FASN expression in cardiomyocytes. Conclusions: Our findings identify FASN as an important regulator of mTOR signalling and histone crotonylation during cardiomyocyte hypertrophy. These results support a potential mechanism linking altered lipid metabolism to epigenetic regulation and pathological cardiac remodelling.

cell biology↗

bioRxiv2026

A conserved Foxp1-Pde4d axis regulates inflammatory responsiveness

Inflammatory responses are heterogeneous, even among cells exposed to a common insult, yet the regulatory mechanisms that distinguish these inflammatory states remain poorly understood. Here, we leveraged inflammatory state heterogeneity to identify a conserved Foxp1-Pde4d regulatory relationship and uncover a role for this axis in preserving inflammatory responsiveness. Genotoxic stress in adipocyte progenitors generated heterogeneous engagement of type-I interferon (IFN) and NF{kappa}B transcriptional programmes, and transcriptome-wide analysis independently identified Foxp1 and the cAMP phosphodiesterase Pde4d among genes associated with lower IFN- and higher NF{kappa}B-associated transcription. ChIP-seq revealed selective loss of Foxp1 occupancy at a Pde4d-associated regulatory element following genotoxic stress, while Foxp1 gain- and loss-of-function established Foxp1 as a positive regulator of Pde4d expression. Remarkably, coupling of Foxp1-Pde4d expression was broadly conserved across vertebrate tissues and damage models. In vivo, Foxp1 loss in zebrafish revealed a striking dissociation between inflammatory state and response capacity: basal NF{kappa}B activity was elevated, yet injury-induced NF{kappa}B activation was markedly blunted and macrophage recruitment impaired. Adenylyl cyclase inhibition restored macrophage recruitment in Foxp1-deficient zebrafish, functionally linking the Foxp1 phenotype to cAMP signalling and supporting a model in which Foxp1-Pde4d regulation preserves inflammatory responsiveness through control of cAMP. Together, these findings show how inflammatory-state heterogeneity can reveal conserved regulatory mechanisms linking basal cellular state to subsequent response capacity.

cell biology↗

bioRxiv2026

The Structural Basis of Genome Silencing: The Inactive X Chromosome Resolved by Electron Spectroscopic Imaging

The eukaryotic nucleus has a hierarchical organization that permits genomic regulation. The genome is packaged as chromatin, which is silenced conditionally as facultative heterochromatin, or more stably silenced as constitutive heterochromatin. The smaller fractions of the genome that contain gene-rich sequences are organized into open chromatin conformations known as euchromatin. The inactive X (Xi) chromosome territory presents a uniquely powerful model system to investigate chromosome-scale gene silencing, as the entire chromosome undergoes coordinated epigenetic repression. The unique chromosome-wide silencing event provides a tractable system for investigating how molecular mechanisms of gene repression are translated into mesoscale structural features. This work builds on previous structural studies of the Xi that have leveraged conventional electron microscopy (EM) and cryo-EM, which have led to remarkable insights into the structural underpinnings of genome silencing. These approaches, however, are unable to directly distinguish chromatin from RNA and protein features. To resolve the molecular composition of the Xi chromosome territory and to provide a model of the structural organization of the chromatin, RNA and protein we analyzed the Xi using Electron Spectroscopic Imaging (ESI). We are able to resolve structural features without the use of contrast enhancing stains, using the distinct elemental signatures of chromatin, RNA and protein and combining them into composite images. By coupling ESI and electron tomography, we can circumvent the projection limitation of EM and provide an unprecedented view of the spatial organization of chromatin fibres in relation to structural features including RNA and proteins in 3D. Additionally, we employed correlative light-microscopy with ESI in physical serial sections and computationally assembled a structural model of the entire Xi chromosome territory revealing an intricate spatial network with distinct chromatin domains, distributed RNA-protein clusters, and identified a large, and previously uncharacterized mesoscale non-chromatin structure. Together, these observations provide new insights into the architecture of the Xi chromosome territory and shed electrons on the structural basis of chromosome-scale genome organization.

cell biology↗